/* Draw secondary structure diagrams given a postscript SS template. * Initial development of this program was for SSU rRNA structures * with templates derived from Gutell's CRW (Comparative RNA Website, * http://www.rna.ccbb.utexas.edu/). * */ #include "esl_config.h" #include #include #include #include #include #include #include "easel.h" #include "esl_arr2.h" #include "esl_arr3.h" #include "esl_distance.h" #include "esl_dmatrix.h" #include "esl_fileparser.h" #include "esl_getopts.h" #include "esl_keyhash.h" #include "esl_msa.h" #include "esl_msafile.h" #include "esl_msafile2.h" #include "esl_sq.h" #include "esl_sqio.h" #include "esl_stack.h" #include "esl_tree.h" #include "esl_vectorops.h" #include "esl_wuss.h" #define SSDRAWINFINITY 987654321 #define ERRBUFSIZE 1024 #define MAXMBWITHOUTFORCE 100 #define ALIMODE 0 #define INDIMODE 1 #define SIMPLEMASKMODE 2 #define INFILEMODE 3 /* CMYK colors, a 4 value array defines a color with values 0..1, * [0] is cyan value, [1] is magenta, [2] is yellow, [3] is black */ #define NCMYK 4 #define ICYAN 0 #define IMGTA 1 #define IYELW 2 #define IBLCK 3 /* indices and sizes for hard-coded color schemes */ #define NSCHEMES 7 #define RB_11_RH_SCHEME 0 /* RainBow, 11 colors, Red High, blue low */ #define RB_11_RL_SCHEME 1 /* RainBow, 11 colors, Red Low, blue high */ #define RB_6_RH_SCHEME 2 /* RainBow, 6 colors, Red High, blue low */ #define RB_6_RL_SCHEME 3 /* RainBow, 6 colors, Red Low, blue high */ #define RB_5_RH_SCHEME 4 /* RainBow, 5 colors, Red High, teal low */ #define RB_5_RL_SCHEME 5 /* RainBow, 5 colors, Red low, teal high */ #define RB_W5_OH_SCHEME 6 /* RainBow with white, 5 colors, orange high, teal low, white lowest */ #define NRB_11_RH_SCHEME 11 #define NRB_11_RL_SCHEME 11 #define NRB_6_RH_SCHEME 6 #define NRB_6_RL_SCHEME 6 #define NRB_5_RH_SCHEME 5 #define NRB_5_RL_SCHEME 5 #define NRB_W5_OH_SCHEME 5 /* the actual CMYK color values for the scheme colors (_C = cyan, _M = magenta, _Y = yellow, _K = black) */ /* the 11-color rainbow scheme */ #define RED2BLUE_1_OF_11_C 0.00 #define RED2BLUE_1_OF_11_M 0.94 #define RED2BLUE_1_OF_11_Y 1.00 #define RED2BLUE_1_OF_11_K 0.00 #define RED2BLUE_2_OF_11_C 0.00 #define RED2BLUE_2_OF_11_M 0.84 #define RED2BLUE_2_OF_11_Y 1.00 #define RED2BLUE_2_OF_11_K 0.00 #define RED2BLUE_3_OF_11_C 0.00 #define RED2BLUE_3_OF_11_M 0.63 #define RED2BLUE_3_OF_11_Y 1.00 #define RED2BLUE_3_OF_11_K 0.00 #define RED2BLUE_4_OF_11_C 0.00 #define RED2BLUE_4_OF_11_M 0.42 #define RED2BLUE_4_OF_11_Y 1.00 #define RED2BLUE_4_OF_11_K 0.00 #define RED2BLUE_5_OF_11_C 0.00 #define RED2BLUE_5_OF_11_M 0.21 #define RED2BLUE_5_OF_11_Y 1.00 #define RED2BLUE_5_OF_11_K 0.00 #define RED2BLUE_6_OF_11_C 0.00 #define RED2BLUE_6_OF_11_M 0.00 #define RED2BLUE_6_OF_11_Y 1.00 #define RED2BLUE_6_OF_11_K 0.00 #define RED2BLUE_7_OF_11_C 0.42 #define RED2BLUE_7_OF_11_M 0.00 #define RED2BLUE_7_OF_11_Y 1.00 #define RED2BLUE_7_OF_11_K 0.00 #define RED2BLUE_8_OF_11_C 0.61 #define RED2BLUE_8_OF_11_M 0.00 #define RED2BLUE_8_OF_11_Y 0.56 #define RED2BLUE_8_OF_11_K 0.22 #define RED2BLUE_9_OF_11_C 0.50 #define RED2BLUE_9_OF_11_M 0.00 #define RED2BLUE_9_OF_11_Y 0.00 #define RED2BLUE_9_OF_11_K 0.50 #define RED2BLUE_10_OF_11_C 0.78 #define RED2BLUE_10_OF_11_M 0.56 #define RED2BLUE_10_OF_11_Y 0.00 #define RED2BLUE_10_OF_11_K 0.22 #define RED2BLUE_11_OF_11_C 0.92 #define RED2BLUE_11_OF_11_M 0.84 #define RED2BLUE_11_OF_11_Y 0.00 #define RED2BLUE_11_OF_11_K 0.08 /* the 6-color rainbow scheme */ /* red */ #define RED2BLUE_1_OF_6_C 0.00 #define RED2BLUE_1_OF_6_M 0.94 #define RED2BLUE_1_OF_6_Y 1.00 #define RED2BLUE_1_OF_6_K 0.00 /* orange-ish */ #define RED2BLUE_2_OF_6_C 0.00 #define RED2BLUE_2_OF_6_M 0.63 #define RED2BLUE_2_OF_6_Y 1.00 #define RED2BLUE_2_OF_6_K 0.00 /* gold-ish */ #define RED2BLUE_3_OF_6_C 0.00 #define RED2BLUE_3_OF_6_M 0.21 #define RED2BLUE_3_OF_6_Y 1.00 #define RED2BLUE_3_OF_6_K 0.00 /* light-green-ish */ #define RED2BLUE_4_OF_6_C 0.42 #define RED2BLUE_4_OF_6_M 0.00 #define RED2BLUE_4_OF_6_Y 1.00 #define RED2BLUE_4_OF_6_K 0.00 /* teal-ish */ #define RED2BLUE_5_OF_6_C 0.50 #define RED2BLUE_5_OF_6_M 0.00 #define RED2BLUE_5_OF_6_Y 0.00 #define RED2BLUE_5_OF_6_K 0.50 /* blue */ #define RED2BLUE_6_OF_6_C 0.92 #define RED2BLUE_6_OF_6_M 0.84 #define RED2BLUE_6_OF_6_Y 0.00 #define RED2BLUE_6_OF_6_K 0.08 /* single colors for one-cell legends */ #define NOC 17 #define CYANOC 0 #define MAGENTAOC 1 #define YELLOWOC 2 #define BLACKOC 3 #define WHITEOC 4 #define LIGHTGREYOC 5 #define GREYOC 6 #define DARKGREYOC 7 #define REDOC 8 #define ORANGEOC 9 #define TEALOC 10 #define LIGHTGREENOC 11 #define GREENOC 12 #define DARKGREENOC 13 #define LIGHTPURPLEOC 14 #define PURPLEOC 15 #define DARKPURPLEOC 16 /* the actual CMYK color values for the single colors (_C = cyan, _M = magenta, _Y = yellow, _K = black) */ #define CYAN_C 1.0 #define CYAN_M 0.0 #define CYAN_Y 0.0 #define CYAN_K 0.0 #define MAGENTA_C 0.0 #define MAGENTA_M 1.0 #define MAGENTA_Y 0.0 #define MAGENTA_K 0.0 #define YELLOW_C 0.0 #define YELLOW_M 0.0 #define YELLOW_Y 1.0 #define YELLOW_K 0.0 #define BLACK_C 0.0 #define BLACK_M 0.0 #define BLACK_Y 0.0 #define BLACK_K 1.0 #define WHITE_C 0.0 #define WHITE_M 0.0 #define WHITE_Y 0.0 #define WHITE_K 0.0 #define LIGHTGREY_C 0.0 #define LIGHTGREY_M 0.0 #define LIGHTGREY_Y 0.0 #define LIGHTGREY_K 0.2 #define GREY_C 0.0 #define GREY_M 0.0 #define GREY_Y 0.0 #define GREY_K 0.5 #define DARKGREY_C 0.0 #define DARKGREY_M 0.0 #define DARKGREY_Y 0.0 #define DARKGREY_K 0.75 #define RED_C 0.0 #define RED_M 1.0 #define RED_Y 1.0 #define RED_K 0.0 #define ORANGE_C 0.0 #define ORANGE_M 0.5 #define ORANGE_Y 1.0 #define ORANGE_K 0.0 #define TEAL_C 0.5 #define TEAL_M 0.0 #define TEAL_Y 0.0 #define TEAL_K 0.5 #define LIGHTGREEN_C 0.5 #define LIGHTGREEN_M 0.0 #define LIGHTGREEN_Y 0.5 #define LIGHTGREEN_K 0.0 #define GREEN_C 1.0 #define GREEN_M 0.0 #define GREEN_Y 1.0 #define GREEN_K 0.0 #define DARKGREEN_C 1.0 #define DARKGREEN_M 0.5 #define DARKGREEN_Y 1.0 #define DARKGREEN_K 0.0 #define LIGHTPURPLE_C 0.3 #define LIGHTPURPLE_M 0.6 #define LIGHTPURPLE_Y 0.0 #define LIGHTPURPLE_K 0.0 #define PURPLE_C 0.5 #define PURPLE_M 1.0 #define PURPLE_Y 0.0 #define PURPLE_K 0.0 #define DARKPURPLE_C 1.0 #define DARKPURPLE_M 1.0 #define DARKPURPLE_Y 0.0 #define DARKPURPLE_K 0.0 /* hard-coded values for the legends */ #define LEG_NBOXES 11 #define LEG_MINFONTSIZE 10 #define SPECIAL_FONT "Courier-BoldOblique" #define LEG_FONT "Courier-Bold" #define LEG_EXTRA_COLUMNS 12 /* how many extra columns we need for printing stats in the legend */ #define COURIER_HEIGHT_WIDTH_RATIO 1.65 #define LEG_EXTRA_TEXT_FONT "Helvetica" /* fonts and other sizes */ #define DEFAULT_FONT "Courier-Bold" #define FOOTER_FONT "Helvetica" #define NUCLEOTIDES_FONT "Courier-Bold" /* NOTE: THIS MUST BE Courier-Bold or Courier, the offsets for drawing cells (CELL_{X,Y}OFFSET_FRACTION) * and placing nucleotides (NUCLEOTIDE_{X,Y}OFFSET_FRACTION_LOWERCASE_GJPQY) depend on it */ /*#define NUCLEOTIDES_FONT "Monaco-Bold"*/ #define POSNTEXT_FONT "Helvetica" #define NUCLEOTIDES_FONTSIZE 8. #define POSNTEXT_FONTSIZE 8. #define LEG_FONTSIZE_UNSCALED 8 #define LEG_EXTRA_TEXT_FONTSIZE_UNSCALED 8 #define HEADER_FONTSIZE_UNSCALED 12 #define HEADER_MODELNAME_MAXCHARS 20 #define TICKS_LINEWIDTH 2. #define BP_LINEWIDTH 1. #define CELLSIZE 8. /* default size of a cell, a single position in the structure diagram */ #define CELLSIZE_INT 8 /* default size of a cell, a single position in the structure diagram */ /* NOTE, *OFFSET_FRACTION* constants below depend on NUCLEOTIDES_FONT being either "Courier-Bold" or "Courier" */ #define CELL_XOFFSET_FRACTION 0.2 #define CELL_YOFFSET_FRACTION 0.2 #define LOWERCASE_LOW_HANGING_CHARS "gjpqy" #define NUCLEOTIDE_YOFFSET_FRACTION_LOWERCASE_LOW_HANGING_CHARS 0.1875 /* postscript info */ #define POSTSCRIPT_PAGEWIDTH 612. #define POSTSCRIPT_PAGEHEIGHT 792. #define PAGE_TOPBUF 30. /* 30 blank pts required at top */ #define PAGE_SIDEBUF 32. /* 32 blank pts required at sides */ #define PAGE_BOTBUF 30. /* 30 blank pts required at bot */ /* cell outline info */ #define OUTLINE_LINEWIDTH_CELL_FRACTION_MIN 0.04 #define OUTLINE_LINEWIDTH_CELL_FRACTION_MAX 0.16 #define NOUTLINETYPES 2 #define OUTLINE_NONE_IDX 0 #define OUTLINE_MIN_IDX 1 #define OUTLINE_MAX_IDX 2 #define OUTLINE_PROCEDURE "box" /* one cell color legends, special values */ #define OCCL_BLANK_COUNT -1 /* Structure: scheme_color_legend * Incept: EPN, Thu Jun 25 20:20:38 2009 * * Parameters describing a one-dimensional legend of colors * from a preset scheme for use in a SSPostscript_t data structure. */ typedef struct scheme_color_legend_s { int scheme; /* preset color scheme index */ int nbins; /* number of colors (bins) in this scheme */ char *text1; /* first line of text for legend, a single string */ char *text2; /* second line of text for legend, a single string */ float *limits; /* [nbins+1] limits for each bin, limits[0] is min value we would expect to see, limits[nbins] is max */ int *counts; /* [nbins] number of cells we've painted each color */ int *counts_masked; /* [nbins] number of cells within mask ('1's) that we've painted each color */ int ints_only_flag; /* TRUE if possible values are only integers, legend values will be drawn differently in this case */ int low_inclusive; /* TRUE if bin 0 is inclusive of limits[0], FALSE if not */ int high_inclusive; /* TRUE if bin[nbins-1] is inclusive of max value, FALSE if not */ int use_mask; /* TRUE to use ps->mask if it is available to draw masked positions differently, FALSE not to */ } SchemeColorLegend_t; /* Structure: onecell_color_legend * Incept: EPN, Tue Sep 30 13:06:15 2008 * * Parameters describing a single colored cell legend for a * SSPostscript_t data structure. */ typedef struct onecell_color_legend_s { float col[NCMYK]; /* [CMYK] color value for the cell */ char *text; /* description text for legend */ char *celltext; /* colored text to use instead of a block, if NULL a colored block will be used */ char *procname; /* name of a procedure for drawing the block, if NULL a colored block will be used */ /* NOTE only one of celltext or procname can be non-NULL */ float *procstack; /* array of stack elements for the procedure */ int nprocstack; /* num els in */ int nres; /* number of nucleotides colored by the color in col[NCMYK] */ int nres_masked; /* number of nucleotides within a mask colored by the color in col[NCMYK] */ int do_separator; /* TRUE to draw a separator line below this one cell color legend, FALSE not to */ int do_no_vspace; /* when printing one cell, legend, don't add any vertical space after it, usually this is FALSE */ } OneCellColorLegend_t; /* Structure: text_legend * Incept: EPN, Mon Apr 19 07:11:44 2010 * * Parameters describing a text section of a legend for a * SSPostscript_t data structure. */ typedef struct text_legend_s { char **text_per_line; /* description text for legend */ int nlines; /* colored text to use instead of a block, if NULL a colored block will be used */ int do_separator; /* TRUE to draw a separator line below this text section, FALSE not to */ } TextLegend_t; /* Structure: ss_postscript * Incept: EPN, Mon Jun 23 15:50:30 2008 * * A clumsy data structure for storing the information that will * become a postscript secondary structure diagram based on a * template created by Robin Gutell and colleagues. * */ typedef struct ss_postscript_s { int npage; /* number of pages in eventual postscript */ char *modelname; /* name of model, read from template file */ int *modeA; /* [0..npage-1] page mode, ALIMODE, INDIMODE, or SIMPLEMASKMODE */ char **descA; /* [0..npage-1] description for each page */ int desc_max_chars; /* max num characters for a page description */ float headerx; /* x coordinate (bottom left corner) of header area */ float headery; /* y coordinate (bottom left corner) of header area */ float headerx_charsize;/* size of a character in x-dimension in the header */ float headery_charsize;/* size of a character in y-dimension in the header */ float headerx_desc; /* x coordinate (bottom left corner) of header area */ int leg_posn; /* consensus position for placing legend, read from template */ int leg_cellsize; /* size of a cell in the legend, (ex. 24 for SSU models) */ float leg_rhs_space;/* extra space to leave to the right of the legend */ float legx_offset; /* offset in x coordinate for placing legend, legx will be ps->rxA[leg_posn-1] + legx_offset */ float legy_offset; /* offset in y coordinate for placing legend, legy will be ps->ryA[leg_posn-1] + legy_offset */ float legx; /* x coordinate (top left corner) of legend area */ float legy; /* y coordinate (top left corner) of legend area */ float cur_legy; /* y coordinate of current line in legend */ float legx_charsize;/* size of a character in x-dimension in the legend */ float legy_charsize;/* size of a character in y-dimension in the legend */ int legx_max_chars; /* max num nucleotides in x direction we can print in legend before running off page */ int legy_max_chars; /* max num nucleotides in y direction we can print in legend before running off page */ int legx_stats; /* x position for printing stats in the legend */ float pagex_max; /* max x position on page */ float pagey_max; /* max y position on page */ float scale; /* scale parameter, read from template file */ char **regurgA; /* [0..nregurg-1][] lines from the template file to regurgitate, these are unchanged. */ int nregurg; /* number of lines (char *'s) in the regurg_textAA 2D array */ char **posntextA; /* [0..i..nposntext-1] string for element i of position text, read from template */ float *posntextxA; /* [0..i..nposntext-1] x value for posntextA[i] */ float *posntextyA; /* [0..i..nposntext-1] y value for posntextA[i] */ int nposntext; /* number of elements in posntextx and posntexty */ float *ticksx1A; /* [0..nticks-1] x begin value for ticks */ float *ticksx2A; /* [0..nticks-1] x end value for ticks */ float *ticksy1A; /* [0..nticks-1] y begin value for ticks */ float *ticksy2A; /* [0..nticks-1] x end value for ticks */ int nticks; /* number of ticks */ float *bpx1A; /* [0..nbp-1] x begin value for bp connect line */ float *bpx2A; /* [0..nbp-1] x end value for bp connect line */ float *bpy1A; /* [0..nbp-1] y begin value for bp connect line */ float *bpy2A; /* [0..nbp-1] x end value for bp connect line */ int nbp; /* number of bp */ float *rxA; /* [0..rflen-1] x coordinate for each nucleotide in the eventual postscript */ float *ryA; /* [0..rflen-1] y coordinate for each nucleotide in the eventual postscript */ int rflen; /* the number of nucleotides in the template file */ char **rAA; /* [0..npage-1][0..rflen-1] nucleotide character in the eventual postscript */ float ***rcolAAA; /* [0..npage-1][0..rflen-1][0..3] color for nucleotide on page p, position c, CMYK in the eventual postscript */ float ***bcolAAA; /* [0..npage-1][0..rflen-1][0..3] color for block on page p, position c, CMYK in the eventual postscript */ char **otypeAA; /* [0..npage-1][0..rflen-1] outline type on page p, position c in the eventual postscript * '0' '1' or '2', OUTLINE_MIN_IDX, OUTLINE_MID_IDX, OUTLINE_MAX_IDX, respectively */ OneCellColorLegend_t ***occlAAA;/* [0..npage-1][0..l..nocclA[p]] ptr to one cell color legend l for page p */ int *nocclA; /* [0..npage-1] number of one cell color legends for each page */ SchemeColorLegend_t **sclAA;/* [0..npage-1] ptr to scheme color legend l for page p, NULL if none */ TextLegend_t ***tlAAA;/* [0..npage-1][0..l..ntlA[p]] ptr to text legend l for page p */ int *ntlA; /* [0..npage-1] number of text legends for page p, NULL if none */ char *mask; /* mask for this postscript, columns which are '0' get drawn differently */ int nalloc; /* number of elements to add to arrays when reallocating */ int msa_nseq; /* number of sequences in the msa, impt b/c msa->nseq will be 0 if --small */ char *msa_cseq_maj;/* [0..rfpos..ps->rflen-1]: consensus sequence for the msa, determined using majority rule */ char *msa_cseq_amb;/* [0..rfpos..ps->rflen-1]: different consensus sequence for the msa, least ambiguous * nt per nongap RF position that represents >= esl_opt_GetReal(go, --athresh) fraction of * nongap nucleotides at position rfpos */ int *msa_ct; /* [1..ps->rflen] CT array for msa this postscript corresponds to, * msa_ct[i] is the position that consensus nucleotide i base pairs to, or 0 if i is unpaired. */ int msa_nbp; /* number of bps read from current MSA (in msa_ct), should equal nbp, but only if bps read from template file */ int *msa_rf2a_map;/* [0..ps->rflen-1] = apos, apos is the alignment position (0..msa->alen-1) that is non-gap RF position rfpos (for rfpos in 0..rflen-1) */ int *msa_a2rf_map;/* [0..ps->msa->alen-1] = rfpos, rfpos is the non-gap RF position (0..ps->rflen) that is alignment position apos (for apos in 0..ps->msa_alen-1) */ int *uaseqlenA; /* [0..ps->msa->nseq-1] unaligned sequence length for all sequences in the MSA, only computed if --indi */ int *seqidxA; /* [0..ps->npage-1] the sequence index in the MSA each page corresponds to, only valid if --indi */ ESL_MSA *msa; /* pointer to MSA this object corresponds to */ const ESL_ALPHABET *abc; /* ptr to alphabet used to decipher gap chars (msa itself is text mode) */ } SSPostscript_t; static SSPostscript_t *create_sspostscript(const ESL_GETOPTS *go); static int setup_sspostscript(SSPostscript_t *ps, char *errbuf); static OneCellColorLegend_t *create_onecell_colorlegend(float *cmykA, int nres, int nres_masked, int do_separator, int do_no_vspace); static SchemeColorLegend_t *create_scheme_colorlegend(int scheme, int ncols, float *limits, int ints_only_flag, int low_inclusive, int high_inclusive, int use_mask); static TextLegend_t *create_text_legend(int nlines, char **text_per_line, int do_separator); static TextLegend_t *create_text_legend_for_consensus_sequence(const ESL_GETOPTS *go, int do_separator); static int add_text_to_scheme_colorlegend(SSPostscript_t *ps, SchemeColorLegend_t *scl, char *text, int legx_max_chars, char *errbuf); static int add_text_to_onecell_colorlegend(SSPostscript_t *ps, OneCellColorLegend_t *occl, char *text, int legx_max_chars, char *errbuf); static int add_celltext_to_onecell_colorlegend(SSPostscript_t *ps, OneCellColorLegend_t *occl, char *celltext, char *errbuf); static int add_procedure_to_onecell_colorlegend(SSPostscript_t *ps, OneCellColorLegend_t *occl, char *procname, float *procstack, int nprocstack, char *errbuf); static int add_page_desc_to_sspostscript(SSPostscript_t *ps, int page, char *text, char *errbuf); static int add_diffmask_page_desc_to_sspostscript(SSPostscript_t *ps, int page, char *mask_file, char *maskdiff_file, char *errbuf); static int draw_sspostscript(FILE *fp, const ESL_GETOPTS *go, char *errbuf, char *command, char *date, float ***hc_scheme, SSPostscript_t *ps); static int draw_legend_column_headers(FILE *fp, SSPostscript_t *ps, int pagenum, char *errbuf); static int draw_onecell_colorlegend(FILE *fp, OneCellColorLegend_t *occl, SSPostscript_t *ps, int occl_idx, int pagenum); static int draw_scheme_colorlegend(const ESL_GETOPTS *go, FILE *fp, SchemeColorLegend_t *scl, float **hc_scheme, SSPostscript_t *ps, int pagenum); static void free_sspostscript(SSPostscript_t *ps); static int add_pages_sspostscript(SSPostscript_t *ps, int ntoadd, int page_mode); static int parse_template_file(char *filename, const ESL_GETOPTS *go, char *errbuf, int msa_rflen, SSPostscript_t **ret_ps); static int parse_template_page(ESL_FILEPARSER *efp, const ESL_GETOPTS *go, char *errbuf, SSPostscript_t **ret_ps); static int parse_modelname_section(ESL_FILEPARSER *efp, char *errbuf, SSPostscript_t *ps); static int parse_legend_section(ESL_FILEPARSER *efp, char *errbuf, SSPostscript_t *ps); static int parse_scale_section(ESL_FILEPARSER *efp, char *errbuf, SSPostscript_t *ps); static int parse_ignore_section(ESL_FILEPARSER *efp, char *errbuf, int *ret_read_showpage); static int parse_regurgitate_section(ESL_FILEPARSER *efp, char *errbuf, SSPostscript_t *ps); static int parse_text_section(ESL_FILEPARSER *efp, char *errbuf, SSPostscript_t *ps); static int parse_lines_section(ESL_FILEPARSER *efp, char *errbuf, SSPostscript_t *ps); static int validate_justread_sspostscript(SSPostscript_t *ps, char *errbuf); static int validate_and_update_sspostscript_given_msa(const ESL_GETOPTS *go, const ESL_ALPHABET *abc, SSPostscript_t *ps, ESL_MSA *msa, int msa_nseq, char *errbuf); static int read_mask_file(char *filename, char *errbuf, char **ret_mask, int *ret_masklen, int *ret_mask_has_internal_zeroes); static void PairCount(const ESL_ALPHABET *abc, double *counters, ESL_DSQ syml, ESL_DSQ symr, double wt); static int get_command(const ESL_GETOPTS *go, char *errbuf, char **ret_command); static int get_date(char *errbuf, char **ret_date); static int set_scheme_values(char *errbuf, float *vec, int ncolvals, float **scheme, float val, SchemeColorLegend_t *scl, int within_mask, int *ret_bi); static int set_onecell_values(char *errbuf, float *vec, int ncolvals, float *onecolor); static int add_mask_to_ss_postscript(SSPostscript_t *ps, char *mask); static int draw_masked_block(FILE *fp, float x, float y, float *colvec, int do_circle_mask, int do_square_mask, int do_x_mask, int do_border, float cellsize); static int draw_header_and_footer(FILE *fp, const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps, int page, int pageidx2print); static void get_insert_info_from_msa(const ESL_ALPHABET *abc, ESL_MSA *msa, int rflen, int **ret_nseq_with_ins_ct, int **ret_nins_ct, int ***ret_per_seq_ins_ct); static void get_insert_info_from_abc_ct(double **abc_ct, ESL_ALPHABET *abc, char *msa_rf, int64_t msa_alen, int rflen, int **ret_nseq_with_ins_ct, int **ret_nins_ct); static void get_insert_info_from_ifile(char *ifile, int rflen, int msa_nseq, ESL_KEYHASH *useme_keyhash, int **ret_nseq_with_ins_ct, int **ret_nins_ct, int ***ret_per_seq_ins_ct, int **ret_soff_ct, int **ret_eoff_ct); static int count_msa(const ESL_ALPHABET *abc, ESL_MSA *msa, char *errbuf, double ***ret_abc_ct, double ****ret_bp_ct, double ***ret_pp_ct, int **ret_spos_ct, int **ret_epos_ct); static int get_consensus_seqs_from_abc_ct(const ESL_GETOPTS *go,SSPostscript_t *ps, char *errbuf, double **abc_ct, ESL_ALPHABET *abc, int64_t msa_alen); static int infocontent_sspostscript(const ESL_GETOPTS *go, ESL_ALPHABET *abc, char *errbuf, SSPostscript_t *ps, double **abc_ct, int msa_nseq, float ***hc_scheme, int hc_scheme_idx, int hc_nbins, float **hc_onecell, int hc_onecell_idx, FILE *tabfp); static int mutual_information_sspostscript(const ESL_GETOPTS *go, ESL_ALPHABET *abc, char *errbuf, SSPostscript_t *ps, double ***bp_ct, int msa_nseq, float ***hc_scheme, int hc_scheme_idx, int hc_nbins, float **hc_onecell, int ss_idx, int zerores_idx, FILE *tabfp); static int delete_sspostscript(const ESL_GETOPTS *go, ESL_ALPHABET *abc, char *errbuf, SSPostscript_t *ps, double **abc_ct, int *span_ct, int msa_nseq, int do_all, float ***hc_scheme, int hc_scheme_idx, int hc_nbins, float **hc_onecell, int hc_zerodel_idx, int hc_fewdel_idx, FILE *tabfp); static int avg_posteriors_sspostscript(const ESL_GETOPTS *go, ESL_ALPHABET *abc, char *errbuf, SSPostscript_t *ps, double **pp_ct, int msa_nseq, float ***hc_scheme, int hc_scheme_idx, int hc_nbins, float **hc_onecell, int hc_onecell_idx, FILE *tabfp); static int insertfreq_sspostscript(const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps, int *nseq_with_ins_ct, int *span_ct, int msa_nseq, float ***hc_scheme, int hc_scheme_idx, int hc_nbins, float **hc_onecell, int hc_zeroins_idx, int hc_fewins_idx, FILE *tabfp); static int insertavglen_sspostscript(const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps, int *nseq_with_ins_ct, int *nins_ct, int *span_ct, int msa_nseq, float ***hc_scheme, int hc_scheme_idx, int hc_nbins, float **hc_onecell, int hc_zeroins_idx, FILE *tabfp); static int span_sspostscript(const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps, int *span_ct, int msa_nseq, float ***hc_scheme, int hc_scheme_idx, int hc_nbins, float **hc_onecell, int zercov_idx, int maxcov_idx, FILE *tabfp); static int individuals_sspostscript(const ESL_GETOPTS *go, ESL_ALPHABET *abc, char *errbuf, SSPostscript_t *ps, double **abc_ct, ESL_MSA *msa, int **per_seq_ins_ct, int do_prob, int do_rescol, float ***hc_scheme, int hc_scheme_idx_s, int hc_scheme_idx_p, int hc_nbins_s, int hc_nbins_p, float **hc_onecell, int extdel_idx_s, int wcbp_idx_s, int gubp_idx_s, int ncbp_idx_s, int dgbp_idx_s, int hgbp_idx_s, int gap_idx_p, FILE *tabfp); static int cons_seq_sspostscript(const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps, float **hc_onecell, int wcbp_idx_s, int gubp_idx_s, int ncbp_idx_s, int dgbp_idx_s, int hgbp_idx_s); static int rf_seq_sspostscript(const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps, ESL_MSA *msa, int do_rescol, float **hc_onecell, int wcbp_idx_s, int gubp_idx_s, int ncbp_idx_s); static int colormask_sspostscript(const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps, ESL_MSA *msa, float **hc_onecell, int incmask_idx, int excmask_idx); static int diffmask_sspostscript(const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps, ESL_MSA *msa, char *mask2, float **hc_onecell, int incboth_idx, int inc1_idx, int inc2_idx, int excboth_idx); static int drawfile2sspostscript(const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps, float ***hc_scheme, int hc_scheme_idx, int hc_nbins); static int expertfile2sspostscript(const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps); static int get_pp_idx(const ESL_ALPHABET *abc, char ppchar); static int get_span_ct(int *msa_rf2a_map, int64_t alen, int rflen, int nseq, int *spos_ct, int *epos_ct, int *srfoff_ct, int *erfoff_ct, int **ret_span_ct); static int is_watson_crick_bp(char i, char j); static int is_gu_or_ug_bp(char i, char j); static int compare_two_cmyk_colors(float acol_C, float acol_M, float acol_Y, float acol_K, float bcol_C, float bcol_M, float bcol_Y, float bcol_K); static void define_outline_procedure(FILE *fp); static char banner[] = "draw postscript secondary structure diagrams"; static char usage[] = "[options] \n\ The must be in Stockholm format."; static ESL_OPTIONS options[] = { /* name type default env range togs reqs incomp help docgroup */ { "-h", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "help; show brief info on version and usage", 1 }, { "-d", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "draw default set of alignment summary diagrams", 1 }, { "--mask", eslARG_INFILE, NULL, NULL, NULL, NULL,NULL, NULL, "for all diagrams, mark masked ('0') columns from mask in ", 1 }, { "--small", eslARG_NONE, NULL, NULL, NULL, NULL,NULL, NULL, "operate in small memory mode (aln must be 1 line/seq Pfam format)", 1 }, { "--cons", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "draw diagram showing the alignment's consensus sequence", 2 }, { "--info", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "draw information content diagram", 2 }, { "--mutinfo",eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "draw base pair mutual information diagram", 2 }, { "--ifreq", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "draw insert frequency diagram", 2 }, { "--iavglen",eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "draw average insert length diagram", 2 }, { "--dall", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "draw delete diagram w/all deletions (incl. terminal deletes)", 2 }, { "--prob", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "draw average posterior probability diagram", 2 }, { "--span", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "draw diagram showing fraction of seqs that span each posn", 2 }, { "--rf", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "draw diagram showing reference (#=GC RF) sequence", 2 }, { "--dint", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "draw delete diagram w/only internal (non-terminal) deletions", 2 }, { "--tabfile",eslARG_OUTFILE,NULL, NULL, NULL, NULL,NULL, NULL, "output per position data in tabular format to file ", 2 }, { "--indi", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, "--small", "draw diagrams for individual sequences in the alignment", 3 }, { "-f", eslARG_NONE, FALSE, NULL, NULL, NULL,"--indi", NULL, "force; w/--indi draw all seqs, even if predicted output >100 Mb", 3 }, { "--no-pp", eslARG_NONE, FALSE, NULL, NULL, NULL,"--indi", NULL, "with --indi, do not draw indi posterior probability diagrams", 9 }, { "--no-bp", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "do not color nucleotides based on basepair type", 9 }, { "--no-ol", eslARG_NONE, FALSE, NULL, NULL, NULL,"--indi", NULL, "w/--indi, do not outline nts that are not most common nt", 9 }, { "--no-ntpp", eslARG_NONE, FALSE, NULL, NULL, NULL,"--indi", "--no-pp", "w/--indi, do not draw nts on individual post prob diagrams", 9 }, { "--no-cnt", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "do not draw consensus nts on alignment summary diagrams", 7 }, { "--cthresh",eslARG_REAL, "0.75", NULL,"0= fraction of seqs", 7 }, { "--cambig", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, "--no-cnt", "allow ambiguous nts in consensus sequence", 7 }, { "--athresh",eslARG_REAL, "0.9", NULL,"0= fraction of seqs", 7 }, { "--mask-u", eslARG_NONE, FALSE, NULL, NULL, NULL,"--mask", "--mask-x","with --mask, mark masked columns as squares", 4 }, { "--mask-x", eslARG_NONE, FALSE, NULL, NULL, NULL,"--mask", "--mask-u","with --mask, mark masked columns as x's", 4 }, { "--mask-a", eslARG_NONE, FALSE, NULL, NULL, NULL,"--mask", NULL, "with --mask-u or --mask-x, draw alternative mask style", 4 }, { "--mask-col", eslARG_NONE, NULL,NULL, NULL, NULL,"--mask", NULL, "w/--mask draw two color diagram denoting masked columns", 5 }, { "--mask-diff",eslARG_INFILE,NULL,NULL, NULL, NULL,"--mask", NULL, "with --mask , compare mask in to mask in ", 5 }, { "--dfile", eslARG_INFILE, NULL,NULL, NULL, NULL,NULL, NULL, "read 'draw file' specifying >=1 diagrams", 6 }, { "--efile", eslARG_INFILE, NULL,NULL, NULL, NULL,NULL, NULL, "read 'expert draw file' specifying >=1 diagrams", 6 }, { "--ifile", eslARG_INFILE, NULL,NULL, NULL, NULL,NULL, NULL, "read insert information from cmalign insert file ", 6 }, { "--no-leg", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "do not draw legend", 8 }, { "--no-head",eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "do not draw header", 8 }, { "--no-foot",eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "do not draw footer", 8 }, { 0,0,0,0,0,0,0,0,0,0 }, }; int main(int argc, char **argv) { ESL_GETOPTS *go = NULL; /* application configuration */ ESL_ALPHABET *abc = NULL; /* biological alphabet */ char *alifile = NULL; /* alignment file name */ char *outfile = NULL; /* output ps file name */ char *templatefile = NULL; /* template file, specifying >= 1 SS diagrams * (each must have a unique consensus length) */ int fmt; /* format code for alifile */ ESL_MSAFILE *afp = NULL; /* open alignment file, normal interface */ ESL_MSAFILE2 *afp2 = NULL; /* open alignment file, legacy small-memory interface */ ESL_MSA *msa = NULL; /* one multiple sequence alignment */ int status; /* easel return code */ int rflen; /* non-gap RF (consensus) length of each alignment */ int apos; /* counter over alignment positions */ char errbuf[ERRBUFSIZE]; /* for printing error messages */ FILE *ofp = NULL; /* output file for postscript */ FILE *tabfp = NULL; /* output file for text data, only set to non-null if --tabfile enabled */ SSPostscript_t *ps = NULL; /* the postscript data structure we create */ int *hc_nbins = NULL; /* hard-coded number of bins (colors) for each possible scheme */ float ***hc_scheme = NULL; /* colors for each pre-defined scheme */ float **hc_onecell = NULL; /* single colors used for binary color schemes */ int z; /* counter */ char *command = NULL; /* string for printing command to stdout */ char *date = NULL; /* date command was executed */ char *mask = NULL; /* first mask we'll use, string of '0's and '1's */ int masklen; /* length of mask */ char *mask2 = NULL; /* second mask we'll use, string of '0's and '1's */ int mask2len; /* length of second mask */ int mask_has_internal_zeroes = FALSE; /* does mask have any '0's with at least '1' on both sides? */ int mask2_has_internal_zeroes = FALSE; /* does mask have any '0's with at least '1' on both sides? */ /* counts of relevant values from the msa */ int *nseq_with_ins_ct = NULL; /* [0..ps->rflen] number of sequences with >=1 insert after each consensus position, only used if --ifreq */ int *nins_ct = NULL; /* [0..ps->rflen] total number of inserted nucleotides (over all seqs) after each consensus position, only used if --ifreq */ int **per_seq_ins_ct = NULL; /* [0..msa->nseq-1][0..ps->rflen] for each sequence, the number of inserts after each consensus position */ double **abc_ct = NULL; /* [0..msa->alen-1][0..abc->K], count of each nucleotide at each position, over all sequences, missing and nonnucleotides are *not counted* */ double ***bp_ct = NULL; /* [0..msa->alen-1][0..abc->Kp][0..abc->Kp], count of each possible base pair at each position, over all sequences, missing and nonnucleotides are *not counted* base pairs are indexed by 'i' for a base pair between positions i and j, where i < j. */ double **pp_ct = NULL; /* [0..msa->alen-1][0..11], count of reach posterior probability (PP) code, over all sequences, gap is 11 */ int *spos_ct = NULL; /* [0..msa->alen-1] per position count of first non-gap position, over all seqs */ int *epos_ct = NULL; /* [0..msa->alen-1] per position count of final non-gap position, over all seqs */ int *srfoff_ct = NULL; /* [0..rfpos..rflen-1], correction for spos_ct for rfpos, derived from ifile, only used if msa has had all insert columns removed */ int *erfoff_ct = NULL; /* [0..rfpos..rflen-1], correction for epos_ct for rfpos, derived from ifile, only used if msa has had all insert columns removed */ int *span_ct = NULL; /* [0..rfpos..rflen-1], number of sequences that 'span' position rfpos */ int64_t msa_alen; /* msa->alen */ int msa_nseq; /* msa->nseq */ /* variables related to small memory mode */ int do_small = TRUE; /* TRUE to operate in small memory mode, FALSE not to */ /* variables storing which pages to print */ int do_default_set = TRUE; /* TRUE if no options telling specifying what pages to draw were selected */ int do_cons = FALSE; int do_rf = FALSE; int do_info = FALSE; int do_mutinfo = FALSE; int do_ifreq = FALSE; int do_iavglen = FALSE; int do_dall = FALSE; int do_dint = FALSE; int do_prob = FALSE; int do_span = FALSE; int do_indi = FALSE; int do_maskcol = FALSE; int do_maskdiff = FALSE; int do_dfile = FALSE; int do_efile = FALSE; int need_span_ct = FALSE; /* TRUE if span_ct must be calculated (if do_dint || do_ifreq || do_iavglen || do_span) */ int tmp_Mb = 0; int predicted_Mb = 0; /* predicted size of the output file, calced if --indi */ /*********************************************** * Parse command line ***********************************************/ go = esl_getopts_Create(options); if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK || esl_opt_VerifyConfig(go) != eslOK) { printf("Failed to parse command line: %s\n", go->errbuf); esl_usage(stdout, argv[0], usage); printf("\nTo see more help on available options, do %s -h\n\n", argv[0]); exit(1); } if (esl_opt_GetBoolean(go, "-h") ) { esl_banner(stdout, argv[0], banner); esl_usage (stdout, argv[0], usage); puts("\n where basic options are:"); esl_opt_DisplayHelp(stdout, go, 1, 2, 80); puts("\noptions for alignment summary diagrams (incompatible with --indi):"); esl_opt_DisplayHelp(stdout, go, 2, 2, 80); puts("\noptions for drawing individual sequences (require --indi):"); esl_opt_DisplayHelp(stdout, go, 3, 2, 80); puts("\noptions for omitting parts of the diagram:"); esl_opt_DisplayHelp(stdout, go, 8, 2, 80); puts("\noptions for drawing simple two color diagrams of masks:"); esl_opt_DisplayHelp(stdout, go, 5, 2, 80); puts("\nexpert options for controlling individual seq diagrams (require --indi):"); esl_opt_DisplayHelp(stdout, go, 9, 2, 80); puts("\nexpert options related to consensus sequence definition:"); esl_opt_DisplayHelp(stdout, go, 7, 2, 80); puts("\nexpert options controlling style of masked positions:"); esl_opt_DisplayHelp(stdout, go, 4, 2, 80); puts("\nexpert options related to input files:"); esl_opt_DisplayHelp(stdout, go, 6, 2, 80); exit(0); } if (esl_opt_ArgNumber(go) != 3) { printf("Incorrect number of command line arguments.\n"); esl_usage(stdout, argv[0], usage); printf("\nTo see more help on available options, do %s -h\n\n", argv[0]); exit(1); } /* Check for incompatible options that aren't simple to check with esl_getopts */ /* --mask-a requires either --mask-x or --mask-u */ if (esl_opt_IsOn(go, "--mask-a") && (! esl_opt_IsOn(go, "--mask-u")) && (! esl_opt_IsOn(go, "--mask-x"))) { esl_fatal("--mask-a requires either --mask-u or mask-x"); } alifile = esl_opt_GetArg(go, 1); templatefile = esl_opt_GetArg(go, 2); outfile = esl_opt_GetArg(go, 3); if((status = get_command(go, errbuf, &command)) != eslOK) esl_fatal(errbuf); if((status = get_date(errbuf, &date)) != eslOK) esl_fatal(errbuf); /****************/ /* Premlinaries */ /****************/ /* allocate and fill predefined one-cell colors, these are hardcoded */ ESL_ALLOC(hc_onecell, sizeof(float *) * NOC); for(z = 0; z < NOC; z++) hc_onecell[z] = NULL; for(z = 0; z < NOC; z++) { ESL_ALLOC(hc_onecell[z], sizeof(float) * NCMYK); } hc_onecell[CYANOC][ICYAN] = CYAN_C; hc_onecell[CYANOC][IMGTA] = CYAN_M; hc_onecell[CYANOC][IYELW] = CYAN_Y; hc_onecell[CYANOC][IBLCK] = CYAN_K; hc_onecell[MAGENTAOC][ICYAN] = MAGENTA_C; hc_onecell[MAGENTAOC][IMGTA] = MAGENTA_M; hc_onecell[MAGENTAOC][IYELW] = MAGENTA_Y; hc_onecell[MAGENTAOC][IBLCK] = MAGENTA_K; hc_onecell[YELLOWOC][ICYAN] = YELLOW_C; hc_onecell[YELLOWOC][IMGTA] = YELLOW_M; hc_onecell[YELLOWOC][IYELW] = YELLOW_Y; hc_onecell[YELLOWOC][IBLCK] = YELLOW_K; hc_onecell[BLACKOC][ICYAN] = BLACK_C; hc_onecell[BLACKOC][IMGTA] = BLACK_M; hc_onecell[BLACKOC][IYELW] = BLACK_Y; hc_onecell[BLACKOC][IBLCK] = BLACK_K; hc_onecell[WHITEOC][ICYAN] = WHITE_C; hc_onecell[WHITEOC][IMGTA] = WHITE_M; hc_onecell[WHITEOC][IYELW] = WHITE_Y; hc_onecell[WHITEOC][IBLCK] = WHITE_K; hc_onecell[LIGHTGREYOC][ICYAN] = LIGHTGREY_C; hc_onecell[LIGHTGREYOC][IMGTA] = LIGHTGREY_M; hc_onecell[LIGHTGREYOC][IYELW] = LIGHTGREY_Y; hc_onecell[LIGHTGREYOC][IBLCK] = LIGHTGREY_K; hc_onecell[GREYOC][ICYAN] = GREY_C; hc_onecell[GREYOC][IMGTA] = GREY_M; hc_onecell[GREYOC][IYELW] = GREY_Y; hc_onecell[GREYOC][IBLCK] = GREY_K; hc_onecell[DARKGREYOC][ICYAN] = DARKGREY_C; hc_onecell[DARKGREYOC][IMGTA] = DARKGREY_M; hc_onecell[DARKGREYOC][IYELW] = DARKGREY_Y; hc_onecell[DARKGREYOC][IBLCK] = DARKGREY_K; hc_onecell[REDOC][ICYAN] = RED_C; hc_onecell[REDOC][IMGTA] = RED_M; hc_onecell[REDOC][IYELW] = RED_Y; hc_onecell[REDOC][IBLCK] = RED_K; hc_onecell[ORANGEOC][ICYAN] = ORANGE_C; hc_onecell[ORANGEOC][IMGTA] = ORANGE_M; hc_onecell[ORANGEOC][IYELW] = ORANGE_Y; hc_onecell[ORANGEOC][IBLCK] = ORANGE_K; hc_onecell[TEALOC][ICYAN] = TEAL_C; hc_onecell[TEALOC][IMGTA] = TEAL_M; hc_onecell[TEALOC][IYELW] = TEAL_Y; hc_onecell[TEALOC][IBLCK] = TEAL_K; hc_onecell[LIGHTGREENOC][ICYAN] = LIGHTGREEN_C; hc_onecell[LIGHTGREENOC][IMGTA] = LIGHTGREEN_M; hc_onecell[LIGHTGREENOC][IYELW] = LIGHTGREEN_Y; hc_onecell[LIGHTGREENOC][IBLCK] = LIGHTGREEN_K; hc_onecell[GREENOC][ICYAN] = GREEN_C; hc_onecell[GREENOC][IMGTA] = GREEN_M; hc_onecell[GREENOC][IYELW] = GREEN_Y; hc_onecell[GREENOC][IBLCK] = GREEN_K; hc_onecell[DARKGREENOC][ICYAN] = DARKGREEN_C; hc_onecell[DARKGREENOC][IMGTA] = DARKGREEN_M; hc_onecell[DARKGREENOC][IYELW] = DARKGREEN_Y; hc_onecell[DARKGREENOC][IBLCK] = DARKGREEN_K; hc_onecell[LIGHTPURPLEOC][ICYAN] = LIGHTPURPLE_C; hc_onecell[LIGHTPURPLEOC][IMGTA] = LIGHTPURPLE_M; hc_onecell[LIGHTPURPLEOC][IYELW] = LIGHTPURPLE_Y; hc_onecell[LIGHTPURPLEOC][IBLCK] = LIGHTPURPLE_K; hc_onecell[PURPLEOC][ICYAN] = PURPLE_C; hc_onecell[PURPLEOC][IMGTA] = PURPLE_M; hc_onecell[PURPLEOC][IYELW] = PURPLE_Y; hc_onecell[PURPLEOC][IBLCK] = PURPLE_K; hc_onecell[DARKPURPLEOC][ICYAN] = DARKPURPLE_C; hc_onecell[DARKPURPLEOC][IMGTA] = DARKPURPLE_M; hc_onecell[DARKPURPLEOC][IYELW] = DARKPURPLE_Y; hc_onecell[DARKPURPLEOC][IBLCK] = DARKPURPLE_K; /***********************************/ /* allocate and fill predefined color schemes, these are hardcoded */ ESL_ALLOC(hc_scheme, sizeof(float **) * NSCHEMES); for (z = 0; z < NSCHEMES; z++) hc_scheme[z] = NULL; ESL_ALLOC(hc_nbins, sizeof(int) * NSCHEMES); hc_nbins[RB_11_RH_SCHEME] = NRB_11_RH_SCHEME; hc_nbins[RB_11_RL_SCHEME] = NRB_11_RL_SCHEME; hc_nbins[RB_6_RH_SCHEME] = NRB_6_RH_SCHEME; hc_nbins[RB_6_RL_SCHEME] = NRB_6_RL_SCHEME; hc_nbins[RB_5_RH_SCHEME] = NRB_5_RH_SCHEME; hc_nbins[RB_5_RL_SCHEME] = NRB_5_RL_SCHEME; hc_nbins[RB_W5_OH_SCHEME] = NRB_W5_OH_SCHEME; /* RB_11_RH_SCHEME RainBow, 11 colors, Red High, blue low */ ESL_ALLOC(hc_scheme[RB_11_RH_SCHEME], sizeof(float *) * NRB_11_RH_SCHEME); for(z = 0; z < NRB_11_RH_SCHEME; z++) hc_scheme[RB_11_RH_SCHEME][z] = NULL; for(z = 0; z < NRB_11_RH_SCHEME; z++) { ESL_ALLOC(hc_scheme[RB_11_RH_SCHEME][z], sizeof(float) * NCMYK); } /* RB_11_RL_SCHEME RainBow, 11 colors, Red Low, blue high */ ESL_ALLOC(hc_scheme[RB_11_RL_SCHEME], sizeof(float *) * NRB_11_RL_SCHEME); for(z = 0; z < NRB_11_RL_SCHEME; z++) hc_scheme[RB_11_RL_SCHEME][z] = NULL; for(z = 0; z < NRB_11_RL_SCHEME; z++) { ESL_ALLOC(hc_scheme[RB_11_RL_SCHEME][z], sizeof(float) * NCMYK); } /* RB_6_RH_SCHEME RainBow, 6 colors, Red High, blue low */ ESL_ALLOC(hc_scheme[RB_6_RH_SCHEME], sizeof(float *) * NRB_6_RH_SCHEME); for(z = 0; z < NRB_6_RH_SCHEME; z++) hc_scheme[RB_6_RH_SCHEME][z] = NULL; for(z = 0; z < NRB_6_RH_SCHEME; z++) { ESL_ALLOC(hc_scheme[RB_6_RH_SCHEME][z], sizeof(float) * NCMYK); } /* RB_6_RL_SCHEME RainBow, 6 colors, Red Low, blue high */ ESL_ALLOC(hc_scheme[RB_6_RL_SCHEME], sizeof(float *) * NRB_6_RL_SCHEME); for(z = 0; z < NRB_6_RL_SCHEME; z++) hc_scheme[RB_6_RL_SCHEME][z] = NULL; for(z = 0; z < NRB_6_RL_SCHEME; z++) { ESL_ALLOC(hc_scheme[RB_6_RL_SCHEME][z], sizeof(float) * NCMYK); } /* RB_5_RH_SCHEME RainBow, 5 colors, Red High, blue low */ ESL_ALLOC(hc_scheme[RB_5_RH_SCHEME], sizeof(float *) * NRB_5_RH_SCHEME); for(z = 0; z < NRB_5_RH_SCHEME; z++) hc_scheme[RB_5_RH_SCHEME][z] = NULL; for(z = 0; z < NRB_5_RH_SCHEME; z++) { ESL_ALLOC(hc_scheme[RB_5_RH_SCHEME][z], sizeof(float) * NCMYK); } /* RB_5_RL_SCHEME RainBow, 5 colors, Red Low, blue high */ ESL_ALLOC(hc_scheme[RB_5_RL_SCHEME], sizeof(float *) * NRB_5_RL_SCHEME); for(z = 0; z < NRB_5_RL_SCHEME; z++) hc_scheme[RB_5_RL_SCHEME][z] = NULL; for(z = 0; z < NRB_5_RL_SCHEME; z++) { ESL_ALLOC(hc_scheme[RB_5_RL_SCHEME][z], sizeof(float) * NCMYK); } /* RB_W5_OH_SCHEME RainBow with white, 5 colors, Orange High, teal low, white lowest */ ESL_ALLOC(hc_scheme[RB_W5_OH_SCHEME], sizeof(float *) * NRB_W5_OH_SCHEME); for(z = 0; z < NRB_W5_OH_SCHEME; z++) hc_scheme[RB_W5_OH_SCHEME][z] = NULL; for(z = 0; z < NRB_W5_OH_SCHEME; z++) { ESL_ALLOC(hc_scheme[RB_W5_OH_SCHEME][z], sizeof(float) * NCMYK); } /***********************************/ /* fill scheme colors */ /* the 5 and 6 color rainbow schemes (the 5 color schemes are identical to the 6 color ones, they just omit blue */ hc_scheme[RB_6_RL_SCHEME][0][ICYAN] = hc_scheme[RB_6_RH_SCHEME][5][ICYAN] = hc_scheme[RB_5_RL_SCHEME][0][ICYAN] = hc_scheme[RB_5_RL_SCHEME][4][ICYAN] = RED2BLUE_1_OF_6_C; hc_scheme[RB_6_RL_SCHEME][0][IMGTA] = hc_scheme[RB_6_RH_SCHEME][5][IMGTA] = hc_scheme[RB_5_RL_SCHEME][0][IMGTA] = hc_scheme[RB_5_RL_SCHEME][4][IMGTA] = RED2BLUE_1_OF_6_M; hc_scheme[RB_6_RL_SCHEME][0][IYELW] = hc_scheme[RB_6_RH_SCHEME][5][IYELW] = hc_scheme[RB_5_RL_SCHEME][0][IYELW] = hc_scheme[RB_5_RL_SCHEME][4][IYELW] = RED2BLUE_1_OF_6_Y; hc_scheme[RB_6_RL_SCHEME][0][IBLCK] = hc_scheme[RB_6_RH_SCHEME][5][IBLCK] = hc_scheme[RB_5_RL_SCHEME][0][IBLCK] = hc_scheme[RB_5_RL_SCHEME][4][IBLCK] = RED2BLUE_1_OF_6_K; hc_scheme[RB_6_RL_SCHEME][1][ICYAN] = hc_scheme[RB_6_RH_SCHEME][4][ICYAN] = hc_scheme[RB_5_RL_SCHEME][1][ICYAN] = hc_scheme[RB_5_RL_SCHEME][3][ICYAN] = RED2BLUE_2_OF_6_C; hc_scheme[RB_6_RL_SCHEME][1][IMGTA] = hc_scheme[RB_6_RH_SCHEME][4][IMGTA] = hc_scheme[RB_5_RL_SCHEME][1][IMGTA] = hc_scheme[RB_5_RL_SCHEME][3][IMGTA] = RED2BLUE_2_OF_6_M; hc_scheme[RB_6_RL_SCHEME][1][IYELW] = hc_scheme[RB_6_RH_SCHEME][4][IYELW] = hc_scheme[RB_5_RL_SCHEME][1][IYELW] = hc_scheme[RB_5_RL_SCHEME][3][IYELW] = RED2BLUE_2_OF_6_Y; hc_scheme[RB_6_RL_SCHEME][1][IBLCK] = hc_scheme[RB_6_RH_SCHEME][4][IBLCK] = hc_scheme[RB_5_RL_SCHEME][1][IBLCK] = hc_scheme[RB_5_RL_SCHEME][3][IBLCK] = RED2BLUE_2_OF_6_K; hc_scheme[RB_6_RL_SCHEME][2][ICYAN] = hc_scheme[RB_6_RH_SCHEME][3][ICYAN] = hc_scheme[RB_5_RL_SCHEME][2][ICYAN] = RED2BLUE_3_OF_6_C; hc_scheme[RB_6_RL_SCHEME][2][IMGTA] = hc_scheme[RB_6_RH_SCHEME][3][IMGTA] = hc_scheme[RB_5_RL_SCHEME][2][IMGTA] = RED2BLUE_3_OF_6_M; hc_scheme[RB_6_RL_SCHEME][2][IYELW] = hc_scheme[RB_6_RH_SCHEME][3][IYELW] = hc_scheme[RB_5_RL_SCHEME][2][IYELW] = RED2BLUE_3_OF_6_Y; hc_scheme[RB_6_RL_SCHEME][2][IBLCK] = hc_scheme[RB_6_RH_SCHEME][3][IBLCK] = hc_scheme[RB_5_RL_SCHEME][2][IBLCK] = RED2BLUE_3_OF_6_K; hc_scheme[RB_6_RL_SCHEME][3][ICYAN] = hc_scheme[RB_6_RH_SCHEME][2][ICYAN] = hc_scheme[RB_5_RL_SCHEME][3][ICYAN] = hc_scheme[RB_5_RL_SCHEME][1][ICYAN] = RED2BLUE_4_OF_6_C; hc_scheme[RB_6_RL_SCHEME][3][IMGTA] = hc_scheme[RB_6_RH_SCHEME][2][IMGTA] = hc_scheme[RB_5_RL_SCHEME][3][IMGTA] = hc_scheme[RB_5_RL_SCHEME][1][IMGTA] = RED2BLUE_4_OF_6_M; hc_scheme[RB_6_RL_SCHEME][3][IYELW] = hc_scheme[RB_6_RH_SCHEME][2][IYELW] = hc_scheme[RB_5_RL_SCHEME][3][IYELW] = hc_scheme[RB_5_RL_SCHEME][1][IYELW] = RED2BLUE_4_OF_6_Y; hc_scheme[RB_6_RL_SCHEME][3][IBLCK] = hc_scheme[RB_6_RH_SCHEME][2][IBLCK] = hc_scheme[RB_5_RL_SCHEME][3][IBLCK] = hc_scheme[RB_5_RL_SCHEME][1][IBLCK] = RED2BLUE_4_OF_6_K; hc_scheme[RB_6_RL_SCHEME][4][ICYAN] = hc_scheme[RB_6_RH_SCHEME][1][ICYAN] = hc_scheme[RB_5_RL_SCHEME][4][ICYAN] = hc_scheme[RB_5_RL_SCHEME][0][ICYAN] = RED2BLUE_5_OF_6_C; hc_scheme[RB_6_RL_SCHEME][4][IMGTA] = hc_scheme[RB_6_RH_SCHEME][1][IMGTA] = hc_scheme[RB_5_RL_SCHEME][4][IMGTA] = hc_scheme[RB_5_RL_SCHEME][0][IMGTA] = RED2BLUE_5_OF_6_M; hc_scheme[RB_6_RL_SCHEME][4][IYELW] = hc_scheme[RB_6_RH_SCHEME][1][IYELW] = hc_scheme[RB_5_RL_SCHEME][4][IYELW] = hc_scheme[RB_5_RL_SCHEME][0][IYELW] = RED2BLUE_5_OF_6_Y; hc_scheme[RB_6_RL_SCHEME][4][IBLCK] = hc_scheme[RB_6_RH_SCHEME][1][IBLCK] = hc_scheme[RB_5_RL_SCHEME][4][IBLCK] = hc_scheme[RB_5_RL_SCHEME][0][IBLCK] = RED2BLUE_5_OF_6_K; hc_scheme[RB_6_RL_SCHEME][5][ICYAN] = hc_scheme[RB_6_RH_SCHEME][0][ICYAN] = RED2BLUE_6_OF_6_C; hc_scheme[RB_6_RL_SCHEME][5][IMGTA] = hc_scheme[RB_6_RH_SCHEME][0][IMGTA] = RED2BLUE_6_OF_6_M; hc_scheme[RB_6_RL_SCHEME][5][IYELW] = hc_scheme[RB_6_RH_SCHEME][0][IYELW] = RED2BLUE_6_OF_6_Y; hc_scheme[RB_6_RL_SCHEME][5][IBLCK] = hc_scheme[RB_6_RH_SCHEME][0][IBLCK] = RED2BLUE_6_OF_6_K; /* the special 4 color, plus white color scheme */ hc_scheme[RB_W5_OH_SCHEME][0][ICYAN] = WHITE_C; hc_scheme[RB_W5_OH_SCHEME][0][IMGTA] = WHITE_M; hc_scheme[RB_W5_OH_SCHEME][0][IYELW] = WHITE_Y; hc_scheme[RB_W5_OH_SCHEME][0][IBLCK] = WHITE_K; hc_scheme[RB_W5_OH_SCHEME][1][ICYAN] = RED2BLUE_5_OF_6_C; hc_scheme[RB_W5_OH_SCHEME][1][IMGTA] = RED2BLUE_5_OF_6_M; hc_scheme[RB_W5_OH_SCHEME][1][IYELW] = RED2BLUE_5_OF_6_Y; hc_scheme[RB_W5_OH_SCHEME][1][IBLCK] = RED2BLUE_5_OF_6_K; hc_scheme[RB_W5_OH_SCHEME][2][ICYAN] = RED2BLUE_4_OF_6_C; hc_scheme[RB_W5_OH_SCHEME][2][IMGTA] = RED2BLUE_4_OF_6_M; hc_scheme[RB_W5_OH_SCHEME][2][IYELW] = RED2BLUE_4_OF_6_Y; hc_scheme[RB_W5_OH_SCHEME][2][IBLCK] = RED2BLUE_4_OF_6_K; hc_scheme[RB_W5_OH_SCHEME][3][ICYAN] = RED2BLUE_3_OF_6_C; hc_scheme[RB_W5_OH_SCHEME][3][IMGTA] = RED2BLUE_3_OF_6_M; hc_scheme[RB_W5_OH_SCHEME][3][IYELW] = RED2BLUE_3_OF_6_Y; hc_scheme[RB_W5_OH_SCHEME][3][IBLCK] = RED2BLUE_3_OF_6_K; hc_scheme[RB_W5_OH_SCHEME][4][ICYAN] = RED2BLUE_2_OF_6_C; hc_scheme[RB_W5_OH_SCHEME][4][IMGTA] = RED2BLUE_2_OF_6_M; hc_scheme[RB_W5_OH_SCHEME][4][IYELW] = RED2BLUE_2_OF_6_Y; hc_scheme[RB_W5_OH_SCHEME][4][IBLCK] = RED2BLUE_2_OF_6_K; /* the 11 color rainbow schemes */ hc_scheme[RB_11_RL_SCHEME][0][ICYAN] = hc_scheme[RB_11_RH_SCHEME][10][ICYAN] = RED2BLUE_1_OF_11_C; hc_scheme[RB_11_RL_SCHEME][0][IMGTA] = hc_scheme[RB_11_RH_SCHEME][10][IMGTA] = RED2BLUE_1_OF_11_M; hc_scheme[RB_11_RL_SCHEME][0][IYELW] = hc_scheme[RB_11_RH_SCHEME][10][IYELW] = RED2BLUE_1_OF_11_Y; hc_scheme[RB_11_RL_SCHEME][0][IBLCK] = hc_scheme[RB_11_RH_SCHEME][10][IBLCK] = RED2BLUE_1_OF_11_K; hc_scheme[RB_11_RL_SCHEME][1][ICYAN] = hc_scheme[RB_11_RH_SCHEME][9][ICYAN] = RED2BLUE_2_OF_11_C; hc_scheme[RB_11_RL_SCHEME][1][IMGTA] = hc_scheme[RB_11_RH_SCHEME][9][IMGTA] = RED2BLUE_2_OF_11_M; hc_scheme[RB_11_RL_SCHEME][1][IYELW] = hc_scheme[RB_11_RH_SCHEME][9][IYELW] = RED2BLUE_2_OF_11_Y; hc_scheme[RB_11_RL_SCHEME][1][IBLCK] = hc_scheme[RB_11_RH_SCHEME][9][IBLCK] = RED2BLUE_2_OF_11_K; hc_scheme[RB_11_RL_SCHEME][2][ICYAN] = hc_scheme[RB_11_RH_SCHEME][8][ICYAN] = RED2BLUE_3_OF_11_C; hc_scheme[RB_11_RL_SCHEME][2][IMGTA] = hc_scheme[RB_11_RH_SCHEME][8][IMGTA] = RED2BLUE_3_OF_11_M; hc_scheme[RB_11_RL_SCHEME][2][IYELW] = hc_scheme[RB_11_RH_SCHEME][8][IYELW] = RED2BLUE_3_OF_11_Y; hc_scheme[RB_11_RL_SCHEME][2][IBLCK] = hc_scheme[RB_11_RH_SCHEME][8][IBLCK] = RED2BLUE_3_OF_11_K; hc_scheme[RB_11_RL_SCHEME][3][ICYAN] = hc_scheme[RB_11_RH_SCHEME][7][ICYAN] = RED2BLUE_4_OF_11_C; hc_scheme[RB_11_RL_SCHEME][3][IMGTA] = hc_scheme[RB_11_RH_SCHEME][7][IMGTA] = RED2BLUE_4_OF_11_M; hc_scheme[RB_11_RL_SCHEME][3][IYELW] = hc_scheme[RB_11_RH_SCHEME][7][IYELW] = RED2BLUE_4_OF_11_Y; hc_scheme[RB_11_RL_SCHEME][3][IBLCK] = hc_scheme[RB_11_RH_SCHEME][7][IBLCK] = RED2BLUE_4_OF_11_K; hc_scheme[RB_11_RL_SCHEME][4][ICYAN] = hc_scheme[RB_11_RH_SCHEME][6][ICYAN] = RED2BLUE_5_OF_11_C; hc_scheme[RB_11_RL_SCHEME][4][IMGTA] = hc_scheme[RB_11_RH_SCHEME][6][IMGTA] = RED2BLUE_5_OF_11_M; hc_scheme[RB_11_RL_SCHEME][4][IYELW] = hc_scheme[RB_11_RH_SCHEME][6][IYELW] = RED2BLUE_5_OF_11_Y; hc_scheme[RB_11_RL_SCHEME][4][IBLCK] = hc_scheme[RB_11_RH_SCHEME][6][IBLCK] = RED2BLUE_5_OF_11_K; hc_scheme[RB_11_RL_SCHEME][5][ICYAN] = hc_scheme[RB_11_RH_SCHEME][5][ICYAN] = RED2BLUE_6_OF_11_C; hc_scheme[RB_11_RL_SCHEME][5][IMGTA] = hc_scheme[RB_11_RH_SCHEME][5][IMGTA] = RED2BLUE_6_OF_11_M; hc_scheme[RB_11_RL_SCHEME][5][IYELW] = hc_scheme[RB_11_RH_SCHEME][5][IYELW] = RED2BLUE_6_OF_11_Y; hc_scheme[RB_11_RL_SCHEME][5][IBLCK] = hc_scheme[RB_11_RH_SCHEME][5][IBLCK] = RED2BLUE_6_OF_11_K; hc_scheme[RB_11_RL_SCHEME][6][ICYAN] = hc_scheme[RB_11_RH_SCHEME][4][ICYAN] = RED2BLUE_7_OF_11_C; hc_scheme[RB_11_RL_SCHEME][6][IMGTA] = hc_scheme[RB_11_RH_SCHEME][4][IMGTA] = RED2BLUE_7_OF_11_M; hc_scheme[RB_11_RL_SCHEME][6][IYELW] = hc_scheme[RB_11_RH_SCHEME][4][IYELW] = RED2BLUE_7_OF_11_Y; hc_scheme[RB_11_RL_SCHEME][6][IBLCK] = hc_scheme[RB_11_RH_SCHEME][4][IBLCK] = RED2BLUE_7_OF_11_K; hc_scheme[RB_11_RL_SCHEME][7][ICYAN] = hc_scheme[RB_11_RH_SCHEME][3][ICYAN] = RED2BLUE_8_OF_11_C; hc_scheme[RB_11_RL_SCHEME][7][IMGTA] = hc_scheme[RB_11_RH_SCHEME][3][IMGTA] = RED2BLUE_8_OF_11_M; hc_scheme[RB_11_RL_SCHEME][7][IYELW] = hc_scheme[RB_11_RH_SCHEME][3][IYELW] = RED2BLUE_8_OF_11_Y; hc_scheme[RB_11_RL_SCHEME][7][IBLCK] = hc_scheme[RB_11_RH_SCHEME][3][IBLCK] = RED2BLUE_8_OF_11_K; hc_scheme[RB_11_RL_SCHEME][8][ICYAN] = hc_scheme[RB_11_RH_SCHEME][2][ICYAN] = RED2BLUE_9_OF_11_C; hc_scheme[RB_11_RL_SCHEME][8][IMGTA] = hc_scheme[RB_11_RH_SCHEME][2][IMGTA] = RED2BLUE_9_OF_11_M; hc_scheme[RB_11_RL_SCHEME][8][IYELW] = hc_scheme[RB_11_RH_SCHEME][2][IYELW] = RED2BLUE_9_OF_11_Y; hc_scheme[RB_11_RL_SCHEME][8][IBLCK] = hc_scheme[RB_11_RH_SCHEME][2][IBLCK] = RED2BLUE_9_OF_11_K; hc_scheme[RB_11_RL_SCHEME][9][ICYAN] = hc_scheme[RB_11_RH_SCHEME][1][ICYAN] = RED2BLUE_10_OF_11_C; hc_scheme[RB_11_RL_SCHEME][9][IMGTA] = hc_scheme[RB_11_RH_SCHEME][1][IMGTA] = RED2BLUE_10_OF_11_M; hc_scheme[RB_11_RL_SCHEME][9][IYELW] = hc_scheme[RB_11_RH_SCHEME][1][IYELW] = RED2BLUE_10_OF_11_Y; hc_scheme[RB_11_RL_SCHEME][9][IBLCK] = hc_scheme[RB_11_RH_SCHEME][1][IBLCK] = RED2BLUE_10_OF_11_K; hc_scheme[RB_11_RL_SCHEME][10][ICYAN] = hc_scheme[RB_11_RH_SCHEME][0][ICYAN] = RED2BLUE_11_OF_11_C; hc_scheme[RB_11_RL_SCHEME][10][IMGTA] = hc_scheme[RB_11_RH_SCHEME][0][IMGTA] = RED2BLUE_11_OF_11_M; hc_scheme[RB_11_RL_SCHEME][10][IYELW] = hc_scheme[RB_11_RH_SCHEME][0][IYELW] = RED2BLUE_11_OF_11_Y; hc_scheme[RB_11_RL_SCHEME][10][IBLCK] = hc_scheme[RB_11_RH_SCHEME][0][IBLCK] = RED2BLUE_11_OF_11_K; /***************************************** * Open the MSA file; determine alphabet; *****************************************/ do_small = esl_opt_GetBoolean(go, "--small") ? TRUE : FALSE; fmt = do_small ? eslMSAFILE_PFAM : eslMSAFILE_STOCKHOLM; abc = esl_alphabet_Create(eslRNA); /* Assert RNA alphabet */ /* is only used for gap counting, I believe * alignments are opened in TEXT mode. */ if (do_small) { status = esl_msafile2_Open(alifile, NULL, &afp2); if (status == eslENOTFOUND) esl_fatal("Alignment file %s doesn't exist or is not readable\n", alifile); else if (status != eslOK) esl_fatal("Alignment file open failed with error %d\n", status); } else { status = esl_msafile_Open(NULL, alifile, NULL, fmt, NULL, &afp); if (status != eslOK) esl_msafile_OpenFailure(afp, status); } /* Read the mask files, if nec */ if(esl_opt_IsOn(go, "--mask")) { if((status = read_mask_file(esl_opt_GetString(go, "--mask"), errbuf, &mask, &masklen, &mask_has_internal_zeroes)) != eslOK) esl_fatal(errbuf); } if(esl_opt_IsOn(go, "--mask-diff")) { if((status = read_mask_file(esl_opt_GetString(go, "--mask-diff"), errbuf, &mask2, &mask2len, &mask2_has_internal_zeroes)) != eslOK) esl_fatal(errbuf); if(masklen != mask2len) esl_fatal("Mask in %f length (%d) differs from mask in %f (%d)!", esl_opt_GetString(go, "--mask"), masklen, esl_opt_GetString(go, "--mask-diff"), mask2len); } /* Open output files, if necessary */ if (esl_opt_IsOn(go, "--tabfile")) { if((tabfp = fopen(esl_opt_GetString(go, "--tabfile"), "w")) == NULL) esl_fatal("Failed to open output file %s\n", esl_opt_GetString(go, "--tabfile")); } /********************** * Read the alignment * **********************/ if (do_small) { status = esl_msafile2_ReadInfoPfam(afp2, NULL, abc, -1, NULL, NULL, &msa, &msa_nseq, &msa_alen, NULL, NULL, NULL, NULL, NULL, &abc_ct, &pp_ct, NULL, NULL, NULL); if (status == eslEFORMAT) esl_fatal("Alignment file parse error:\n%s\n", afp2->errbuf); else if (status == eslEINVAL) esl_fatal("Alignment file parse error:\n%s\n", afp2->errbuf); else if (status == eslEOF) esl_fatal("No alignments found in file %s\n", alifile); else if (status != eslOK) esl_fatal("Alignment file read failed with error code %d\n%s", status, afp2); msa->alen = msa_alen; } else { status = esl_msafile_Read(afp, &msa); /* if ! do_small, we read full aln into memory */ if (status != eslOK) esl_msafile_ReadFailure(afp, status); msa_nseq = msa->nseq; msa_alen = msa->alen; } if(msa->rf == NULL) esl_fatal("First MSA in %s does not have RF annotation.", alifile); /* determine non-gap RF length (consensus length) */ rflen = 0; for(apos = 0; apos < msa->alen; apos++) { if(esl_abc_CIsResidue(abc, msa->rf[apos])) { rflen++; } } /* We've read the alignment, now read the template postscript file (we do this second b/c the RF len of the alignment tells us which postscript template to use) */ if((status = parse_template_file(templatefile, go, errbuf, rflen, &ps) != eslOK)) esl_fatal(errbuf); /************************************************************************************************************** * Now that we have the msa and know what template we're using, determine what type of pages we'll be drawing * **************************************************************************************************************/ /* do_default_set: this is TRUE if either -d is enabled AND/OR zero of: * {--info, --mutinfo, --ifreq, --iavglen, --dall, --dint, --span, --mask-col, --mask-diff, * --dfile, --efile, --cons, --prob, --rf, --indi} are enabled. * When do_default_set is TRUE, we draw cons, info, mutinfo, ifreq, iavglen, dall, and prob * (if the alignment has posterior probabilities). * * Careful: this block assumes that all boolean options are OFF (FALSE) by default */ do_default_set = TRUE; if(esl_opt_GetBoolean(go, "--info")) { do_info = TRUE; do_default_set = FALSE; } if(esl_opt_GetBoolean(go, "--mutinfo")) { do_mutinfo = TRUE; do_default_set = FALSE; } if(esl_opt_GetBoolean(go, "--ifreq")) { do_ifreq = TRUE; do_default_set = FALSE; } if(esl_opt_GetBoolean(go, "--iavglen")) { do_iavglen = TRUE; do_default_set = FALSE; } if(esl_opt_GetBoolean(go, "--dall")) { do_dall = TRUE; do_default_set = FALSE; } if(esl_opt_GetBoolean(go, "--dint")) { do_dint = TRUE; do_default_set = FALSE; } if(esl_opt_GetBoolean(go, "--prob")) { do_prob = TRUE; do_default_set = FALSE; } if(esl_opt_GetBoolean(go, "--span")) { do_span = TRUE; do_default_set = FALSE; } if(esl_opt_GetBoolean(go, "--mask-col")) { do_maskcol = TRUE; do_default_set = FALSE; } if(esl_opt_IsOn (go, "--mask-diff")) { do_maskdiff = TRUE; do_default_set = FALSE; } if(esl_opt_IsOn (go, "--dfile")) { do_dfile = TRUE; do_default_set = FALSE; } if(esl_opt_IsOn (go, "--efile")) { do_efile = TRUE; do_default_set = FALSE; } if(esl_opt_GetBoolean(go, "--cons")) { do_cons = TRUE; do_default_set = FALSE; } if(esl_opt_GetBoolean(go, "--rf")) { if(msa->rf == NULL) esl_fatal("--rf selected by msa does not have #=GC RF annotation"); do_rf = TRUE; do_default_set = FALSE; } if(esl_opt_GetBoolean(go, "--indi")) { do_indi = TRUE; do_default_set = FALSE; /* Predict size of indi output file, based on two data points: * 2000 page tRNA rflen=71 is 35 Mb, 2000 page archaeal SSU rflen 1508 is 560 Mb, * =~ 0.0002 Mb per page per rfpos */ predicted_Mb = (int) (ps->rflen * 0.0002 * msa_nseq); if(! esl_opt_GetBoolean(go, "--no-pp")) predicted_Mb *= 2; /* round to nearest 10 Mb */ tmp_Mb = 10; while(tmp_Mb < predicted_Mb) tmp_Mb += 10; predicted_Mb = tmp_Mb; if(predicted_Mb > MAXMBWITHOUTFORCE && (! esl_opt_GetBoolean(go, "-f"))) { esl_fatal("WARNING: drawing individual seqs and msa has %d seqs in it,\noutput postcript file will be large (~%d Mb).\nUse -f to override this warning and do it anyway.", msa_nseq, predicted_Mb); } } /* if -d: if we've made do_default_set as FALSE, we set it back to TRUE */ if(esl_opt_GetBoolean(go, "-d")) do_default_set = TRUE; if(do_default_set) { /* set default pages */ do_cons = do_info = do_mutinfo = do_ifreq = do_iavglen = do_dall = TRUE; if((do_small && pp_ct != NULL) || (msa->pp != NULL)) do_prob = TRUE; } /* determine if tabfile was incorrectly used */ if(tabfp != NULL && do_info == FALSE && do_mutinfo == FALSE && do_ifreq == FALSE && do_prob == FALSE && do_iavglen == FALSE && do_dall == FALSE && do_dint == FALSE && do_span == FALSE && do_indi == FALSE) { esl_fatal("--tabfile only makes sense w/0 other options, or with >= 1 of --info,--mutinfo,--ifreq,--iavglen,--prob,--dall,--dint,--span,--indi"); } need_span_ct = (do_dint || do_span || do_ifreq || do_iavglen) ? TRUE : FALSE; if(do_small && (do_dint || do_span || do_ifreq || do_iavglen || do_mutinfo)) { /* If we're in small mem mode, now that we know msa->rf and msa->ss_cons, * we do a second read of the msa to get bpct, spos_ct and epos_ct, * but only if we need them (if --span, --dint, or --mutinfo). * To do this, we close the alifile and reopen it, so we can read the 1st * alignment again. */ esl_msafile2_Close(afp2); status = esl_msafile2_Open(alifile, NULL, &afp2); if (status == eslENOTFOUND) esl_fatal("2nd pass, alignment file %s doesn't exist or is not readable\n", alifile); else if (status == eslEFORMAT) esl_fatal("2nd pass, couldn't determine format of alignment %s\n", alifile); else if (status != eslOK) esl_fatal("2nd pass, alignment file open failed with error %d\n", status); status = esl_msafile2_ReadInfoPfam(afp2, NULL, abc, msa_alen, msa->rf, msa->ss_cons, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, &bp_ct, &spos_ct, &epos_ct); if (status == eslEFORMAT) esl_fatal("2nd pass, Alignment file parse error:\n%s\n", afp2->errbuf); else if (status == eslEINVAL) esl_fatal("2nd pass, Alignment file parse error:\n%s\n", afp2->errbuf); else if (status == eslEOF) esl_fatal("2nd pass, No alignments found in file %s\n", alifile); else if (status != eslOK) esl_fatal("2nd pass, Alignment file read failed with error code %d\n", status); } /* if we get here, the postscript file has been successfully read; now we open the output file */ if(ofp == NULL) { /* open postscript output file for writing */ if ((ofp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open output postscript file %s\n", esl_opt_GetArg(go, 2)); } /* determine position for header and legend */ if((status = setup_sspostscript(ps, errbuf) != eslOK)) esl_fatal(errbuf); if(ps->rflen == 0) esl_fatal("MSA has consensus (non-gap RF) length of %d which != template file consensus length of %d.", rflen, ps->rflen); if(rflen != ps->rflen) esl_fatal("MSA has consensus (non-gap RF) length of %d which != template file consensus length of %d.", rflen, ps->rflen); /* add the mask if there is one */ if(mask != NULL) add_mask_to_ss_postscript(ps, mask); if(mask != NULL && ps->rflen != masklen) esl_fatal("MSA has consensus (non-gap RF) length of %d which != lane mask length of %d from mask file %s.", rflen, masklen, esl_opt_GetString(go, "--mask")); if ((status = validate_and_update_sspostscript_given_msa(go, abc, ps, msa, msa_nseq, errbuf)) != eslOK) esl_fatal(errbuf); /* get the information we need from the alignment */ if(! do_small) { /* derive counts from the msa for postscript diagrams, we do this our functions for drawing diagrams work in small mem or big mem mode */ if((status = count_msa(abc, msa, errbuf, &(abc_ct), &(bp_ct), (do_prob ? &(pp_ct) : NULL), &(spos_ct), &(epos_ct))) != eslOK) esl_fatal(errbuf); } if (esl_opt_GetBoolean(go, "--prob") && pp_ct == NULL) esl_fatal("--prob requires all sequences have PP annotation"); /* read the insert file, if nec, we have to do this before we determine the span count in case inserts have been removed from the msa, * in which case the spos_ct and epos_ct's from either count_msa or esl_msafile2_ReadInfoPfam() could be slightly incorrect, we'll use * srfoff_ct and erfoff_ct from get_insert_info_from_ifile() to correct them when we derive span_ct from spos_ct and epos_ct together in get_span_ct(). */ if(esl_opt_IsOn(go, "--ifile")) { get_insert_info_from_ifile((esl_opt_GetString(go, "--ifile")), ps->rflen, msa_nseq, NULL, &(nseq_with_ins_ct), &(nins_ct), NULL, &srfoff_ct, &erfoff_ct); /* dies with esl_fatal() upon an error */ } /* determine span count */ if(need_span_ct) { if((status = get_span_ct(ps->msa_rf2a_map, msa_alen, ps->rflen, msa_nseq, spos_ct, epos_ct, srfoff_ct, erfoff_ct, &span_ct)) != eslOK) esl_fatal("Out of memory, getting span_ct array."); } /* determine consensus sequence */ if((status = get_consensus_seqs_from_abc_ct(go, ps, errbuf, abc_ct, abc, msa_alen)) != eslOK) esl_fatal(errbuf); /* step through each type of page, creating it if nec */ if(do_cons) { /* this will work in either small memory or normal memory mode */ if((status = cons_seq_sspostscript(go, errbuf, ps, hc_onecell, BLACKOC, /* one-cell legend, watson-crick bp color */ GREENOC, /* one-cell legend, G-U or U-G bp color */ REDOC, /* one-cell legend, color for noncanonical bps */ LIGHTPURPLEOC, /* one-cell legend, internal double-gap bp color */ LIGHTPURPLEOC)) != eslOK) /* one-cell legend, internal half-gap bp color, only relevant if do_rescol == TRUE */ esl_fatal(errbuf); } if(do_rf) { /* this will work in either small memory or normal memory mode */ if((status = rf_seq_sspostscript(go, errbuf, ps, msa, (! esl_opt_GetBoolean(go, "--no-bp")), hc_onecell, BLACKOC, /* one-cell legend, watson-crick bp color, only relevant if do_rescol == TRUE */ GREENOC, /* one-cell legend, G-U or U-G bp color, only relevant if do_rescol == TRUE */ REDOC)) != eslOK) /* one-cell legend, color for noncanonical bps */ esl_fatal(errbuf); } if(do_info) { if((status = infocontent_sspostscript(go, abc, errbuf, ps, abc_ct, msa_nseq, hc_scheme, RB_6_RL_SCHEME, hc_nbins[RB_6_RL_SCHEME], hc_onecell, LIGHTGREYOC, tabfp)) != eslOK) esl_fatal(errbuf); } if(do_mutinfo) { /* mutual info page */ if((status = mutual_information_sspostscript(go, abc, errbuf, ps, bp_ct, msa_nseq, hc_scheme, RB_6_RH_SCHEME, hc_nbins[RB_6_RH_SCHEME], hc_onecell, GREYOC, LIGHTGREYOC, tabfp)) != eslOK) esl_fatal(errbuf); } if(do_ifreq || do_iavglen) { /* insert frequency page */ /* first, determine number of sequences with inserts after each position, 3 different ways depending on command line options */ if(esl_opt_IsOn(go, "--ifile")) { /* read the insert file from cmalign */ /* we've already read the ifile above, and filled nseq_with_ins_ct, but we check here */ if(nseq_with_ins_ct == NULL) esl_fatal("Internal error, --ifile selected, but not read"); } else if (do_small) { /* use abc_ct to derive nseq_with_ins_ct */ get_insert_info_from_abc_ct(abc_ct, abc, msa->rf, msa_alen, ps->rflen, &(nseq_with_ins_ct), &(nins_ct)); /* dies with esl_fatal() upon an error */ } else { get_insert_info_from_msa(abc, msa, ps->rflen, &(nseq_with_ins_ct), &(nins_ct), NULL); /* dies with esl_fatal() upon an error */ } /* now draw the insert diagram */ if(do_ifreq) { if((status = insertfreq_sspostscript(go, errbuf, ps, nseq_with_ins_ct, span_ct, msa_nseq, hc_scheme, RB_6_RH_SCHEME, hc_nbins[RB_6_RH_SCHEME], hc_onecell, LIGHTGREYOC, GREYOC, tabfp)) != eslOK) esl_fatal(errbuf); } if(do_iavglen) { if((status = insertavglen_sspostscript(go, errbuf, ps, nseq_with_ins_ct, nins_ct, span_ct, msa_nseq, hc_scheme, RB_6_RH_SCHEME, hc_nbins[RB_6_RH_SCHEME], hc_onecell, LIGHTGREYOC, tabfp)) != eslOK) esl_fatal(errbuf); } } if(do_dall) { /* make a new postscript page marking all deletes */ if((status = delete_sspostscript(go, abc, errbuf, ps, abc_ct, span_ct, msa_nseq, TRUE, hc_scheme, RB_6_RH_SCHEME, hc_nbins[RB_6_RH_SCHEME], hc_onecell, LIGHTGREYOC, DARKGREYOC, tabfp)) != eslOK) esl_fatal(errbuf); } if(do_dint) { /* internal deletes */ if((status = delete_sspostscript(go, abc, errbuf, ps, abc_ct, span_ct, msa_nseq, FALSE, hc_scheme, RB_6_RH_SCHEME, hc_nbins[RB_6_RH_SCHEME], hc_onecell, LIGHTGREYOC, DARKGREYOC, tabfp)) != eslOK) esl_fatal(errbuf); } if(do_prob && pp_ct != NULL) { /* avg post prob */ if((status = avg_posteriors_sspostscript(go, abc, errbuf, ps, pp_ct, msa_nseq, hc_scheme, RB_6_RL_SCHEME, hc_nbins[RB_6_RL_SCHEME], hc_onecell, LIGHTGREYOC, tabfp)) != eslOK) esl_fatal(errbuf); } if(do_span) { /* span */ if((status = span_sspostscript(go, errbuf, ps, span_ct, msa_nseq, hc_scheme, RB_6_RL_SCHEME, hc_nbins[RB_6_RL_SCHEME], hc_onecell, LIGHTGREYOC, BLACKOC, tabfp)) != eslOK) esl_fatal(errbuf); } if(do_maskcol) { /* Paint positions excluded by the mask magenta, unless the mask has zero internal exclusions. * Such a mask is a 'truncating' mask, that excludes only a 5' contiguous set of columns, and a 3' contiguous set of columns, in this case paint excluded positions light grey. */ if((status = colormask_sspostscript(go, errbuf, ps, msa, hc_onecell, BLACKOC, (mask_has_internal_zeroes ? MAGENTAOC : LIGHTGREYOC))) != eslOK) esl_fatal(errbuf); } if(do_maskdiff) { if((status = diffmask_sspostscript(go, errbuf, ps, msa, mask2, hc_onecell, BLACKOC, CYANOC, MAGENTAOC, LIGHTGREYOC)) != eslOK) esl_fatal(errbuf); } if(do_dfile) { if((status = drawfile2sspostscript(go, errbuf, ps, hc_scheme, RB_6_RH_SCHEME, hc_nbins[RB_6_RH_SCHEME])) != eslOK) esl_fatal(errbuf); } if(do_efile) { if((status = expertfile2sspostscript(go, errbuf, ps)) != eslOK) esl_fatal(errbuf); } if(do_indi) { /* we're printing all individual seqs */ /* get insert info we'll use in individuals_sspostscript() */ if(esl_opt_IsOn(go, "--ifile")) { /* read the insert file from cmalign, with info from all seqs */ get_insert_info_from_ifile((esl_opt_GetString(go, "--ifile")), ps->rflen, msa_nseq, NULL, NULL, NULL, &(per_seq_ins_ct), NULL, NULL); /* dies with esl_fatal() upon an error */ } else { get_insert_info_from_msa(abc, msa, ps->rflen, NULL, NULL, &per_seq_ins_ct); /* dies with esl_fatal() upon an error */ } /* we have msa and per_seq_ins_ct for all possible combos of --small and --ifile, * draw the individual sequence pages */ if((status = individuals_sspostscript(go, abc, errbuf, ps, abc_ct, msa, per_seq_ins_ct, ((! esl_opt_GetBoolean(go, "--no-pp")) && (msa->pp != NULL)), /* do_prob? draw pp pages? */ (! esl_opt_GetBoolean(go, "--no-bp")), /* do_rescol: paint nucleotides different colors based on basepair type? */ hc_scheme, RB_W5_OH_SCHEME, RB_6_RL_SCHEME, hc_nbins[RB_W5_OH_SCHEME], hc_nbins[RB_6_RL_SCHEME], hc_onecell, LIGHTGREYOC, /* one-cell legend, 5'/3' flush color */ BLACKOC, /* one-cell legend, watson-crick bp color, only relevant if do_rescol == TRUE */ GREENOC, /* one-cell legend, G-U or U-G bp color, only relevant if do_rescol == TRUE */ REDOC, /* one-cell legend, non-canonical bp color, only relevant if do_rescol == TRUE */ LIGHTPURPLEOC, /* one-cell legend, internal double-gap bp color, only relevant if do_rescol == TRUE */ LIGHTPURPLEOC, /* one-cell legend, internal half-gap bp color, only relevant if do_rescol == TRUE */ LIGHTGREYOC, /* one-cell legend, color for gap in post prob pages */ tabfp)) != eslOK) esl_fatal(errbuf); } if((status = draw_sspostscript(ofp, go, errbuf, command, date, hc_scheme, ps)) != eslOK) esl_fatal(errbuf); free(command); fclose(ofp); printf("# %d page postscript saved to file %s.\n", ps->npage, outfile); /* Cleanup, normal return */ if(tabfp != NULL) { fclose(tabfp); if(do_indi && (do_info || do_mutinfo || do_ifreq || do_iavglen || do_dall || do_dint || do_prob || do_span)) { printf("# Per-position and per-sequence data saved to tab-delimited text file %s.\n", esl_opt_GetString(go, "--tabfile")); } else if (do_indi) { printf("# Per-sequence data saved to tab-delimited text file %s.\n", esl_opt_GetString(go, "--tabfile")); } else { printf("# Per-position data saved to tab-delimited text file %s.\n", esl_opt_GetString(go, "--tabfile")); } } esl_arr2_Destroy((void **) abc_ct, msa? msa->alen:0); esl_arr2_Destroy((void **) pp_ct, msa? msa->alen:0); esl_arr3_Destroy((void ***) bp_ct, msa? msa->alen:0, abc? abc->Kp: 0); esl_arr2_Destroy((void **) per_seq_ins_ct, msa_nseq); esl_free(spos_ct); esl_free(epos_ct); esl_free(srfoff_ct); esl_free(erfoff_ct); esl_free(span_ct); esl_free(nseq_with_ins_ct); esl_free(mask); esl_free(date); esl_free(hc_nbins); free_sspostscript(ps); esl_alphabet_Destroy(abc); esl_msafile_Close(afp); esl_msafile2_Close(afp2); esl_getopts_Destroy(go); for(z = 0; z < NOC; z++) esl_free(hc_onecell[z]); esl_free(hc_onecell); for(z = 0; z < NRB_11_RH_SCHEME; z++) esl_free(hc_scheme[RB_11_RH_SCHEME][z]); for(z = 0; z < NRB_11_RL_SCHEME; z++) esl_free(hc_scheme[RB_11_RL_SCHEME][z]); for(z = 0; z < NRB_6_RH_SCHEME; z++) esl_free(hc_scheme[RB_6_RH_SCHEME][z]); for(z = 0; z < NRB_6_RL_SCHEME; z++) esl_free(hc_scheme[RB_6_RL_SCHEME][z]); for(z = 0; z < NRB_5_RH_SCHEME; z++) esl_free(hc_scheme[RB_5_RH_SCHEME][z]); for(z = 0; z < NRB_5_RL_SCHEME; z++) esl_free(hc_scheme[RB_5_RL_SCHEME][z]); for(z = 0; z < NRB_W5_OH_SCHEME; z++) esl_free(hc_scheme[RB_W5_OH_SCHEME][z]); for(z = 0; z < NSCHEMES; z++) { esl_free(hc_scheme[z]); } free(hc_scheme); esl_msa_Destroy(msa); return 0; ERROR: esl_fatal("Memory allocation error in main()."); return eslFAIL;/* silence compiler warning about void return*/ } /* Function: create_sspostscript() * * Purpose: Create and initialize a SS postscript data structure. * Return: ps */ static SSPostscript_t * create_sspostscript(const ESL_GETOPTS *go) { int status; SSPostscript_t *ps; ESL_ALLOC(ps, sizeof(SSPostscript_t)); ps->npage = 0; ps->modelname = NULL; ps->modeA = NULL; ps->descA = NULL; ps->headerx = 0.; ps->headery = 0.; ps->headerx_desc = 0.; ps->headerx_charsize = 0.; ps->headery_charsize = 0.; ps->desc_max_chars = 0; ps->leg_posn = -1; ps->leg_cellsize = -1; ps->leg_rhs_space = 0.; ps->legx_offset = 0.; ps->legy_offset = 0.; ps->legx = 0.; ps->legy = 0.; ps->cur_legy = 0.; ps->legx_charsize = 0.; ps->legy_charsize = 0.; ps->legx_max_chars = 0; ps->legx_stats = 0.; ps->pagex_max = 0.; ps->pagey_max = 0.; ps->scale = -1.; /* we'll check if this is still negative after reading the template file, if so it's an error */ ps->regurgA = NULL; ps->nregurg = 0; ps->posntextA = NULL; ps->posntextxA = ps->posntextyA = NULL; ps->nposntext = 0; ps->ticksx1A = ps->ticksx2A = ps->ticksy1A = ps->ticksy2A = NULL; ps->nticks = 0; ps->bpx1A = ps->bpx2A = ps->bpy1A = ps->bpy2A = NULL; ps->nbp = 0; ps->rxA = ps->ryA = NULL; ps->rflen = 0; ps->rAA = NULL; ps->rcolAAA = NULL; ps->bcolAAA = NULL; ps->otypeAA = NULL; ps->occlAAA = NULL; ps->nocclA = NULL; ps->sclAA = NULL; ps->tlAAA = NULL; ps->ntlA = NULL; ps->mask = NULL; ps->nalloc = 50; ps->msa_cseq_maj = NULL; ps->msa_cseq_amb = NULL; ps->msa_ct = NULL; ps->msa_nbp = 0; ps->msa_rf2a_map = NULL; ps->msa_a2rf_map = NULL; ps->uaseqlenA = NULL; ps->seqidxA = NULL; ps->msa = NULL; ps->abc = NULL; return ps; ERROR: esl_fatal("create_sspostscript(): memory allocation error."); return NULL; /* NEVERREACHED */ } /* Function: setup_sspostscript() * * Purpose: Determine positions for header and legend in a SSPostscript_t() * Return: eslOK */ static int setup_sspostscript(SSPostscript_t *ps, char *errbuf) { float xroom, yroom; float header_max_chars; if(ps->rflen == 0) ESL_FAIL(eslEINVAL, errbuf, "Failed to ready any nucleotides in template file."); /* set up legx, legy, this is a hack (takes advantage of position of 3' nucleotide in all SSU models) */ ps->legx = ps->rxA[ps->leg_posn-1] + ps->legx_offset; ps->legy = ps->ryA[ps->leg_posn-1] + ps->legy_offset; ps->cur_legy = ps->legy; ps->pagex_max = POSTSCRIPT_PAGEWIDTH / ps->scale; ps->pagey_max = POSTSCRIPT_PAGEHEIGHT / ps->scale; ps->headerx = 0. + PAGE_SIDEBUF; ps->headery = ps->pagey_max - PAGE_TOPBUF - ((HEADER_FONTSIZE_UNSCALED) / ps->scale); /* determine max number of nucleotides we can print before we run off the page in the legend section */ ps->legx_charsize = (LEG_FONTSIZE_UNSCALED / COURIER_HEIGHT_WIDTH_RATIO) / ps->scale; ps->legy_charsize = (LEG_FONTSIZE_UNSCALED) / ps->scale; xroom = ps->pagex_max - ps->legx - (ps->leg_cellsize - ps->legx_charsize); yroom = ps->pagey_max - ps->legy - (ps->leg_cellsize - ps->legy_charsize); ps->legx_max_chars = (int) (xroom / ps->legx_charsize); ps->legy_max_chars = (int) (yroom / ps->legy_charsize); ps->legx_stats = ps->pagex_max - PAGE_SIDEBUF - ps->leg_rhs_space - (LEG_EXTRA_COLUMNS * ps->legx_charsize); /* determine max size of description that will fit in header */ //header_fontwidth = (HEADER_FONTSIZE_UNSCALED / COURIER_HEIGHT_WIDTH_RATIO) / ps->scale; // SRE: appears to be unused. ps->headerx_charsize = (HEADER_FONTSIZE_UNSCALED / COURIER_HEIGHT_WIDTH_RATIO) / ps->scale; header_max_chars = (int) ((ps->pagex_max - 2*PAGE_SIDEBUF) / ps->headerx_charsize); ps->headery_charsize = (HEADER_FONTSIZE_UNSCALED) / ps->scale; ps->desc_max_chars = header_max_chars - (HEADER_MODELNAME_MAXCHARS + 6 + 6 + 8 +2); /*6,6,8 for #pos,#bps,#seq plus 2 spaces each, plus 2 for after name */ ps->headerx_desc = ps->pagex_max - PAGE_SIDEBUF - (ps->desc_max_chars * ps->headerx_charsize); return eslOK; } /* Function: free_sspostscript() * * Purpose: Free a SS postscript data structure. * Return: (void) */ static void free_sspostscript(SSPostscript_t *ps) { int i, p, c, l, l2; if(ps->modelname != NULL) free(ps->modelname); if(ps->modeA != NULL) free(ps->modeA); if(ps->descA != NULL) { for(i = 0; i < ps->npage; i++) { if(ps->descA[i] != NULL) { free(ps->descA[i]); } } free(ps->descA); } if(ps->regurgA != NULL) { for(i = 0; i < ps->nregurg; i++) { if(ps->regurgA[i] != NULL) { free(ps->regurgA[i]); } } free(ps->regurgA); } if(ps->posntextA != NULL) { for(i = 0; i < ps->nposntext; i++) free(ps->posntextA[i]); free(ps->posntextA); } if(ps->posntextxA != NULL) free(ps->posntextxA); if(ps->posntextyA != NULL) free(ps->posntextyA); if(ps->ticksx1A != NULL) free(ps->ticksx1A); if(ps->ticksy1A != NULL) free(ps->ticksy1A); if(ps->ticksx2A != NULL) free(ps->ticksx2A); if(ps->ticksy2A != NULL) free(ps->ticksy2A); if(ps->bpx1A != NULL) free(ps->bpx1A); if(ps->bpy1A != NULL) free(ps->bpy1A); if(ps->bpx2A != NULL) free(ps->bpx2A); if(ps->bpy2A != NULL) free(ps->bpy2A); if(ps->rxA != NULL) free(ps->rxA); if(ps->ryA != NULL) free(ps->ryA); if(ps->rAA != NULL) { for(p = 0; p < ps->npage; p++) if(ps->rAA[p] != NULL) free(ps->rAA[p]); free(ps->rAA); } if(ps->rcolAAA != NULL) { for(p = 0; p < ps->npage; p++) { if(ps->rcolAAA[p] != NULL) { for(c = 0; c < ps->rflen; c++) free(ps->rcolAAA[p][c]); free(ps->rcolAAA[p]); } } free(ps->rcolAAA); } if(ps->bcolAAA != NULL) { for(p = 0; p < ps->npage; p++) { if(ps->bcolAAA[p] != NULL) { for(c = 0; c < ps->rflen; c++) free(ps->bcolAAA[p][c]); free(ps->bcolAAA[p]); } } free(ps->bcolAAA); } if(ps->otypeAA != NULL) { for(p = 0; p < ps->npage; p++) { if(ps->otypeAA[p] != NULL) { free(ps->otypeAA[p]); } } free(ps->otypeAA); } if(ps->occlAAA != NULL) { for(p = 0; p < ps->npage; p++) { if(ps->occlAAA[p] != NULL) { for(l = 0; l < ps->nocclA[p]; l++) { if(ps->occlAAA[p][l]->text != NULL) free(ps->occlAAA[p][l]->text); if(ps->occlAAA[p][l]->celltext != NULL) free(ps->occlAAA[p][l]->celltext); if(ps->occlAAA[p][l]->procname != NULL) free(ps->occlAAA[p][l]->procname); if(ps->occlAAA[p][l]->procstack != NULL) free(ps->occlAAA[p][l]->procstack); free(ps->occlAAA[p][l]); /* the rest is statically allocated memory */ } free(ps->occlAAA[p]); } } free(ps->occlAAA); } if(ps->sclAA != NULL) { for(p = 0; p < ps->npage; p++) { if(ps->sclAA[p] != NULL) { if(ps->sclAA[p]->limits != NULL) free(ps->sclAA[p]->limits); if(ps->sclAA[p]->counts != NULL) free(ps->sclAA[p]->counts); if(ps->sclAA[p]->counts_masked != NULL) free(ps->sclAA[p]->counts_masked); if(ps->sclAA[p]->text1 != NULL) free(ps->sclAA[p]->text1); if(ps->sclAA[p]->text2 != NULL) free(ps->sclAA[p]->text2); free(ps->sclAA[p]); /* statically allocated memory */ } } free(ps->sclAA); } if(ps->tlAAA != NULL) { for(p = 0; p < ps->npage; p++) { if(ps->tlAAA[p] != NULL) { for(l = 0; l < ps->ntlA[p]; l++) { for(l2 = 0; l2 < ps->tlAAA[p][l]->nlines; l2++) { free(ps->tlAAA[p][l]->text_per_line[l2]); } free(ps->tlAAA[p][l]); /* the rest is statically allocated memory */ } free(ps->tlAAA[p]); } } free(ps->tlAAA); } if(ps->ntlA != NULL) free(ps->ntlA); if(ps->nocclA != NULL) free(ps->nocclA); if(ps->msa_cseq_maj != NULL) free(ps->msa_cseq_maj); if(ps->msa_cseq_amb != NULL) free(ps->msa_cseq_amb); if(ps->msa_ct != NULL) free(ps->msa_ct); if(ps->msa_rf2a_map != NULL) free(ps->msa_rf2a_map); if(ps->msa_a2rf_map != NULL) free(ps->msa_a2rf_map); if(ps->mask != NULL) free(ps->mask); if(ps->seqidxA != NULL) free(ps->seqidxA); if(ps->uaseqlenA != NULL) free(ps->uaseqlenA); free(ps); return; } /* Function: create_onecell_colorlegend() * * Purpose: Create and initialize a one cell color legend data structure. * As a special case, pass nres as OCCL_BLANK_COUNT if you don't * want a count printed for this one cell. * Return: occl */ static OneCellColorLegend_t * create_onecell_colorlegend(float *col, int nres, int nres_masked, int do_separator, int do_no_vspace) { int status; OneCellColorLegend_t *occl; ESL_ALLOC(occl, sizeof(OneCellColorLegend_t)); /* initialize */ esl_vec_FSet(occl->col, NCMYK, 0.); occl->text = NULL; occl->celltext = NULL; occl->procname = NULL; occl->procstack = NULL; occl->nprocstack = 0; /* set caller specified values */ esl_vec_FCopy(col, NCMYK, occl->col); occl->nres = nres; occl->nres_masked = nres_masked; occl->do_separator = do_separator; occl->do_no_vspace = do_no_vspace; return occl; ERROR: esl_fatal("create_onecell_colorlegend(): memory allocation error."); return NULL; /* NEVERREACHED */ } /* Function: create_onecell_colorlegend() * * Purpose: Create and initialize a one cell color legend data structure. * Return: occl */ static TextLegend_t * create_text_legend(int nlines, char **text_per_line, int do_separator) { int status; TextLegend_t *tl; int i; ESL_ALLOC(tl, sizeof(TextLegend_t)); /* initialize */ tl->text_per_line = NULL; /* set caller specified values */ tl->nlines = nlines; tl->do_separator = do_separator; ESL_ALLOC(tl->text_per_line, sizeof(char *) * nlines); for(i = 0; i < nlines; i++) { if((status = esl_strdup(text_per_line[i], -1, &(tl->text_per_line[i]))) != eslOK) esl_fatal("create_text_legend(), error copying text"); } return tl; ERROR: esl_fatal("create_text_legend(): memory allocation error."); return NULL; /* NEVERREACHED */ } /* Function: create_text_legend_for_consensus_sequence() * * Purpose: Create text explaining how a consensus sequence is calculated * for the legend, and return it in the form of a TextLegend_t * object. * * Return: tl */ static TextLegend_t * create_text_legend_for_consensus_sequence(const ESL_GETOPTS *go, int do_separator) { int status; TextLegend_t *tl; int i; int nlines; char **text; if(esl_opt_GetBoolean(go, "--cambig")) { nlines = 5; ESL_ALLOC(text, sizeof(char *) * nlines); for(i = 0; i < nlines; i++) { text[i] = NULL; } if((status = esl_strcat(&(text[0]), -1, "Consensus nucleotides (nt) are displayed, calculated", -1)) != eslOK) esl_fatal("create_text_legend_for_consensus_sequence(), error copying text"); ESL_ALLOC(text[1], sizeof(char) * (strlen("as the least ambiguous nt that represents >= 1.00") + 1)); sprintf(text[1], "as the least ambiguous nt that represents >= %0.2f", esl_opt_GetReal(go, "--athresh")); if((status = esl_strcat(&(text[2]), -1, "of all non-gap nts at each position.", -1)) != eslOK) esl_fatal("create_text_legend_for_consensus_sequence(), error copying text"); if((status = esl_strcat(&(text[3]), -1, "K=G|U, M=A|C, R=A|G, S=C|G, Y=C|U, W=A|U", -1)) != eslOK) esl_fatal("create_text_legend_for_consensus_sequence(), error copying text"); if((status = esl_strcat(&(text[4]), -1, "B=C|G|U, D=A|G|U, H=A|C|U, V=A|C|G, N=A|C|G|U", -1)) != eslOK) esl_fatal("create_text_legend_for_consensus_sequence(), error copying text"); } else { /* --cambig not enabled, majority rule was used */ nlines = 4; ESL_ALLOC(text, sizeof(char *) * nlines); for(i = 0; i < nlines; i++) { text[i] = NULL; } if((status = esl_strcat(&(text[0]), -1, "Consensus nucleotides (nt) are displayed, defined", -1)) != eslOK) esl_fatal("create_text_legend_for_consensus_sequence(), error copying text"); if((status = esl_strcat(&(text[1]), -1, "as the most frequent nt at each position.", -1)) != eslOK) esl_fatal("create_text_legend_for_consensus_sequence(), error copying text"); ESL_ALLOC(text[2], sizeof(char) * (strlen("Capitalized nts occur in >= 1.00 fraction of sequences") + 1)); sprintf(text[2], "Capitalized nts occur in >= %0.2f fraction of sequences", esl_opt_GetReal(go, "--cthresh")); if((status = esl_strcat(&(text[3]), -1, "that do not have a gap at the position.", -1)) != eslOK) esl_fatal("create_text_legend_for_consensus_sequence(), error copying text"); } tl = create_text_legend(nlines, text, do_separator); for(i = 0; i < nlines; i++) { free(text[i]); } free(text); return tl; ERROR: esl_fatal("create_text_legend(): memory allocation error."); return NULL; /* NEVERREACHED */ } /* Function: create_scheme_colorlegend() * * Purpose: Create and initialize a scheme color legend data structure. * Return: scl */ static SchemeColorLegend_t * create_scheme_colorlegend(int scheme, int nbins, float *limits, int ints_only_flag, int low_inclusive, int high_inclusive, int use_mask) { int status; SchemeColorLegend_t *scl; int i; int *counts; int *counts_masked; ESL_ALLOC(scl, sizeof(SchemeColorLegend_t)); /* initialize */ scl->text1 = NULL; scl->text2 = NULL; /* set caller specified values */ scl->scheme = scheme; scl->nbins = nbins; ESL_ALLOC(scl->limits, sizeof(float) * (nbins+1)); for(i = 0; i <= nbins; i++) { scl->limits[i] = limits[i]; } ESL_ALLOC(counts, sizeof(int) * nbins); ESL_ALLOC(counts_masked, sizeof(int) * nbins); esl_vec_ISet(counts, nbins, 0); esl_vec_ISet(counts_masked, nbins, 0); scl->counts = counts; scl->counts_masked = counts_masked; scl->ints_only_flag = ints_only_flag; scl->low_inclusive = low_inclusive; scl->high_inclusive = high_inclusive; scl->use_mask = use_mask; return scl; ERROR: esl_fatal("create_scheme_colorlegend(): memory allocation error."); return NULL; /* NEVERREACHED */ } /* Function: add_text_to_scheme_colorlegend() * * Purpose: Add text to an existing scheme color legend data structure. * Throws: Exception if the text is too long. */ int add_text_to_scheme_colorlegend(SSPostscript_t *ps, SchemeColorLegend_t *scl, char *text, int legx_max_chars, char *errbuf) { int status; int i, idx; int max_chars_per_line; if(scl->text1 != NULL) esl_fatal("add_text_to_scheme_colorlegend(), text already exists!\n"); if(scl->text2 != NULL) esl_fatal("add_text_to_scheme_colorlegend(), text already exists!\n"); if(text == NULL) esl_fatal("add_text_to_scheme_colorlegend(), passed in text is NULL!\n"); max_chars_per_line = ps->legx_max_chars - ((int) ps->leg_rhs_space / ps->legx_charsize) - ((int) (PAGE_SIDEBUF / ps->legx_charsize)) - LEG_EXTRA_COLUMNS - 2; if(((int) strlen(text)) <= max_chars_per_line) { /* case 1, entire text can fit in one line */ if((status = esl_strdup(text, -1, &(scl->text1))) != eslOK) esl_fatal("add_text_to_scheme_colorlegend(), error copying text"); return eslOK; } else if(((int) strlen(text)) > ((2 * max_chars_per_line) - 6)) { /* case 2, entire text can't even fit in two lines, * (this is inexact doesn't account for size of words which is an issue b/c we break at newline, * this is why I have the extra '- 6'); */ ESL_FAIL(eslEINVAL, errbuf, "add_text_to_scheme_colorlegend(), text is %d chars, max allowed is %d (%s)\n", (int) strlen(text), ((2 * max_chars_per_line) - 6), text); } else { /* split it up into two lines */ idx = max_chars_per_line - 1; while(text[idx] != ' ') { idx--; if(idx < 0) ESL_FAIL(eslEINVAL, errbuf, "add_text_to_scheme_colorlegend(), couldn't find a breakpoint for splitting the string (%s)\n", text); } /* copy first string into text1 */ ESL_ALLOC(scl->text1, sizeof(char) * (idx+1)); for(i = 0; i < idx; i++) scl->text1[i] = text[i]; scl->text1[idx] = '\0'; /* copy remainder into text2 */ int len = (int) strlen(text); idx++; ESL_ALLOC(scl->text2, sizeof(char) * (len - idx+1)); for(i = idx; i < len; i++) scl->text2[i-idx] = text[i]; scl->text2[len-idx] = '\0'; } return eslOK; ERROR: ESL_FAIL(status, errbuf, "Error adding text to scheme_colorlegend probably out of memory"); } /* Function: add_text_to_onecell_colorlegend() * * Purpose: Add text to an existing one cell color legend data structure. * Throws: Exception if the text is too long. */ int add_text_to_onecell_colorlegend(SSPostscript_t *ps, OneCellColorLegend_t *occl, char *text, int legx_max_chars, char *errbuf) { int status; int max_chars_per_line; if(occl->text != NULL) esl_fatal("add_text_to_onecell_colorlegend(), text description already exists!\n"); if(text == NULL) esl_fatal("add_text_to_onecell_colorlegend(), passed in text is NULL!\n"); max_chars_per_line = legx_max_chars - LEG_EXTRA_COLUMNS - 2 - ((int) (((float) ps->leg_cellsize * 1.5) / ps->legx_charsize)); /*printf("max: %d cur: %d text: %s\n", max_chars_per_line, (int) strlen(text), text);*/ if(((int) strlen(text)) > (max_chars_per_line)) { ESL_FAIL(eslEINVAL, errbuf, "add_text_to_onecell_colorlegend(), text is %d chars, max allowed is %d (%s)\n", (int) strlen(text), max_chars_per_line, text); } if((status = esl_strdup(text, -1, &(occl->text))) != eslOK) esl_fatal("add_text_to_onecell_colorlegend(), error copying text"); return eslOK; } /* Function: add_celltext_to_onecell_colorlegend() * * Purpose: Add cell text to an existing one cell color legend data structure. */ int add_celltext_to_onecell_colorlegend(SSPostscript_t *ps, OneCellColorLegend_t *occl, char *celltext, char *errbuf) { int status; if(occl->celltext != NULL) esl_fatal("add_celltext_to_onecell_colorlegend(), cell text already exists!\n"); if(celltext == NULL) esl_fatal("add_celltext_to_onecell_colorlegend(), passed in celltext is NULL!\n"); if((status = esl_strdup(celltext, -1, &(occl->celltext))) != eslOK) esl_fatal("add_celltext_to_onecell_colorlegend(), error copying text"); return eslOK; } /* Function: add_procedure_to_onecell_colorlegend() * * Purpose: Add procedure for drawing one cell to an existing one cell color legend data structure. */ int add_procedure_to_onecell_colorlegend(SSPostscript_t *ps, OneCellColorLegend_t *occl, char *procname, float *procstack, int nprocstack, char *errbuf) { int status; int i; if(occl->celltext != NULL) esl_fatal("add_procedure_to_onecell_colorlegend(), cell text already exists!\n"); if(occl->procname != NULL) esl_fatal("add_procedure_to_onecell_colorlegend(), procedure text already exists!\n"); if(occl->procstack != NULL) esl_fatal("add_procedure_to_onecell_colorlegend(), procedure stack already exists!\n"); if(procname == NULL) esl_fatal("add_procedure_to_onecell_colorlegend(), passed in procname is NULL!\n"); if(procstack == NULL) esl_fatal("add_procedure_to_onecell_colorlegend(), passed in procstack is NULL!\n"); if((status = esl_strdup(procname, -1, &(occl->procname))) != eslOK) esl_fatal("add_procedure_to_onecell_colorlegend(), error copying text"); ESL_ALLOC(occl->procstack, sizeof(float) * nprocstack); for(i = 0; i < nprocstack; i++) occl->procstack[i] = procstack[i]; occl->nprocstack = nprocstack; return eslOK; ERROR: return eslEMEM; } /* Function: add_page_desc_to_sspostscript() * * Purpose: Add text describing a particular page of a postscript object. * Throws: Exception if the text is too long. */ int add_page_desc_to_sspostscript(SSPostscript_t *ps, int page, char *text, char *errbuf) { int status; int i, j; int max_both_lines; if(ps->descA[page] != NULL) ESL_FAIL(eslEINVAL, errbuf, "add_page_desc_to_sspostscript(), description for page %d already exists!\n", page); if(text == NULL) ESL_FAIL(eslEINVAL, errbuf, "add_page_desc_to_sspostscript(), passed in text is NULL!\n"); max_both_lines =(2. * ps->desc_max_chars); if(ps->modeA[page] == INDIMODE || ps->modeA[page] == SIMPLEMASKMODE) max_both_lines--; /* b/c we have to add a '-' to split up the larger strings onto 2 lines */ /* check to see if we can fit the text onto two lines of max width ps->desc_max_chars */ int textlen = (int) strlen(text); if(textlen <= ps->desc_max_chars) { /* fine, this will fit on one line */ if((status = esl_strdup(text, -1, &(ps->descA[page]))) != eslOK) ESL_FAIL(eslEINVAL, errbuf, "add_page_desc_to_sspostscript(), error copying text"); } else if (textlen <= max_both_lines) { if(ps->modeA[page] == ALIMODE) { /* maybe fine, make sure there's a break point (space ' ') that will break this string into two strings of length <= ps->desc_max_chars */ i = ps->desc_max_chars; while(text[i] != ' ' && text[i] != '-') { i--; if(i < 0) ESL_FAIL(eslEINVAL, errbuf, "add_page_desc_to_sspostscript(), first word of text (%s) is more than max allowed of %d chars", text, ps->desc_max_chars); } /* found last space before max width, make sure it breaks the line up into two chunks of valid size */ if((textlen - (i+1)) <= ps->desc_max_chars) { /* we're good */ if((status = esl_strdup(text, -1, &(ps->descA[page]))) != eslOK) ESL_FAIL(eslEINVAL, errbuf, "add_page_desc_to_sspostscript(), error copying text"); ps->descA[page][i] = '\n'; /* so we can remember where the break is */ } else ESL_FAIL(eslEINVAL, errbuf, "add_page_desc_to_sspostscript(), couldn't find (' ') for splitting text into two chunks (%s)", text); } else { /* INDIMODE or SIMPLEMASKMODE, sequence/mask name bigger than 1 line, but not 2, we put a '-' in it at the end of line 1 and add a '\n' so we remember where it was */ ESL_ALLOC(ps->descA[page], sizeof(char) * (textlen + 3)); /* +3 so we have space for the extra '-' and '\n' */ for(i = 0; i < ps->desc_max_chars; i++) ps->descA[page][i] = text[i]; i = ps->desc_max_chars; ps->descA[page][i] = '-'; i++; ps->descA[page][i] = '\n'; for(i = ps->desc_max_chars; i < textlen; i++) ps->descA[page][i+2] = text[i]; ps->descA[page][textlen+2] = '\0'; } } else /* the text won't fit on two lines */ if(ps->modeA[page] != INDIMODE) { /* not fine, this won't fit on two lines */ ESL_FAIL(eslEINVAL, errbuf, "add_page_desc_to_sspostscript(), text is %d chars, max allowed is %d (%s)\n", textlen, max_both_lines, text); } else { /* INDIMODE or SIMPLEMASKMODE, sequence/mask name exceeds max, we put a '-' in it at the end of line 1 and truncate it */ ESL_ALLOC(ps->descA[page], sizeof(char) * (max_both_lines + 2)); /* +2 so we have space for the extra '\n' (which we won't print), and the '\0' */ /* first look to see if there's a space before desc_max_chars, this will never happen for a seq name, but may for a mask description */ j = ps->desc_max_chars; while(text[j] != ' ' && j > 0) { j--; } if(j == 0) { j = ps->desc_max_chars; } /* no space */ for(i = 0; i < j; i++) ps->descA[page][i] = text[i]; i = j; if(j == ps->desc_max_chars && text[j] != ' ') { ps->descA[page][i] = '-'; } i++; ps->descA[page][i] = '\n'; for(i = j; i < j + ps->desc_max_chars; i++) ps->descA[page][i+2] = text[i]; ps->descA[page][i+2] = '\0'; } return eslOK; ERROR: ESL_FAIL(status, errbuf, "add_page_desc_to_sspostscript() error, probably out of memory."); } /* Function: add_diffmask_page_desc_to_sspostscript() * * Purpose: Add text describing a diff mask page of a postscript object. * Throws: Exception if the text is too long. */ int add_diffmask_page_desc_to_sspostscript(SSPostscript_t *ps, int page, char *mask_file, char *maskdiff_file, char *errbuf) { int status; int i; char *mask1desc = NULL; char *mask2desc = NULL; int len2copy; int mask_file_len; int maskdiff_file_len; void *tmp; if(ps->mask == NULL) ESL_FAIL(eslEINVAL, errbuf, "add_diffmask_page_desc_to_sspostscript(), ps->mask is NULL\n"); if(ps->descA[page] != NULL) ESL_FAIL(eslEINVAL, errbuf, "add_diffmask_page_desc_to_sspostscript(), description for page %d already exists!\n", page); if(maskdiff_file == NULL) ESL_FAIL(eslEINVAL, errbuf, "add_diffmask_page_desc_to_sspostscript(), passed in maskdiff_file is NULL!\n"); /* check to see if we can fit the text onto two lines of max width ps->desc_max_chars */ mask_file_len = (int) strlen(ps->mask); maskdiff_file_len = (int) strlen(maskdiff_file); if((status = esl_strcat(&(mask1desc), -1, "mask 1: ", -1)) != eslOK) ESL_FAIL(eslEINVAL, errbuf, "add_diffmask_page_desc_to_sspostscript(), error copying text"); if((mask_file_len + 8) <= ps->desc_max_chars) { /* this will fit on one line */ if((status = esl_strcat(&(mask1desc), -1, mask_file, -1)) != eslOK) ESL_FAIL(eslEINVAL, errbuf, "add_diffmask_page_desc_to_sspostscript(), error copying text"); } else { /* won't fit on one line, include as much as we can */ len2copy = ps->desc_max_chars - 8 - 3; /* 8 is for "mask 1: " at beginning, 3 is for "..." at end */ ESL_RALLOC(mask1desc, tmp, sizeof(char) * ps->desc_max_chars+1); for(i = 0; i < len2copy; i++) { mask1desc[8+i] = mask_file[i]; } mask1desc[8+len2copy] = '.'; mask1desc[8+len2copy+1] = '.'; mask1desc[8+len2copy+2] = '.'; mask1desc[8+len2copy+3] = '\0'; } /* repeat for mask 2 */ if((status = esl_strcat(&(mask2desc), -1, "mask 2: ", -1)) != eslOK) ESL_FAIL(eslEINVAL, errbuf, "add_diffmask_page_desc_to_sspostscript(), error copying text"); if((maskdiff_file_len + 8) <= ps->desc_max_chars) { /* this will fit on one line */ if((status = esl_strcat(&(mask2desc), -1, maskdiff_file, -1)) != eslOK) ESL_FAIL(eslEINVAL, errbuf, "add_diffmask_page_desc_to_sspostscript(), error copying text"); } else { /* won't fit on one line, include as much as we can */ len2copy = ps->desc_max_chars - 8 - 3; /* 8 is for "mask 1: " at beginning, 3 is for "..." at end */ ESL_RALLOC(mask2desc, tmp, sizeof(char) * ps->desc_max_chars+1); for(i = 0; i < len2copy; i++) { mask2desc[8+i] = maskdiff_file[i]; } mask2desc[8+len2copy] = '.'; mask2desc[8+len2copy+1] = '.'; mask2desc[8+len2copy+2] = '.'; mask2desc[8+len2copy+3] = '\0'; } /* concatenate them in ps->descA[page] */ if((status = esl_strcat(&(ps->descA[page]), -1, mask1desc, -1)) != eslOK) ESL_FAIL(eslEINVAL, errbuf, "add_diffmask_page_desc_to_sspostscript(), error copying text"); if((status = esl_strcat(&(ps->descA[page]), -1, "\n", -1)) != eslOK) ESL_FAIL(eslEINVAL, errbuf, "add_diffmask_page_desc_to_sspostscript(), error copying text"); if((status = esl_strcat(&(ps->descA[page]), -1, mask2desc, -1)) != eslOK) ESL_FAIL(eslEINVAL, errbuf, "add_diffmask_page_desc_to_sspostscript(), error copying text"); free(mask1desc); free(mask2desc); return eslOK; ERROR: ESL_FAIL(status, errbuf, "add_page_desc_to_sspostscript() error, probably out of memory."); } /* Function: add_mask_to_sspostscript * * Purpose: Add a mask to a sspostscript object. */ int add_mask_to_ss_postscript(SSPostscript_t *ps, char *mask) { int status; if(ps->mask != NULL) { esl_fatal("add_mask_to_ss_postscript(), mask is non-null!\n"); } if(mask == NULL) esl_fatal("add_mask_to_ss_postscript(), passed in mask is NULL!\n"); if((status = esl_strdup(mask, -1, &(ps->mask))) != eslOK) esl_fatal("add_mask_to_ss_postscript(), error copying mask"); return eslOK; } /* Function: draw_legend_column_headers() * * Purpose: Draw the legend column headers. * Return: eslOK */ static int draw_legend_column_headers(FILE *fp, SSPostscript_t *ps, int pagenum, char *errbuf) { int status; int i; float x, y; // float legend_fontsize; char *cur_string; int cur_width = 0; //legend_fontsize = LEG_FONTSIZE_UNSCALED / ps->scale; x = ps->legx; y = ps->cur_legy; if(ps->mask != NULL && ps->modeA[pagenum] == ALIMODE) { y -= 1.25 * (float) ps->leg_cellsize; } /*fprintf(fp, "/%s findfont %f scalefont setfont\n", SPECIAL_FONT, legend_fontsize);*/ fprintf(fp, "%% begin legend column headers\n"); fprintf(fp, "(%s) %.2f %.2f moveto show\n", "LEGEND", x, (y + ((float) ps->leg_cellsize * .25))); /*fprintf(fp, "/%s findfont %f scalefont setfont\n", LEG_FONT, legend_fontsize);*/ x = ps->legx_stats; y = ps->cur_legy; cur_width = ps->legx_max_chars - ((int) ps->leg_rhs_space / ps->legx_charsize) - ((int) (PAGE_SIDEBUF / ps->legx_charsize)) - LEG_EXTRA_COLUMNS - 2; ESL_ALLOC(cur_string, sizeof(char) * (cur_width+1)); for(i = 0; i < cur_width; i++) cur_string[i] = '-'; cur_string[cur_width] = '\0'; if(ps->mask != NULL && ps->modeA[pagenum] == ALIMODE) { fprintf(fp, "(%4s %4s) %.2f %.2f moveto show\n", "", "incl", x, (y + ((float) ps->leg_cellsize * .25))); y -= 0.625 * (float) ps->leg_cellsize; fprintf(fp, "(%4s %4s) %.2f %.2f moveto show\n", "", " by ", x, (y + ((float) ps->leg_cellsize * .25))); y -= 0.625 * (float) ps->leg_cellsize; fprintf(fp, "(%4s %4s) %.2f %.2f moveto show\n", "all", "mask", x, (y + ((float) ps->leg_cellsize * .25))); y -= 0.625 * (float) ps->leg_cellsize; fprintf(fp, "(%s) %.2f %.2f moveto show\n", cur_string, ps->legx, (y + ((float) ps->leg_cellsize * .25))); fprintf(fp, "(---- ----) %.2f %.2f moveto show\n", x, (y + ((float) ps->leg_cellsize * .25))); } else { fprintf(fp, "(%5s) %.2f %.2f moveto show\n", "count", x, (y + ((float) ps->leg_cellsize * .25))); y -= 0.625 * (float) ps->leg_cellsize; fprintf(fp, "(%s) %.2f %.2f moveto show\n", cur_string, ps->legx, (y + ((float) ps->leg_cellsize * .25))); fprintf(fp, "(-----) %.2f %.2f moveto show\n", x, (y + ((float) ps->leg_cellsize * .25))); } ps->cur_legy = y - (1.0 * (float) ps->leg_cellsize); fprintf(fp, "%% end legend column headers\n\n"); free(cur_string); return eslOK; ERROR: ESL_FAIL(status, errbuf, "ERROR drawing legend column headers, probably out of memory."); } /* Function: draw_onecell_colorlegend() * * Purpose: Print a one cell color legend to an open file. * Return: eslOK, dies if we run out of memory. */ static int draw_onecell_colorlegend(FILE *fp, OneCellColorLegend_t *occl, SSPostscript_t *ps, int occl_idx, int pagenum) { int status; float x, y; int cp, i; float fontsize; char *cur_string; int cur_width = 0; /* object is valid, print it */ x = ps->legx; y = ps->cur_legy; /* print cell */ fprintf(fp, "%% begin one cell color legend\n"); if(occl->celltext == NULL && occl->procname == NULL) { /* print a colored block as the cell */ fprintf(fp, "newpath\n"); fprintf(fp, " %.2f %.2f moveto", x, y); fprintf(fp, " 0 %.3f rlineto %.3f 0 rlineto 0 %.3f rlineto closepath\n", (float) ps->leg_cellsize, (float) ps->leg_cellsize, (-1 * (float) ps->leg_cellsize)); fprintf(fp, " "); for(cp = 0; cp < NCMYK; cp++) fprintf(fp, "%.2f ", occl->col[cp]); fprintf(fp, "setcmykcolor\n"); fprintf(fp, " fill\n"); /* draw a small box outlining the colored block we just drew */ /*fprintf(fp, "%.2f setlinewidth\n", (ps->leg_cellsize / 24.)); fprintf(fp, "newpath\n"); fprintf(fp, " %.2f %.2f moveto", x, y); fprintf(fp, " 0 %.3f rlineto %.3f 0 rlineto 0 %.3f rlineto closepath\n", (float) ps->leg_cellsize, (float) ps->leg_cellsize, (-1 * (float) ps->leg_cellsize)); fprintf(fp, " "); fprintf(fp, " %.4f %.4f %.4f %.4f setcmykcolor\n", 0., 0., 0., 1.); fprintf(fp, " stroke\n");*/ } else if (occl->procname != NULL) { fprintf(fp, "%.2f %.2f ", x, y); for(i = 0; i < occl->nprocstack; i++) { fprintf(fp, "%.2f ", occl->procstack[i]); } fprintf(fp, "%s\n", occl->procname); } else if (occl->celltext != NULL){ /* fontsize = (float) ps->leg_cellsize / strlen(occl->celltext); */ fontsize = (float) ps->leg_cellsize / 2; fprintf(fp, "/%s findfont %f scalefont setfont\n", NUCLEOTIDES_FONT, fontsize); for(cp = 0; cp < NCMYK; cp++) fprintf(fp, "%.2f ", occl->col[cp]); fprintf(fp, "setcmykcolor\n"); fprintf(fp, "(%s) %.2f %.2f moveto show\n", occl->celltext, x, y + ((float) ps->leg_cellsize * 0.25)); } if(occl->celltext == NULL || (strlen(occl->celltext) > 0)) { /* if we printed a block or text, modify x, so text for the legend is indented appropriately */ x += (float) ps->leg_cellsize * 1.5; } fontsize = LEG_FONTSIZE_UNSCALED / ps->scale; /* print text for this legend */ if(occl->text != NULL) { /* back to black */ fprintf(fp, " 0.00 0.00 0.00 1.00 setcmykcolor\n"); fprintf(fp, "/%s findfont %f scalefont setfont\n", LEG_FONT, fontsize); fprintf(fp, "(%s) %.2f %.2f moveto show\n", occl->text, x, y + ((float) ps->leg_cellsize * 0.25)); /* print stats */ if(occl->nres != OCCL_BLANK_COUNT) { x = ps->legx_stats; if(ps->mask != NULL && ps->modeA[pagenum] == ALIMODE) { fprintf(fp, "(%4d %4d) %.2f %.2f moveto show\n", occl->nres, occl->nres_masked, x, y + ((float) ps->leg_cellsize * 0.25)); } else { fprintf(fp, "(%5d) %.2f %.2f moveto show\n", occl->nres, x, y + ((float) ps->leg_cellsize * 0.25)); } } } /* reset color to black */ fprintf(fp, " %.4f %.4f %.4f %.4f setcmykcolor\n", 0., 0., 0., 1.); if(occl->do_separator) { cur_width = ps->legx_max_chars - ((int) ps->leg_rhs_space / ps->legx_charsize) - ((int) (PAGE_SIDEBUF / ps->legx_charsize)) - LEG_EXTRA_COLUMNS - 2; ESL_ALLOC(cur_string, sizeof(char) * (cur_width+1)); for(i = 0; i < cur_width; i++) cur_string[i] = '-'; cur_string[cur_width] = '\0'; fprintf(fp, "(%s) %.2f %.2f moveto show\n", cur_string, ps->legx, (y - ((float) ps->leg_cellsize * 0.5))); fprintf(fp, "(-----) %.2f %.2f moveto show\n", (float) ps->legx_stats, (y - ((float) ps->leg_cellsize * 0.5))); y -= (float) ps->leg_cellsize * 0.5; free(cur_string); } /* y -= (float) ps->leg_cellsize * 1.5; */ if(occl->do_no_vspace) { y -= (float) (ps->leg_cellsize / COURIER_HEIGHT_WIDTH_RATIO) * 1.25; } else { y -= (float) ps->leg_cellsize * 1.25; } ps->cur_legy = y; fprintf(fp, "%% end one cell color legend\n\n"); return eslOK; ERROR: esl_fatal("ERROR drawing one cell legend, probably out of memory."); return eslEMEM; /* never reached */ } /* Function: draw_scheme_colorlegend() * * Purpose: Print a scheme color legend to an open file. * Return: eslOK */ static int draw_scheme_colorlegend(const ESL_GETOPTS *go, FILE *fp, SchemeColorLegend_t *scl, float **hc_scheme, SSPostscript_t *ps, int pagenum) { float x, y; int cp; int c,i,n1s; float fontsize; int do_circle_mask, do_square_mask, do_x_mask, do_border; int do_mask; float old_x; do_mask = ((ps->mask != NULL) && (scl->use_mask)) ? TRUE : FALSE; do_border = (!esl_opt_GetBoolean(go, "--mask-a")); do_circle_mask = do_square_mask = do_x_mask = FALSE; if(esl_opt_GetBoolean(go, "--mask-u")) { do_square_mask = TRUE; } else if(esl_opt_GetBoolean(go, "--mask-x")) { do_x_mask = TRUE; } else do_circle_mask = TRUE; x = ps->legx; y = ps->cur_legy; //y = ps->legy - (ps->nocclA[pagenum] * ((float) ps->leg_cellsize * 1.5)); fontsize = LEG_FONTSIZE_UNSCALED / ps->scale; fprintf(fp, "%% begin color scheme legend\n"); fprintf(fp, "/%s findfont %f scalefont setfont\n", LEG_FONT, fontsize); fprintf(fp, " 0.00 0.00 0.00 1.00 setcmykcolor\n"); float colvec[NCMYK]; colvec[0] = colvec[1] = colvec[2] = 0.; colvec[3] = 1.0; if(do_mask) { /* print cells showing difference between masked and unmasked */ /*x -= (float) ps->leg_cellsize;*/ /*y -= (float) ps->leg_cellsize;*/ fprintf(fp, "%.1f setlinewidth\n", (float) ps->leg_cellsize/4.); fprintf(fp, "newpath\n"); fprintf(fp, " %.2f %.2f moveto", x, y); fprintf(fp, " 0 %.3f rlineto %.3f 0 rlineto 0 %.3f rlineto closepath\n", (float) ps->leg_cellsize, (float) ps->leg_cellsize, (-1 * (float) ps->leg_cellsize)); fprintf(fp, " "); for(cp = 0; cp < NCMYK; cp++) { fprintf(fp, "%.2f ", colvec[cp]); } fprintf(fp, "setcmykcolor\n"); fprintf(fp, " fill\n"); /* print label */ x += (float) ps->leg_cellsize * 1.5; y += (float) ps->leg_cellsize * 0.625; fprintf(fp, "(included by mask) %.2f %.2f moveto show\n", x, y); y -= (float) ps->leg_cellsize * 0.625; fprintf(fp, "((all colors)) %.2f %.2f moveto show\n", x, y); x -= (float) ps->leg_cellsize * 1.5; /* print stats for included by mask */ old_x = x; n1s = 0; for(i = 0; i < ps->rflen; i++) if(ps->mask[i] == '1') n1s++; x = ps->legx_stats; y += (float) ps->leg_cellsize * 0.3125; fprintf(fp, "(%4d %4d) %.2f %.2f moveto show\n", n1s, n1s, x, y); y -= (float) ps->leg_cellsize * 0.3125; x = old_x; y -= (float) ps->leg_cellsize * 1.5; draw_masked_block(fp, x, y, colvec, do_circle_mask, do_square_mask, do_x_mask, do_border, (float) ps->leg_cellsize); x += (float) ps->leg_cellsize * 1.5; y += (float) ps->leg_cellsize * 0.625; fprintf(fp, "(excluded by mask) %.2f %.2f moveto show\n", x, y); y -= (float) ps->leg_cellsize * 0.625; fprintf(fp, "((all colors)) %.2f %.2f moveto show\n", x, y); /* print stats for excluded by mask */ x = ps->legx_stats; y += (float) ps->leg_cellsize * 0.3125; fprintf(fp, "(%4d %4d) %.2f %.2f moveto show\n", ps->rflen-n1s, 0, x, y); y -= (float) ps->leg_cellsize * 1.8125; x = ps->legx; } /* print text for this legend */ if(scl->text1 != NULL) { if(scl->text2 == NULL) { fprintf(fp, "(%s:) %.2f %.2f moveto show\n", scl->text1, x, (y + ((float) ps->leg_cellsize * .25))); } else { fprintf(fp, "(%s) %.2f %.2f moveto show\n", scl->text1, x, (y + ((float) ps->leg_cellsize * .25))); y -= (float) ps->leg_cellsize * 0.625; fprintf(fp, "(%s:) %.2f %.2f moveto show\n", scl->text2, x, (y + ((float) ps->leg_cellsize * .25))); } } y -= (float) ps->leg_cellsize; /* print scheme color cells and labels next to them */ for(c = 0; c < scl->nbins; c++) { fprintf(fp, "newpath\n"); fprintf(fp, " %.2f %.2f moveto", x, y); fprintf(fp, " 0 %.3f rlineto %.3f 0 rlineto 0 %.3f rlineto closepath\n", (float) ps->leg_cellsize, (float) ps->leg_cellsize, (-1 * (float) ps->leg_cellsize)); fprintf(fp, " "); for(cp = 0; cp < NCMYK; cp++) { fprintf(fp, "%.2f ", hc_scheme[c][cp]); } fprintf(fp, "setcmykcolor\n"); fprintf(fp, " fill\n"); /* draw a small box outlining the colored block we just drew */ /*fprintf(fp, "%.2f setlinewidth\n", (ps->leg_cellsize / 24.)); fprintf(fp, "newpath\n"); fprintf(fp, " %.2f %.2f moveto", x, y); fprintf(fp, " 0 %.3f rlineto %.3f 0 rlineto 0 %.3f rlineto closepath\n", (float) ps->leg_cellsize, (float) ps->leg_cellsize, (-1 * (float) ps->leg_cellsize)); fprintf(fp, " "); fprintf(fp, " %.4f %.4f %.4f %.4f setcmykcolor\n", 0., 0., 0., 1.); fprintf(fp, " stroke\n");*/ /* print label */ x += (float) ps->leg_cellsize * 1.5; y += (float) ps->leg_cellsize * 0.25; fprintf(fp, " 0.00 0.00 0.00 1.00 setcmykcolor\n"); if(esl_FCompare(scl->limits[c+1], SSDRAWINFINITY, eslSMALLX1) == eslOK) { /* max value is infinity, special case */ if(c != scl->nbins-1) esl_fatal("ERROR when drawing color legend, limits[%d] is INFINITY, but this is reserved only for the max limit", c+1); if(scl->ints_only_flag) fprintf(fp, "(>=%d) %.2f %.2f moveto show\n", (int) scl->limits[c], x, y); else fprintf(fp, "(>=%3.f) %.2f %.2f moveto show\n", scl->limits[c], x, y); } else if(scl->ints_only_flag) { if(c == scl->nbins-1) { fprintf(fp, "(\\[%d-%d\\]) %.2f %.2f moveto show\n", (int) scl->limits[c], (int) scl->limits[c+1], x, y); } else if(esl_FCompare(scl->limits[c], scl->limits[c+1]-1, eslSMALLX1) == eslOK) { /* next limit is exactly 1 plus cur limit, don't do range, define single int */ if(compare_two_cmyk_colors(hc_scheme[c][ICYAN], hc_scheme[c][IMGTA], hc_scheme[c][IYELW], hc_scheme[c][IBLCK], WHITE_C, WHITE_M, WHITE_Y, WHITE_K)) { /* color is white and won't show up on our white background, so we explicitly state (blank) next to it's color value */ fprintf(fp, "(\\(blank\\) %d) %.2f %.2f moveto show\n", (int) scl->limits[c], x, y); } else { fprintf(fp, "(%d) %.2f %.2f moveto show\n", (int) scl->limits[c], x, y); } } else { fprintf(fp, "(\\[%d-%d\\]) %.2f %.2f moveto show\n", (int) scl->limits[c], (int) scl->limits[c+1]-1, x, y); } } else { if(c == scl->nbins-1) fprintf(fp, "(\\[%.3f-%.3f\\%c) %.2f %.2f moveto show\n", scl->limits[c], scl->limits[c+1], (scl->high_inclusive ? ']' : ')'), x, y); else if(c == 0) fprintf(fp, "(\\%c%.3f-%.3f\\)) %.2f %.2f moveto show\n", (scl->low_inclusive ? '[' : '('), scl->limits[c], scl->limits[c+1], x, y); else fprintf(fp, "(\\[%.3f-%.3f\\)) %.2f %.2f moveto show\n", scl->limits[c], scl->limits[c+1], x, y); } /* print stats */ old_x = x; x = ps->legx_stats; if(do_mask) { fprintf(fp, "(%4d %4d) %.2f %.2f moveto show\n", scl->counts[c], scl->counts_masked[c], x, y); } else { fprintf(fp, "(%5d) %.2f %.2f moveto show\n", scl->counts[c], x, y); } x = old_x - (float) ps->leg_cellsize * 1.5; y -= (float) ps->leg_cellsize * 0.25; y -= (float) ps->leg_cellsize; } /* reset color to black */ fprintf(fp, " %.4f %.4f %.4f %.4f setcmykcolor\n", 0., 0., 0., 1.); fprintf(fp, "%% end color scheme legend\n\n"); ps->cur_legy = y; return eslOK; } /* Function: draw_text_section_in_legend() * * Purpose: Print a text section in the legend section. * Return: eslOK, dies if we run out of memory. */ static int draw_text_section_in_legend(FILE *fp, TextLegend_t *tl, SSPostscript_t *ps, int tl_idx, int pagenum) { int status; float x, y; int i; float fontsize; char *cur_string; int cur_width = 0; x = ps->legx; y = ps->cur_legy; /* print cell */ fprintf(fp, "%% begin text legend\n"); fontsize = LEG_EXTRA_TEXT_FONTSIZE_UNSCALED / ps->scale; /* print text for this legend */ /* back to black */ fprintf(fp, " 0.00 0.00 0.00 1.00 setcmykcolor\n"); fprintf(fp, "/%s findfont %f scalefont setfont\n", LEG_EXTRA_TEXT_FONT, fontsize); for(i = 0; i < tl->nlines; i++) { fprintf(fp, "(%s) %.2f %.2f moveto show\n", tl->text_per_line[i], x, y); y -= (float) fontsize * 1.25; } if(tl->do_separator) { cur_width = ps->legx_max_chars - ((int) (PAGE_SIDEBUF / ps->legx_charsize)) - LEG_EXTRA_COLUMNS - 2; ESL_ALLOC(cur_string, sizeof(char) * (cur_width+1)); for(i = 0; i < cur_width; i++) cur_string[i] = '-'; cur_string[cur_width] = '\0'; fprintf(fp, "(%s) %.2f %.2f moveto show\n", cur_string, ps->legx, (y - ((float) ps->leg_cellsize * 0.5))); fprintf(fp, "(-----) %.2f %.2f moveto show\n", (float) ps->legx_stats, (y - ((float) ps->leg_cellsize * 0.5))); y -= (float) ps->leg_cellsize * 0.5; free(cur_string); } ps->cur_legy = y - (1.0 * (float) ps->leg_cellsize); fprintf(fp, "%% end text legend\n\n"); return eslOK; ERROR: esl_fatal("ERROR drawing text legend, probably out of memory."); return eslEMEM; /* never reached */ } /* Function: draw_sspostscript() * * Purpose: Print a SS postscript data structure. * Return: eslOK on success; * eslEINCOMPAT if ps->npage == 0 */ static int draw_sspostscript(FILE *fp, const ESL_GETOPTS *go, char *errbuf, char *command, char *date, float ***hc_scheme, SSPostscript_t *ps) { int status; int p, pi, i, c, l; int do_circle_mask, do_square_mask, do_x_mask, do_border; int *page_orderA; if(ps->modelname == NULL) ESL_FAIL(eslEINVAL, errbuf, "Error, failed to read modelname from template file."); do_border = (!esl_opt_GetBoolean(go, "--mask-a")); do_circle_mask = do_square_mask = do_x_mask = FALSE; if(esl_opt_GetBoolean(go, "--mask-u")) { do_square_mask = TRUE; } else if(esl_opt_GetBoolean(go, "--mask-x")) { do_x_mask = TRUE; } else do_circle_mask = TRUE; if(ps->npage == 0) ESL_FAIL(eslEINCOMPAT, errbuf, "draw_sspostscript, ps->npage == 0\n"); /* determine print order of pages, currently this is just 0..npage-1 */ ESL_ALLOC(page_orderA, sizeof(int) * ps->npage); for(pi = 0; pi < ps->npage; pi++) page_orderA[pi] = pi; /* define procedures */ fprintf(fp, "%% ------------------------------------------------------------\n"); fprintf(fp, "%% Procedure definitions\n"); define_outline_procedure(fp); fprintf(fp, "%% ------------------------------------------------------------\n"); /* draw the pages */ for(pi = 0; pi < ps->npage; pi++) { p = page_orderA[pi]; ps->cur_legy = ps->legy; /* print postscript comment header, only visible if viewed in text mode */ fprintf(fp, "%% ------------------------------------------------------------\n"); fprintf(fp, "%% Postscript file created by esl-ssdraw (page %d of %d)\n", pi+1, ps->npage); fprintf(fp, "%% ------------------------------------------------------------\n"); fprintf(fp, "%% msafile: %s (%d seqs)\n", esl_opt_GetArg(go, 1), ps->msa_nseq); fprintf(fp, "%% templatefile: %s\n", esl_opt_GetArg(go, 2)); fprintf(fp, "%% modelname: %s\n", ps->modelname); fprintf(fp, "%% consensus-len: %d\n", ps->rflen); if(esl_opt_IsOn(go, "--mask")) { fprintf(fp, "%% maskfile: %s\n", esl_opt_GetString(go, "--mask")); } if(esl_opt_IsOn(go, "--mask-diff")) { fprintf(fp, "%% difffile: %s\n", esl_opt_GetString(go, "--mask-diff")); } if(esl_opt_IsOn(go, "--dfile")) { fprintf(fp, "%% dfile: %s\n", esl_opt_GetString(go, "--dfile")); } if(esl_opt_IsOn(go, "--efile")) { fprintf(fp, "%% efile: %s\n", esl_opt_GetString(go, "--efile")); } if(esl_opt_IsOn(go, "--ifile")) { fprintf(fp, "%% ifile: %s\n", esl_opt_GetString(go, "--ifile")); } fprintf(fp, "%%\n"); /* scale section */ fprintf(fp, "%.2f %.2f scale\n\n", ps->scale, ps->scale); /* header section */ if((status = draw_header_and_footer(fp, go, errbuf, ps, p, pi+1)) != eslOK) return status; /* regurgitated section */ if(ps->regurgA != NULL) { fprintf(fp, "%% begin regurgitate\n"); for(i = 0; i < ps->nregurg; i++) fprintf(fp, "%s", ps->regurgA[i]); fprintf(fp, "%% end regurgitate\n\n"); } /* 'text positiontext' section */ for(i = 0; i < ps->nposntext; i++) { if(i == 0) { fprintf(fp, "%% begin text positiontext\n"); fprintf(fp, "/%s findfont %.2f scalefont setfont\n", POSNTEXT_FONT, POSNTEXT_FONTSIZE); fprintf(fp, "0.00 0.00 0.00 1.00 setcmykcolor\n"); /* black */ } fprintf(fp, "%s %.2f %.2f moveto show\n", ps->posntextA[i], ps->posntextxA[i], ps->posntextyA[i]); if(i == (ps->nposntext-1)) { fprintf(fp, "%% end text positiontext\n\n"); } } /* 'lines bpconnects' section */ for(i = 0; i < ps->nbp; i++) { if(i == 0) { fprintf(fp, "%% begin lines bpconnects\n"); fprintf(fp, "%.2f setlinewidth\n", BP_LINEWIDTH); fprintf(fp, "0.00 0.00 0.00 1.00 setcmykcolor\n"); /* black */ } fprintf(fp, "%.2f %.2f %.2f %.2f newpath moveto lineto stroke\n", ps->bpx1A[i], ps->bpy1A[i], ps->bpx2A[i], ps->bpy2A[i]); if(i == (ps->nbp-1)) { fprintf(fp, "%% end lines bpconnects\n\n"); } } /* print out remainder of the page */ /* fprintf(fp, "%% begin ignore\n"); */ fprintf(fp, "0.00 0.00 0.00 1.00 setcmykcolor\n"); /* set to black */ fprintf(fp, "/%s findfont %f scalefont setfont\n\n", LEG_FONT, LEG_FONTSIZE_UNSCALED / ps->scale); /* draw legend headers, if we have a legend (only legend text doesn't require legend headers) */ if((ps->nocclA[p] > 0) || (ps->sclAA != NULL && ps->sclAA[p] != NULL)) { if(! (esl_opt_GetBoolean(go, "--no-leg"))) { if((status = draw_legend_column_headers(fp, ps, p, errbuf)) != eslOK) return status; } } /* print one cell color legends, if any */ if(ps->occlAAA != NULL && ps->occlAAA[p] != NULL) { for(l = 0; l < ps->nocclA[p]; l++) { if(! (esl_opt_GetBoolean(go, "--no-leg"))) { draw_onecell_colorlegend(fp, ps->occlAAA[p][l], ps, l, p); } } } /* print scheme color legends, if any */ if(ps->sclAA != NULL && ps->sclAA[p] != NULL) { if(! (esl_opt_GetBoolean(go, "--no-leg"))) { draw_scheme_colorlegend(go, fp, ps->sclAA[p], hc_scheme[ps->sclAA[p]->scheme], ps, p); } } /* print text legends, if any */ if(ps->tlAAA != NULL && ps->tlAAA[p] != NULL) { for(l = 0; l < ps->ntlA[p]; l++) { if(! (esl_opt_GetBoolean(go, "--no-leg"))) { draw_text_section_in_legend(fp, ps->tlAAA[p][l], ps, l, p); } } } if(ps->bcolAAA != NULL && ps->bcolAAA[p] != NULL) { fprintf(fp, "%% begin colored positions\n"); if(ps->mask != NULL && ps->modeA[p] != SIMPLEMASKMODE && ps->modeA[p] != INDIMODE) { fprintf(fp, "2.0 setlinewidth\n"); if(do_border && do_x_mask) { fprintf(fp, "1.0 setlinewidth\n"); } if(do_border && do_square_mask) { fprintf(fp, "2.0 setlinewidth\n"); } if(do_border && do_circle_mask) { fprintf(fp, "2.5 setlinewidth\n"); } for(c = 0; c < ps->rflen; c++) { fprintf(fp, "%snucleotide %d\n", "%", c+1); if(ps->mask[c] == '0') { draw_masked_block(fp, ps->rxA[c]-1., ps->ryA[c]-1., ps->bcolAAA[p][c], do_circle_mask, do_square_mask, do_x_mask, do_border, CELLSIZE); } else { /* cell is within mask, ps->mask[c] == '1' */ fprintf(fp, "newpath\n"); fprintf(fp, " %.2f %.2f moveto", ps->rxA[c] - (CELLSIZE * CELL_XOFFSET_FRACTION), ps->ryA[c] - (CELLSIZE * CELL_YOFFSET_FRACTION)); fprintf(fp, " 0 %d rlineto %d 0 rlineto 0 %d rlineto closepath\n", CELLSIZE_INT, CELLSIZE_INT, -1 * CELLSIZE_INT); fprintf(fp, " %.2f %.2f %.2f %.2f setcmykcolor\n", ps->bcolAAA[p][c][0], ps->bcolAAA[p][c][1], ps->bcolAAA[p][c][2], ps->bcolAAA[p][c][3]); fprintf(fp, " fill\n"); } } fprintf(fp, "1.00 setlinewidth\n"); } else { /* no mask, all cells are printed the same */ for(c = 0; c < ps->rflen; c++) { fprintf(fp, "%snucleotide %d\n", "%", c+1); fprintf(fp, "newpath\n"); fprintf(fp, " %.2f %.2f moveto", ps->rxA[c] - (CELLSIZE * CELL_XOFFSET_FRACTION), ps->ryA[c] - (CELLSIZE * CELL_YOFFSET_FRACTION)); fprintf(fp, " 0 %d rlineto %d 0 rlineto 0 %d rlineto closepath\n", CELLSIZE_INT, CELLSIZE_INT, -1 * CELLSIZE_INT); fprintf(fp, " %.2f %.2f %.2f %.2f setcmykcolor\n", ps->bcolAAA[p][c][0], ps->bcolAAA[p][c][1], ps->bcolAAA[p][c][2], ps->bcolAAA[p][c][3]); fprintf(fp, " fill\n"); } } /* back to black */ fprintf(fp, " 0.00 0.00 0.00 1.00 setcmykcolor\n"); fprintf(fp, "%% end colored positions\n\n"); } if(ps->rAA[p] != NULL) { fprintf(fp, "/%s findfont %f scalefont setfont\n", NUCLEOTIDES_FONT, NUCLEOTIDES_FONTSIZE); fprintf(fp, " 0.00 0.00 0.00 1.00 setcmykcolor\n"); /* reset color as black */ fprintf(fp, "%% begin text nucleotides\n"); if(ps->rcolAAA[p] != NULL) { for(c = 0; c < ps->rflen; c++) { fprintf(fp, " %.2f %.2f %.2f %.2f setcmykcolor ", ps->rcolAAA[p][c][0], ps->rcolAAA[p][c][1], ps->rcolAAA[p][c][2], ps->rcolAAA[p][c][3]); if(strchr(LOWERCASE_LOW_HANGING_CHARS, ps->rAA[p][c]) != NULL) { fprintf(fp, "(%c) %.2f %.2f moveto show", ps->rAA[p][c], ps->rxA[c], ps->ryA[c] + (CELLSIZE * NUCLEOTIDE_YOFFSET_FRACTION_LOWERCASE_LOW_HANGING_CHARS)); /* handle lowercase low hanging chars ("gjpqy") nucleotides special, so they're centered in the box! */ } else if(ps->rAA[p][c] != ' ') { fprintf(fp, "(%c) %.2f %.2f moveto show", ps->rAA[p][c], ps->rxA[c], ps->ryA[c]); } fprintf(fp, "\n"); } } else { /* ps->rcolAAA[p] is NULL */ for(c = 0; c < ps->rflen; c++) { if(strchr(LOWERCASE_LOW_HANGING_CHARS, ps->rAA[p][c]) != NULL) { fprintf(fp, "(%c) %.2f %.2f moveto show", ps->rAA[p][c], ps->rxA[c], ps->ryA[c] + (CELLSIZE * NUCLEOTIDE_YOFFSET_FRACTION_LOWERCASE_LOW_HANGING_CHARS)); /* handle lowercase low hanging chars ("gjpqy") nucleotides special, so they're centered in the box! */ } else if(ps->rAA[p][c] != ' ') { fprintf(fp, "(%c) %.2f %.2f moveto show", ps->rAA[p][c], ps->rxA[c], ps->ryA[c]); } fprintf(fp, "\n"); } } fprintf(fp, "%% end text nucleotides\n"); fprintf(fp, " 0.000 0.000 0.000 1.000 setcmykcolor\n"); /* reset color as black */ } if(ps->otypeAA != NULL && ps->otypeAA[p] != NULL) { fprintf(fp, "%% begin outlines\n"); for(c = 0; c < ps->rflen; c++) { if(ps->otypeAA[p][c] != OUTLINE_NONE_IDX) { /* push x and y and cellsize onto stack */ fprintf(fp, "%.2f %.2f %.2f", ps->rxA[c] - (CELLSIZE * CELL_XOFFSET_FRACTION), ps->ryA[c] - (CELLSIZE * CELL_YOFFSET_FRACTION), CELLSIZE); if(ps->otypeAA[p][c] == OUTLINE_MIN_IDX) { fprintf(fp, " %.2f %s\n", OUTLINE_LINEWIDTH_CELL_FRACTION_MIN * CELLSIZE, OUTLINE_PROCEDURE); } else if(ps->otypeAA[p][c] == OUTLINE_MAX_IDX) { fprintf(fp, " %.2f %s\n", OUTLINE_LINEWIDTH_CELL_FRACTION_MAX * CELLSIZE, OUTLINE_PROCEDURE); } } } fprintf(fp, "%% end outlines\n"); fprintf(fp, " 0.000 0.000 0.000 1.000 setcmykcolor\n"); /* reset color as black */ } /* 'lines positionsticks' section, drawn last so they're not buried beneath other objects */ for(i = 0; i < ps->nticks; i++) { if(i == 0) { fprintf(fp, "%% begin lines positionticks\n"); fprintf(fp, "%.2f setlinewidth\n", TICKS_LINEWIDTH); fprintf(fp, "0.00 0.00 0.00 1.00 setcmykcolor\n"); /* black */ } fprintf(fp, "%.2f %.2f %.2f %.2f newpath moveto lineto stroke\n", ps->ticksx1A[i], ps->ticksy1A[i], ps->ticksx2A[i], ps->ticksy2A[i]); if(i == (ps->nticks-1)) { fprintf(fp, "%% end lines positionticks\n\n"); } } fprintf(fp, "showpage\n\n"); /* fprintf(fp, "%% end ignore\n\n"); */ } free(page_orderA); return eslOK; ERROR: ESL_FAIL(eslEINVAL, errbuf, "draw_sspostscript() error, probably out of memory."); } /* parse_template_file * * Read secondary structure templates from a postscript * template file derived from the Gutell CRW website until * the one that corresponds to our alignment is found, * (defined as the first template structure that has the * same consensus length as the passed in ) * or we run out structure templates. This function * repeatedly calls parse_template() which actually parses * the templates. * * If we run out of structure templates of anything is * invalid in any of the templates in the file, we * return a non-eslOK status code to caller and fill * errbuf with the error message. * * Returns: eslOK on success. */ int parse_template_file(char *filename, const ESL_GETOPTS *go, char *errbuf, int msa_rflen, SSPostscript_t **ret_ps) { int status; ESL_FILEPARSER *efp; SSPostscript_t *ps; int found_match = FALSE; if (esl_fileparser_Open(filename, NULL, &efp) != eslOK) esl_fatal("ERROR, failed to open template file %s in parse_template_file\n", filename); esl_fileparser_SetCommentChar(efp, '#'); status = eslOK; while((found_match == FALSE) && (status == eslOK)) { status = parse_template_page(efp, go, errbuf, &ps); if((status != eslOK) && (status != eslEOF)) { esl_fileparser_Close(efp); return status; } if(ps->rflen == msa_rflen) { found_match = TRUE; } else { free_sspostscript(ps); } } if(found_match == FALSE) { esl_fileparser_Close(efp); esl_fatal("ERROR, did not find template structure to match alignment consensus length of %d in:\n%s\n", msa_rflen, filename); } /* if we get here, we've found a match */ /* validate the template we just read */ if((status = validate_justread_sspostscript(ps, errbuf)) != eslOK) return status; esl_fileparser_Close(efp); *ret_ps = ps; return eslOK; } /* parse_template_page * * Read a single secondary structure template page for a * single CM from a postscript template file derived from the * Gutell CRW website. This function is called repeatedly * on the same file to read multiple structure templates. * The logic is to keep reading until we find one with the * same consensus length as our input alignment. * * The structure template is read in sections. * Each section begins with a line like this: * % begin * * list of valid tokens for : * modelname * legcoords * scale * regurgitate * ignore * lines * text * * if is lines or text, then is read, * valid tokens for if is 'text' * positiontext * nucleotides * * valid tokens for if is 'lines' * positionticks * bpconnects * * The 'regurgitate' lines are stored, but never changed. * The 'ignore' lines are not even stored. * All other lines are stored in data structures that * can be manipulated (though not all are at this point). * * If anything is invalid, we return a non-eslOK status code * to caller. * * Returns: eslOK on success. */ int parse_template_page(ESL_FILEPARSER *efp, const ESL_GETOPTS *go, char *errbuf, SSPostscript_t **ret_ps) { int status; char *tok; int toklen; SSPostscript_t *ps = NULL; int read_showpage = FALSE; int reached_eof = FALSE; /* Create the postscript object */ ps = create_sspostscript(go); while ((read_showpage == FALSE) && ((status = esl_fileparser_GetToken(efp, &tok, &toklen)) == eslOK)) { if(strcmp(tok, "%") == 0) { if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) == eslOK) { if(strcmp(tok, "begin") == 0) { if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) == eslOK) { if(strcmp(tok, "modelname") == 0) { if((status = parse_modelname_section(efp, errbuf, ps)) != eslOK) return status; } else if(strcmp(tok, "legend") == 0) { /*printf("parsing legend\n");*/ if((status = parse_legend_section(efp, errbuf, ps)) != eslOK) return status; } else if(strcmp(tok, "scale") == 0) { /*printf("parsing scale\n");*/ if((status = parse_scale_section(efp, errbuf, ps)) != eslOK) return status; } else if(strcmp(tok, "ignore") == 0) { /*printf("parsing ignore\n");*/ if((status = parse_ignore_section(efp, errbuf, &read_showpage)) != eslOK) return status; } else if(strcmp(tok, "regurgitate") == 0) { /*printf("parsing regurgitate\n");*/ if((status = parse_regurgitate_section(efp, errbuf, ps)) != eslOK) return status; } else if(strcmp(tok, "text") == 0) { /*printf("parsing text\n");*/ if((status = parse_text_section(efp, errbuf, ps)) != eslOK) return status; } else if(strcmp(tok, "lines") == 0) { /*printf("parsing lines\n");*/ if((status = parse_lines_section(efp, errbuf, ps)) != eslOK) return status; } else { ESL_FAIL(eslEINVAL, errbuf, "parse_template_page(), error, unknown section type %s.", tok); } } else { ESL_FAIL(eslEINVAL, errbuf, "parse_template_page(), error last read line number %d.", efp->linenumber); } } else { ESL_FAIL(eslEINVAL, errbuf, "parse_template_page(), expected line beginning with %%%% begin, but read tok: %s instead of begin, last read line number %d.", tok, efp->linenumber); } } else { ESL_FAIL(eslEINVAL, errbuf, "parse_template_page(), ran out of tokens early, error last read line number %d.", efp->linenumber); } } else { ESL_FAIL(eslEINVAL, errbuf, "parse_template_page(), expected line beginning with %%%%, read tok: %s, last read line number %d.", tok, efp->linenumber); } } if(read_showpage == FALSE && status != eslEOF) { ESL_FAIL(status, errbuf, "parse_template_page(), error, ran out of tokens, but not at end of file?, last read line number %d.", efp->linenumber); } if(status == eslEOF) reached_eof = TRUE; *ret_ps = ps; if(reached_eof) return eslEOF; else return eslOK; } /* parse_modelname_section * * Parse the modelname section of a template postscript file. * If anything is invalid, we return a non-eslOK status code * to caller. * * Returns: eslOK on success. */ int parse_modelname_section(ESL_FILEPARSER *efp, char *errbuf, SSPostscript_t *ps) { int status; char *tok; int toklen; char *curstr = NULL; int curlen = 0; int ntok = 0; /* this section should be exactly 3 lines, one of which we've already read, * here's an example, next token should be the first 0.65 * % begin modelname * % archaea * % end scale */ if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing modelname section, reading token 1 of 3"); if (strcmp(tok, "%") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing modelname section, middle line token 1 should be a percent sign but it's %s", tok); /* read remainder of line, this is the model name */ while ((status = esl_fileparser_GetTokenOnLine(efp, &tok, &toklen)) == eslOK) { if(ntok > 0) { if((status = esl_strcat(&curstr, curlen, " ", 1)) != eslOK) ESL_FAIL(status, errbuf, "parse_modelname_section(), error parsing model name."); curlen += 1; } if((status = esl_strcat(&curstr, curlen, tok, toklen)) != eslOK) ESL_FAIL(status, errbuf, "parse_modelname_section(), error parsing model name."); curlen += toklen; ntok++; } ESL_ALLOC(ps->modelname, sizeof(char) * (curlen+1)); strcpy(ps->modelname, curstr); /* next line should be '% end modelname' */ if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing modelname section, reading end line token 1 of 3"); if (strcmp(tok, "%") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing modelname section, end line token 1 of 3 should be a percent sign but it's %s", tok); if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing modelname section, reading end line token 2 of 3"); if (strcmp(tok, "end") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing modelname section, end line token 2 of 3 should be 'end' but it's %s", tok); if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing modelname section, reading end line token 3 of 3"); if (strcmp(tok, "modelname") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing modelname section, end line token 3 of 3 should be 'modelname' but it's %s", tok); if(curstr != NULL) free(curstr); return eslOK; ERROR: ESL_FAIL(status, errbuf, "Error, parsing modelname section, memory error?"); } /* parse_legend_section * * Parse the legend (legend coordinates) section of a template postscript file. * If anything is invalid, we return a non-eslOK status code * to caller. * * Returns: eslOK on success. */ int parse_legend_section(ESL_FILEPARSER *efp, char *errbuf, SSPostscript_t *ps) { int status; char *tok; int toklen; /* this section should be exactly 3 lines, one of which we've already read, * five tokens of the middle line are * this tells us to put the top-left corner of the legend at * ps->legx[rfpos] + x_offset, ps->legy[rfpos] + y_offset, * and have the RHS of the buffer end points before the RHS of the page * cellsize is the size of the cells in the legend * here's an example, first token we'll read should be '%', followed by '1508' * % begin legend * % 1508 24. -24. 12 0. * % end legend */ if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing legend section, reading token 1 of 6"); if (strcmp(tok, "%") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing legend section, middle line token 1 should be a percent sign but it's %s", tok); if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing legend section, reading token 2 of 6"); ps->leg_posn = atoi(tok); if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing legend section, reading token 3 of 6"); ps->legx_offset = atof(tok); if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing legend section, reading token 4 of 6"); ps->legy_offset = atof(tok); if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing legend section, reading token 5 of 6"); ps->leg_cellsize = atoi(tok); if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing legend section, reading token 6 of 6"); ps->leg_rhs_space = atof(tok); /* read '% end legend' line */ if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing legend section, reading token 3 of 3"); if (strcmp(tok, "%") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing legend section, end line token 1 of 3 should be a percent sign but it's %s", tok); if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing legend section, reading end line token 2 of 3"); if (strcmp(tok, "end") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing legend section, end line token 2 of 3 should be 'end' but it's %s", tok); if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing legend section, reading end line token 3 of 3"); if (strcmp(tok, "legend") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing legend section, end line token 3 of 3 should be 'legend' but it's %s", tok); return eslOK; } /* parse_scale_section * * Parse the scale section of a template postscript file. * If anything is invalid, we return a non-eslOK status code * to caller. * * Returns: eslOK on success. */ int parse_scale_section(ESL_FILEPARSER *efp, char *errbuf, SSPostscript_t *ps) { int status; char *tok; int toklen; /* this section should be exactly 3 lines, one of which we've already read, * here's an example, next token should be the first 0.65 * % begin scale * 0.65 0.65 scale * % end scale */ if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing scale section, reading token 1 of 3"); ps->scale = atof(tok); if(ps->scale < 0.) ESL_FAIL(status, errbuf, "Error, parsing scale section, scale must be positive real number, read %s\n", tok); if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing scale section, reading token 2 of 3"); if(esl_FCompare(ps->scale, atof(tok), eslSMALLX1) != eslOK) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing scale section, x and y scales are not equal %.2f != %.2f", ps->scale, atof(tok)); if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing scale section, reading token 3 of 3"); if (strcmp(tok, "scale") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing scale section, token 3 of 3 should be 'scale' but it's %s", tok); if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing scale section, reading end line token 1 of 3"); if (strcmp(tok, "%") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing scale section, end line token 1 of 3 should be a percent sign but it's %s", tok); if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing scale section, reading end line token 2 of 3"); if (strcmp(tok, "end") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing scale section, end line token 2 of 3 should be 'end' but it's %s", tok); if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing scale section, reading end line token 3 of 3"); if (strcmp(tok, "scale") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing scale section, end line token 3 of 3 should be 'scale' but it's %s", tok); return eslOK; } /* parse_ignore_section * * Parse an ignore section of a template postscript file. * We ignore this data. This function's purpose is to read * tokens until we see the "% end ignore" line signalling * the end of the ignore section. * * As a special case, if any line iss a single token, 'showpage', we * set *ret_read_showpage as TRUE upon return. This signals to caller * that the current page is finished. * * Returns: eslOK on success. */ int parse_ignore_section(ESL_FILEPARSER *efp, char *errbuf, int *ret_read_showpage) { int status; char *tok; int keep_reading = TRUE; int read_showpage = FALSE; while((keep_reading) && (status = esl_fileparser_NextLine(efp) == eslOK)) { /* we're going to keep reading until we've read the line that is '% end ignore', 3 tokens, '%', then 'end', then 'ignore' */ if(((status = esl_fileparser_GetToken(efp, &tok, NULL)) == eslOK) && (strcmp(tok, "%") == 0)) { /* first token is '%' */ if(((status = esl_fileparser_GetToken(efp, &tok, NULL)) == eslOK) && (strcmp(tok, "end") == 0)) { /* second token is 'end' */ if(((status = esl_fileparser_GetToken(efp, &tok, NULL)) == eslOK) && (strcmp(tok, "ignore") == 0)) { /* final token is 'end' */ keep_reading = FALSE; status = eslOK; } } } else if(strcmp(tok, "showpage") == 0) { /* first token is 'showpage' */ read_showpage = TRUE; } } if(status == eslEOF) ESL_FAIL(status, errbuf, "Error, parsing ignore section, finished file looking for '%%%% end ignore' line"); if(status != eslOK) ESL_FAIL(status, errbuf, "Error, parsing ignore section, last line number read %d", efp->linenumber); *ret_read_showpage = read_showpage; return eslOK; } /* parse_regurgitate_section * * Parse a regurgitate section of a template postscript file. * If anything is invalid, we return a non-eslOK status code * to caller. * * Returns: eslOK on success. */ int parse_regurgitate_section(ESL_FILEPARSER *efp, char *errbuf, SSPostscript_t *ps) { int status; char *tok; int toklen; int seen_end = FALSE; char *curstr = NULL; char *newstr; int nalloc = ps->nregurg; int curlen; void *tmp; int ntok = 0; while (((status = esl_fileparser_NextLine(efp)) == eslOK) && (!seen_end)) { curlen = ntok = 0; while ((status = esl_fileparser_GetTokenOnLine(efp, &tok, &toklen)) == eslOK) { if (strcmp(tok, "%") == 0) { /* should be the end, make sure it's properly formatted */ if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing regurgitate section, read %%%% prefixed line without ' end regurgitate' after it"); if (strcmp(tok, "end") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing regurgitate section, read %%%% prefixed line without ' end regurgitate' after it"); if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing regurgitate section, read %%%% prefixed line without ' end regurgitate' after it"); if (strcmp(tok, "regurgitate") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing regurgitate section, read %%%% prefixed line without ' end regurgitate' after it"); seen_end = TRUE; break; } else { if(ntok > 0) { if((status = esl_strcat(&curstr, curlen, " ", 1)) != eslOK) ESL_FAIL(status, errbuf, "parse_regurgitate_section(), error (2)."); curlen += 1; } if((status = esl_strcat(&curstr, curlen, tok, toklen)) != eslOK) ESL_FAIL(status, errbuf, "parse_regurgitate_section(), error (1)."); curlen += toklen; ntok++; } } if(seen_end) break; if((status = esl_strcat(&curstr, curlen, "\n", 1)) != eslOK) ESL_FAIL(status, errbuf, "parse_regurgitate_section(), error (3)."); curlen += 1; ESL_ALLOC(newstr, sizeof(char) * (curlen+1)); strcpy(newstr, curstr); if(ps->nregurg == nalloc) { nalloc += ps->nalloc; ESL_RALLOC(ps->regurgA, tmp, sizeof(char *) * nalloc); } ps->regurgA[ps->nregurg++] = newstr; free(curstr); curstr = NULL; } if(status == eslEOF) ESL_FAIL(status, errbuf, "Error, parsing regurgitate section, finished file looking for '%%%% end regurgitate' line"); if(status != eslOK) ESL_FAIL(status, errbuf, "Error, parsing regurgitate section, last line number read %d", efp->linenumber); return eslOK; ERROR: ESL_FAIL(status, errbuf, "Memory error parsing regurgitate section"); } /* parse_text_section * * Parse a text section of a template postscript file. * If anything is invalid, we return a non-eslOK status code * to caller. * * Returns: eslOK on success. */ int parse_text_section(ESL_FILEPARSER *efp, char *errbuf, SSPostscript_t *ps) { int status; char *tok; int toklen; int seen_end = FALSE; int nalloc; void *tmp; int do_posntext = FALSE; int do_nucleotides = FALSE; int i; /* find out which section we're in, 'posntext' or 'nucleotides' */ if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing text section, last line %d\n", efp->linenumber); if (strcmp(tok, "positiontext") == 0) { do_posntext = TRUE; nalloc = ps->nposntext; } else if (strcmp(tok, "nucleotides") == 0) { do_nucleotides = TRUE; nalloc = ps->rflen; } /* Parse each line. example line: * (G) 168.00 392.00 moveto show */ while (((status = esl_fileparser_NextLine(efp)) == eslOK) && (!seen_end)) { if((status = esl_fileparser_GetTokenOnLine(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing text section, each non-comment line should be 5-tokens ending with 'show'"); if (tok[0] == '%') { /* comment line, could be the end, check if it's '% end text {positiontext,nucleotides}', if not, ignore it */ if(strcmp(tok, "%") == 0) { /* first token is '%', keep checking */ if(((status = esl_fileparser_GetToken(efp, &tok, &toklen)) == eslOK) && (strcmp(tok, "end") == 0)) { /* second token is 'end', keep checking */ if(((status = esl_fileparser_GetToken(efp, &tok, &toklen)) == eslOK) && (strcmp(tok, "text") == 0)) { /* third token is 'end', keep checking */ if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) == eslOK) { /* has a fourth token, keep checking */ if(do_posntext && strcmp(tok, "positiontext") == 0) seen_end = TRUE; if(do_nucleotides && strcmp(tok, "nucleotides") == 0) seen_end = TRUE; } } } } } else { /* we're reading a non-comment line, tok is the string, if do_posntext, we store it, else we discard it */ if(do_posntext) { if(ps->nposntext == nalloc) { ESL_RALLOC(ps->posntextA, tmp, sizeof(char *) * (nalloc + ps->nalloc)); ESL_RALLOC(ps->posntextxA, tmp, sizeof(float) * (nalloc + ps->nalloc)); ESL_RALLOC(ps->posntextyA, tmp, sizeof(float) * (nalloc + ps->nalloc)); for(i = nalloc; i < nalloc + ps->nalloc; i++) ps->posntextA[i] = NULL; nalloc += ps->nalloc; } if((status = esl_strdup(tok, -1, &(ps->posntextA[ps->nposntext]))) != eslOK) goto ERROR; } if(do_nucleotides && ps->rflen == nalloc) { ESL_RALLOC(ps->rxA, tmp, sizeof(float) * (nalloc + ps->nalloc)); ESL_RALLOC(ps->ryA, tmp, sizeof(float) * (nalloc + ps->nalloc)); nalloc += ps->nalloc; } /* get x */ if((status = esl_fileparser_GetTokenOnLine(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing text section, each non-comment line should be 5 tokens ending with 'show'"); if(do_posntext) ps->posntextxA[ps->nposntext] = atof(tok); if(do_nucleotides) ps->rxA[ps->rflen] = atof(tok); /* get y */ if((status = esl_fileparser_GetTokenOnLine(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing text section, each non-comment line should be 5 tokens ending with 'show'"); if(do_posntext) ps->posntextyA[ps->nposntext] = atof(tok); if(do_nucleotides) ps->ryA[ps->rflen] = atof(tok); /* verify moveto */ if((status = esl_fileparser_GetTokenOnLine(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing text section, each non-comment line should be 5 tokens ending with 'show'"); if (strcmp(tok, "moveto") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing text main section, fourth token should be 'moveto', line %d", efp->linenumber); /* verify show */ if((status = esl_fileparser_GetTokenOnLine(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing text section, each non-comment line should be 5 tokens ending with 'show'"); if (strcmp(tok, "show") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing text main section, fifth token should be 'show', line %d", efp->linenumber); if(do_posntext) ps->nposntext++; if(do_nucleotides) ps->rflen++; } } if(!seen_end) { if(do_posntext) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing text positiontext section, didn't see '%%%% end text positiontext' line: %d\n", efp->linenumber); if(do_nucleotides) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing text positiontext section, didn't see '%%%% end text nucleotides' line: %d\n", efp->linenumber); } if(status == eslEOF && do_posntext) ESL_FAIL(status, errbuf, "Error, parsing text section, finished file looking for '%%%% end text positiontext' line"); if(status == eslEOF && do_nucleotides) ESL_FAIL(status, errbuf, "Error, parsing text section, finished file looking for '%%%% end text nucleotides' line"); if(status != eslOK) ESL_FAIL(status, errbuf, "Error, parsing text section, last line number read %d", efp->linenumber); return eslOK; ERROR: ESL_FAIL(status, errbuf, "Memory error parsing text section"); } /* parse_lines_section * * Parse a lines section of a template postscript file. * If anything is invalid, we return a non-eslOK status code * to caller. * * Returns: eslOK on success. */ int parse_lines_section(ESL_FILEPARSER *efp, char *errbuf, SSPostscript_t *ps) { int status; char *tok; int toklen; int seen_end = FALSE; int nalloc; void *tmp; int do_ticks = FALSE; int do_bpconnects = FALSE; /* find out which section we're in, 'positionticks' or 'bpconnects' */ if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing lines section, last line %d\n", efp->linenumber); if (strcmp(tok, "positionticks") == 0) { do_ticks = TRUE; nalloc = ps->nticks; } else if (strcmp(tok, "bpconnects") == 0) { do_bpconnects = TRUE; nalloc = ps->nbp; } else ESL_FAIL(status, errbuf, "Error, parsing lines section unrecognized type: %s ('bpconnects' or 'positionticks' expected)\n", tok); /* Parse each line. example line: * 151.82 331.76 148.86 338.65 newpath moveto lineto stroke */ while (((status = esl_fileparser_NextLine(efp)) == eslOK) && (!seen_end)) { if((status = esl_fileparser_GetTokenOnLine(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing lines main section should include 5-tokens ending with 'show'"); if (strcmp(tok, "%") == 0) { /* should be the end, make sure it's properly formatted */ if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing lines section, read %%%% prefixed line without ' end lines' after it"); if (strcmp(tok, "end") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing lines section, read %%%% prefixed line without ' end lines' after it"); if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing lines section, read %%%% prefixed line without ' end lines' after it"); if (strcmp(tok, "lines") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing lines section, read %%%% prefixed line without ' end lines' after it"); if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing lines section, read %%%% prefixed line without ' end lines' after it"); if(do_ticks) { if (strcmp(tok, "positionticks") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing lines section, read %%%% prefixed line without ' end lines positionticks' after it"); } if(do_bpconnects) { if (strcmp(tok, "bpconnects") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing lines section, read %%%% prefixed line without ' end lines bpconnects' after it"); } seen_end = TRUE; break; } /* if we get here, we haven't seen the end, we're reading a normal line, tok is the first x coord, we record this */ /* first we expand our arrays if nec */ if(do_ticks && ps->nticks == nalloc) { nalloc += ps->nalloc; ESL_RALLOC(ps->ticksx1A, tmp, sizeof(float) * nalloc); ESL_RALLOC(ps->ticksy1A, tmp, sizeof(float) * nalloc); ESL_RALLOC(ps->ticksx2A, tmp, sizeof(float) * nalloc); ESL_RALLOC(ps->ticksy2A, tmp, sizeof(float) * nalloc); } if(do_bpconnects && ps->nbp == nalloc) { nalloc += ps->nalloc; ESL_RALLOC(ps->bpx1A, tmp, sizeof(float) * nalloc); ESL_RALLOC(ps->bpy1A, tmp, sizeof(float) * nalloc); ESL_RALLOC(ps->bpx2A, tmp, sizeof(float) * nalloc); ESL_RALLOC(ps->bpy2A, tmp, sizeof(float) * nalloc); } /* store x1 */ if(do_ticks) ps->ticksx1A[ps->nticks] = atof(tok); if(do_bpconnects) ps->bpx1A[ps->nbp] = atof(tok); /* get y1 */ if((status = esl_fileparser_GetTokenOnLine(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing lines main section should include 8-tokens ending with 'stroke'"); if(do_ticks) ps->ticksy1A[ps->nticks] = atof(tok); if(do_bpconnects) ps->bpy1A[ps->nbp] = atof(tok); /* get x2 */ if((status = esl_fileparser_GetTokenOnLine(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing lines main section should include 8-tokens ending with 'stroke'"); if(do_ticks) ps->ticksx2A[ps->nticks] = atof(tok); if(do_bpconnects) ps->bpx2A[ps->nbp] = atof(tok); /* get y2 */ if((status = esl_fileparser_GetTokenOnLine(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing lines main section should include 8-tokens ending with 'stroke'"); if(do_ticks) ps->ticksy2A[ps->nticks] = atof(tok); if(do_bpconnects) ps->bpy2A[ps->nbp] = atof(tok); /* verify newpath */ if((status = esl_fileparser_GetTokenOnLine(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing lines main section should include 8-tokens ending with 'stroke'"); if (strcmp(tok, "newpath") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing lines main section, fifth token should be 'newpath', line %d", efp->linenumber); /* verify moveto */ if((status = esl_fileparser_GetTokenOnLine(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing lines main section should include 8-tokens ending with 'stroke'"); if (strcmp(tok, "moveto") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing lines main section, sixth token should be 'moveto', line %d", efp->linenumber); /* verify lineto */ if((status = esl_fileparser_GetTokenOnLine(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing lines main section should include 8-tokens ending with 'stroke'"); if (strcmp(tok, "lineto") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing lines main section, seventh token should be 'lineto', line %d", efp->linenumber); /* verify stroke */ if((status = esl_fileparser_GetTokenOnLine(efp, &tok, &toklen)) != eslOK) ESL_FAIL(status, errbuf, "Error, parsing lines main section should include 8-tokens ending with 'stroke'"); if (strcmp(tok, "stroke") != 0) ESL_FAIL(eslEINVAL, errbuf, "Error, parsing lines main section, eigth token should be 'stroke', line %d", efp->linenumber); if(do_ticks) ps->nticks++; if(do_bpconnects) ps->nbp++; } if(!seen_end) ESL_FAIL(status, errbuf, "Error, parsing lines section, didn't see end! line: %d\n", efp->linenumber); if(status == eslEOF && do_ticks) ESL_FAIL(status, errbuf, "Error, parsing lines section, finished file looking for '%%%% end lines positionticks' line"); if(status == eslEOF && do_bpconnects) ESL_FAIL(status, errbuf, "Error, parsing lines section, finished file looking for '%%%% end lines bpconnects' line"); if(status != eslOK) ESL_FAIL(status, errbuf, "Error, parsing lines section, last line number read %d", efp->linenumber); return eslOK; ERROR: ESL_FAIL(status, errbuf, "Memory error parsing lines section"); } /* Function: individuals_sspostscript() * * Purpose: Fill a postscript data structure with info for individual seqs and * possibly their posteriors in the MSA. * Return: eslOK on success. * * per_seq_ins_ct - [0..i..msa->nseq-1][0..rfpos..rflen] number of inserts * insert after each nongap RF position per sequence. * If rfpos == 0: # inserts BEFORE first position. * If rfpos == n: # inserts after position rfpos n * This is off-by-one with respect to msa->rf for example, * msa->rf[n] is the 'n-1'th nucleotide of the RF annotation. */ static int individuals_sspostscript(const ESL_GETOPTS *go, ESL_ALPHABET *abc, char *errbuf, SSPostscript_t *ps, double **abc_ct, ESL_MSA *msa, int **per_seq_ins_ct, int do_prob, int do_rescol, float ***hc_scheme, int hc_scheme_idx_s, int hc_scheme_idx_p, int hc_nbins_s, int hc_nbins_p, float **hc_onecell, int extdel_idx_s, int wcbp_idx_s, int gubp_idx_s, int ncbp_idx_s, int dgbp_idx_s, int hgbp_idx_s, int gap_idx_p, FILE *tabfp) { int status; int p, i, pp, ai; int rfpos, apos, lpos, rpos, lrfpos, rrfpos; int orig_npage = ps->npage; int new_npage; /* variables for the sequence pages */ int nextdel_s = 0; /* number of external deletes (3' and 5' flush deletes) */ int nwc_s = 0; /* number of Watson/Crick (A:U,U:A,C:G,G:C) basepairs */ int ngu_s = 0; /* number of G:U,U:G basepairs (2 * num G-U,U-G bps) */ int nnc_s = 0; /* number of non-canonical basepairs (A:A,A:C,A:G,C:A,C:C,C:U,G:A,G:G,U:C,U:U) */ int ndgi_s = 0; /* number of internal double-gap basepairs */ int nhgi_s = 0; /* number of internal half-gap basepairs */ int ndge_s = 0; /* number of external double-gap basepairs */ int nhge_s = 0; /* number of external half-gap basepairs */ float *limits_s; /* [nbins+1] limits for each bin, limits[0] is min value we would expect to see, limits[nbins] is max */ int nins_s; /* number of inserts after the current rfpos for current sequence */ int spos, epos; /* first/final nongap position for cur sequence */ int apos_is_internal; /* is apos within spos..epos?, if not it's an external deletion */ int lpos_is_internal; /* is lpos within spos..epos?, if not it's an external deletion */ int rpos_is_internal; /* is rpos within spos..epos?, if not it's an external deletion */ int namewidth; /* length in chars of longest seq name we'll print */ char *namedashes = NULL; int ni; double cur_cfreq; int noutline_min = 0; /* number of positions with minimal outline */ int noutline_max = 0; /* number of positions with maximal outline */ int noutline_bp_good = 0; /* number of WC/GU basepairs that have left and/or right half outlined, consensus is WC/GU */ int noutline_bp_bad = 0; /* number of NC basepairs that have left and/or right half outlined, consensus is WC/GU */ int maj_bp_is_wc_or_gu; /* TRUE if current consensus bp is a watson-crick of GU in majority consensus sequence */ float *stack; /* postscript stack for outline procedure */ /* variables for the postprob pages */ int ngap_p = 0; int ngap_masked_p = 0; float *limits_p; int within_mask; float ppavgA[11]; int ppidx; int do_prob_res = FALSE; /* set to TRUE if --no-ntpp is NOT enabled */ int do_outline = FALSE; /* set to TRUE if --no-nt is NOT enabled */ int noccl; /* number of one-cell color legends depends on value of do_prob_res and do_ouline */ /* contract check */ if(do_prob) { if(msa->pp == NULL) ESL_FAIL(eslEINVAL, errbuf, "internal error, individuals_sspostscript() do_prob == TRUE, msa->pp == FALSE"); for(i = 0; i < msa->nseq; i++) { if(msa->pp[i] == NULL) ESL_FAIL(eslEINVAL, errbuf, "with --indi, either all or none of the selected sequences must have PP annotation, seq %d does not", i); } do_prob_res = (! esl_opt_GetBoolean(go, "--no-ntpp")); } do_outline = (! esl_opt_GetBoolean(go, "--no-ol")); /* PP values, hard coded */ ppavgA[0] = 0.025; ppavgA[1] = 0.10; ppavgA[2] = 0.20; ppavgA[3] = 0.30; ppavgA[4] = 0.40; ppavgA[5] = 0.50; ppavgA[6] = 0.60; ppavgA[7] = 0.70; ppavgA[8] = 0.80; ppavgA[9] = 0.90; ppavgA[10] = 0.975; /* determine number of pages we'll add */ new_npage = do_prob ? msa->nseq*2 : msa->nseq; if((status = add_pages_sspostscript(ps, new_npage, INDIMODE)) != eslOK) ESL_FAIL(status, errbuf, "memory error adding pages to the postscript object."); /* add the pages carefully, we allocate posterior pages and seq pages differently */ for(p = orig_npage; p < ps->npage; p++) { /* allocate seq page */ ESL_ALLOC(ps->rAA[p], sizeof(char) * (ps->rflen+1)); if(do_rescol) ESL_ALLOC(ps->rcolAAA[p], sizeof(float *) * ps->rflen); if(do_outline) { ESL_ALLOC(ps->otypeAA[p], sizeof(char) * ps->rflen); for(rfpos = 0; rfpos < ps->rflen; rfpos++) ps->otypeAA[p][rfpos] = OUTLINE_NONE_IDX; } ESL_ALLOC(ps->bcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->sclAA[p], sizeof(SchemeColorLegend_t) * 1); noccl = 2; if (do_rescol) noccl += 5; if (do_outline) noccl += 7; ESL_ALLOC(ps->occlAAA[p], sizeof(OneCellColorLegend_t *) * noccl); for(rfpos = 0; rfpos < ps->rflen; rfpos++) { if(do_rescol) ESL_ALLOC(ps->rcolAAA[p][rfpos], sizeof(float) * NCMYK); /* CMYK colors */ ESL_ALLOC(ps->bcolAAA[p][rfpos], sizeof(float) * NCMYK); /* CMYK colors */ } if(do_prob) { /* allocate postprob page */ p++; ESL_ALLOC(ps->rAA[p], sizeof(char) * (ps->rflen+1)); ESL_ALLOC(ps->bcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->sclAA[p], sizeof(SchemeColorLegend_t) * 1); ESL_ALLOC(ps->occlAAA[p], sizeof(OneCellColorLegend_t *) * 1); if(do_prob_res) ESL_ALLOC(ps->rcolAAA[p], sizeof(float *) * ps->rflen); for(rfpos = 0; rfpos < ps->rflen; rfpos++) { ESL_ALLOC(ps->bcolAAA[p][rfpos], sizeof(float) * NCMYK); /* CMYK colors */ if(do_prob_res) ESL_ALLOC(ps->rcolAAA[p][rfpos], sizeof(float) * NCMYK); /* CMYK colors */ } } } /* setup seq limits */ ESL_ALLOC(limits_s, sizeof(float) * (hc_nbins_s+1)); limits_s[0] = 0; limits_s[1] = 1; limits_s[2] = 2; limits_s[3] = 5; limits_s[4] = 10; limits_s[5] = SSDRAWINFINITY; /* setup pp limits */ ESL_ALLOC(limits_p, sizeof(float) * (hc_nbins_p+1)); limits_p[0] = 0.0; limits_p[1] = 0.35; limits_p[2] = 0.55; limits_p[3] = 0.75; limits_p[4] = 0.85; limits_p[5] = 0.95; limits_p[6] = 1.00; /* allocate the uaseqlenA data structure to store unaligned seq lengths */ if(ps->uaseqlenA != NULL) { free(ps->uaseqlenA); ps->uaseqlenA = NULL; } ESL_ALLOC(ps->uaseqlenA, sizeof(int) * msa->nseq); esl_vec_ISet(ps->uaseqlenA, msa->nseq, 0); if(tabfp != NULL) { /* determine max length of a name */ namewidth = 8; /* length of 'seq name' */ for(i = 0; i < msa->nseq; i++) { namewidth = ESL_MAX(namewidth, strlen(msa->sqname[i])); } ESL_ALLOC(namedashes, sizeof(char) * namewidth+1); namedashes[namewidth] = '\0'; for(ni = 0; ni < namewidth; ni++) namedashes[ni] = '-'; fprintf(tabfp, "# -----------------------\n"); fprintf(tabfp, "# Per-sequence statistics\n"); fprintf(tabfp, "# -----------------------\n"); fprintf(tabfp, "# This section includes %d non #-prefixed lines, one for each sequence\n", ps->rflen); fprintf(tabfp, "# printed to the output postscript file.\n"); fprintf(tabfp, "# Each line includes %d tokens, separated by whitespace:\n", do_outline ? 15 : 11); fprintf(tabfp, "# \ttoken 1: 'perseq' (tag defining line type to ease parsing)\n"); fprintf(tabfp, "# \ttoken 2: sequence name\n"); fprintf(tabfp, "# \ttoken 3: spos: aligned position of first (5'-most) nongap nucleotide in sequence\n"); fprintf(tabfp, "# \ttoken 4: epos: aligned position of final (3'-most) nongap nucleotide in sequence\n"); fprintf(tabfp, "# \ttoken 5: number of Watson-Crick basepairs (A-U, C-G, G-C, or U-A) in the sequence\n"); fprintf(tabfp, "# \ttoken 6: number of G-U or U-G basepairs in the sequence\n"); fprintf(tabfp, "# \ttoken 7: number of non-canonical basepairs (A-A, A-C, A-G, C-A, C-C, C-U, G-A, G-G, U-C, U-U) in the sequence\n"); fprintf(tabfp, "# \ttoken 8: number of internal half-gap basepairs in the sequence\n"); fprintf(tabfp, "# \ttoken 9: number of internal double-gap basepairs in the sequence\n"); fprintf(tabfp, "# \ttoken 10: number of external half-gap basepairs in the sequence\n"); fprintf(tabfp, "# \ttoken 11: number of external double-gap basepairs in the sequence\n"); if(do_outline) { fprintf(tabfp, "# \ttoken 12: number of nt changes relative to majority rule consensus sequence\n"); fprintf(tabfp, "# \ttoken 13: subset of token 12 for which consensus nt occurs in > 0.75 of nongap sequences\n"); fprintf(tabfp, "# \ttoken 14: number of internal basepairs in seq that differ from majority rule consensus basepair\n"); fprintf(tabfp, "# \t *and* consensus bp is Watson-Crick, G-U or U-G\n"); fprintf(tabfp, "# \ttoken 15: subset of token 14 which are Watson-Crick, G-U or U-G in seq\n"); } fprintf(tabfp, "#\n"); fprintf(tabfp, "# Alignment length: %" PRId64 " (this is max possible value for tokens 3 and 4)\n", msa->alen); fprintf(tabfp, "# Number of consensus basepairs: %d (this is max possible value for tokens 5-11)\n", ps->nbp); fprintf(tabfp, "# A basepair between positions i and j for sequence s is a half-gap basepair if s has\n"); fprintf(tabfp, "# a gap at either position i or j, but not both. It is a double-gap basepair if it has\n"); fprintf(tabfp, "# a gap at both positions i and j.\n"); fprintf(tabfp, "# A basepair between i:j is 'internal' for sequence s if if spos <= i and epos >= j.\n"); fprintf(tabfp, "# Otherwise, basepair i:j is 'external' for sequence s.\n"); fprintf(tabfp, "# All basepairs that are nongaps in both i and j are necessarily internal.\n"); fprintf(tabfp, "#\n"); fprintf(tabfp, "# %6s %-*s %4s %4s %4s %4s %4s %4s %4s %4s %4s", "type", namewidth, "seq name", "spos", "epos", "nwc", "ngu", "nnc", "nhgi", "ndgi", "nhge", "ndge"); if(do_outline) { fprintf(tabfp, " %4s %4s %5s %5s", "ndf", "nrdf", "nbpdf", "nbpcp"); } fprintf(tabfp, "\n"); fprintf(tabfp, "# %6s %-*s %4s %4s %4s %4s %4s %4s %4s %4s %4s", "------", namewidth, namedashes, "----", "----", "----", "----", "----", "----", "----", "----", "----"); if(do_outline) { fprintf(tabfp, " %4s %4s %5s %5s", "----", "----", "-----", "-----"); } fprintf(tabfp, "\n"); } /* Step through each seq, first fill seq page, then possibly postprob page */ ai = 0; pp = orig_npage-1; for(i = 0; i < msa->nseq; i++) { /************************** * Draw the sequence page * **************************/ pp++; spos = epos = -1; /* determine first and final non-gap position */ for(apos = 0; apos < msa->alen; apos++) { /* find first non-gap RF position */ if((! esl_abc_CIsGap(abc, msa->aseq[i][apos]))) { spos = apos; break; } } for(apos = msa->alen-1; apos >= 0; apos--) { if((! esl_abc_CIsGap(abc, msa->aseq[i][apos]))) { epos = apos; break; } } ps->sclAA[pp] = create_scheme_colorlegend(hc_scheme_idx_s, hc_nbins_s, limits_s, TRUE, TRUE, TRUE, FALSE); /* init one cell legend counters */ nextdel_s = nwc_s = ngu_s = nnc_s = ndgi_s = nhgi_s = ndge_s = nhge_s = noutline_min = noutline_max = noutline_bp_good = noutline_bp_bad = 0; ai++; for(rfpos = 0; rfpos < ps->rflen; rfpos++) { apos = ps->msa_rf2a_map[rfpos]; nins_s = per_seq_ins_ct[i][rfpos+1]; apos_is_internal = TRUE; /* set to FALSE below if apos < spos || apos > epos */ if(! esl_abc_CIsGap(abc, msa->aseq[i][apos])) ps->uaseqlenA[i]++; ps->uaseqlenA[i] += nins_s; ps->rAA[pp][rfpos] = msa->aseq[i][apos]; if(do_outline) { if((! esl_abc_CIsGap(abc, msa->aseq[i][apos])) && /* aseq is not a gap at this posn */ (esl_abc_CIsCanonical(abc, ps->msa_cseq_maj[rfpos])) && /* cseq is canonical at this posn */ (toupper(msa->aseq[i][apos]) != toupper(ps->msa_cseq_maj[rfpos]))) { /* aseq != cseq at this posn */ cur_cfreq = abc_ct[apos][esl_abc_DigitizeSymbol(abc, toupper(ps->msa_cseq_maj[rfpos]))] / esl_vec_DSum(abc_ct[apos], abc->K); if(cur_cfreq > 0.75) { ps->otypeAA[pp][rfpos] = OUTLINE_MAX_IDX; noutline_max++; } else { ps->otypeAA[pp][rfpos] = OUTLINE_MIN_IDX; noutline_min++; } } } /* printf("ps->rAA[%3d][%4d]: %c\n", pp, rfpos, ps->rAA[pp][rfpos]); */ if((spos != -1 && epos != -1) && /* this should always be true, unless seq has length 0! */ (apos < spos || apos > epos)) { if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_onecell[extdel_idx_s])) != eslOK) return status; nextdel_s++; apos_is_internal = FALSE; } else { /* color insert value */ if((status = set_scheme_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_scheme[hc_scheme_idx_s], nins_s, ps->sclAA[pp], TRUE, NULL)) != eslOK) return status; } if(do_rescol || tabfp != NULL) { if(ps->msa_ct[(rfpos+1)] == 0) { if(do_rescol) { /* single-stranded nucleotide or gap, draw same color as Watson-Cricks */ if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[wcbp_idx_s])) != eslOK) return status; } } else { /* consensus basepaired nucleotide */ lpos = apos; rpos = ps->msa_rf2a_map[ps->msa_ct[rfpos+1]-1]; lrfpos = rfpos; rrfpos = ps->msa_ct[rfpos+1]-1; maj_bp_is_wc_or_gu = ((is_watson_crick_bp(ps->msa_cseq_maj[lrfpos], ps->msa_cseq_maj[rrfpos])) || (is_gu_or_ug_bp(ps->msa_cseq_maj[lrfpos], ps->msa_cseq_maj[rrfpos]))) ? TRUE : FALSE; lpos_is_internal = apos_is_internal; rpos_is_internal = TRUE; /* we set to FALSE below if nec */ if((spos != -1 && epos != -1) && /* this should always be true, unless seq has length 0! */ (rpos < spos || rpos > epos)) { rpos_is_internal = FALSE; } if(lpos_is_internal && rpos_is_internal) { /* BP is either Watson-Crick, G:U/U:G, non-canonical, internal double-gap bp or internal half-gap bp */ if(is_watson_crick_bp(msa->aseq[i][lpos], msa->aseq[i][rpos])) { /* watson-crick */ if(do_rescol) { if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[wcbp_idx_s])) != eslOK) return status; } if(lpos < rpos) nwc_s++; if(do_outline && (lpos > rpos) && maj_bp_is_wc_or_gu) { /* check if this seq has a different WC or GU bp than the majority consensus */ if((ps->otypeAA[pp][lrfpos] != OUTLINE_NONE_IDX) || (ps->otypeAA[pp][rrfpos] != OUTLINE_NONE_IDX)) { noutline_bp_good++; } } } else if(is_gu_or_ug_bp(msa->aseq[i][lpos], msa->aseq[i][rpos])) { /* G:U or U:G */ if(do_rescol) { if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[gubp_idx_s])) != eslOK) return status; } if(lpos < rpos) ngu_s++; if(do_outline && (lpos > rpos) && maj_bp_is_wc_or_gu) { if((ps->otypeAA[pp][lrfpos] != OUTLINE_NONE_IDX) || (ps->otypeAA[pp][rrfpos] != OUTLINE_NONE_IDX)) { noutline_bp_good++; } } } else if ((! esl_abc_CIsResidue(abc, msa->aseq[i][lpos])) && (! esl_abc_CIsResidue(abc, msa->aseq[i][rpos]))) { /* internal double-gap basepair */ if(do_rescol) { if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[dgbp_idx_s])) != eslOK) return status; } if(lpos < rpos) ndgi_s++; if(do_outline && (lpos > rpos) && maj_bp_is_wc_or_gu) { if((ps->otypeAA[pp][lrfpos] != OUTLINE_NONE_IDX) || (ps->otypeAA[pp][rrfpos] != OUTLINE_NONE_IDX)) { noutline_bp_bad++; } } } else if ((! esl_abc_CIsResidue(abc, msa->aseq[i][lpos])) || (! esl_abc_CIsResidue(abc, msa->aseq[i][rpos]))) { /* internal half-gap basepair */ if(do_rescol) { if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[hgbp_idx_s])) != eslOK) return status; } if(lpos < rpos) nhgi_s++; if(do_outline && (lpos > rpos) && maj_bp_is_wc_or_gu) { if((ps->otypeAA[pp][lrfpos] != OUTLINE_NONE_IDX) || (ps->otypeAA[pp][rrfpos] != OUTLINE_NONE_IDX)) { noutline_bp_bad++; } } } else { /* non-canonical */ if(do_rescol) { if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[ncbp_idx_s])) != eslOK) return status; } if(lpos < rpos) nnc_s++; if(do_outline && (lpos > rpos) && maj_bp_is_wc_or_gu) { if((ps->otypeAA[pp][lrfpos] != OUTLINE_NONE_IDX) || (ps->otypeAA[pp][rrfpos] != OUTLINE_NONE_IDX)) { noutline_bp_bad++; } } } } /* end of (if(lpos_is_internal && rpos_is_internal)) */ else { /* we'll draw this nucleotide as black */ if ((! esl_abc_CIsResidue(abc, msa->aseq[i][lpos])) && (! esl_abc_CIsResidue(abc, msa->aseq[i][rpos]))) { /* external double-gap basepair */ ndge_s++; } if ((! esl_abc_CIsResidue(abc, msa->aseq[i][lpos])) || (! esl_abc_CIsResidue(abc, msa->aseq[i][rpos]))) { /* external half-gap basepair */ nhge_s++; } if(do_rescol) { if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[BLACKOC])) != eslOK) return status; } } } } } ps->rAA[pp][ps->rflen] = '\0'; ps->seqidxA[pp] = i; ps->nocclA[pp] = 0; if(tabfp != NULL) { fprintf(tabfp, " perseq %-*s %4d %4d %4d %4d %4d %4d %4d %4d %4d", namewidth, msa->sqname[i], spos+1, epos+1, nwc_s, ngu_s, nnc_s, nhgi_s, ndgi_s, nhge_s, ndge_s); if(do_outline) { fprintf(tabfp, " %4d %4d %5d %5d", noutline_min + noutline_max, noutline_max, noutline_bp_good + noutline_bp_bad, noutline_bp_good); } fprintf(tabfp, "\n"); } /* if nec, add one-cell color legends for different bp types */ if(do_rescol) { /* add one-cell color legend for watson-crick basepairs */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[wcbp_idx_s], nwc_s, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], "Watson-Crick basepair (WC bp)", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_celltext_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "C-G", errbuf)) != eslOK) return status; ps->nocclA[pp]++; /* add one-cell color legend for G-U, U-G basepairs */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[gubp_idx_s], ngu_s, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], "G-U or U-G bp", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_celltext_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "G-U", errbuf)) != eslOK) return status; ps->nocclA[pp]++; /* add one-cell color legend for non-canonical basepairs */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[ncbp_idx_s], nnc_s, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], "non-canonical bp", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_celltext_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "A-A", errbuf)) != eslOK) return status; ps->nocclA[pp]++; /* add one-cell color legend for internal half-gap basepairs */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[hgbp_idx_s], nhgi_s, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], "internal half-gap bp", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_celltext_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "A--", errbuf)) != eslOK) return status; ps->nocclA[pp]++; /* add one-cell color legend for internal double-gap basepairs */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[dgbp_idx_s], ndgi_s, OCCL_BLANK_COUNT, TRUE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], "internal double-gap bp", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_celltext_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "---", errbuf)) != eslOK) return status; ps->nocclA[pp]++; } /* if nec, add one page cell legend for the two outline types */ if(do_outline) { /* add a psuedo-one-cell color legends, the explanatory text for outlines: */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[BLACKOC], OCCL_BLANK_COUNT, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], "Positions != to most common nt x:", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_celltext_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "", errbuf)) != eslOK) return status; ps->nocclA[pp]++; /* allocate our stack for the procedure */ ESL_ALLOC(stack, sizeof(float) * 2); stack[0] = ps->leg_cellsize; stack[1] = ps->leg_cellsize * OUTLINE_LINEWIDTH_CELL_FRACTION_MIN; /* add one-cell color legend for minimal outline */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[BLACKOC], noutline_min, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], "!= x and freq(x) < 0.75", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_procedure_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], OUTLINE_PROCEDURE, stack, 2, errbuf)) != eslOK) return status; ps->nocclA[pp]++; stack[1] = ps->leg_cellsize * OUTLINE_LINEWIDTH_CELL_FRACTION_MAX; /* add one-cell color legend for maximal outline */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[BLACKOC], noutline_max, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], "!= x and freq(x) >= 0.75", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_procedure_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], OUTLINE_PROCEDURE, stack, 2, errbuf)) != eslOK) return status; ps->nocclA[pp]++; /* add a psuedo-one-cell color legends, the explanatory text for outline basepairs: */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[BLACKOC], OCCL_BLANK_COUNT, OCCL_BLANK_COUNT, FALSE, TRUE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], "Number of bps != most common bp a:b", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_celltext_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "", errbuf)) != eslOK) return status; ps->nocclA[pp]++; /* add a psuedo-one-cell color legends, the explanatory text for outline basepairs: */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[BLACKOC], OCCL_BLANK_COUNT, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], "and a:b is Watson-Crick, GU or UG:", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_celltext_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "", errbuf)) != eslOK) return status; ps->nocclA[pp]++; ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[BLACKOC], noutline_bp_good, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], " Watson-Crick, GU or UG but != a:b", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_celltext_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "", errbuf)) != eslOK) return status; ps->nocclA[pp]++; ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[BLACKOC], noutline_bp_bad, OCCL_BLANK_COUNT, TRUE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], " non-canonical or w/gap and != a:b", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_celltext_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "", errbuf)) != eslOK) return status; ps->nocclA[pp]++; } /* add description to ps */ if((status = add_text_to_scheme_colorlegend(ps, ps->sclAA[pp], "# inserted nucleotides after each consensus position", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_page_desc_to_sspostscript(ps, pp, msa->sqname[i], errbuf)) != eslOK) return status; /* done with seq page */ /* add one-cell color legend for external gaps (deletes) */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[extdel_idx_s], nextdel_s, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "5'/3'-flush gaps", ps->legx_max_chars, errbuf)) != eslOK) return status; ps->nocclA[pp]++; /*************************************** * Draw the posterior probability page * ***************************************/ if(do_prob) { /* contract checked that msa->pp[i] is non-NULL */ pp++; ps->sclAA[pp] = create_scheme_colorlegend(hc_scheme_idx_p, hc_nbins_p, limits_p, FALSE, TRUE, TRUE, FALSE); ngap_p = 0; ngap_masked_p = (ps->mask == NULL) ? -1 : 0; for(rfpos = 0; rfpos < ps->rflen; rfpos++) { apos = ps->msa_rf2a_map[rfpos]; if(do_prob_res) { ps->rAA[pp][rfpos] = msa->aseq[i][apos]; if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[WHITEOC])) != eslOK) return status; } else { ps->rAA[pp][rfpos] = ' '; /* no need to add color to a ' ' */ } if(! esl_abc_CIsGap(abc, msa->aseq[i][apos])) { if((ppidx = get_pp_idx(abc, msa->pp[i][apos])) == -1) ESL_FAIL(eslEFORMAT, errbuf, "bad #=GR PP char: %c", msa->pp[i][apos]); if(ppidx == 11) ESL_FAIL(eslEFORMAT, errbuf, "nongap nucleotide: %c, annotated with gap #=GR PP char: %c", msa->aseq[i][apos], msa->pp[i][apos]); within_mask = (ps->mask != NULL && ps->mask[rfpos] == '1') ? TRUE : FALSE; if((status = set_scheme_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_scheme[hc_scheme_idx_p], ppavgA[ppidx], ps->sclAA[pp], within_mask, NULL)) != eslOK) return status; } else { if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_onecell[gap_idx_p])) != eslOK) return status; ngap_p++; if(ps->mask != NULL && ps->mask[rfpos] == '1') ngap_masked_p++; } } /* add one-cell color legend */ ps->occlAAA[pp][0] = create_onecell_colorlegend(hc_onecell[gap_idx_p], ngap_p, ngap_masked_p, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][0], "gap", ps->legx_max_chars, errbuf)) != eslOK) return status; ps->nocclA[pp] = 1; if((status = add_text_to_scheme_colorlegend(ps, ps->sclAA[pp], "posterior probability \\(alignment confidence\\)", ps->legx_max_chars, errbuf)) != eslOK) return status; ps->seqidxA[pp] = i; if((status = add_page_desc_to_sspostscript(ps, pp, msa->sqname[i], errbuf)) != eslOK) return status; ps->rAA[pp][ps->rflen] = '\0'; } } /* end of for(i = 0; i < msa->nseq; i++) */ free(limits_s); free(limits_p); return eslOK; ERROR: ESL_FAIL(status, errbuf, "individuals_sspostscript(): memory allocation error."); return status; /* NEVERREACHED */ } /* Function: cons_seq_sspostscript() * * Purpose: Fill a postscript data structure with 1 new page, the consensus sequence. * Return: eslOK on success. */ static int cons_seq_sspostscript(const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps, float **hc_onecell, int wcbp_idx_s, int gubp_idx_s, int ncbp_idx_s, int dgbp_idx_s, int hgbp_idx_s) { int status; int p, pp; int rfpos, lpos, rpos; int orig_npage = ps->npage; int nwc_s; /* number of watson-crick bps */ int ngu_s; /* number of GU/UG bps */ int nnc_s; /* number of noncanonical bps */ int ndgi_s = 0; /* number of internal double-gap basepairs */ int nhgi_s = 0; /* number of internal half-gap basepairs */ int spos, epos; /* first/final nongap position for consensus sequence */ int lpos_is_internal; /* is lpos within spos..epos?, if not it's an external deletion */ int rpos_is_internal; /* is rpos within spos..epos?, if not it's an external deletion */ int lpos_is_gap; /* is lpos a gap */ int rpos_is_gap; /* is rpos a gap */ nwc_s = ngu_s = nnc_s = ndgi_s = nhgi_s = 0; if((status = add_pages_sspostscript(ps, 1, INDIMODE)) != eslOK) ESL_FAIL(status, errbuf, "memory error adding pages to the postscript object."); for(p = orig_npage; p < ps->npage; p++) { ESL_ALLOC(ps->rAA[p], sizeof(char) * ps->rflen); ESL_ALLOC(ps->tlAAA[p], sizeof(TextLegend_t *) * 1); } /* fill ps->rAA with nucleotides and gaps for RF sequence */ pp = orig_npage; for(rfpos = 0; rfpos < ps->rflen; rfpos++) { ps->rAA[pp][rfpos] = esl_opt_GetBoolean(go, "--cambig") ? ps->msa_cseq_amb[rfpos] : ps->msa_cseq_maj[rfpos]; } if((! esl_opt_GetBoolean(go, "--cambig")) && (! esl_opt_GetBoolean(go, "--no-bp"))) { spos = epos = -1; /* determine first and final non-gap position */ for(rfpos = 0; rfpos < ps->rflen; rfpos++) { /* find first non-gap RF position */ if(! esl_abc_CIsGap(ps->abc, ps->msa_cseq_maj[rfpos])) { spos = rfpos; break; } } for(rfpos = ps->rflen-1; rfpos >= 0; rfpos--) { if(! esl_abc_CIsGap(ps->abc, ps->msa_cseq_maj[rfpos])) { epos = rfpos; break; } } ESL_ALLOC(ps->rcolAAA[pp], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->occlAAA[pp], sizeof(OneCellColorLegend_t *) * 5); for(rfpos = 0; rfpos < ps->rflen; rfpos++) { ESL_ALLOC(ps->rcolAAA[pp][rfpos], sizeof(float) * NCMYK); /* CMYK colors */ if(ps->msa_ct[(rfpos+1)] == 0) { /* single stranded */ /* single-stranded nucleotide or gap, draw same color as Watson-Cricks */ if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[wcbp_idx_s])) != eslOK) return status; } else { /* basepair, either watson-crick, GU/UG, or non-canonical */ lpos = rfpos; rpos = ps->msa_ct[rfpos+1]-1; lpos_is_internal = ((lpos < spos) || (lpos > epos)) ? FALSE : TRUE; rpos_is_internal = ((rpos < spos) || (rpos > epos)) ? FALSE : TRUE; lpos_is_gap = esl_abc_CIsGap(ps->abc, ps->msa_cseq_maj[lpos]) ? TRUE : FALSE; rpos_is_gap = esl_abc_CIsGap(ps->abc, ps->msa_cseq_maj[rpos]) ? TRUE : FALSE; if(lpos_is_internal && rpos_is_internal) { /* BP is either Watson-Crick, G:U/U:G, non-canonical, internal double-gap bp or internal half-gap bp */ if(is_watson_crick_bp(ps->msa_cseq_maj[lpos], ps->msa_cseq_maj[rpos])) { /* watson-crick */ if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[wcbp_idx_s])) != eslOK) return status; if(lpos < rpos) nwc_s++; } else if(is_gu_or_ug_bp(ps->msa_cseq_maj[lpos], ps->msa_cseq_maj[rpos])) { /* G:U or U:G */ if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[gubp_idx_s])) != eslOK) return status; if(lpos < rpos) ngu_s++; } else if (lpos_is_gap && rpos_is_gap) { /* internal double-gap basepair */ if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[dgbp_idx_s])) != eslOK) return status; if(lpos < rpos) ndgi_s++; } else if (lpos_is_gap || rpos_is_gap) { /* internal double-gap basepair */ if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[hgbp_idx_s])) != eslOK) return status; if(lpos < rpos) nhgi_s++; } else { /* non-canonical */ if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[ncbp_idx_s])) != eslOK) return status; if(lpos < rpos) nnc_s++; } } /* end of (if(lpos_is_internal && rpos_is_internal)) */ else { /* either the left half of the bp is before the first nongap nt, * or the right half of the bp is after the final nongap nt, * for both cases, draw the nt as black, and don't count it as * any type of basepair */ if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[BLACKOC])) != eslOK) return status; } } } /* add one-cell color legend for watson-crick basepairs */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[wcbp_idx_s], nwc_s, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], "Watson-Crick basepair (bp)", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_celltext_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "C-G", errbuf)) != eslOK) return status; ps->nocclA[pp]++; /* add one-cell color legend for G-U, U-G basepairs */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[gubp_idx_s], ngu_s, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], "G-U or U-G bp", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_celltext_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "G-U", errbuf)) != eslOK) return status; ps->nocclA[pp]++; /* add one-cell color legend for non-canonical basepairs */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[ncbp_idx_s], nnc_s, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], "non-canonical bp", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_celltext_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "A-A", errbuf)) != eslOK) return status; ps->nocclA[pp]++; /* add one-cell color legend for internal half-gap basepairs */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[hgbp_idx_s], nhgi_s, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], "internal half-gap bp", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_celltext_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "A--", errbuf)) != eslOK) return status; ps->nocclA[pp]++; /* add one-cell color legend for internal double-gap basepairs */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[dgbp_idx_s], ndgi_s, OCCL_BLANK_COUNT, TRUE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], "internal double-gap bp", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_celltext_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "---", errbuf)) != eslOK) return status; ps->nocclA[pp]++; } /* add description to ps */ if((status = add_page_desc_to_sspostscript(ps, pp, "alignment consensus sequence", errbuf)) != eslOK) return status; /* add text legend explaining how consensus nucleotides are determined */ ps->tlAAA[pp][0] = create_text_legend_for_consensus_sequence(go, FALSE); ps->ntlA[pp] = 1; return eslOK; ERROR: ESL_FAIL(status, errbuf, "cons_seq_sspostscript(): memory allocation error."); return status; /* NEVERREACHED */ } /* Function: rf_seq_sspostscript() * * Purpose: Fill a postscript data structure with 1 new page, the RF sequence. * Return: eslOK on success. */ static int rf_seq_sspostscript(const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps, ESL_MSA *msa, int do_rescol, float **hc_onecell, int wcbp_idx_s, int gubp_idx_s, int ncbp_idx_s) { int status; int p, pp; int rfpos, apos, lpos, rpos; int orig_npage = ps->npage; int seen_canonical = FALSE; int nwc_s; /* number of watson-crick bps */ int ngu_s; /* number of GU/UG bps */ int nnc_s; /* number of noncanonical bps */ nwc_s = ngu_s = nnc_s = 0; if((status = add_pages_sspostscript(ps, 1, INDIMODE)) != eslOK) ESL_FAIL(status, errbuf, "memory error adding pages to the postscript object."); for(p = orig_npage; p < ps->npage; p++) { ESL_ALLOC(ps->rAA[p], sizeof(char) * ps->rflen); } /* fill ps->rAA with nucleotides and gaps for RF sequence */ pp = orig_npage; for(rfpos = 0; rfpos < ps->rflen; rfpos++) { apos = ps->msa_rf2a_map[rfpos]; if(esl_abc_CIsCanonical(ps->abc, msa->rf[apos])) seen_canonical = TRUE; ps->rAA[pp][rfpos] = msa->rf[apos]; } /* if seen_canonical is still FALSE, the reference sequences is probably all 'x's, so we don't color by bp type */ if(do_rescol && seen_canonical) { /* determine color for the nucleotide, depends if it is single-stranded or basepaired */ ESL_ALLOC(ps->rcolAAA[pp], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->occlAAA[pp], sizeof(OneCellColorLegend_t *) * 3); for(rfpos = 0; rfpos < ps->rflen; rfpos++) { ESL_ALLOC(ps->rcolAAA[pp][rfpos], sizeof(float) * NCMYK); /* CMYK colors */ apos = ps->msa_rf2a_map[rfpos]; if(ps->msa_ct[(rfpos+1)] == 0) { /* single stranded */ /* single-stranded nucleotide or gap, draw same color as Watson-Cricks */ if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[wcbp_idx_s])) != eslOK) return status; } else { /* basepair, either watson-crick, GU/UG, or non-canonical */ lpos = apos; rpos = ps->msa_rf2a_map[ps->msa_ct[rfpos+1]-1]; if(is_watson_crick_bp(msa->rf[lpos], msa->rf[rpos])) { /* watson-crick */ if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[wcbp_idx_s])) != eslOK) return status; if(lpos < rpos) nwc_s++; } else if(is_gu_or_ug_bp(msa->rf[lpos], msa->rf[rpos])) { /* G:U or U:G */ if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[gubp_idx_s])) != eslOK) return status; if(lpos < rpos) ngu_s++; } else { /* non-canonical */ if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[ncbp_idx_s])) != eslOK) return status; if(lpos < rpos) nnc_s++; } } } /* add one-cell color legend for watson-crick basepairs */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[wcbp_idx_s], nwc_s, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], "Watson-Crick basepair (bp)", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_celltext_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "C-G", errbuf)) != eslOK) return status; ps->nocclA[pp]++; /* add one-cell color legend for G-U, U-G basepairs */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[gubp_idx_s], ngu_s, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], "G-U or U-G bp", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_celltext_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "G-U", errbuf)) != eslOK) return status; ps->nocclA[pp]++; /* add one-cell color legend for non-canonical basepairs */ ps->occlAAA[pp][ps->nocclA[pp]] = create_onecell_colorlegend(hc_onecell[ncbp_idx_s], nnc_s, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend (ps, ps->occlAAA[pp][ps->nocclA[pp]], "non-canonical bp", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_celltext_to_onecell_colorlegend(ps, ps->occlAAA[pp][ps->nocclA[pp]], "A-A", errbuf)) != eslOK) return status; ps->nocclA[pp]++; } /* add description to ps */ if((status = add_page_desc_to_sspostscript(ps, pp, "*REFERENCE* (\"#=GC RF\")", errbuf)) != eslOK) return status; return eslOK; ERROR: ESL_FAIL(status, errbuf, "rf_seq_sspostscript(): memory allocation error."); return status; /* NEVERREACHED */ } /* count_msa() * * Given an msa, count nucleotides, post probs, basepairs, and consensus start and end * positions and store them in , , , * , and . * * [0..apos..alen-1][0..abc->K]: * - per position count of each symbol in alphabet over all seqs. * * [0..apos..alen-1][0..abc->Kp-1][0..abc->Kp-1] * - per (non-pknotted) consensus basepair count of each possible basepair * over all seqs basepairs are indexed by 'i' the minimum of 'i:j' for a * pair between i and j, where i < j. Note that non-canonicals and * gaps and the like are all stored independently. * * [0..apos..alen-1][0..10] * - per position count of each posterior probability code over all seqs. * * [0..apos..alen-1] * - per position count of first nongap position over all seqs. * * [0..apos..alen-1] * - per position count of final nongap position over all seqs. * * A 'gap' has a looser defintion than in esl_abc here, esl_abc's gap, * missing nucleotides and nonnucleotides are all considered 'gaps' here. * * If we encounter an error, we return non-eslOK status and fill * errbuf with error message. * * Returns eslOK upon success. */ int count_msa(const ESL_ALPHABET *abc, ESL_MSA *msa, char *errbuf, double ***ret_abc_ct, double ****ret_bp_ct, double ***ret_pp_ct, int **ret_spos_ct, int **ret_epos_ct) { int status; double **abc_ct = NULL; double ***bp_ct = NULL; int *spos_ct = NULL; int *epos_ct = NULL; int apos, i, j, x, epos; ESL_DSQ *tmp_dsq = NULL; int seen_start = FALSE; /* variables related to getting bp counts */ int *ct = NULL; /* 0..alen-1 base pair partners array for current sequence */ char *ss_nopseudo = NULL; /* no-pseudoknot version of structure */ int nppvals = 12; /* '0'-'9' = 0-9, '*' = 10, gap = '11' */ double **pp_ct = NULL; /* [0..alen-1][0..nppvals-1] per position count of each possible PP char over all seqs */ int ppidx; /* contract check, msa should be in text mode and have ss_cons */ if(msa->flags & eslMSA_DIGITAL) ESL_FAIL(eslEINVAL, errbuf, "count_msa() contract violation, MSA is digitized"); if(msa->ss_cons == NULL) ESL_FAIL(eslEINVAL, errbuf, "the alignment lacks SS_cons annotation"); /* allocate pp_ct array, if nec */ if(ret_pp_ct != NULL && msa->pp != NULL) { ESL_ALLOC(pp_ct, sizeof(double *) * msa->alen); for(apos = 0; apos < msa->alen; apos++) { ESL_ALLOC(pp_ct[apos], sizeof(double) * nppvals); esl_vec_DSet(pp_ct[apos], nppvals, 0.); } } /* get ct array which defines the consensus base pairs */ ESL_ALLOC(ct, sizeof(int) * (msa->alen+1)); ESL_ALLOC(ss_nopseudo, sizeof(char) * (msa->alen+1)); esl_wuss_nopseudo(msa->ss_cons, ss_nopseudo); if ((status = esl_wuss2ct(ss_nopseudo, msa->alen, ct)) != eslOK) ESL_FAIL(status, errbuf, "Consensus structure string is inconsistent."); ESL_ALLOC(tmp_dsq, (msa->alen+2) * sizeof(ESL_DSQ)); ESL_ALLOC(abc_ct, sizeof(double *) * msa->alen); ESL_ALLOC(bp_ct, sizeof(double **) * msa->alen); for(apos = 0; apos < msa->alen; apos++) { ESL_ALLOC(abc_ct[apos], sizeof(double) * (abc->K+1)); esl_vec_DSet(abc_ct[apos], (abc->K+1), 0.); /* careful ct is indexed 1..alen, not 0..alen-1 */ if(ct[(apos+1)] > (apos+1)) { /* apos+1 is an 'i' in an i:j pair, where i < j */ ESL_ALLOC(bp_ct[apos], sizeof(double *) * (abc->Kp)); for(x = 0; x < abc->Kp; x++) { ESL_ALLOC(bp_ct[apos][x], sizeof(double) * (abc->Kp)); esl_vec_DSet(bp_ct[apos][x], abc->Kp, 0.); } } else { /* apos+1 is not an 'i' in an i:j pair, where i < j, set to NULL */ bp_ct[apos] = NULL; } } ESL_ALLOC(spos_ct, sizeof(int) * msa->alen); ESL_ALLOC(epos_ct, sizeof(int) * msa->alen); esl_vec_ISet(spos_ct, msa->alen, 0); esl_vec_ISet(epos_ct, msa->alen, 0); for(i = 0; i < msa->nseq; i++) { seen_start = FALSE; epos = 0; // all seqs should have at least one residue, so we only need to initialize epos to make static analyzers happy. if((status = esl_abc_Digitize(abc, msa->aseq[i], tmp_dsq)) != eslOK) ESL_FAIL(status, errbuf, "problem digitizing sequence %d", i); for(apos = 0; apos < msa->alen; apos++) { /* update appropriate abc count, careful, tmp_dsq ranges from 1..msa->alen (not 0..msa->alen-1) */ if((status = esl_abc_DCount(abc, abc_ct[apos], tmp_dsq[apos+1], 1.0)) != eslOK) ESL_FAIL(status, errbuf, "problem counting nucleotide %d of seq %d", apos, i); if(! esl_abc_XIsGap(abc, tmp_dsq[apos+1])) { if(! seen_start) { spos_ct[apos]++; seen_start = TRUE; } epos = apos; // as noted above: must get called at least once per seq. } /* get bp count, if nec */ if(bp_ct[apos] != NULL) { /* our flag for whether position (apos+1) is an 'i' in an i:j pair where i < j */ j = ct[apos+1] - 1; /* ct is indexed 1..alen */ bp_ct[apos][tmp_dsq[(apos+1)]][tmp_dsq[(j+1)]]++; } } epos_ct[epos]++; /* get PP counts, if nec */ if(ret_pp_ct != NULL) { if(msa->pp[i] == NULL) ESL_FAIL(eslEINVAL, errbuf, "--prob requires all sequences in the alignment have PP, seq %d does not.", i+1); for(apos = 0; apos < msa->alen; apos++) { /* update appropriate pp count, careful, tmp_dsq ranges from 1..msa->alen (not 0..msa->alen-1) */ if((ppidx = get_pp_idx(abc, msa->pp[i][apos])) == -1) ESL_FAIL(eslEFORMAT, errbuf, "bad #=GR PP char: %c", msa->pp[i][apos]); pp_ct[apos][ppidx] += 1.; } } } *ret_abc_ct = abc_ct; *ret_bp_ct = bp_ct; *ret_spos_ct = spos_ct; *ret_epos_ct = epos_ct; if(ret_pp_ct != NULL) *ret_pp_ct = pp_ct; /* we only allocated pp_ct if ret_pp_ct != NULL */ esl_free(tmp_dsq); esl_free(ss_nopseudo); esl_free(ct); return eslOK; ERROR: esl_arr2_Destroy((void **) abc_ct, msa? msa->alen:0); esl_arr2_Destroy((void **) pp_ct, msa? msa->alen:0); esl_arr3_Destroy((void ***) bp_ct, msa? msa->alen:0, abc? abc->Kp:0); esl_free(spos_ct); esl_free(epos_ct); esl_free(tmp_dsq); ESL_FAIL(status, errbuf, "Error, out of memory while counting important values in the msa."); return status; /* NEVERREACHED */ } /* Function: infocontent_sspostscript() * * Purpose: Fill a postscript data structure with 1 new page, colored squares indicating * the information content of each consensus column. * * Return: eslOK on success. */ static int infocontent_sspostscript(const ESL_GETOPTS *go, ESL_ALPHABET *abc, char *errbuf, SSPostscript_t *ps, double **abc_ct, int msa_nseq, float ***hc_scheme, int hc_scheme_idx, int hc_nbins, float **hc_onecell, int hc_onecell_idx, FILE *tabfp) { int status; int p, pp, c; int rfpos, apos; int orig_npage = ps->npage; double *tmp_obs = NULL; double *ent = NULL; double *bg = NULL; float *limits = NULL; int zero_obs; int nonecell = 0; int nonecell_masked = 0; int within_mask; int bi; /* bin index for current position */ int l; if((status = add_pages_sspostscript(ps, 1, ALIMODE)) != eslOK) ESL_FAIL(status, errbuf, "memory error adding pages to the postscript object."); for(p = orig_npage; p < ps->npage; p++) { ESL_ALLOC(ps->bcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->sclAA[p], sizeof(SchemeColorLegend_t) * 1); ESL_ALLOC(ps->occlAAA[p], sizeof(OneCellColorLegend_t *) * 1); if(! esl_opt_GetBoolean(go, "--no-cnt")) { ESL_ALLOC(ps->rAA[p], sizeof(char) * ps->rflen); ESL_ALLOC(ps->rcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->tlAAA[p], sizeof(TextLegend_t *) * 1); } for(c = 0; c < ps->rflen; c++) { ESL_ALLOC(ps->bcolAAA[p][c], sizeof(float) * NCMYK); /* CMYK colors */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { ESL_ALLOC(ps->rcolAAA[p][c], sizeof(float) * NCMYK); /* CMYK colors */ } } } ESL_ALLOC(ent, sizeof(double) * ps->rflen); ESL_ALLOC(bg, sizeof(double) * abc->K); esl_vec_DSet(bg, abc->K, 1./(abc->K)); ESL_ALLOC(tmp_obs, sizeof(double) * abc->K); esl_vec_DSet(tmp_obs, abc->K, 0.); pp = orig_npage; /* add color legend */ ESL_ALLOC(limits, sizeof(float) * (hc_nbins+1)); limits[0] = 0.0; limits[1] = 0.4; limits[2] = 0.8; limits[3] = 1.2; limits[4] = 1.6; limits[5] = 1.99; limits[6] = 2.00; ps->sclAA[pp] = create_scheme_colorlegend(hc_scheme_idx, hc_nbins, limits, FALSE, TRUE, TRUE, TRUE); if(tabfp != NULL) { fprintf(tabfp, "# ------------------------\n"); fprintf(tabfp, "# Information content data\n"); fprintf(tabfp, "# ------------------------\n"); fprintf(tabfp, "# This section includes %d non #-prefixed lines, one for each consensus position\n", ps->rflen); fprintf(tabfp, "# in the alignment and corresponding template.\n"); fprintf(tabfp, "# Each line includes %d tokens, separated by whitespace:\n", ps->mask == NULL ? 5 : 6); fprintf(tabfp, "# \ttoken 1: 'infocontent' (tag defining line type to ease parsing)\n"); fprintf(tabfp, "# \ttoken 2: consensus position (starting at 1)\n"); fprintf(tabfp, "# \ttoken 3: information content for position (bits)\n"); fprintf(tabfp, "# \ttoken 4: number of non-gap nucleotides in position (max possible is %d (num seqs in aln))\n", msa_nseq); fprintf(tabfp, "# \ttoken 5: bin index this positions falls in (see bin values below)\n"); if(ps->mask != NULL) { fprintf(tabfp, "# \ttoken 6: '1' if position is included by mask, '0' if not\n"); } fprintf(tabfp, "#\n"); fprintf(tabfp, "# Information content is calculated as 2.0 - H, where\n"); fprintf(tabfp, "# H = - \\sum_x p_x \\log_2 p_x, for x in {A, C, G, U}\n"); fprintf(tabfp, "# p_x is the frequency of x for *non-gap* nucleotides at the position.\n"); fprintf(tabfp, "# For example, p_A in a column that includes 4 As, 3 Cs, 2 Gs, 1 U and 5 gaps\n"); fprintf(tabfp, "# would be 4/10 = 0.4.\n"); fprintf(tabfp, "# Maximum possible value for token 3 is %d, the number of sequences in the file.\n", msa_nseq); fprintf(tabfp, "#\n"); fprintf(tabfp, "# Value ranges for bins:\n"); fprintf(tabfp, "# \tbin 0: special case, 0 non-gap nucleotides in this position\n"); for(l = 0; l < hc_nbins; l++) { fprintf(tabfp, "# \tbin %2d: [%.3f-%.3f%s information per position (bits)\n", l+1, limits[l], limits[l+1], (l == hc_nbins-1) ? "]" : ")"); } fprintf(tabfp, "#\n"); fprintf(tabfp, "# %11s %6s %8s %10s %3s", "type", "cpos", "info", "nongap", "bin"); if(ps->mask != NULL) fprintf(tabfp, " %4s", "mask"); fprintf(tabfp, "\n"); fprintf(tabfp, "# %11s %6s %8s %10s %3s", "-----------", "------", "--------", "----------", "---"); if(ps->mask != NULL) fprintf(tabfp, " %4s", "----"); fprintf(tabfp, "\n"); } if(ps->mask == NULL) nonecell_masked = -1; /* special flag */ for(rfpos = 0; rfpos < ps->rflen; rfpos++) { apos = ps->msa_rf2a_map[rfpos]; esl_vec_DCopy(abc_ct[apos], abc->K, tmp_obs); /* only copy first abc->K values, don't copy gaps */ zero_obs = (esl_DCompare(esl_vec_DSum(tmp_obs, abc->K), 0., eslSMALLX1) == eslOK) ? TRUE : FALSE; esl_vec_DNorm(tmp_obs, abc->K); ent[rfpos] = esl_vec_DEntropy(bg, abc->K) - esl_vec_DEntropy(tmp_obs, abc->K); if(zero_obs) { if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_onecell[hc_onecell_idx])) != eslOK) return status; nonecell++; if(ps->mask != NULL && ps->mask[rfpos] == '1') nonecell_masked++; bi = -1; } else { within_mask = (ps->mask != NULL && ps->mask[rfpos] == '1') ? TRUE : FALSE; if((status = set_scheme_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_scheme[hc_scheme_idx], ent[rfpos], ps->sclAA[pp], within_mask, &bi)) != eslOK) return status; } /* fill in info for the consensus nucleotide */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { if(ps->mask == NULL || ps->mask[rfpos] == '1') { ps->rAA[pp][rfpos] = esl_opt_GetBoolean(go, "--cambig") ? ps->msa_cseq_amb[rfpos] : ps->msa_cseq_maj[rfpos]; if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[WHITEOC])) != eslOK) return status; } else { /* position is a '0' in the mask, leave it blank (' ') */ ps->rAA[pp][rfpos] = ' '; if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[WHITEOC])) != eslOK) return status; } } if(tabfp != NULL) { fprintf(tabfp, " infocontent %6d %8.5f %10d %3d", rfpos+1, ent[rfpos], (int) esl_vec_DSum(abc_ct[apos], abc->K), bi+1); if(ps->mask != NULL) fprintf(tabfp, " %4d", ps->mask[rfpos] == '1' ? 1 : 0); fprintf(tabfp, "\n"); } } /* add one-cell color legend */ ps->occlAAA[pp][0] = create_onecell_colorlegend(hc_onecell[hc_onecell_idx], nonecell, nonecell_masked, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][0], "100% gaps", ps->legx_max_chars, errbuf)) != eslOK) return status; ps->nocclA[pp] = 1; /* add text to legend */ /*sprintf(text, "information content (bits) (total: %.2f bits)", esl_vec_DSum(ent, ps->rflen));*/ if((status = add_text_to_scheme_colorlegend(ps, ps->sclAA[pp], "information content (bits)", ps->legx_max_chars, errbuf)) != eslOK) return status; /* add the consensus nucleotide explanation text section to the legend */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { ps->tlAAA[pp][0] = create_text_legend_for_consensus_sequence(go, FALSE); ps->ntlA[pp] = 1; } /* add description to ps */ if((status = add_page_desc_to_sspostscript(ps, pp, "information content per position", errbuf)) != eslOK) return status; free(ent); free(tmp_obs); free(bg); free(limits); if(tabfp != NULL) fprintf(tabfp, "//\n"); return eslOK; ERROR: ESL_FAIL(status, errbuf, "infocontent_sspostscript(): memory allocation error."); return status; /* NEVERREACHED */ } /* Function: delete_sspostscript() * * Purpose: Fill a postscript data structure with a new page w/colored squares indicating * the number of sequences with gaps (deletions) at each consensus column. * If do_all is TRUE the page shows all deletions. If false only 'internal' deletions, * those that come after the first occupied consensus column of each sequence and * before the final occupied consensus column for each sequence, are shown. * * Return: eslOK on success. */ static int delete_sspostscript(const ESL_GETOPTS *go, ESL_ALPHABET *abc, char *errbuf, SSPostscript_t *ps, double **abc_ct, int *span_ct, int msa_nseq, int do_all, float ***hc_scheme, int hc_scheme_idx, int hc_nbins, float **hc_onecell, int hc_zerodel_idx, int hc_fewdel_idx, FILE *tabfp) { int status; int p, pp, c, l, bi; int rfpos, apos; int orig_npage = ps->npage; double dfreq; int nzerodel = 0; int nzerodel_masked = 0; int nfewdel = 0; int nfewdel_masked = 0; int within_mask; float *limits = NULL; float fewdel_thresh; float n_ext_del; /* msa_nseq - span_ct[rfpos], number of external deletions */ if(ps->mask == NULL) { nzerodel_masked = -1; /* special flag */ nfewdel_masked = -1; /* special flag */ } if((status = add_pages_sspostscript(ps, 1, ALIMODE)) != eslOK) ESL_FAIL(status, errbuf, "memory error adding pages to the postscript object."); for(p = orig_npage; p < ps->npage; p++) { ESL_ALLOC(ps->bcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->sclAA[p], sizeof(SchemeColorLegend_t) * 1); ESL_ALLOC(ps->occlAAA[p], sizeof(OneCellColorLegend_t *) * 2); if(! esl_opt_GetBoolean(go, "--no-cnt")) { ESL_ALLOC(ps->rAA[p], sizeof(char) * ps->rflen); ESL_ALLOC(ps->rcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->tlAAA[p], sizeof(TextLegend_t *) * 1); } for(c = 0; c < ps->rflen; c++) { ESL_ALLOC(ps->bcolAAA[p][c], sizeof(float) * NCMYK); /* CMYK colors */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { ESL_ALLOC(ps->rcolAAA[p][c], sizeof(float) * NCMYK); /* CMYK colors */ } } } pp = orig_npage; /* add color legend */ ESL_ALLOC(limits, sizeof(float) * (hc_nbins+1)); fewdel_thresh = 0.001; /* positions with delete freq < this value will be painted specially (dark grey) */ limits[0] = fewdel_thresh; limits[1] = 0.05; limits[2] = 0.20; limits[3] = 0.35; limits[4] = 0.50; limits[5] = 0.75; limits[6] = 1.00; ps->sclAA[pp] = create_scheme_colorlegend(hc_scheme_idx, hc_nbins, limits, FALSE, FALSE, TRUE, TRUE); if(tabfp != NULL) { if(do_all) { fprintf(tabfp, "# -----------\n"); fprintf(tabfp, "# Delete data\n"); fprintf(tabfp, "# -----------\n"); fprintf(tabfp, "# This section includes %d non #-prefixed lines, one for each consensus position\n", ps->rflen); fprintf(tabfp, "# in the alignment and corresponding template.\n"); fprintf(tabfp, "# Each line includes %d tokens, separated by whitespace:\n", ps->mask == NULL ? 4 : 5); fprintf(tabfp, "# \ttoken 1: 'deleteall' (tag defining line type to ease parsing)\n"); fprintf(tabfp, "# \ttoken 2: consensus position (starting at 1)\n"); fprintf(tabfp, "# \ttoken 3: frequency of deletions (gaps) for position\n"); fprintf(tabfp, "# \ttoken 4: bin index this positions falls in (see bin values below)\n"); if(ps->mask != NULL) { fprintf(tabfp, "# \ttoken 5: '1' if position is included by mask, '0' if not\n"); } fprintf(tabfp, "#\n"); fprintf(tabfp, "# A sequence s has a 'delete' at consensus position x if position\n"); fprintf(tabfp, "# x is a gap for aligned sequence s.\n"); fprintf(tabfp, "# Total number of sequences in the alignment is %d\n", msa_nseq); fprintf(tabfp, "#\n"); fprintf(tabfp, "# Value ranges for bins:\n"); fprintf(tabfp, "# \tbin 0: special case, 0 sequences have a delete at position\n"); fprintf(tabfp, "# \tbin 1: special case, < %.5f fraction of sequences have internal deletes at position\n", fewdel_thresh); for(l = 0; l < hc_nbins; l++) { fprintf(tabfp, "# \tbin %2d: [%.3f-%.3f%s frequency of deletes per position\n", l+2, limits[l], limits[l+1], (l == hc_nbins-1) ? "]" : ")"); } fprintf(tabfp, "#\n"); fprintf(tabfp, "# %9s %6s %8s %3s", "type", "cpos", "dfreq", "bin"); if(ps->mask != NULL) fprintf(tabfp, " %4s", "mask"); fprintf(tabfp, "\n"); fprintf(tabfp, "# %9s %6s %8s %3s", "---------", "------", "--------", "---"); if(ps->mask != NULL) fprintf(tabfp, " %4s", "----"); fprintf(tabfp, "\n"); } else { /* ! do_all (internal deletes only) */ fprintf(tabfp, "# --------------------\n"); fprintf(tabfp, "# Internal delete data\n"); fprintf(tabfp, "# --------------------\n"); fprintf(tabfp, "# This section includes %d non #-prefixed lines, one for each consensus position\n", ps->rflen); fprintf(tabfp, "# in the alignment and corresponding template.\n"); fprintf(tabfp, "# Each line includes %d tokens, separated by whitespace:\n", ps->mask == NULL ? 5 : 6); fprintf(tabfp, "# \ttoken 1: 'deleteint' (tag defining line type to ease parsing)\n"); fprintf(tabfp, "# \ttoken 2: consensus position (starting at 1)\n"); fprintf(tabfp, "# \ttoken 3: frequency of internal deletions (gaps) for position\n"); fprintf(tabfp, "# \ttoken 4: number of sequences that span (begin at or prior to and end at or after) position (max is %d)\n", msa_nseq); fprintf(tabfp, "# \ttoken 5: bin index this positions falls in (see bin values below)\n"); if(ps->mask != NULL) fprintf(tabfp, "# \ttoken 6: '1' if position is included by mask, '0' if not\n"); fprintf(tabfp, "#\n"); fprintf(tabfp, "# A sequence s has an 'internal delete' at consensus position 'x' that is actual alignment position 'a' if\n"); fprintf(tabfp, "# x is a gap for aligned sequence s, and s has at least one non-gap nucleotide aligned to a position 'b' <= 'a'\n"); fprintf(tabfp, "# and at least one non-gap nucleotide aligned to a position 'c' >= 'a'\n"); fprintf(tabfp, "#\n"); fprintf(tabfp, "# Value ranges for bins:\n"); fprintf(tabfp, "# \tbin 0: special case, 0 sequences have an internal delete at position\n"); fprintf(tabfp, "# \tbin 1: special case, < %.5f fraction of sequences have internal deletes at position\n", fewdel_thresh); for(l = 0; l < hc_nbins; l++) { fprintf(tabfp, "# \tbin %2d: [%.3f-%.3f%s frequency of internal deletes per position\n", l+2, limits[l], limits[l+1], (l == hc_nbins-1) ? "]" : ")"); } fprintf(tabfp, "#\n"); fprintf(tabfp, "# %9s %6s %8s %10s %3s", "type", "cpos", "dfreq", "nspan", "bin"); if(ps->mask != NULL) fprintf(tabfp, " %4s", "mask"); fprintf(tabfp, "\n"); fprintf(tabfp, "# %9s %6s %8s %10s %3s", "---------", "------", "--------", "----------", "---"); if(ps->mask != NULL) fprintf(tabfp, " %4s", "----"); fprintf(tabfp, "\n"); } } /* draw delete page */ for(rfpos = 0; rfpos < ps->rflen; rfpos++) { apos = ps->msa_rf2a_map[rfpos]; n_ext_del = do_all ? -1. : (float) (msa_nseq - span_ct[rfpos]); /* num external deletes is num seqs minus number of seqs that 'span' apos, see function header comments for explanation */ if((( do_all) && ( abc_ct[apos][abc->K] < eslSMALLX1)) || /* abc_ct[apos][abc->K] == 0 */ ((!do_all) && ((abc_ct[apos][abc->K] - n_ext_del) < eslSMALLX1))) { /* abc_ct[apos][abc->K] == n_ext_del (all deletes are external) */ if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_onecell[hc_zerodel_idx])) != eslOK) return status; nzerodel++; if(ps->mask != NULL && ps->mask[rfpos] == '1') nzerodel_masked++; bi = -2; /* special case */ dfreq = 0.; } else { within_mask = (ps->mask != NULL && ps->mask[rfpos] == '1') ? TRUE : FALSE; dfreq = do_all ? ( abc_ct[apos][abc->K] / (float) msa_nseq) : ((abc_ct[apos][abc->K] - n_ext_del) / (float) msa_nseq); /* printf("do_all: %d rfpos: %d dfreq: %.2f\n", do_all, rfpos, dfreq); */ if (dfreq < fewdel_thresh) { if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_onecell[hc_fewdel_idx])) != eslOK) return status; nfewdel++; if(ps->mask != NULL && ps->mask[rfpos] == '1') nfewdel_masked++; bi = -1; /* special case */ } else { if((status = set_scheme_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_scheme[hc_scheme_idx], dfreq, ps->sclAA[pp], within_mask, &bi)) != eslOK) return status; } } /* fill in info for the consensus nucleotide */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { if(ps->mask == NULL || ps->mask[rfpos] == '1') { ps->rAA[pp][rfpos] = esl_opt_GetBoolean(go, "--cambig") ? ps->msa_cseq_amb[rfpos] : ps->msa_cseq_maj[rfpos]; if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[WHITEOC])) != eslOK) return status; } else { /* position is a '0' in the mask, leave it blank (' ') */ ps->rAA[pp][rfpos] = ' '; if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[WHITEOC])) != eslOK) return status; } } if(tabfp != NULL) { if(do_all) fprintf(tabfp, " deleteall %6d %8.5f %3d", rfpos+1, dfreq, bi+2); else fprintf(tabfp, " deleteint %6d %8.5f %10d %3d", rfpos+1, dfreq, span_ct[rfpos], bi+2); if(ps->mask != NULL) fprintf(tabfp, " %4d", ps->mask[rfpos] == '1' ? 1 : 0); fprintf(tabfp, "\n"); } } /* add one-cell color legend */ ps->occlAAA[pp][0] = create_onecell_colorlegend(hc_onecell[hc_zerodel_idx], nzerodel, nzerodel_masked, FALSE, FALSE); ps->occlAAA[pp][1] = create_onecell_colorlegend(hc_onecell[hc_fewdel_idx], nfewdel, nfewdel_masked, FALSE, FALSE); ps->nocclA[pp] = 2; if(do_all) { if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][0], "zero deletions", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][1], "< 0.001 seqs have delete", ps->legx_max_chars, errbuf)) != eslOK) return status; } else { if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][0], "zero internal deletions", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][1], "< 0.001 seqs have delete", ps->legx_max_chars, errbuf)) != eslOK) return status; } /* add color legend and description */ if(do_all) { /*sprintf(text, "fraction seqs w/deletes ('-'=0 deletes; avg/seq: %.2f)", (float) esl_vec_ISum(dct, ps->rflen) / (float) msa_nseq);*/ if((status = add_text_to_scheme_colorlegend(ps, ps->sclAA[pp], "fraction of seqs with deletes", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_page_desc_to_sspostscript(ps, ps->npage-1, "frequency of deletions at each position", errbuf)) != eslOK) return status; } else { /* !do_all, only internal deletes counted */ /*sprintf(text, "fraction seqs w/internal deletes ('-'=0; avg/seq: %.2f)", (float) esl_vec_ISum(dct_internal, ps->rflen) / (float) msa_nseq);*/ if((status = add_text_to_scheme_colorlegend(ps, ps->sclAA[pp], "fraction of seqs w/internal deletions", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_page_desc_to_sspostscript(ps, ps->npage-1, "frequency of internal deletions in each position", errbuf)) != eslOK) return status; } /* add the consensus nucleotide explanation text section to the legend */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { ps->tlAAA[pp][0] = create_text_legend_for_consensus_sequence(go, FALSE); ps->ntlA[pp] = 1; } free(limits); if(tabfp != NULL) fprintf(tabfp, "//\n"); return eslOK; ERROR: ESL_FAIL(status, errbuf, "delete_sspostscript(): memory allocation error."); return status; /* NEVERREACHED */ } /* Function: insertfreq_sspostscript() * * Purpose: Fill a postscript data structure with 1 new page, with colors * indicating the fraction of seqs with inserts after each * position. * * Return: eslOK on success. */ static int insertfreq_sspostscript(const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps, int *nseq_with_ins_ct, int *span_ct, int msa_nseq, float ***hc_scheme, int hc_scheme_idx, int hc_nbins, float **hc_onecell, int hc_zeroins_idx, int hc_fewins_idx, FILE *tabfp) { int status; int p, pp, c, l; int rfpos; int orig_npage = ps->npage; //int apos; int nzeroins = 0; int nzeroins_masked = 0; int nfewins = 0; int nfewins_masked = 0; float *limits; int within_mask; float ifreq; int bi; float fewins_thresh; if(ps->mask == NULL) { nzeroins_masked = -1; /* special flag */ nfewins_masked = -1; /* special flag */ } if((status = add_pages_sspostscript(ps, 1, ALIMODE)) != eslOK) ESL_FAIL(status, errbuf, "memory error adding pages to the postscript object."); for(p = orig_npage; p < ps->npage; p++) { ESL_ALLOC(ps->bcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->sclAA[p], sizeof(SchemeColorLegend_t) * 1); ESL_ALLOC(ps->occlAAA[p], sizeof(OneCellColorLegend_t *) * 2); if(! esl_opt_GetBoolean(go, "--no-cnt")) { ESL_ALLOC(ps->rAA[p], sizeof(char) * ps->rflen); ESL_ALLOC(ps->rcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->tlAAA[p], sizeof(TextLegend_t *) * 1); } for(c = 0; c < ps->rflen; c++) { ESL_ALLOC(ps->bcolAAA[p][c], sizeof(float) * NCMYK); /* CMYK colors */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { ESL_ALLOC(ps->rcolAAA[p][c], sizeof(float) * NCMYK); /* CMYK colors */ } } } pp = orig_npage; /* add color legend */ ESL_ALLOC(limits, sizeof(float) * (hc_nbins+1)); fewins_thresh = 0.001; limits[0] = fewins_thresh; limits[1] = 0.01; limits[2] = 0.05; limits[3] = 0.10; limits[4] = 0.20; limits[5] = 0.50; limits[6] = 1.00; ps->sclAA[pp] = create_scheme_colorlegend(hc_scheme_idx, hc_nbins, limits, FALSE, FALSE, TRUE, TRUE); if(tabfp != NULL) { fprintf(tabfp, "# ---------------------\n"); fprintf(tabfp, "# Insert frequency data\n"); fprintf(tabfp, "# ---------------------\n"); fprintf(tabfp, "# This section includes %d non #-prefixed lines, one for each possible insert position\n", ps->rflen+1); fprintf(tabfp, "# after each of the %d consensus positions and one more for inserts prior to the first consensus position.\n", ps->rflen); fprintf(tabfp, "# Each line includes %d tokens, separated by whitespace:\n", ps->mask == NULL ? 5 : 6); fprintf(tabfp, "# \ttoken 1: 'insertfreq' (tag defining line type to ease parsing)\n"); fprintf(tabfp, "# \ttoken 2: consensus position after which inserts occur ('0' == before posn 1)\n"); fprintf(tabfp, "# \ttoken 3: fraction of sequences that span (see defn of span below) with >= 1 inserted nucleotides after position\n"); fprintf(tabfp, "# \ttoken 4: number of sequences that span (begin at or prior to and end at or after) position (max is %d)\n", msa_nseq); fprintf(tabfp, "# \ttoken 5: bin index this positions falls in (see bin values below)\n"); if(ps->mask != NULL) { fprintf(tabfp, "# \ttoken 6: '1' if position is included by mask, '0' if not\n"); } fprintf(tabfp, "#\n"); fprintf(tabfp, "# Total number of sequences in the alignment is %d\n", msa_nseq); fprintf(tabfp, "#\n"); fprintf(tabfp, "# A sequence s spans consensus position 'x' that is actual alignment position 'a' if s has\n"); fprintf(tabfp, "# at least one non-gap nucleotide aligned to a position 'b' <= 'a' and\n"); fprintf(tabfp, "# at least one non-gap nucleotide aligned to a position 'c' >= 'a'\n"); fprintf(tabfp, "#\n"); fprintf(tabfp, "# Value ranges for bins:\n"); fprintf(tabfp, "# \tbin -1: special case, reserved for inserts before position 1,\n"); fprintf(tabfp, "# \t these are NOT SHOWN in the postscript diagram (!)\n"); fprintf(tabfp, "# \tbin 0: special case, 0 sequences have inserts after this position\n"); fprintf(tabfp, "# \tbin 1: special case, < %.5f fraction of sequences have inserts after this position\n", fewins_thresh); for(l = 0; l < hc_nbins; l++) { fprintf(tabfp, "# \tbin %2d: [%.3f-%.3f%s fraction of sequences with >= 1 inserts after each position\n", l+2, limits[l], limits[l+1], (l == hc_nbins-1) ? "]" : ")"); } fprintf(tabfp, "#\n"); fprintf(tabfp, "# %10s %6s %8s %10s %3s", "type", "cpos", "ifreq", "nspan", "bin"); if(ps->mask != NULL) fprintf(tabfp, " %4s", "mask"); fprintf(tabfp, "\n"); fprintf(tabfp, "# %10s %6s %8s %10s %3s", "----------", "------", "--------", "----------", "---"); if(ps->mask != NULL) fprintf(tabfp, " %4s", "----"); fprintf(tabfp, "\n"); } /* print info on inserts before rfpos 1 to tabfile, if nec */ if(tabfp != NULL) { //apos = ps->msa_rf2a_map[0]; if(nseq_with_ins_ct[0] > span_ct[0]) ESL_FAIL(eslERANGE, errbuf, "drawing insert page, rfpos: 0 nseq_with_ins_ct (%d) exceeds span_ct (%d)", nseq_with_ins_ct[0], span_ct[0]); ifreq = (float) nseq_with_ins_ct[0] / (float) span_ct[0]; fprintf(tabfp, " insertfreq %6d %8.5f %10d %3d", 0, ifreq, span_ct[0], -1); if(ps->mask != NULL) fprintf(tabfp, " %4d", 0); fprintf(tabfp, "\n"); } for(rfpos = 0; rfpos < ps->rflen; rfpos++) { //apos = ps->msa_rf2a_map[rfpos]; if(nseq_with_ins_ct[rfpos+1] > span_ct[rfpos]) ESL_FAIL(eslERANGE, errbuf, "drawing insert page, rfpos: %d nseq_with_ins_ct (%d) exceeds span_ct (%d)", rfpos, nseq_with_ins_ct[rfpos+1], span_ct[rfpos]); ifreq = (float) nseq_with_ins_ct[rfpos+1] / (float) span_ct[rfpos]; /* note we don't need to add one to span_ct, it is [0..rflen-1] */ if(nseq_with_ins_ct[(rfpos+1)] == 0) { /* careful, nseq_with_ins_ct goes from 1..rflen, its off-by-one with other arrays */ if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_onecell[hc_zeroins_idx])) != eslOK) return status; nzeroins++; if(ps->mask != NULL && ps->mask[rfpos] == '1') nzeroins_masked++; bi = -2; /* special case */ } else if (ifreq < fewins_thresh) { if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_onecell[hc_fewins_idx])) != eslOK) return status; nfewins++; if(ps->mask != NULL && ps->mask[rfpos] == '1') nfewins_masked++; bi = -1; /* special case */ } else { within_mask = (ps->mask != NULL && ps->mask[rfpos] == '1') ? TRUE : FALSE; if((status = set_scheme_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_scheme[hc_scheme_idx], ifreq, ps->sclAA[pp], within_mask, &bi)) != eslOK) return status; } /* printf("rfpos: %5d ifreq: %.3f\n", rfpos, ifreq); */ /* fill in info for the consensus nucleotide */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { if(ps->mask == NULL || ps->mask[rfpos] == '1') { ps->rAA[pp][rfpos] = esl_opt_GetBoolean(go, "--cambig") ? ps->msa_cseq_amb[rfpos] : ps->msa_cseq_maj[rfpos]; if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[WHITEOC])) != eslOK) return status; } else { /* position is a '0' in the mask, leave it blank (' ') */ ps->rAA[pp][rfpos] = ' '; if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[WHITEOC])) != eslOK) return status; } } if(tabfp != NULL) { fprintf(tabfp, " insertfreq %6d %8.5f %10d %3d", rfpos+1, ifreq, span_ct[rfpos], bi+1); if(ps->mask != NULL) fprintf(tabfp, " %4d", ps->mask[rfpos] == '1' ? 1 : 0); fprintf(tabfp, "\n"); } } /* add one-cell color legend */ ps->occlAAA[pp][0] = create_onecell_colorlegend(hc_onecell[hc_zeroins_idx], nzeroins, nzeroins_masked, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][0], "zero insertions", ps->legx_max_chars, errbuf)) != eslOK) return status; ps->occlAAA[pp][1] = create_onecell_colorlegend(hc_onecell[hc_fewins_idx], nfewins, nfewins_masked, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][1], "< 0.001 seqs have insert", ps->legx_max_chars, errbuf)) != eslOK) return status; ps->nocclA[pp] = 2; /* add color legend */ if((status = add_text_to_scheme_colorlegend(ps, ps->sclAA[pp], "fraction of seqs w/insertions", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_page_desc_to_sspostscript(ps, ps->npage-1, "frequency of insertions after each position", errbuf)) != eslOK) return status; /* add the consensus nucleotide explanation text section to the legend */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { ps->tlAAA[pp][0] = create_text_legend_for_consensus_sequence(go, FALSE); ps->ntlA[pp] = 1; } free(limits); if(tabfp != NULL) fprintf(tabfp, "//\n"); return eslOK; ERROR: ESL_FAIL(status, errbuf, "insertfreq_sspostscript(): memory allocation error."); return status; /* NEVERREACHED */ } /* Function: insertavglen_sspostscript() * * Purpose: Fill a postscript data structure with 1 new page, with colors * indicating the average length of inserts after each * position. * * Return: eslOK on success. */ static int insertavglen_sspostscript(const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps, int *nseq_with_ins_ct, int *nins_ct, int *span_ct, int msa_nseq, float ***hc_scheme, int hc_scheme_idx, int hc_nbins, float **hc_onecell, int hc_zeroins_idx, FILE *tabfp) { int status; int p, pp, c, l; int rfpos; int orig_npage = ps->npage; //int apos; int nzeroins = 0; int nzeroins_masked = 0; float *limits; int within_mask; float ifreq; float iavglen; int bi; if(ps->mask == NULL) nzeroins_masked = -1; /* special flag */ if((status = add_pages_sspostscript(ps, 1, ALIMODE)) != eslOK) ESL_FAIL(status, errbuf, "memory error adding pages to the postscript object."); for(p = orig_npage; p < ps->npage; p++) { ESL_ALLOC(ps->bcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->sclAA[p], sizeof(SchemeColorLegend_t) * 1); ESL_ALLOC(ps->occlAAA[p], sizeof(OneCellColorLegend_t *) * 1); if(! esl_opt_GetBoolean(go, "--no-cnt")) { ESL_ALLOC(ps->rAA[p], sizeof(char) * ps->rflen); ESL_ALLOC(ps->rcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->tlAAA[p], sizeof(TextLegend_t *) * 1); } for(c = 0; c < ps->rflen; c++) { ESL_ALLOC(ps->bcolAAA[p][c], sizeof(float) * NCMYK); /* CMYK colors */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { ESL_ALLOC(ps->rcolAAA[p][c], sizeof(float) * NCMYK); /* CMYK colors */ } } } pp = orig_npage; /* add color legend */ ESL_ALLOC(limits, sizeof(float) * (hc_nbins+1)); limits[0] = 1.00; limits[1] = 1.01; limits[2] = 1.50; limits[3] = 3.00; limits[4] = 4.00; limits[5] = 10.00; limits[6] = SSDRAWINFINITY; ps->sclAA[pp] = create_scheme_colorlegend(hc_scheme_idx, hc_nbins, limits, FALSE, TRUE, FALSE, TRUE); if(tabfp != NULL) { fprintf(tabfp, "# --------------------------\n"); fprintf(tabfp, "# Average insert length data\n"); fprintf(tabfp, "# --------------------------\n"); fprintf(tabfp, "# This section includes %d non #-prefixed lines, one for each possible insert position\n", ps->rflen+1); fprintf(tabfp, "# after each of the %d consensus positions and one more for inserts prior to the first consensus position.\n", ps->rflen); fprintf(tabfp, "# Each line includes %d tokens, separated by whitespace:\n", ps->mask == NULL ? 5 : 6); fprintf(tabfp, "# \ttoken 1: 'insertlen' (tag defining line type to ease parsing)\n"); fprintf(tabfp, "# \ttoken 2: consensus position after which inserts occur ('0' == before posn 1)\n"); fprintf(tabfp, "# \ttoken 3: average number of inserted nucleotides after each position for those seqs with >=1 inserted nucleotides)\n"); fprintf(tabfp, "# \ttoken 4: fraction of sequences that span (see defn of span below) with >= 1 inserted nucleotides after position\n"); fprintf(tabfp, "# \ttoken 5: number of sequences that span (begin at or prior to and end at or after) position (max is %d)\n", msa_nseq); fprintf(tabfp, "# \ttoken 6: bin index this positions falls in (see bin values below)\n"); if(ps->mask != NULL) { fprintf(tabfp, "# \ttoken 7: '1' if position is included by mask, '0' if not\n"); } fprintf(tabfp, "#\n"); fprintf(tabfp, "# Total number of sequences in the alignment is %d\n", msa_nseq); fprintf(tabfp, "#\n"); fprintf(tabfp, "# A sequence s spans consensus position 'x' that is actual alignment position 'a' if s has\n"); fprintf(tabfp, "# at least one non-gap nucleotide aligned to a position 'b' <= 'a' and\n"); fprintf(tabfp, "# at least one non-gap nucleotide aligned to a position 'c' >= 'a'\n"); fprintf(tabfp, "#\n"); fprintf(tabfp, "# Value ranges for bins:\n"); fprintf(tabfp, "# \tbin -1: special case, reserved for inserts before position 1,\n"); fprintf(tabfp, "# \t these are NOT SHOWN in the postscript diagram (!)\n"); fprintf(tabfp, "# \tbin 0: special case, 0 sequences have inserts after this position\n"); for(l = 0; l < hc_nbins; l++) { fprintf(tabfp, "# \tbin %2d: [%.3f-%.3f%s average insert length after each position\n", l+1, limits[l], limits[l+1], (l == hc_nbins-1) ? "]" : ")"); } fprintf(tabfp, "#\n"); fprintf(tabfp, "# %12s %6s %8s %8s %10s %3s", "type", "cpos", "iavglen", "ifreq", "nspan", "bin"); if(ps->mask != NULL) fprintf(tabfp, " %4s", "mask"); fprintf(tabfp, "\n"); fprintf(tabfp, "# %12s %6s %8s %8s %10s %3s", "------------", "------", "--------", "--------", "----------", "---"); if(ps->mask != NULL) fprintf(tabfp, " %4s", "----"); fprintf(tabfp, "\n"); } /* print info on inserts before rfpos 1 to tabfile, if nec */ if(tabfp != NULL) { //apos = ps->msa_rf2a_map[0]; if(nseq_with_ins_ct[0] > span_ct[0]) ESL_FAIL(eslERANGE, errbuf, "drawing insert page, rfpos: 0 nseq_with_ins_ct (%d) exceeds span_ct (%d)", nseq_with_ins_ct[0], span_ct[0]); ifreq = (span_ct[0] == 0) ? 0. : (float) nseq_with_ins_ct[0] / (float) span_ct[0]; iavglen = (nseq_with_ins_ct[0] == 0) ? 0. : (float) nins_ct[0] / (float) nseq_with_ins_ct[0]; fprintf(tabfp, " insertavglen %6d %8.4f %8.5f %10d %3d", 0, iavglen, ifreq, span_ct[0], -1); if(ps->mask != NULL) fprintf(tabfp, " %4d", 0); fprintf(tabfp, "\n"); } for(rfpos = 0; rfpos < ps->rflen; rfpos++) { //apos = ps->msa_rf2a_map[rfpos]; if(nseq_with_ins_ct[rfpos+1] > span_ct[rfpos]) ESL_FAIL(eslERANGE, errbuf, "drawing insert page, rfpos: %d nseq_with_ins_ct (%d) exceeds span_ct (%d)", rfpos, nseq_with_ins_ct[rfpos+1], span_ct[rfpos]); ifreq = (span_ct[rfpos] == 0) ? 0. : (float) nseq_with_ins_ct[rfpos+1] / (float) span_ct[rfpos]; iavglen = (nseq_with_ins_ct[rfpos+1] == 0) ? 0. : (float) nins_ct[rfpos+1] / (float) nseq_with_ins_ct[rfpos+1]; /* printf("rfpos: %5d ifreq: %.3f iavglen: %.3f nins: %10d nseq: %10d\n", rfpos, ifreq, iavglen, nins_ct[rfpos+1], nseq_with_ins_ct[rfpos+1]); */ if(nseq_with_ins_ct[(rfpos+1)] == 0) { /* careful, nseq_with_ins_ct goes from 1..rflen, its off-by-one with other arrays */ if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_onecell[hc_zeroins_idx])) != eslOK) return status; nzeroins++; if(ps->mask != NULL && ps->mask[rfpos] == '1') nzeroins_masked++; bi = -1; /* special case */ } else { within_mask = (ps->mask != NULL && ps->mask[rfpos] == '1') ? TRUE : FALSE; if((status = set_scheme_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_scheme[hc_scheme_idx], iavglen, ps->sclAA[pp], within_mask, &bi)) != eslOK) return status; } /* fill in info for the consensus nucleotide */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { if(ps->mask == NULL || ps->mask[rfpos] == '1') { ps->rAA[pp][rfpos] = esl_opt_GetBoolean(go, "--cambig") ? ps->msa_cseq_amb[rfpos] : ps->msa_cseq_maj[rfpos]; if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[WHITEOC])) != eslOK) return status; } else { /* position is a '0' in the mask, leave it blank (' ') */ ps->rAA[pp][rfpos] = ' '; if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[WHITEOC])) != eslOK) return status; } } if(tabfp != NULL) { fprintf(tabfp, " insertavglen %6d %8.4f %8.5f %10d %3d", rfpos+1, iavglen, ifreq, span_ct[rfpos], bi+1); if(ps->mask != NULL) fprintf(tabfp, " %4d", ps->mask[rfpos] == '1' ? 1 : 0); fprintf(tabfp, "\n"); } } /* add one-cell color legend */ ps->occlAAA[pp][0] = create_onecell_colorlegend(hc_onecell[hc_zeroins_idx], nzeroins, nzeroins_masked, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][0], "zero insertions", ps->legx_max_chars, errbuf)) != eslOK) return status; ps->nocclA[pp] = 1; /* add color legend */ if((status = add_text_to_scheme_colorlegend(ps, ps->sclAA[pp], "average insertion length", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_page_desc_to_sspostscript(ps, ps->npage-1, "average insertion length after each position", errbuf)) != eslOK) return status; /* add the consensus nucleotide explanation text section to the legend */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { ps->tlAAA[pp][0] = create_text_legend_for_consensus_sequence(go, FALSE); ps->ntlA[pp] = 1; } free(limits); if(tabfp != NULL) fprintf(tabfp, "//\n"); return eslOK; ERROR: ESL_FAIL(status, errbuf, "insertavglen_sspostscript(): memory allocation error."); return status; /* NEVERREACHED */ } /* Function: span_sspostscript() * * Purpose: Fill a postscript data structure with 1 new page, with colors * indicating the fraction of seqs that 'span' each consensus * position. A consensus position cpos is spanned by a sequence x if * if at least 1 nucleotide in x is aligned to a consensus position <= cpos * *and* at least 1 nucleotide in x is aligned to a consensus position >= cpos. * * Return: eslOK on success. */ static int span_sspostscript(const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps, int *span_ct, int msa_nseq, float ***hc_scheme, int hc_scheme_idx, int hc_nbins, float **hc_onecell, int zerocov_idx, int maxcov_idx, FILE *tabfp) { int status; int p, pp, c, l; int rfpos; int orig_npage = ps->npage; int nzerocov = 0; int nzerocov_masked = 0; int nmaxcov = 0; int nmaxcov_masked = 0; float *limits; int within_mask; float cfract; int bi; if(ps->mask == NULL) nzerocov_masked = nmaxcov_masked = -1; /* special flag */ if((status = add_pages_sspostscript(ps, 1, ALIMODE)) != eslOK) ESL_FAIL(status, errbuf, "memory error adding pages to the postscript object."); for(p = orig_npage; p < ps->npage; p++) { ESL_ALLOC(ps->bcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->sclAA[p], sizeof(SchemeColorLegend_t) * 1); ESL_ALLOC(ps->occlAAA[p], sizeof(OneCellColorLegend_t *) * 2); if(! esl_opt_GetBoolean(go, "--no-cnt")) { ESL_ALLOC(ps->rAA[p], sizeof(char) * ps->rflen); ESL_ALLOC(ps->rcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->tlAAA[p], sizeof(TextLegend_t *) * 1); } for(c = 0; c < ps->rflen; c++) { ESL_ALLOC(ps->bcolAAA[p][c], sizeof(float) * NCMYK); /* CMYK colors */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { ESL_ALLOC(ps->rcolAAA[p][c], sizeof(float) * NCMYK); /* CMYK colors */ } } } pp = orig_npage; /* add color legend */ ESL_ALLOC(limits, sizeof(float) * (hc_nbins+1)); limits[0] = 0.0; limits[1] = 0.167; limits[2] = 0.333; limits[3] = 0.500; limits[4] = 0.667; limits[5] = 0.833; limits[6] = 1.00; ps->sclAA[pp] = create_scheme_colorlegend(hc_scheme_idx, hc_nbins, limits, FALSE, FALSE, FALSE, TRUE); if(tabfp != NULL) { fprintf(tabfp, "# ---------\n"); fprintf(tabfp, "# Span data\n"); fprintf(tabfp, "# ---------\n"); fprintf(tabfp, "# This section includes %d non #-prefixed lines, one for each consensus position\n", ps->rflen); fprintf(tabfp, "# in the alignment and corresponding template.\n"); fprintf(tabfp, "# Each line includes %d tokens, separated by whitespace:\n", ps->mask == NULL ? 4 : 5); fprintf(tabfp, "# \ttoken 1: 'span' (tag defining line type to ease parsing)\n"); fprintf(tabfp, "# \ttoken 2: consensus position (starting at 1)\n"); fprintf(tabfp, "# \ttoken 3: fraction of sequences that 'span' position\n"); fprintf(tabfp, "# \ttoken 4: bin index this positions falls in (see bin values below)\n"); if(ps->mask != NULL) { fprintf(tabfp, "# \ttoken 5: '1' if position is included by mask, '0' if not\n"); } fprintf(tabfp, "#\n"); fprintf(tabfp, "# A sequence s spans consensus position 'x' that is actual alignment position 'a' if s has\n"); fprintf(tabfp, "# at least one non-gap nucleotide aligned to a position 'b' <= 'a' and\n"); fprintf(tabfp, "# at least one non-gap nucleotide aligned to a position 'c' >= 'a'\n"); fprintf(tabfp, "#\n"); fprintf(tabfp, "# Value ranges for bins:\n"); fprintf(tabfp, "# \tbin 0: special case, 0 sequences span this position\n"); fprintf(tabfp, "# \tbin 1: special case, all %d sequences span this position\n", msa_nseq); for(l = 0; l < hc_nbins; l++) { fprintf(tabfp, "# \tbin %2d: [%.3f-%.3f%s fraction of sequences that span each position\n", l+2, limits[l], limits[l+1], (l == hc_nbins-1) ? "]" : ")"); } fprintf(tabfp, "#\n"); fprintf(tabfp, "# %4s %6s %8s %3s", "type", "cpos", "span", "bin"); if(ps->mask != NULL) fprintf(tabfp, " %4s", "mask"); fprintf(tabfp, "\n"); fprintf(tabfp, "# %4s %6s %8s %3s", "----", "------", "--------", "---"); if(ps->mask != NULL) fprintf(tabfp, " %4s", "----"); fprintf(tabfp, "\n"); } for(rfpos = 0; rfpos < ps->rflen; rfpos++) { if(span_ct[rfpos] == 0) { if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_onecell[zerocov_idx])) != eslOK) return status; nzerocov++; if(ps->mask != NULL && ps->mask[rfpos] == '1') nzerocov_masked++; cfract = 0.; bi = -2; } else if(span_ct[rfpos] == msa_nseq) { if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_onecell[maxcov_idx])) != eslOK) return status; nmaxcov++; if(ps->mask != NULL && ps->mask[rfpos] == '1') nmaxcov_masked++; cfract = 1.; bi = -1; } else { within_mask = (ps->mask != NULL && ps->mask[rfpos] == '1') ? TRUE : FALSE; cfract = (float) span_ct[rfpos] / (float) msa_nseq; if((status = set_scheme_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_scheme[hc_scheme_idx], cfract, ps->sclAA[pp], within_mask, &bi)) != eslOK) return status; } /* fill in info for the consensus nucleotide */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { if(ps->mask == NULL || ps->mask[rfpos] == '1') { ps->rAA[pp][rfpos] = esl_opt_GetBoolean(go, "--cambig") ? ps->msa_cseq_amb[rfpos] : ps->msa_cseq_maj[rfpos]; if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[WHITEOC])) != eslOK) return status; } else { /* position is a '0' in the mask, leave it blank (' ') */ ps->rAA[pp][rfpos] = ' '; if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[WHITEOC])) != eslOK) return status; } } if(tabfp != NULL) { fprintf(tabfp, " span %6d %8.5f %3d", rfpos+1, cfract, bi+2); if(ps->mask != NULL) fprintf(tabfp, " %4d", ps->mask[rfpos] == '1' ? 1 : 0); fprintf(tabfp, "\n"); } } /* add one-cell color legend for zero span positions */ ps->occlAAA[pp][0] = create_onecell_colorlegend(hc_onecell[zerocov_idx], nzerocov, nzerocov_masked, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][0], "no sequences span", ps->legx_max_chars, errbuf)) != eslOK) return status; /* add one-cell color legend for maximum span positions */ ps->occlAAA[pp][1] = create_onecell_colorlegend(hc_onecell[maxcov_idx], nmaxcov, nmaxcov_masked, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][1], "100% of seqs span", ps->legx_max_chars, errbuf)) != eslOK) return status; ps->nocclA[pp] = 2; /* add color legend */ if((status = add_text_to_scheme_colorlegend(ps, ps->sclAA[pp], "fraction of seqs that span each position", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_page_desc_to_sspostscript(ps, ps->npage-1, "fraction of sequences that span each position", errbuf)) != eslOK) return status; /* add the consensus nucleotide explanation text section to the legend */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { ps->tlAAA[pp][0] = create_text_legend_for_consensus_sequence(go, FALSE); ps->ntlA[pp] = 1; } free(limits); if(tabfp != NULL) fprintf(tabfp, "//\n"); return eslOK; ERROR: ESL_FAIL(status, errbuf, "span_sspostscript(): memory allocation error."); return status; /* NEVERREACHED */ } /* Function: avg_posteriors_sspostscript() * * Purpose: Fill a postscript data structure with info average posterior probabilities in the MSA. * Return: eslOK on success. */ static int avg_posteriors_sspostscript(const ESL_GETOPTS *go, ESL_ALPHABET *abc, char *errbuf, SSPostscript_t *ps, double **pp_ct, int msa_nseq, float ***hc_scheme, int hc_scheme_idx, int hc_nbins, float **hc_onecell, int hc_onecell_idx, FILE *tabfp) { int status; int p; int rfpos; int pp; float *limits; /* bin limits for the color scheme */ int nonecell_allgap = 0; int nonecell_allgap_masked = 0; int within_mask; int orig_npage = ps->npage; float ppavgA[11]; int l; int apos; double nnongap; double ppsum; int ppidx; double ppavg; int bi; ppavgA[0] = 0.025; ppavgA[1] = 0.10; ppavgA[2] = 0.20; ppavgA[3] = 0.30; ppavgA[4] = 0.40; ppavgA[5] = 0.50; ppavgA[6] = 0.60; ppavgA[7] = 0.70; ppavgA[8] = 0.80; ppavgA[9] = 0.90; ppavgA[10] = 0.975; if(ps->mask == NULL) { nonecell_allgap_masked = -1; } /* special flag */ if((status = add_pages_sspostscript(ps, 1, ALIMODE)) != eslOK) ESL_FAIL(status, errbuf, "memory error adding pages to the postscript object."); for(p = orig_npage; p < ps->npage; p++) { ESL_ALLOC(ps->bcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->sclAA[p], sizeof(SchemeColorLegend_t) * 1); ESL_ALLOC(ps->occlAAA[p], sizeof(OneCellColorLegend_t *) * 1); if(! esl_opt_GetBoolean(go, "--no-cnt")) { ESL_ALLOC(ps->rAA[p], sizeof(char) * ps->rflen); ESL_ALLOC(ps->rcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->tlAAA[p], sizeof(TextLegend_t *) * 1); } for(rfpos = 0; rfpos < ps->rflen; rfpos++) { ESL_ALLOC(ps->bcolAAA[p][rfpos], sizeof(float) * NCMYK); /* CMYK colors */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { ESL_ALLOC(ps->rcolAAA[p][rfpos], sizeof(float) * NCMYK); /* CMYK colors */ } } } ESL_ALLOC(limits, sizeof(float) * (hc_nbins+1)); limits[0] = 0.0; limits[1] = 0.70; limits[2] = 0.80; limits[3] = 0.85; limits[4] = 0.90; limits[5] = 0.95; limits[6] = 1.00; if(tabfp != NULL) { fprintf(tabfp, "# ----------------------------------\n"); fprintf(tabfp, "# Average posterior probability data\n"); fprintf(tabfp, "# ----------------------------------\n"); fprintf(tabfp, "# This section includes %d non #-prefixed lines, one for each consensus position\n", ps->rflen); fprintf(tabfp, "# in the alignment and corresponding template.\n"); fprintf(tabfp, "# Each line includes %d tokens, separated by whitespace:\n", ps->mask == NULL ? 5 : 6); fprintf(tabfp, "# \ttoken 1: 'avgpostprob' (tag defining line type to ease parsing)\n"); fprintf(tabfp, "# \ttoken 2: consensus position (starting at 1)\n"); fprintf(tabfp, "# \ttoken 3: average posterior probability of non-gap nucleotides for position\n"); fprintf(tabfp, "# \ttoken 4: number of non-gap nucleotides in position (max possible is %d (num seqs in aln))\n", msa_nseq); fprintf(tabfp, "# \ttoken 5: bin index this positions falls in (see bin values below)\n"); if(ps->mask != NULL) fprintf(tabfp, "# \ttoken 6: '1' if position is included by mask, '0' if not\n"); fprintf(tabfp, "#\n"); fprintf(tabfp, "# Posterior probability (PP) values in the alignment file can have 12 possible values,\n"); fprintf(tabfp, "# the average per position is calculated by defining each as the average of its range given\n"); fprintf(tabfp, "# below. (For example, a '8' which indicates PP between 0.75 and 0.85 is treated as 0.8).\n"); fprintf(tabfp, "# \t'.': gap, corresponds to a gap in the sequence (not counted)\n"); fprintf(tabfp, "# \t'0': posterior probability of between 0.00 and 0.05\n"); fprintf(tabfp, "# \t'1': posterior probability of between 0.05 and 0.15\n"); fprintf(tabfp, "# \t'2': posterior probability of between 0.15 and 0.25\n"); fprintf(tabfp, "# \t'3': posterior probability of between 0.25 and 0.35\n"); fprintf(tabfp, "# \t'4': posterior probability of between 0.35 and 0.45\n"); fprintf(tabfp, "# \t'5': posterior probability of between 0.45 and 0.55\n"); fprintf(tabfp, "# \t'6': posterior probability of between 0.55 and 0.65\n"); fprintf(tabfp, "# \t'7': posterior probability of between 0.65 and 0.75\n"); fprintf(tabfp, "# \t'8': posterior probability of between 0.75 and 0.85\n"); fprintf(tabfp, "# \t'9': posterior probability of between 0.85 and 0.95\n"); fprintf(tabfp, "# \t'*': posterior probability of between 0.95 and 1.00\n"); fprintf(tabfp, "#\n"); fprintf(tabfp, "# Value ranges for bins:\n"); fprintf(tabfp, "# \tbin 0: special case, 0 sequences have a non-gap nucleotide at position\n"); for(l = 0; l < hc_nbins; l++) { fprintf(tabfp, "# \tbin %2d: [%.3f-%.3f%s average posterior probability per position\n", l+1, limits[l], limits[l+1], (l == hc_nbins-1) ? "]" : ")"); } fprintf(tabfp, "#\n"); fprintf(tabfp, "# %11s %6s %8s %10s %3s", "type", "cpos", "avgpp", "nongap", "bin"); if(ps->mask != NULL) fprintf(tabfp, " %4s", "mask"); fprintf(tabfp, "\n"); fprintf(tabfp, "# %11s %6s %8s %10s %3s", "-----------", "------", "--------", "----------", "---"); if(ps->mask != NULL) fprintf(tabfp, " %4s", "----"); fprintf(tabfp, "\n"); } /* step through each sequence and each column, collecting stats */ pp = orig_npage; ps->sclAA[pp] = create_scheme_colorlegend(hc_scheme_idx, hc_nbins, limits, FALSE, TRUE, TRUE, TRUE); for(rfpos = 0; rfpos < ps->rflen; rfpos++) { apos = ps->msa_rf2a_map[rfpos]; nnongap = esl_vec_DSum(pp_ct[apos], 11); if(esl_FCompare(nnongap, 0., eslSMALLX1) == eslOK) { /* effectively 0.0, all gaps */ if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_onecell[hc_onecell_idx])) != eslOK) return status; nonecell_allgap++; if(ps->mask != NULL && ps->mask[rfpos] == '1') nonecell_allgap_masked++; bi = -1; ppavg = 0.; } else { /* at least 1 non-gap nucleotide in this position */ if(esl_FCompare(nnongap, pp_ct[apos][10], eslSMALLX1)) { /* all nongap nucleotides have highest possible posterior probability */ } else { } ppsum = 0.; for(ppidx = 0; ppidx < 11; ppidx++) { ppsum += pp_ct[apos][ppidx] * ppavgA[ppidx]; /* Note: PP value is considered average of range, not minimum ('9' == 0.90 (0.95-0.85/2) */ } ppavg = ppsum / nnongap; within_mask = (ps->mask != NULL && ps->mask[rfpos] == '1') ? TRUE : FALSE; if((status = set_scheme_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_scheme[hc_scheme_idx], ppavg, ps->sclAA[pp], within_mask, &bi)) != eslOK) return status; } /* fill in info for the consensus nucleotide */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { if(ps->mask == NULL || ps->mask[rfpos] == '1') { ps->rAA[pp][rfpos] = esl_opt_GetBoolean(go, "--cambig") ? ps->msa_cseq_amb[rfpos] : ps->msa_cseq_maj[rfpos]; if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[WHITEOC])) != eslOK) return status; } else { /* position is a '0' in the mask, leave it blank (' ') */ ps->rAA[pp][rfpos] = ' '; if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[WHITEOC])) != eslOK) return status; } } if(tabfp != NULL) { fprintf(tabfp, " avgpostprob %6d %8.5f %10d %3d", rfpos+1, ppavg, (int) nnongap, bi+1); if(ps->mask != NULL) fprintf(tabfp, " %4d", ps->mask[rfpos] == '1' ? 1 : 0); fprintf(tabfp, "\n"); } } /* add one-cell color legend for all gap positions */ ps->occlAAA[pp][0] = create_onecell_colorlegend(hc_onecell[hc_onecell_idx], nonecell_allgap, nonecell_allgap_masked, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][0], "100% gaps", ps->legx_max_chars, errbuf)) != eslOK) return status; ps->nocclA[pp] = 1; /* add color legend */ if((status = add_text_to_scheme_colorlegend(ps, ps->sclAA[pp], "average posterior probability \\(confidence\\)", ps->legx_max_chars,errbuf)) != eslOK) return status; /* add the consensus nucleotide explanation text section to the legend */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { ps->tlAAA[pp][0] = create_text_legend_for_consensus_sequence(go, FALSE); ps->ntlA[pp] = 1; } /* add description to ps */ if((status = add_page_desc_to_sspostscript(ps, pp, "average posterior probability per position", errbuf)) != eslOK) return status; free(limits); if(tabfp != NULL) fprintf(tabfp, "//\n"); return eslOK; ERROR: return status; } /* Function: colormask_sspostscript() * * Purpose: Fill a postscript data structure with 1 new page based on a lanemask, each column * is either black (if included, a '1' in the mask) or pink (not included, a '0' in the * mask. * * Return: eslOK on success. */ static int colormask_sspostscript(const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps, ESL_MSA *msa, float **hc_onecell, int incmask_idx, int excmask_idx) { int status; int p, pp, c; int cpos; int orig_npage = ps->npage; int ncols_inside_mask = 0; int ncols_outside_mask = 0; char *mask_desc = NULL; char *mask_file = NULL; if(ps->mask == NULL) ESL_FAIL(eslEINVAL, errbuf, "ps->mask is null when trying to draw maskcol page"); if((status = add_pages_sspostscript(ps, 1, SIMPLEMASKMODE)) != eslOK) ESL_FAIL(eslEINVAL, errbuf, "memory error adding pages to the postscript object."); for(p = orig_npage; p < ps->npage; p++) { ESL_ALLOC(ps->rAA[p], sizeof(char) * ps->rflen); ESL_ALLOC(ps->bcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->occlAAA[p], sizeof(OneCellColorLegend_t *) * 2); for(c = 0; c < ps->rflen; c++) { ESL_ALLOC(ps->bcolAAA[p][c], sizeof(float) * NCMYK); /* CMYK colors */ } } pp = orig_npage; for(cpos = 0; cpos < ps->rflen; cpos++) { if(ps->mask[cpos] == '1') { /* included */ if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][cpos], NCMYK, hc_onecell[incmask_idx])) != eslOK) return status; ncols_inside_mask++; } else if(ps->mask[cpos] == '0') { if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][cpos], NCMYK, hc_onecell[excmask_idx])) != eslOK) return status; ncols_outside_mask++; } else ESL_FAIL(eslEINVAL, errbuf, "--mask mask char number %d is not a 1 nor a 0, but a %c\n", cpos, ps->mask[cpos]); ps->rAA[pp][cpos] = ' '; } /* add color legend */ ps->occlAAA[pp][0] = create_onecell_colorlegend(hc_onecell[incmask_idx], ncols_inside_mask, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][0], "columns included by mask", ps->legx_max_chars, errbuf)) != eslOK) return status; ps->occlAAA[pp][1] = create_onecell_colorlegend(hc_onecell[excmask_idx], ncols_outside_mask, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][1], "columns excluded by mask", ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = esl_strcat(&(mask_desc), -1, "mask file: ", -1)) != eslOK) ESL_FAIL(status, errbuf, "error copying mask file name string");; if((status = esl_FileTail(esl_opt_GetString(go, "--mask"), FALSE, &mask_file)) != eslOK) ESL_FAIL(status, errbuf, "error copying mask file name string (probably out of memory)."); if((strlen(mask_file) + strlen(mask_desc)) > (ps->desc_max_chars*2 - 2)) { /* desc would be too long, shorten mask_file so desc is legal */ /* the -5 below is so we can add '...' to end */ if((status = esl_strcat(&(mask_desc), -1, mask_file, ((ps->desc_max_chars*2) - strlen(mask_desc) - 5))) != eslOK) ESL_FAIL(status, errbuf, "error copying mask file name string"); if((status = esl_strcat(&(mask_desc), -1, "...", 3)) != eslOK) ESL_FAIL(status, errbuf, "error copying mask file name string"); } else { /* desc will not be too long */ if((status = esl_strcat(&(mask_desc), -1, mask_file, -1)) != eslOK) ESL_FAIL(status, errbuf, "error copying mask file name string"); } free(mask_file); if((status = add_page_desc_to_sspostscript(ps, pp, mask_desc, errbuf)) != eslOK) return status; ps->nocclA[pp] = 2; return eslOK; ERROR: ESL_FAIL(status, errbuf, "colormask_sspostscript(): memory allocation error."); return status; /* NEVERREACHED */ } /* Function: diffmask_sspostscript() * * Purpose: Fill a postscript data structure with 1 new page based on a comparison between * two masks one in ps->mask the other in , each position becomes * one of four colors, one for each of the four possible combinations of 0 and 1. * * Return: eslOK on success. */ static int diffmask_sspostscript(const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps, ESL_MSA *msa, char *mask2, float **hc_onecell, int incboth_idx, int inc1_idx, int inc2_idx, int excboth_idx) { int status; int p, pp, c; int cpos; int orig_npage = ps->npage; int ncols_in_both = 0; int ncols_out_both = 0; int ncols_in_1_out_2 = 0; int ncols_out_1_in_2 = 0; if(ps->mask == NULL) ESL_FAIL(eslEINVAL, errbuf, "ps->mask is null when trying to draw maskdiff page"); if((status = add_pages_sspostscript(ps, 1, SIMPLEMASKMODE)) != eslOK) ESL_FAIL(eslEINVAL, errbuf, "memory error adding pages to the postscript object."); for(p = orig_npage; p < ps->npage; p++) { ESL_ALLOC(ps->rAA[p], sizeof(char) * ps->rflen); ESL_ALLOC(ps->bcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->occlAAA[p], sizeof(OneCellColorLegend_t *) * 4); for(c = 0; c < ps->rflen; c++) { ESL_ALLOC(ps->bcolAAA[p][c], sizeof(float) * NCMYK); /* CMYK colors */ } } pp = orig_npage; for(cpos = 0; cpos < ps->rflen; cpos++) { if(ps->mask[cpos] == '1' && mask2[cpos] == '1') { if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][cpos], NCMYK, hc_onecell[incboth_idx])) != eslOK) return status; ncols_in_both++; } else if(ps->mask[cpos] == '1' && mask2[cpos] == '0') { if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][cpos], NCMYK, hc_onecell[inc1_idx])) != eslOK) return status; ncols_in_1_out_2++; } else if(ps->mask[cpos] == '0' && mask2[cpos] == '1') { if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][cpos], NCMYK, hc_onecell[inc2_idx])) != eslOK) return status; ncols_out_1_in_2++; } else if(ps->mask[cpos] == '0' && mask2[cpos] == '0') { if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][cpos], NCMYK, hc_onecell[excboth_idx])) != eslOK) return status; ncols_out_both++; } else if(ps->mask[cpos] != '0' && ps->mask[cpos] != '1') ESL_FAIL(eslEINVAL, errbuf, "--mask-col char number %d is not a 1 nor a 0, but a %c\n", cpos, ps->mask[cpos]); else if(mask2[cpos] != '0' && mask2[cpos] != '1') ESL_FAIL(eslEINVAL, errbuf, "--mask-diff char number %d is not a 1 nor a 0, but a %c\n", cpos, mask2[cpos]); ps->rAA[pp][cpos] = ' '; } /* add color legend */ ps->occlAAA[pp][0] = create_onecell_colorlegend(hc_onecell[incboth_idx], ncols_in_both, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][0], "included by both masks", ps->legx_max_chars, errbuf)) != eslOK) return status; ps->occlAAA[pp][1] = create_onecell_colorlegend(hc_onecell[inc1_idx], ncols_in_1_out_2, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][1], "incl mask 1, excl mask 2", ps->legx_max_chars, errbuf)) != eslOK) return status; ps->occlAAA[pp][2] = create_onecell_colorlegend(hc_onecell[inc2_idx], ncols_out_1_in_2, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][2], "excl mask 1, incl mask 1", ps->legx_max_chars, errbuf)) != eslOK) return status; ps->occlAAA[pp][3] = create_onecell_colorlegend(hc_onecell[excboth_idx], ncols_out_both, OCCL_BLANK_COUNT, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][3], "excluded by both masks", ps->legx_max_chars, errbuf)) != eslOK) return status; ps->nocclA[pp] = 4; if((status = add_diffmask_page_desc_to_sspostscript(ps, pp, esl_opt_GetString(go, "--mask"), esl_opt_GetString(go, "--mask-diff"), errbuf)) != eslOK) return status; return eslOK; ERROR: ESL_FAIL(status, errbuf, "diffmask_sspostscript(): memory allocation error."); return status; /* NEVERREACHED */ } /* Function: add_pages_sspostscript() * * Purpose: Add and initialize blank pages to a postscript object. */ int add_pages_sspostscript(SSPostscript_t *ps, int ntoadd, int page_mode) { int status; void *tmp; int p; if(ps->npage == 0) { assert(ps->rAA == NULL); assert(ps->bcolAAA == NULL); ESL_ALLOC(ps->rAA, sizeof(char *) * (ps->npage + ntoadd)); ESL_ALLOC(ps->rcolAAA, sizeof(float **) * (ps->npage + ntoadd)); ESL_ALLOC(ps->bcolAAA, sizeof(float **) * (ps->npage + ntoadd)); ESL_ALLOC(ps->otypeAA, sizeof(char *) * (ps->npage + ntoadd)); ESL_ALLOC(ps->occlAAA, sizeof(OneCellColorLegend_t **) * (ps->npage + ntoadd)); ESL_ALLOC(ps->nocclA, sizeof(int) * (ps->npage + ntoadd)); ESL_ALLOC(ps->tlAAA, sizeof(TextLegend_t **) * (ps->npage + ntoadd)); ESL_ALLOC(ps->ntlA, sizeof(int) * (ps->npage + ntoadd)); ESL_ALLOC(ps->sclAA, sizeof(SchemeColorLegend_t *) * (ps->npage + ntoadd)); ESL_ALLOC(ps->descA, sizeof(char *) * (ps->npage + ntoadd)); ESL_ALLOC(ps->modeA, sizeof(int) * (ps->npage + ntoadd)); ESL_ALLOC(ps->seqidxA, sizeof(int) * (ps->npage + ntoadd)); } else { assert(ps->rAA != NULL); assert(ps->bcolAAA != NULL); assert(ps->rcolAAA != NULL); ESL_RALLOC(ps->rAA, tmp, sizeof(char *) * (ps->npage + ntoadd)); ESL_RALLOC(ps->rcolAAA,tmp, sizeof(float **) * (ps->npage + ntoadd)); ESL_RALLOC(ps->bcolAAA,tmp, sizeof(float **) * (ps->npage + ntoadd)); ESL_RALLOC(ps->otypeAA,tmp, sizeof(char *) * (ps->npage + ntoadd)); ESL_RALLOC(ps->occlAAA,tmp, sizeof(OneCellColorLegend_t ***) * (ps->npage + ntoadd)); ESL_RALLOC(ps->nocclA, tmp, sizeof(int) * (ps->npage + ntoadd)); ESL_RALLOC(ps->tlAAA, tmp, sizeof(TextLegend_t ***) * (ps->npage + ntoadd)); ESL_RALLOC(ps->ntlA, tmp, sizeof(int) * (ps->npage + ntoadd)); ESL_RALLOC(ps->sclAA, tmp, sizeof(SchemeColorLegend_t **) * (ps->npage + ntoadd)); ESL_RALLOC(ps->descA, tmp, sizeof(char *) * (ps->npage + ntoadd)); ESL_RALLOC(ps->modeA, tmp, sizeof(int) * (ps->npage + ntoadd)); ESL_RALLOC(ps->seqidxA,tmp, sizeof(int) * (ps->npage + ntoadd)); } for(p = ps->npage; p < (ps->npage + ntoadd); p++) { ps->rAA[p] = NULL; ps->rcolAAA[p] = NULL; ps->bcolAAA[p] = NULL; ps->otypeAA[p] = NULL; ps->occlAAA[p] = NULL; ps->nocclA[p] = 0; ps->tlAAA[p] = NULL; ps->ntlA[p] = 0; ps->sclAA[p] = NULL; ps->descA[p] = NULL; ps->modeA[p] = page_mode; ps->seqidxA[p] = -1; } ps->npage += ntoadd; return eslOK; ERROR: return status; } /* read_mask_file * * Given an open file pointer, read the first token of the * file and return it as *ret_mask. Also return length of * mask in *ret_masklen, and a flag indicating whether or * not the mask has any internal zeroes in *ret_mask_has_internal_zeroes. * An internal '0' is one that occurs between at least one * 5' and one 3' '1' * * Returns: eslOK on success. */ int read_mask_file(char *filename, char *errbuf, char **ret_mask, int *ret_masklen, int *ret_mask_has_internal_zeroes) { int status; ESL_FILEPARSER *efp; char *tok; char *mask; int toklen; int n; /* for determining if we have internal zeroes */ int seen_1 = FALSE; /* becomes TRUE when we see first (5'-most) '1' */ int seen_1_then_0 = FALSE; /* becomes TRUE when we see first (5'-most) '0' that is 3' of first '1' */ int seen_1_then_0_then_1 = FALSE; /* becomes TRUE when we see first (5'-most) '1' that is 3' of first '0' that is 3' of first '1' */ if (esl_fileparser_Open(filename, NULL, &efp) != eslOK) ESL_FAIL(eslFAIL, errbuf, "failed to open %s in read_mask_file\n", filename); esl_fileparser_SetCommentChar(efp, '#'); if((status = esl_fileparser_GetToken(efp, &tok, &toklen)) != eslOK) ESL_FAIL(eslFAIL, errbuf, "failed to read a single token from %s\n", filename); ESL_ALLOC(mask, sizeof(char) * (toklen+1)); for(n = 0; n < toklen; n++) { mask[n] = tok[n]; if(mask[n] == '0') { if((seen_1) && (!seen_1_then_0)) { seen_1_then_0 = TRUE; } } else if (mask[n] == '1') { if(!seen_1) { seen_1 = TRUE; } if((seen_1) && (seen_1_then_0) && (!seen_1_then_0_then_1)) { seen_1_then_0_then_1 = TRUE; } } else { ESL_FAIL(eslEINVAL, errbuf, "character %d of mask file is invalid: %c (must be a '1' or a '0')\n", n, mask[n]); } mask[n] = tok[n]; } mask[n] = '\0'; *ret_mask = mask; *ret_masklen= toklen; *ret_mask_has_internal_zeroes = seen_1_then_0_then_1; esl_fileparser_Close(efp); return eslOK; ERROR: return eslEMEM; } /* Function: mutual_information_sspostscript() * * Purpose: Fill a postscript data structure with 1 new page, colored squares indicating * the mutual information of each base paired consensus column. * mutual information is the extra information gained from modelling * the pair together (info of vector of bps, size 16) versus separately (sum * of info of the two independent vector of singlets, size 4). * * Return: eslOK on success. */ static int mutual_information_sspostscript(const ESL_GETOPTS *go, ESL_ALPHABET *abc, char *errbuf, SSPostscript_t *ps, double ***bp_ct, int msa_nseq, float ***hc_scheme, int hc_scheme_idx, int hc_nbins, float **hc_onecell, int ss_idx, int zerores_idx, FILE *tabfp) { int status; int p, pp, c, i; int rfpos, apos; int orig_npage = ps->npage; double *bg, *bg_pair; double bg_ent, bg_pair_ent; double *obs_left, *obs_right, *obs_pair; double ent_left, ent_right, ent_pair; int j; ESL_DSQ lres; ESL_DSQ rres; double nres; int nss = 0; int nzerores = 0; int nss_masked = 0; int nzerores_masked = 0; int i_within_mask, j_within_mask; int i_bi, j_bi; float *limits; int l; int idx =1; if(ps->mask == NULL) nss_masked = nzerores_masked = -1; /* special flag */ if((status = add_pages_sspostscript(ps, 1, ALIMODE)) != eslOK) ESL_FAIL(status, errbuf, "memory error adding pages to the postscript object."); for(p = orig_npage; p < ps->npage; p++) { ESL_ALLOC(ps->bcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->sclAA[p], sizeof(SchemeColorLegend_t) * 1); ESL_ALLOC(ps->occlAAA[p], sizeof(OneCellColorLegend_t *) * 2); if(! esl_opt_GetBoolean(go, "--no-cnt")) { ESL_ALLOC(ps->rAA[p], sizeof(char) * ps->rflen); ESL_ALLOC(ps->rcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->tlAAA[p], sizeof(TextLegend_t *) * 1); } for(c = 0; c < ps->rflen; c++) { ESL_ALLOC(ps->bcolAAA[p][c], sizeof(float) * NCMYK); /* CMYK colors */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { ESL_ALLOC(ps->rcolAAA[p][c], sizeof(float) * NCMYK); /* CMYK colors */ } } } pp = orig_npage; /* add color legend */ ESL_ALLOC(limits, sizeof(float) * (hc_nbins+1)); limits[0] = 0.0; limits[1] = 0.167; limits[2] = 0.333; limits[3] = 0.500; limits[4] = 0.667; limits[5] = 0.833; limits[6] = 1.000; ps->sclAA[pp] = create_scheme_colorlegend(hc_scheme_idx, hc_nbins, limits, FALSE, TRUE, TRUE, TRUE); if(tabfp != NULL) { fprintf(tabfp, "# -----------------------\n"); fprintf(tabfp, "# Mutual information data\n"); fprintf(tabfp, "# -----------------------\n"); fprintf(tabfp, "# This section includes %d non #-prefixed lines, one for each consensus position\n", ps->rflen); fprintf(tabfp, "# in the alignment and corresponding template.\n"); fprintf(tabfp, "# Each line includes %d tokens, separated by whitespace:\n", ps->mask == NULL ? 9 : 11); fprintf(tabfp, "# \ttoken 1: 'mutualinfo' (tag defining line type to ease parsing)\n"); fprintf(tabfp, "# \ttoken 2: base pair index\n"); fprintf(tabfp, "# \ttoken 3: 5' consensus position of base pair (starting at 1)\n"); fprintf(tabfp, "# \ttoken 4: 3' consensus position of base pair (starting at 1)\n"); fprintf(tabfp, "# \ttoken 5: sequence information content at 5' position (bits)\n"); fprintf(tabfp, "# \ttoken 6: sequence information content at 3' position (bits)\n"); fprintf(tabfp, "# \ttoken 7: mutual information of the base pair (bits)\n"); fprintf(tabfp, "# \ttoken 8: number of sequences with non-gap at 5' and 3' posn (max possible is %d)\n", msa_nseq); fprintf(tabfp, "# \ttoken 8: number of sequences with non-gap at 5' and 3' position\n"); fprintf(tabfp, "# \ttoken 9: bin index this positions falls in (see bin values below).\n"); if(ps->mask != NULL) { fprintf(tabfp, "# \ttoken 10: '1' if 5' position is included by mask, '0' if not\n"); fprintf(tabfp, "# \ttoken 11: '1' if 3' position is included by mask, '0' if not\n"); } fprintf(tabfp, "#\n"); fprintf(tabfp, "# Information content is calculated as 2.0 - H, where\n"); fprintf(tabfp, "# H = - \\sum_x p_x \\log_2 p_x, for x in {A, C, G, U}\n"); fprintf(tabfp, "# p_x is the frequency of x for *non-gap* nucleotides at the position.\n"); fprintf(tabfp, "# Only nucleotides for sequences which have a non-gap nucleotide at both\n"); fprintf(tabfp, "# the 5' and 3' positions of the pair are counted.\n"); fprintf(tabfp, "# Mutual information is calculated as\n"); fprintf(tabfp, "# \\sum_{x,y} p_{x,y} \\log_2 ((p_x * p_y) / p_{x,y}\n"); fprintf(tabfp, "# Value ranges for bins:\n"); fprintf(tabfp, "# \tbin 0: special case, 0 sequences have non-gaps at both 5' and 3' position of pair\n"); for(l = 0; l < hc_nbins; l++) { fprintf(tabfp, "# \tbin %2d: [%.3f-%.3f%s mutual information per position (bits)\n", l+1, limits[l], limits[l+1], (l == hc_nbins-1) ? "]" : ")"); } fprintf(tabfp, "#\n"); fprintf(tabfp, "# %10s %4s %5s %5s %8s %8s %9s %10s %3s", "type", "idx", "5'pos", "3'pos", "5'info", "3'info", "mutinfo/2", "nongap", "bin"); if(ps->mask != NULL) fprintf(tabfp, " %6s %6s", "5'mask", "3'mask"); fprintf(tabfp, "\n"); fprintf(tabfp, "# %10s %4s %5s %5s %8s %8s %9s %10s %3s", "----------", "----", "-----", "-----", "--------", "--------", "---------", "----------", "---"); if(ps->mask != NULL) fprintf(tabfp, " %6s %6s", "------", "------"); fprintf(tabfp, "\n"); } /* determine background entropy */ ESL_ALLOC(bg, sizeof(double) * abc->K); ESL_ALLOC(bg_pair, sizeof(double) * abc->K*abc->K); esl_vec_DSet(bg, abc->K, 1./(abc->K)); esl_vec_DSet(bg_pair, abc->K*abc->K, 1./(abc->K*abc->K)); bg_pair_ent = esl_vec_DEntropy(bg_pair, abc->K*abc->K); bg_ent = esl_vec_DEntropy(bg, abc->K); free(bg); free(bg_pair); ESL_ALLOC(obs_left, sizeof(double) * (abc->K)); ESL_ALLOC(obs_right, sizeof(double) * (abc->K)); ESL_ALLOC(obs_pair, sizeof(double) * (abc->K*abc->K)); /* get observed nucleotides and base pairs at each rfpos */ for(rfpos = 0; rfpos < ps->rflen; rfpos++) { esl_vec_DSet(obs_left, abc->K, 0.); esl_vec_DSet(obs_right, abc->K, 0.); esl_vec_DSet(obs_pair, abc->K*abc->K, 0.); i = rfpos; nres = 0.; apos = ps->msa_rf2a_map[rfpos]; /* check if we're base paired */ if(ps->msa_ct[rfpos+1] != 0) { /* printf("msa_ct rfpos+1: %d %d\n", rfpos+1, ps->msa_ct[rfpos+1]); */ if(ps->msa_ct[rfpos+1] > (rfpos+1)) { /* rfpos is left half of base pair */ /* add up contributions of all possible base pairs, * we have to be careful to skip nucleotides that are gaps, missing or nonnucleotides in * EITHER left or right half of the bp. * We use the raw counts from msa_count() as the wt, (bp_ct[apos][lres][rres]) */ j = ps->msa_ct[i+1] - 1; for(lres = 0; lres < abc->K; lres++) { for(rres = 0; rres < abc->K; rres++) { /* printf("apos: %d rfpos: %d lres: %d rres: %d bp_ct[][][]: %.5f\n", apos, rfpos, lres, rres, bp_ct[apos][lres][rres]);*/ esl_abc_DCount(abc, obs_left, lres, bp_ct[apos][lres][rres]); esl_abc_DCount(abc, obs_right, rres, bp_ct[apos][lres][rres]); PairCount(abc, obs_pair, lres, rres, bp_ct[apos][lres][rres]); nres += bp_ct[apos][lres][rres]; } } for(lres = abc->K+1; lres < abc->Kp-2; lres++) { /* do all degenerates and 'any' (N) */ for(rres = abc->K+1; rres < abc->Kp-2; rres++) { /* do all degenerates and 'any' (N) */ esl_abc_DCount(abc, obs_left, lres, bp_ct[apos][lres][rres]); esl_abc_DCount(abc, obs_right, rres, bp_ct[apos][lres][rres]); PairCount(abc, obs_pair, lres, rres, bp_ct[apos][lres][rres]); nres += bp_ct[apos][lres][rres]; } } /* esl_vec_DDump(stdout, obs_left, abc->K, NULL); esl_vec_DDump(stdout, obs_right, abc->K, NULL); esl_vec_DDump(stdout, obs_pair, abc->K*abc->K, NULL); */ esl_vec_DNorm(obs_left, abc->K); esl_vec_DNorm(obs_right, abc->K); esl_vec_DNorm(obs_pair, abc->K*abc->K); ent_left = bg_ent - esl_vec_DEntropy(obs_left, abc->K); ent_right = bg_ent - esl_vec_DEntropy(obs_right, abc->K); ent_pair = bg_pair_ent - esl_vec_DEntropy(obs_pair, abc->K*abc->K); /* printf("lpos: %5d rpos: %5d entP: %8.3f entL: %8.3f entR: %8.3f nres: %.2f ", i+1, j+1, ent_pair, ent_left, ent_right, nres); */ ent_pair -= ent_left + ent_right; ent_pair /= 2.; /* printf("Final: %8.3f\n", ent_pair); */ /* To verify that the ent_pair is mutual information, calculated a different way, uncomment the following block */ /* double mi = 0; for(lres = 0; lres < abc->K; lres++) { for(rres = 0; rres < abc->K; rres++) { if(obs_pair[lres*abc->K+rres] > eslSMALLX1) { mi += obs_pair[lres*abc->K+rres] * (1.44269504 * log((obs_pair[lres*abc->K+rres])/(obs_left[lres] * obs_right[rres]))); printf("mi: %.2f obs_left %.2f obs_right: %.2f obs_pair %.2f \n", mi, obs_left[lres], obs_right[rres], obs_pair[lres*abc->K+rres]); } } } printf("MI/2: %.2f EP: %.2f %.2f\n", mi/2., ent_pair, (mi/2.) - ent_pair); */ if(ent_pair < (-1. * eslSMALLX1)) { ESL_FAIL(eslEINCONCEIVABLE, errbuf, "pair information < 0.: %f (lpos: %d rpos: %d)\n", ent_pair, i, j); } if(esl_DCompare(nres, 0., eslSMALLX1) == eslOK) { /* nres is 0 */ if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][i], NCMYK, hc_onecell[zerores_idx])) != eslOK) return status; if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][j], NCMYK, hc_onecell[zerores_idx])) != eslOK) return status; nzerores += 2; if(ps->mask != NULL && ps->mask[i] == '1') nzerores_masked++; if(ps->mask != NULL && ps->mask[j] == '1') nzerores_masked++; if(tabfp != NULL) { fprintf(tabfp, " mutualinfo %4d %5d %5d %8.5f %8.5f %9.5f %10d %3d", idx++, i+1, j+1, 0., 0., 0., 0, 0); if(ps->mask != NULL) fprintf(tabfp, " %6d %6d", ((ps->mask == NULL || ps->mask[i] == '1') ? 1 : 0), ((ps->mask == NULL || ps->mask[j] == '1') ? 1 : 0)); fprintf(tabfp, "\n"); } } else { i_within_mask = (ps->mask != NULL && ps->mask[i] == '1') ? TRUE : FALSE; j_within_mask = (ps->mask != NULL && ps->mask[j] == '1') ? TRUE : FALSE; if((status = set_scheme_values(errbuf, ps->bcolAAA[pp][i], NCMYK, hc_scheme[hc_scheme_idx], ent_pair, ps->sclAA[pp], i_within_mask, &i_bi)) != eslOK) return status; if((status = set_scheme_values(errbuf, ps->bcolAAA[pp][j], NCMYK, hc_scheme[hc_scheme_idx], ent_pair, ps->sclAA[pp], j_within_mask, &j_bi)) != eslOK) return status; if(tabfp != NULL) { fprintf(tabfp, " mutualinfo %4d %5d %5d %8.5f %8.5f %9.5f %10d %3d", idx++, i+1, j+1, ent_left, ent_right, ent_pair, (int) nres, i_bi+1); if(ps->mask != NULL) fprintf(tabfp, " %6d %6d", ((ps->mask == NULL || ps->mask[i] == '1') ? 1 : 0), ((ps->mask == NULL || ps->mask[j] == '1') ? 1 : 0)); fprintf(tabfp, "\n"); } } } /* end of if(ps->msa_ct[rfpos+1] > (rfpos+1)) { */ } else { /* single stranded, paint grey */ nss++; if(ps->mask != NULL && ps->mask[rfpos] == '1') nss_masked++; if((status = set_onecell_values(errbuf, ps->bcolAAA[pp][rfpos], NCMYK, hc_onecell[ss_idx])) != eslOK) return status; } /* fill in info for the consensus nucleotide */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { if(ps->mask == NULL || ps->mask[rfpos] == '1') { ps->rAA[pp][rfpos] = esl_opt_GetBoolean(go, "--cambig") ? ps->msa_cseq_amb[rfpos] : ps->msa_cseq_maj[rfpos]; if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[WHITEOC])) != eslOK) return status; } else { /* position is a '0' in the mask, leave it blank (' ') */ ps->rAA[pp][rfpos] = ' '; if((status = set_onecell_values(errbuf, ps->rcolAAA[pp][rfpos], NCMYK, hc_onecell[WHITEOC])) != eslOK) return status; } } } /* add text to the one cell legend */ ps->occlAAA[pp][0] = create_onecell_colorlegend(hc_onecell[ss_idx], nss, nss_masked, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][0], "single-stranded", ps->legx_max_chars, errbuf)) != eslOK) return status; /* add text to the second one cell legend */ ps->occlAAA[pp][1] = create_onecell_colorlegend(hc_onecell[zerores_idx], nzerores, nzerores_masked, FALSE, FALSE); if((status = add_text_to_onecell_colorlegend(ps, ps->occlAAA[pp][1], "0 complete basepairs", ps->legx_max_chars, errbuf)) != eslOK) return status; ps->nocclA[pp] = 2; /* add text to the scheme legend */ if((status = add_text_to_scheme_colorlegend(ps, ps->sclAA[pp], "mutual information per position (bits)", ps->legx_max_chars, errbuf)) != eslOK) return status; /* add the consensus nucleotide explanation text section to the legend */ if(! esl_opt_GetBoolean(go, "--no-cnt")) { ps->tlAAA[pp][0] = create_text_legend_for_consensus_sequence(go, FALSE); ps->ntlA[pp] = 1; } /* add description to ps */ if((status = add_page_desc_to_sspostscript(ps, pp, "mutual information per basepaired position", errbuf)) != eslOK) return status; free(limits); free(obs_left); free(obs_right); free(obs_pair); if(tabfp != NULL) fprintf(tabfp, "//\n"); return eslOK; ERROR: ESL_FAIL(status, errbuf, "mutual_information_sspostscript(): memory allocation error."); return status; /* NEVERREACHED */ } /* Function: PairCount() * Date: SRE, Tue Aug 1 10:34:20 2000 [St. Louis] * * Purpose: Given a possibly degenerate symbol code for left * and right symbols in a pair, increment a symbol * counter array appropriately. * * Args: abc - pointer to the internal alphabet * counters - vector to count into [0..abc->K^2-1] * syml - index of left symbol [0..abc->sym_iupac-1] * symr - index of right symbol [0..abc->sym_iupac-1] * wt - weight to use for the count (often 1.0). * * Returns: void */ static void PairCount(const ESL_ALPHABET *abc, double *counters, ESL_DSQ syml, ESL_DSQ symr, double wt) { int status; if (syml < abc->K && symr < abc->K) { counters[(int) (syml * abc->K + symr)] += wt; return; } else { int l,r; double *left = NULL; double *right = NULL; ESL_ALLOC(left, sizeof(double) * abc->K); ESL_ALLOC(right, sizeof(double) * abc->K); esl_vec_DSet(left, abc->K, 0.); esl_vec_DSet(right, abc->K, 0.); esl_abc_DCount(abc, left, syml, 1.0); esl_abc_DCount(abc, right, symr, 1.0); for (l = 0; l < abc->K; l++) for (r = 0; r < abc->K; r++) counters[l*abc->K +r] += left[l] * right[r] * wt; free(left); free(right); } return; ERROR: esl_fatal("Memory error"); } /* Function: get_command * Date: EPN, Fri Jan 25 13:56:10 2008 * * Purpose: Return the command used to call esl-ssdraw * in . * * Returns: eslOK on success; eslEMEM on allocation failure. */ static int get_command(const ESL_GETOPTS *go, char *errbuf, char **ret_command) { int status; int i; char *command = NULL; for (i = 0; i < go->argc; i++) { /* copy all command line options and args */ if((status = esl_strcat(&(command), -1, go->argv[i], -1)) != eslOK) goto ERROR; if(i < (go->argc-1)) if((status = esl_strcat(&(command), -1, " ", 1)) != eslOK) goto ERROR; } *ret_command = command; return eslOK; ERROR: ESL_FAIL(status, errbuf, "get_command(): memory allocation error."); return status; } /* Function: get_date * Date: EPN, Fri Jan 25 13:59:22 2008 * * Purpose: Return a string that gives the current date. * * Returns: eslOK on success; eslEMEM on allocation failure. */ static int get_date(char *errbuf, char **ret_date) { int status; time_t date = time(NULL); char *sdate = NULL; if((status = esl_strdup(ctime(&date), -1, &sdate)) != eslOK) goto ERROR; esl_strchop(sdate, -1); /* doesn't return anything but eslOK */ *ret_date = sdate; return eslOK; ERROR: ESL_FAIL(status, errbuf, "get_date() error status: %d, probably out of memory.", status); return status; } /* Function: set_scheme_values() * * Purpose: Set color values from a predefined scheme given min, max, * value and number of colors. */ static int set_scheme_values(char *errbuf, float *vec, int ncolvals, float **scheme, float val, SchemeColorLegend_t *scl, int within_mask, int *ret_bi) { float min, max; int ci, bi; min = scl->limits[0]; max = scl->limits[scl->nbins]; if((min-val) > eslSMALLX1) { ESL_FAIL(eslEINVAL, errbuf, "set_scheme_values(), val: %.4f < min: %.4f\n", val, min); } if((val-max) > eslSMALLX1) { ESL_FAIL(eslEINVAL, errbuf, "set_scheme_values(), val: %.4f > max: %.4f\n", val, max); } bi = 0; while((bi < (scl->nbins-1)) && ((val > scl->limits[bi+1]) || /* val exceeds limits[bi+1] OR */ (esl_FCompare(val, scl->limits[bi+1], eslSMALLX1) == eslOK))) { /* val equals limits[bi+1] */ bi++; } /* printf("%.3f %d (%.3f)\n", val, bi, scl->limits[bi+1]); */ scl->counts[bi]++; if(within_mask) scl->counts_masked[bi]++; for(ci = 0; ci < ncolvals; ci++) { vec[ci] = scheme[bi][ci]; } if(ret_bi != NULL) *ret_bi = bi; return eslOK; } /* Function: set_onecell_values() * * Purpose: Set color values as a predefined single * color. */ static int set_onecell_values(char *errbuf, float *vec, int ncolvals, float *onecolor) { int ci; for(ci = 0; ci < ncolvals; ci++) { vec[ci] = onecolor[ci]; } return eslOK; } /* Function: draw_masked_block() * * Purpose: Given coords, color, and mask style options draw a masked block. */ static int draw_masked_block(FILE *fp, float x, float y, float *colvec, int do_circle_mask, int do_square_mask, int do_x_mask, int do_border, float cellsize) { if (do_circle_mask) { if(do_border) { fprintf(fp, "newpath\n"); fprintf(fp, " %.2f %.2f %.1f 0 360 arc closepath\n", x + (cellsize/2.), y + (cellsize/2.), cellsize * (3./8.)); fprintf(fp, " %.4f %.4f %.4f %.4f setcmykcolor\n", colvec[0], colvec[1], colvec[2], colvec[3]); fprintf(fp, " stroke\n"); } else { fprintf(fp, "newpath\n"); fprintf(fp, " %.2f %.2f %.1f 0 360 arc closepath\n", x + (cellsize/2.), y + (cellsize/2.), cellsize * (3./8.)); fprintf(fp, " %.4f %.4f %.4f %.4f setcmykcolor\n", colvec[0], colvec[1], colvec[2], colvec[3]); fprintf(fp, " fill\n"); } } else if(do_square_mask) { if(do_border) { fprintf(fp, "newpath\n"); fprintf(fp, " %.2f %.2f moveto", x +1., y +1.); fprintf(fp, " 0 %.1f rlineto %.1f 0 rlineto 0 -%.1f rlineto closepath\n", cellsize*0.75, cellsize*0.75, cellsize*0.75); fprintf(fp, " %.4f %.4f %.4f %.4f setcmykcolor\n", colvec[0], colvec[1], colvec[2], colvec[3]); fprintf(fp, " stroke\n"); } else { fprintf(fp, "newpath\n"); fprintf(fp, " %.2f %.2f moveto", x + 1.5, y + 1.5); fprintf(fp, " 0 %.1f rlineto %.1f 0 rlineto 0 -%.1f rlineto closepath\n", cellsize*(5./8.), cellsize*(5./8.), cellsize*(5./8.)); fprintf(fp, " %.4f %.4f %.4f %.4f setcmykcolor\n", colvec[0], colvec[1], colvec[2], colvec[3]); fprintf(fp, " fill\n"); } } else if (do_x_mask) { if(do_border) { fprintf(fp, "newpath\n"); fprintf(fp, " %.2f %.2f moveto", x, y); fprintf(fp, " 0 %.1f rlineto %.1f 0 rlineto 0 -%.1f rlineto closepath\n", cellsize, cellsize, cellsize); fprintf(fp, " %.4f %.4f %.4f %.4f setcmykcolor\n", colvec[0], colvec[1], colvec[2], colvec[3]); fprintf(fp, " fill\n"); fprintf(fp, " %.4f %.4f %.4f %.4f setcmykcolor\n", 0., 0., 0., 0.); fprintf(fp, "newpath\n"); fprintf(fp, " %.2f %.2f moveto", x, y); fprintf(fp, " %.1f %.1f rlineto closepath\n", cellsize, cellsize); fprintf(fp, " stroke\n"); fprintf(fp, " %.2f %.2f moveto", x + cellsize, y); fprintf(fp, " -%.1f %.1f rlineto closepath\n", cellsize, cellsize); fprintf(fp, " stroke\n"); } else { fprintf(fp, "newpath\n"); fprintf(fp, " %.4f %.4f %.4f %.4f setcmykcolor\n", colvec[0], colvec[1], colvec[2], colvec[3]); fprintf(fp, " %.2f %.2f moveto", x, y); fprintf(fp, " %.1f %.1f rlineto closepath\n", cellsize, cellsize); fprintf(fp, " stroke\n"); fprintf(fp, "newpath\n"); fprintf(fp, " %.2f %.2f moveto", x + cellsize, y); fprintf(fp, " -%.1f %.1f rlineto closepath\n", cellsize, cellsize); fprintf(fp, " stroke\n"); } } return eslOK; } /* Function: validate_justread_sspostscript() * * Purpose: Validate a sspostscript just created by parsing * a template file. Nothing fancy here, just make * sure all we've written everything we expect. */ static int validate_justread_sspostscript(SSPostscript_t *ps, char *errbuf) { if(ps->modelname == NULL) ESL_FAIL(eslEINVAL, errbuf, "Error, failed to read modelname from template file."); if(ps->nbp == 0) ESL_FAIL(eslEINVAL, errbuf, "Error, failed to read 'lines bpconnects' section from template file."); if(ps->scale < 0) ESL_FAIL(eslEINVAL, errbuf, "Error, failed to read scale from template file."); if(ps->rflen == 0) ESL_FAIL(eslEINVAL, errbuf, "Error, failed to read 'text nucleotides' section from template file."); if(ps->leg_posn == -1) ESL_FAIL(eslEINVAL, errbuf, "Error, failed to read 'legend' section from template file."); if(ps->leg_cellsize == -1) ESL_FAIL(eslEINVAL, errbuf, "Error, failed to read 'legend' section from template file."); /* Stuff we don't currently require, but we may want to eventually */ /*if(ps->nposntext == 0) ESL_FAIL(eslEINVAL, errbuf, "validate_justread_sspostscript(), failed to read 'text positiontext' section from template file.");*/ /*if(ps->nticks == 0) ESL_FAIL(eslEINVAL, errbuf, "validate_justread_sspostscript(), failed to read 'lines positionticks' section from template file.");*/ /*if(ps->nbp == 0) ESL_FAIL(eslEINVAL, errbuf, "validate_justread_sspostscript(), failed to read 'lines bpconnects' section from template file.");*/ return eslOK; } /* Function: validate_and_update_sspostscript_given_msa() * * Purpose: Validate that a sspostscript works with a MSA. */ static int validate_and_update_sspostscript_given_msa(const ESL_GETOPTS *go, const ESL_ALPHABET *abc, SSPostscript_t *ps, ESL_MSA *msa, int msa_nseq, char *errbuf) { int status; int *msa_ct; int msa_nbp = 0; int *tmp_ct; int apos, rfpos_i, rfpos_j, rfpos; int *rf2a_map = NULL; int *a2rf_map = NULL; int rflen = 0; ps->msa = msa; ps->abc = abc; /* contract check */ if(msa->rf == NULL) ESL_FAIL(eslEINVAL, errbuf, "Error, msa does not have RF annotation."); if(msa->ss_cons == NULL) ESL_FAIL(eslEINVAL, errbuf, "Error, msa does not have SS_cons annotation."); /* count non-gap RF columns */ for(apos = 0; apos < msa->alen; apos++) { if(esl_abc_CIsResidue(abc, msa->rf[apos])) rflen++; } if(ps->rflen != rflen) ESL_FAIL(eslEINVAL, errbuf, "validate_and_update_sspostscript_given_msa(), expected consensus length of %d in MSA, but read %d\n", ps->rflen, rflen); /* build map of non-gap RF positions to alignment positions and vice versa */ ESL_ALLOC(rf2a_map, sizeof(int) * rflen); ESL_ALLOC(a2rf_map, sizeof(int) * msa->alen); esl_vec_ISet(a2rf_map, msa->alen, -1); rfpos = 0; for(apos = 0; apos < msa->alen; apos++) { if(esl_abc_CIsResidue(abc, msa->rf[apos])) { rf2a_map[rfpos] = apos; a2rf_map[apos] = rfpos; rfpos++; } } /* get the CT array for this msa */ ESL_ALLOC(tmp_ct, sizeof(int) * (msa->alen+1)); if (esl_wuss2ct(msa->ss_cons, msa->alen, tmp_ct) != eslOK) ESL_FAIL(eslEINVAL, errbuf, "Problem getting ct from SS_cons, does first alignment of MSA file have SS_cons annotation?"); ESL_ALLOC(msa_ct, sizeof(int) * (rflen+1)); esl_vec_ISet(msa_ct, rflen+1, 0); /* convert tmp_ct which is in alignment coords [1..alen] to non-gap RF coords [1..rflen]*/ for(apos = 0; apos < msa->alen; apos++) { if(tmp_ct[apos+1] > (apos+1)) { rfpos_i = a2rf_map[apos]; rfpos_j = a2rf_map[tmp_ct[apos+1]-1]; if(rfpos_i != -1 && rfpos_j != -1) { /* a consensus basepair */ msa_ct[rfpos_i+1] = rfpos_j+1; msa_ct[rfpos_j+1] = rfpos_i+1; msa_nbp++; } } } free(tmp_ct); if(ps->nbp != 0 && ps->nbp != msa_nbp) ESL_FAIL(eslEINVAL, errbuf, "validate_and_update_sspostscript_given_msa(), expected %d basepairs in MSA's SS_cons, but read %d\n", ps->nbp, msa_nbp); /* for(rfpos = 0; rfpos < rflen; rfpos++) printf("ct %5d %5d\n", rfpos, msa_ct[rfpos+1]-1); */ if(ps->msa_ct != NULL) { free(ps->msa_ct); ps->msa_ct = NULL;} if(ps->msa_rf2a_map != NULL) { free(ps->msa_rf2a_map); ps->msa_rf2a_map = NULL; } if(ps->msa_a2rf_map != NULL) { free(ps->msa_a2rf_map); ps->msa_a2rf_map = NULL; } ps->msa_ct = msa_ct; ps->msa_nbp = msa_nbp; ps->msa_ct = msa_ct; ps->msa_rf2a_map = rf2a_map; ps->msa_a2rf_map = a2rf_map; ps->msa_nseq = msa_nseq; return eslOK; ERROR: ESL_FAIL(status, errbuf, "validate_and_update_sspostscript_given_msa(), error status %d, probably out of memory.\n", status); return status; } /* Function: draw_header_and_footer() * * Purpose: Draw header for a page */ static int draw_header_and_footer(FILE *fp, const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps, int page, int pageidx2print) { int status; int i, split_idx; float x, y; float header_fontsize; int model_width, desc_width, desc_column_width; char *model_dashes, *desc_dashes, *desc2print; char *desc_string = NULL; float xmodel; char *model2print = NULL; float footer_fontsize, footerx_charsize; header_fontsize = HEADER_FONTSIZE_UNSCALED / ps->scale; fprintf(fp, "%% begin header section\n"); fprintf(fp, "/%s findfont %.2f scalefont setfont\n", DEFAULT_FONT, header_fontsize); fprintf(fp, "0.00 0.00 0.00 1.00 setcmykcolor\n"); /* black */ if(! (esl_opt_GetBoolean(go, "--no-head"))) { model_width = ESL_MAX(strlen("model"), (int) strlen(ps->modelname)); if(model_width > HEADER_MODELNAME_MAXCHARS) { ESL_ALLOC(model2print, sizeof(char) * (HEADER_MODELNAME_MAXCHARS+1)); for(i = 0; i < (HEADER_MODELNAME_MAXCHARS-3); i++) model2print[i] = ps->modelname[i]; model2print[HEADER_MODELNAME_MAXCHARS-3] = '.'; model2print[HEADER_MODELNAME_MAXCHARS-2] = '.'; model2print[HEADER_MODELNAME_MAXCHARS-1] = '.'; model2print[HEADER_MODELNAME_MAXCHARS] = '\0'; } else { if((status = esl_strdup(ps->modelname, -1, &(model2print))) != eslOK) ESL_FAIL(eslEINVAL, errbuf, "draw_header_and_footer(), error copying modelname"); } model_width = ESL_MIN(model_width, HEADER_MODELNAME_MAXCHARS); ESL_ALLOC(model_dashes, sizeof(char) * (model_width+1)); for(i = 0; i < model_width; i++) model_dashes[i] = '-'; model_dashes[model_width] = '\0'; if(ps->modeA[page] == ALIMODE || ps->modeA[page] == SIMPLEMASKMODE) { if((status = esl_strdup("description", -1, &(desc_string))) != eslOK) ESL_FAIL(eslEINVAL, errbuf, "draw_header_and_footer(), error copying description"); } else if(ps->modeA[page] == INDIMODE) { if((status = esl_strdup("sequence name", -1, &(desc_string))) != eslOK) ESL_FAIL(eslEINVAL, errbuf, "draw_header_and_footer(), error copying description"); } xmodel = ps->headerx_desc - (ps->headerx_charsize * (model_width + 6 + 6 + 8 + 2)); /*6,6,8 for #pos,#bps,#seq|seqlen) plus 2 spaces each, first 2 for 2 spaces before desc*/ x = xmodel; y = ps->headery; fprintf(fp, "(%-*s %4s %4s) %.2f %.2f moveto show\n", model_width, "model", "#pos", "#bps", x, y); y -= header_fontsize * 0.75; fprintf(fp, "(%-*s %4s %4s) %.2f %.2f moveto show\n", model_width, model_dashes, "----", "----", x, y); y -= header_fontsize * 0.75; fprintf(fp, "(%-*s %4d %4d) %.2f %.2f moveto show\n", model_width, model2print, ps->rflen, ps->msa_nbp, x, y); free(model_dashes); x += (model_width + 6 + 6 +2) * ps->headerx_charsize; if(ps->modeA[page] == ALIMODE) { y+= header_fontsize * 1.5; fprintf(fp, "(%6s) %.2f %.2f moveto show\n", "#seqs", x, y); y -= header_fontsize * 0.75; fprintf(fp, "(%6s) %.2f %.2f moveto show\n", "------", x, y); y -= header_fontsize * 0.75; fprintf(fp, "(%6d) %.2f %.2f moveto show", ps->msa_nseq, x, y); } else if(ps->modeA[page] == INDIMODE && (ps->seqidxA[page] != -1)) { /* ps->seqidxA[page] == -1 if we're printing the consensus sequence */ y+= header_fontsize * 1.5; fprintf(fp, "(%6s) %.2f %.2f moveto show\n", "seqlen", x, y); y -= header_fontsize * 0.75; fprintf(fp, "(%6s) %.2f %.2f moveto show\n", "------", x, y); y -= header_fontsize * 0.75; fprintf(fp, "(%6d) %.2f %.2f moveto show", ps->uaseqlenA[ps->seqidxA[page]], x, y); } if(ps->descA[page] != NULL) { x = ps->headerx_desc; y += 2. * header_fontsize * 0.75; desc_width = ESL_MAX((int) strlen(desc_string), (int) strlen(ps->descA[page])); if(desc_width > ps->desc_max_chars) { /* split into two lines, the add_page_desc_to_sspostscript() function added a '\n' where the split should be */ i = 0; while(ps->descA[page][i] != '\n') { i++; if(i >= desc_width) ESL_FAIL(eslEINVAL, errbuf, "drawing header, failed to find split point from add_page_desc_to_() in two-line description (%s)", ps->descA[page]); } split_idx = i; desc_column_width = split_idx; } else desc_column_width = desc_width; ESL_ALLOC(desc_dashes, sizeof(char) * (desc_column_width+1)); for(i = 0; i < desc_column_width; i++) desc_dashes[i] = '-'; desc_dashes[desc_column_width] = '\0'; fprintf(fp, "(%-*s) %.2f %.2f moveto show\n", desc_column_width, desc_string, x, y); y -= header_fontsize * 0.75; free(desc_string); fprintf(fp, "(%-*s) %.2f %.2f moveto show\n", desc_column_width, desc_dashes, x, y); y -= header_fontsize * 0.75; free(desc_dashes); if(desc_width > ps->desc_max_chars) { ESL_ALLOC(desc2print, sizeof(char) * (split_idx+1)); for(i = 0; i < split_idx; i++) desc2print[i] = ps->descA[page][i]; desc2print[split_idx] = '\0'; fprintf(fp, "(%-*s) %.2f %.2f moveto show\n", desc_column_width, desc2print, x, y); free(desc2print); x = ps->headerx_desc; y-= ps->headery_charsize * 1; ESL_ALLOC(desc2print, sizeof(char) * ((desc_width - split_idx) -1+1)); for(i = split_idx+1; i < desc_width; i++) desc2print[(i-(split_idx+1))] = ps->descA[page][i]; desc2print[(desc_width-(split_idx+1))] = '\0'; fprintf(fp, "(%-*s) %.2f %.2f moveto show\n", desc_column_width, desc2print, x, y); free(desc2print); } else { fprintf(fp, "(%-*s) %.2f %.2f moveto show\n", desc_width, ps->descA[page], x, y); } } /* masked row of header goes here if desired */ } fprintf(fp, "%% end header section\n\n"); /* draw footer */ footer_fontsize = LEG_FONTSIZE_UNSCALED / ps->scale; footerx_charsize = ps->legx_charsize; if(! (esl_opt_GetBoolean(go, "--no-foot"))) { fprintf(fp, "%% begin footer section\n"); fprintf(fp, "/%s findfont %.2f scalefont setfont\n", FOOTER_FONT, footer_fontsize); /* draw alignment file name in lower left hand corner */ if(ps->mask != NULL) { if(esl_opt_GetString(go, "--mask-diff") != NULL) { fprintf(fp, "(alignment file: %s; mask 1 file: %s; mask 2 file: %s;) %.2f %.2f moveto show\n", esl_opt_GetArg(go, 1), esl_opt_GetString(go, "--mask"), esl_opt_GetString(go, "--mask-diff"), PAGE_SIDEBUF, PAGE_BOTBUF); } else { fprintf(fp, "(alignment file: %s; mask file: %s;) %.2f %.2f moveto show\n", esl_opt_GetArg(go, 1), esl_opt_GetString(go, "--mask"), PAGE_SIDEBUF, PAGE_BOTBUF); } } else { fprintf(fp, "(alignment file: %s) %.2f %.2f moveto show\n", esl_opt_GetArg(go, 1), PAGE_SIDEBUF, PAGE_BOTBUF); } /* put page number */ /* determine ndigits */ int tmp, ndigits; tmp = pageidx2print; ndigits = 1; while(tmp >= 10) { tmp /= 10; ndigits++; } x = ps->pagex_max - (PAGE_SIDEBUF) - (footerx_charsize * (5 + ndigits)); fprintf(fp, "(page %d) %.2f %.2f moveto show\n", pageidx2print, x, PAGE_BOTBUF); fprintf(fp, "%% end footer section\n\n"); } if(model2print != NULL) free(model2print); return eslOK; ERROR: ESL_FAIL(eslEINVAL, errbuf, "draw_header_and_footer(), memory error."); } /* Function: get_insert_info_from_msa * Date: EPN, Fri Dec 4 13:52:53 2009 * * Read an MSA with #=GC RF annotation defining * consensus columns and count how many insertions * occur after each consensus column for each sequence. * * msa - the alignment * rflen - expected nongap RF length (consensus length) * ret_nseq_with_ins_ct - [0..rflen] number of sequences with >= 1 * insert after each position. NULL if unwanted. * ret_nins_ct - [0..rflen] total number of inserted nucleotides * after each position. NULL if unwanted. * ret_per_seq_ins_ct - [0..i..msa->nseq-1][0..rflen] number of inserts * insert after each position per sequence. NULL if unwanted. * * Returns void. Dies with an informative error message upon an error. */ void get_insert_info_from_msa(const ESL_ALPHABET *abc, ESL_MSA *msa, int rflen, int **ret_nseq_with_ins_ct, int **ret_nins_ct, int ***ret_per_seq_ins_ct) { int status; int i; int *nseq_with_ins_ct = NULL; int *nins_ct = NULL; int **per_seq_ins_ct = NULL; int rfpos, apos; /* contract check */ if(msa->rf == NULL) esl_fatal("Error in get_insert_info_from_msa(), msa->rf is NULL."); /* allocate and initialize */ ESL_ALLOC(nseq_with_ins_ct, sizeof(int) * (rflen+1)); esl_vec_ISet(nseq_with_ins_ct, rflen+1, 0); ESL_ALLOC(nins_ct, sizeof(int) * (rflen+1)); esl_vec_ISet(nins_ct, rflen+1, 0); ESL_ALLOC(per_seq_ins_ct, sizeof(int *) * (msa->nseq)); for(i = 0; i < msa->nseq; i++) { ESL_ALLOC(per_seq_ins_ct[i], sizeof(int) * (rflen+1)); esl_vec_ISet(per_seq_ins_ct[i], (rflen+1), 0); } /* fill per_seq_ins_ct, nseq_with_ins_ct */ rfpos = 0; for(apos = 0; apos < msa->alen; apos++) { if(esl_abc_CIsResidue(abc, msa->rf[apos])) { rfpos++; if(rfpos > rflen) esl_fatal("Error in get_insert_info_from_msa(), expected consensus length (%d) is incorrect."); } else { for(i = 0; i < msa->nseq; i++) { if(! esl_abc_CIsGap(abc, msa->aseq[i][apos])) { per_seq_ins_ct[i][rfpos]++; nins_ct[rfpos]++; if(per_seq_ins_ct[i][rfpos] == 1) nseq_with_ins_ct[rfpos]++; } } } } if(ret_nseq_with_ins_ct != NULL) *ret_nseq_with_ins_ct = nseq_with_ins_ct; else free(nseq_with_ins_ct); if(ret_nins_ct != NULL) *ret_nins_ct = nins_ct; else free(nins_ct); if(ret_per_seq_ins_ct != NULL) *ret_per_seq_ins_ct = per_seq_ins_ct; else esl_arr2_Destroy((void **) per_seq_ins_ct, msa->nseq); return; ERROR: esl_fatal("Error in get_insert_info_from_msa(), memory allocation error."); return; /* NEVERREACHED */ } /* Function: get_insert_info_from_ifile * Date: EPN, Fri Dec 4 14:49:12 2009 * * Read a file output from Infernal's cmalign * when run with '--matchonly --ifile ' and * fill *ret_ict[0..rflen][0..msa->nseq-1] number * of inserts after each consensus position for * each sequence. * * We also keep track of cases where a count of * the first and final nongap positions of all sequence * per column would be incorrect IF the msa were * to have all insert columns removed. These corrections * are stored and returned in srfoff_ct and erfoff_ct * as explained below. * * Format of an insert file (from the commented header of an ifile): * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * This file includes 2+ non-'#' pre-fixed lines per model used for alignment, * where is the number of sequences in the target file. * The first non-'#' prefixed line per model includes 2 tokens, separated by a single space (' '): * The first token is the model name and the second is the consensus length of the model (). * The following lines include (4+3*) whitespace delimited tokens per line. * The format for these lines is: * .... .... * indicating has >= 1 inserted nucleotides after different consensus positions, * is the name of the sequence * is the unaligned length of the sequence * is the first (5'-most) consensus position filled by a nongap for this sequence (-1 if 0 nongap consensus posns) * is the final (3'-most) consensus position filled by a nongap for this sequence (-1 if 0 nongap consensus posns) * is the unaligned length of the sequence * is a consensus position (between 1 and ; if 0 inserts occur before 1st consensus posn) * is the *unaligned* position (b/t 1 and ) in of the first inserted nucleotide after . * is the number of inserted nucleotides after position for . * Lines for sequences with 0 inserted nucleotides will include only . * The final non-'#' prefixed line per model includes only '//', indicating the end of info for a model. * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * * Example: * ~~~~~~~~~~~~~~~~~~~~~~~~~~ * tRNA 71 * tRNA-1 67 1 71 17 15 1 * tRNA-2 71 1 71 20 20 1 * tRNA-3 70 1 71 45 41 3 46 44 1 * tRNA-4 71 1 71 * tRNA-5 69 1 71 46 44 1 * tRNA-6 70 1 71 * tRNA-7 67 1 71 * tRNA-8 71 1 71 17 16 1 * tRNA-9 67 1 71 * tRNA-10 73 1 71 45 44 4 * ~~~~~~~~~~~~~~~~~~~~~~~~~~ * * ifile - name of ifile * rflen - expected nongap RF length (consensus length) * msa_nseq - expected number of sequences * useme_keyhash - keyhash with names of sequences for which we will store insert info * if NULL, we store insert info for all seqs. * ret_nseq_with_ins_ct - [0..rflen] number of sequences with >= 1 inserts * after each RF position. * Note [0] is before first posn, [1] is after first posn, [rflen] is after last one * ret_nins_ct - [0..rflen] total number of inserted nucleotides (over all seqs) after each RF position. * Note [0] is before first posn, [1] is after first posn, [rflen] is after last one * ret_per_seq_ins_ct - [0..i..msa->nseq-1][0..rflen number of inserts * after each position for each sequence. * Filled here. * * ret_srfoff_ct - [0..rfpos..rflen-1] count adjustment to make to a spos_ct[rfpos] if it * were obtained from an alignment with inserts removed, this value is +, * where is : -1 times the number of sequences that have their first nongap * RF position as rfpos, but include an insert before an rfpos2 < rfpos. * and is : +1 times the number of sequences that have their first nongap * RF position as rfpos3, but have an insert before rfpos < rfpos3. * We can only determine these cases when we read the ifile, since the * msa has had inserts removed. * NOTE a nasty off-by-one: RF (consensus) positions in the ifile are indexed 1..rflen * * ret_erfoff_ct - [0..rfpos..rflen-1] count adjustment to make to a epos_ct[rfpos] if it * were obtained from an alignment with inserts removed, this value is +, * where is : -1 times the number of sequences that have their final nongap * RF position as rfpos, but include an insert after an rfpos2 > rfpos. * and is : +1 times the number of sequences that have their final nongap * RF position as rfpos3, but have an insert after rfpos > rfpos3. * We can only determine these cases when we read the ifile, since the * msa has had inserts removed. * NOTE a nasty off-by-one: RF (consensus) positions in the ifile are indexed 1..rflen * * Returns void. Dies with an informative error message on an error. */ void get_insert_info_from_ifile(char *ifile, int rflen, int msa_nseq, ESL_KEYHASH *useme_keyhash, int **ret_nseq_with_ins_ct, int **ret_nins_ct, int ***ret_per_seq_ins_ct, int **ret_srfoff_ct, int **ret_erfoff_ct) { int status; ESL_FILEPARSER *efp; char *tok; int nseq_read = 0; int nseq_stored = 0; int **per_seq_ins_ct = NULL; int *nins_ct = NULL; int *nseq_with_ins_ct = NULL; int nins; int i; int rfpos; /* current nongap RF position */ int uapos; /* unaligned position for current sequence */ int seen_model_name_line = FALSE; int seen_end_of_model_line = FALSE; int nseq2store; /* number of seqs we'll store insert info on */ int seqlen; /* sequence length for current sequence, read from ifile */ int spos; /* first (5'-most) nongap consensus position for current sequence, read from ifile */ int epos; /* final (3'-most) nongap consensus position for current sequence, read from ifile */ int *srfoff_ct = NULL; /* [0..rfpos..rflen-1] correction for spos_ct[rfpos], add this value to spos_ct * to correct the miscounting that occurs if the msa has had all inserts removed, but * an insert file with insert info has been supplied and is read in this function */ int *erfoff_ct = NULL; /* [0..rfpos..rflen-1] correction for epos_ct[rfpos] (analagous to srfoff_ct) */ int already_handled_special_spos = FALSE; int prv_e_increment, prv_e_decrement; if (esl_fileparser_Open(ifile, NULL, &efp) != eslOK) esl_fatal("Error: failed to open insert file %s\n", ifile); esl_fileparser_SetCommentChar(efp, '#'); /* determine how many sequences we'll be storing info for */ nseq2store = (useme_keyhash == NULL) ? msa_nseq : esl_keyhash_GetNumber(useme_keyhash); /* allocate and initialize */ ESL_ALLOC(nseq_with_ins_ct, sizeof(int) * (rflen+1)); esl_vec_ISet(nseq_with_ins_ct, rflen+1, 0); ESL_ALLOC(nins_ct, sizeof(int) * (rflen+1)); esl_vec_ISet(nins_ct, rflen+1, 0); if(ret_srfoff_ct != NULL) { ESL_ALLOC(srfoff_ct, sizeof(int) * rflen); esl_vec_ISet(srfoff_ct, rflen, 0); } if(ret_erfoff_ct != NULL) { ESL_ALLOC(erfoff_ct, sizeof(int) * rflen); esl_vec_ISet(erfoff_ct, rflen, 0); } if(ret_per_seq_ins_ct != NULL) { ESL_ALLOC(per_seq_ins_ct, sizeof(int *) * (nseq2store)); for(i = 0; i < nseq2store; i++) { ESL_ALLOC(per_seq_ins_ct[i], sizeof(int) * (rflen+1)); esl_vec_ISet(per_seq_ins_ct[i], (rflen+1), 0); } } /* Read the file, verify that it contains the correct number of sequences and the * consensus length(s) listed in the file agrees with expected rflen. * Special care is taken to allow concatenated ifiles, so we may see more than * one // lines, but the total number of seqs should match what we expect. */ i = 0; while (esl_fileparser_NextLine(efp) == eslOK) { if (esl_fileparser_GetTokenOnLine(efp, &tok, NULL) != eslOK) { if(seen_model_name_line) esl_fatal("Error reading insert file, failed to read seq name on line %d of file %s\n", efp->linenumber, ifile); else esl_fatal("Error reading insert file, failed to read model name on line %d of file %s\n", efp->linenumber, ifile); } if(! seen_model_name_line) { /* this should be a special line, 2 tokens: , verify that is what we expect */ seen_model_name_line = TRUE; seen_end_of_model_line = FALSE; if (esl_fileparser_GetTokenOnLine(efp, &tok, NULL) != eslOK) { esl_fatal("Error reading insert file, failed to read consensus length on line %d of file %s\n", efp->linenumber, ifile); } if(rflen != atoi(tok)) { esl_fatal("Error reading insert file, read consensus length of %d on line %d of file %s, but expected length %d\n", atoi(tok), efp->linenumber, ifile, rflen); } } else if (strncmp(tok, "//", 2) == 0) { /* end of data for an ifile, but we may have concatenated them, so we keep going */ seen_model_name_line = FALSE; seen_end_of_model_line = TRUE; } else { /* should be a seq line with 1+3*n tokens, ... , n can be 0 */ /* determine if we're using this sequence */ i++; if(useme_keyhash == NULL || (esl_keyhash_Lookup(useme_keyhash, tok, -1, NULL) == eslOK)) { already_handled_special_spos = FALSE; /* initialize */ prv_e_decrement = prv_e_increment = -1; /* initialize */ if(esl_fileparser_GetTokenOnLine(efp, &tok, NULL) != eslOK) esl_fatal("Error reading insert file, failed to read unaligned length for sequence on line %d of file %s.\n", efp->linenumber, ifile); seqlen = atoi(tok); if(esl_fileparser_GetTokenOnLine(efp, &tok, NULL) != eslOK) esl_fatal("Error reading insert file, failed to read first nongap consensus position for sequence on line %d of file %s.\n", efp->linenumber, ifile); spos = atoi(tok); if(spos > rflen) esl_fatal("Error reading insert file, read spos of %d that exceeds expected consensus length %d on line %d of file %s.\n", spos, rflen, efp->linenumber, ifile); if(esl_fileparser_GetTokenOnLine(efp, &tok, NULL) != eslOK) esl_fatal("Error reading insert file, failed to read final nongap consensus position for sequence on line %d of file %s.\n", efp->linenumber, ifile); epos = atoi(tok); if(epos > rflen) esl_fatal("Error reading insert file, read epos of %d that exceeds expected consensus length %d on line %d of file %s.\n", epos, rflen, efp->linenumber, ifile); if(spos == -1 && epos != -1) esl_fatal("insert file is corrupt, spos is -1 but epos is not -1, on line %d\n", efp->linenumber); if(spos != -1 && epos == -1) esl_fatal("insert file is corrupt, spos is not -1 but epos is -1, on line %d\n", efp->linenumber); while(esl_fileparser_GetTokenOnLine(efp, &tok, NULL) == eslOK) { /* rfpos */ rfpos = atoi(tok); if(rfpos > rflen) esl_fatal("Error reading insert file, read insert info for position %d that exceeds expected consensus length %d on line %d of file %s.\n", rfpos, rflen, efp->linenumber, ifile); /* uapos */ if((status = esl_fileparser_GetTokenOnLine(efp, &tok, NULL)) != eslOK) esl_fatal("Error reading insert file, didn't read unaligned sequence position for rfpos %d on line %d of file %s.\n", rfpos, efp->linenumber, ifile); uapos = atoi(tok); if(uapos > seqlen) esl_fatal("Error reading insert file, read insert info for position %d that exceeds expected sequence length %d on line %d of file %s.\n", rfpos, seqlen, efp->linenumber, ifile); /* nins */ if((status = esl_fileparser_GetTokenOnLine(efp, &tok, NULL)) != eslOK) esl_fatal("Error reading insert file, didn't read number of inserts for position %d on line %d of file %s.\n", rfpos, efp->linenumber, ifile); nins = atoi(tok); nins_ct[rfpos] += nins; if(per_seq_ins_ct != NULL) per_seq_ins_ct[nseq_stored][rfpos] = nins; if(nins > 0) nseq_with_ins_ct[rfpos]++; /* nins should always be > 0, but why not check? */ /* check for special cases where a spos_ct and epos_ct read from a de-inserted msa would be incorrect */ if(spos != -1) { /* Note, if spos == -1 (then epos also == -1, we checked above), then there are 0 nongap consensus positions for * this sequence, and the spos and epos counts were never incremented for this sequence, so they don't need to be corrected. */ /* First check if this insert is before spos-1 */ if(srfoff_ct != NULL) { if((rfpos < (spos-1)) && (! already_handled_special_spos)) { /* we've got an insert *after* a position rfpos < (spos-1) for minimal rfpos */ /* Any function that counted the first RF position for this sequence if inserts were * removed thought it was spos, but an insert exists after rfpos<(spos-1), which means there * was an insert after rfpos, then a gap in at least 1 consensus position before the * first nongap consensus nucleotide at cpos. * NOTE a nasty off-by-one: RF (consensus) positions in the ifile are indexed 1..rflen, whereas srfoff_ct is 0..rflen-1 */ srfoff_ct[(spos-1)]--; /* this position was overcounted */ srfoff_ct[(rfpos-1)+1]++; /* this position was undercounted, we do +1 because insert occured after rfpos */ /* printf("decremented srfoff_ct[%d] for seq %d\n", spos-1, i); printf("incremented srfoff_ct[%d] for seq %d\n", rfpos-1+1, i); */ already_handled_special_spos = TRUE; /* if another rfpos is less than (spos-1) we don't care, we already fixed s_rfoff_ct */ } } /* Now check if this insert is after epos */ if(erfoff_ct != NULL) { if(rfpos > epos) { /* we've got an insert *after* a position rfpos > epos */ /* Any function that counted the final RF position for this sequence if inserts were * removed thought it was epos, but an insert exists after rfpos>epos, which means there * was a gap in at least one consensus position cpos > epos (cpos <= rfpos) and then inserts * after rfpos. * NOTE a nasty off-by-one: RF (consensus) positions in the ifile are indexed 1..rflen, whereas srfoff_ct is 0..rflen-1 */ erfoff_ct[(epos-1)]--; /* this position was overcounted */ erfoff_ct[(rfpos-1)]++; /* this position was undercounted */ /* BUT, be careful, we could have already entered this 'if' for this sequence, if so we need to negate * the previous time we incremented and decremented. * NOTE this case and corresponding code only applies to epos (not spos) b/c with spos * its the first case only that we want to handle (which is why we use the already_handled_special_spos FLAG) */ if(prv_e_decrement != -1 && prv_e_increment != -1) { erfoff_ct[prv_e_increment]--; /* undo increment with a decrement */ erfoff_ct[prv_e_decrement]++; /* undo decrement with an increment */ prv_e_decrement = (epos-1); prv_e_increment = (rfpos-1); } } } } } nseq_stored++; } nseq_read++; if(nseq_read > msa_nseq) esl_fatal("Error reading insert file, read info for more sequences than expected (%d) at line %d of file %s.", msa_nseq, efp->linenumber, ifile); } } esl_fileparser_Close(efp); /* end of file, make sure we read a '//' at the end of it */ if(! seen_end_of_model_line) esl_fatal("Error reading insert file, didn't read the special '//' line at the end of file %s.\n", rfpos, efp->linenumber, ifile); /* if useme_keyhash != NULL, make sure we read all the seqs we wanted to */ if((useme_keyhash != NULL) && (nseq_stored != nseq2store)) { esl_fatal("Error reading insert file, wanted to read insert info on %d seqs, but only found %d of them in the insert file %s\n", nseq2store, nseq_stored, ifile); } if(nseq_read != msa_nseq) esl_fatal("Error reading insert file, expected to read info on %d seqs, but only found %d in the insert file %s\n", msa_nseq, nseq_read, ifile); if (ret_nins_ct) *ret_nins_ct = nins_ct; else esl_free(nins_ct); if (ret_nseq_with_ins_ct) *ret_nseq_with_ins_ct = nseq_with_ins_ct; else esl_free(nseq_with_ins_ct); if (ret_srfoff_ct) *ret_srfoff_ct = srfoff_ct; else esl_free(srfoff_ct); if (ret_erfoff_ct) *ret_erfoff_ct = erfoff_ct; else esl_free(erfoff_ct); if (ret_per_seq_ins_ct) *ret_per_seq_ins_ct = per_seq_ins_ct; else esl_arr2_Destroy((void **) per_seq_ins_ct, msa_nseq); return; ERROR: esl_fatal("Memory allocation error while reading insert file %s.", ifile); return;; /* NEVERREACHED */ } /* Function: get_insert_info_from_abc_ct * Date: EPN, Tue Jan 19 09:32:30 2010 * * Given an abc_ct array: * [0..apos..alen-1][0..abc->K]: per position count of * each symbol in alphabet over all seqs. * * Determine the number of sequences with >= 1 inserted * nucleotides after each RF position. * * IMPORTANT NOTE: This is done based on the assumption that inserts * have been systematically placed in the MSA by a program like * Infernal or HMMER and that the maximum number of nongap nucleotides in * any insert position after rfpos is the number of sequences with >=1 * insert nucleotides after rfpos. However, if the alignments were not * generated from HMMER nor Infernal, or have been modified, the * inserts may not follow this rule (the rule, in other words is that * there is always 1 insert column after each nongap RF position rfpos * that includes a nucleotide from all sequences that have >= 1 inserted * nucleotides after rfpos). * * abc_ct - [0..apos..msa_alen-1][0..abc->K] count of each nucleotide in each position * abc - the alphabet * msa_rf - msa->rf, the reference annotation * msa->alen - length of alignment * rflen - expected nongap RF length (consensus length) * ret_nseq_with_ins_ct - [0..rflen] number of sequences with >= 1 * insert after each position. NULL if unwanted. * ret_nins_ct - [0..rflen] total number of inserted nucleotides (over * all sequences after each position. NULL if unwanted. * * Returns void. Dies with an informative error message upon an error. */ void get_insert_info_from_abc_ct(double **abc_ct, ESL_ALPHABET *abc, char *msa_rf, int64_t msa_alen, int rflen, int **ret_nseq_with_ins_ct, int **ret_nins_ct) { int status; int *nins_ct; int *nseq_with_ins_ct; int nins, nmaxins; int rfpos, apos; /* allocate and initialize */ ESL_ALLOC(nseq_with_ins_ct, sizeof(int) * (rflen+1)); esl_vec_ISet(nseq_with_ins_ct, rflen+1, 0); ESL_ALLOC(nins_ct, sizeof(int) * (rflen+1)); esl_vec_ISet(nins_ct, rflen+1, 0); nmaxins = 0; rfpos = 0; for(apos = 0; apos < msa_alen; apos++) { if(esl_abc_CIsResidue(abc, msa_rf[apos])) { nseq_with_ins_ct[rfpos] = nmaxins; nmaxins = 0; rfpos++; if(rfpos > rflen) esl_fatal("Error in get_insert_info_from_abc_ct(), expected consensus length (%d) is incorrect."); } else { nins = (int) esl_vec_DSum(abc_ct[apos], abc->K); nins_ct[rfpos] += nins; nmaxins = ESL_MAX(nmaxins, nins); } } /* get max_nseq with inserts after the final position */ nseq_with_ins_ct[rfpos] = nmaxins; if(ret_nins_ct != NULL) *ret_nins_ct = nins_ct; else free(nins_ct); if(ret_nseq_with_ins_ct != NULL) *ret_nseq_with_ins_ct = nseq_with_ins_ct; else free(nseq_with_ins_ct); return; ERROR: esl_fatal("Error in get_insert_info_from_abc_ct(), memory allocation error."); return; /* NEVERREACHED */ } /* get_pp_idx * * Given a #=GR PP or #=GC PP_cons character, return the appropriate index * in a pp_ct[] vector. * '0' return 0; * '1' return 1; * '2' return 2; * '3' return 3; * '4' return 4; * '5' return 5; * '6' return 6; * '7' return 7; * '8' return 8; * '9' return 9; * '*' return 10; * gap return 11; * * Anything else (including missing or nonnucleotide) return -1; */ int get_pp_idx(const ESL_ALPHABET *abc, char ppchar) { if(esl_abc_CIsGap(abc, ppchar)) return 11; if(ppchar == '*') return 10; if(ppchar == '9') return 9; if(ppchar == '8') return 8; if(ppchar == '7') return 7; if(ppchar == '6') return 6; if(ppchar == '5') return 5; if(ppchar == '4') return 4; if(ppchar == '3') return 3; if(ppchar == '2') return 2; if(ppchar == '1') return 1; if(ppchar == '0') return 0; return -1; } /* spos_and_epos2span_ct * * Given two arrays, spos_ct[0..apos..alen-1] and epos_ct[0..apos..alen-1], * specifying the number of sequences for which the first and last non-gap * position is apos, calculate the number of sequences that 'span' each RF * position. A sequence spans position rfpos which is actually alignment * position apos, it has at least one nongap nucleotide in a position x <= apos, * and at least one nucleotide in a position y, y >= apos. * * As a special case, if alen == rflen and srfoff_ct != NULL and erfoff_ct != NULL, * then we've read an insert file (with --ifile) which has given us information * that we'll use to update spos_ct and epos_ct. In this case, the inserts * have been removed from the alignment but it is possible that spos_ct and * epos_ct have miscounted some positions (see get_insert_info_from_ifile() * for more info). * * span_ct: [0..rfpos..ps->msa->rflen-1] number of sequences that 'span' each position rfpos * have >= 1 nucleotide at a position apos before rf2a_map[rfpos] and >= 1 nucleotide at * any position apos >= rf2a_map[rfpos], */ int get_span_ct(int *msa_rf2a_map, int64_t alen, int rflen, int nseq, int *spos_ct, int *epos_ct, int *srfoff_ct, int *erfoff_ct, int **ret_span_ct) { int status; int *nseq_start_after_rfpos = NULL; int *nseq_end_before_rfpos = NULL; int *span_ct = NULL; int rfpos; int do_correction; int apos, nxt_apos, prv_apos; ESL_ALLOC(span_ct, sizeof(int) * rflen); ESL_ALLOC(nseq_start_after_rfpos, sizeof(int) * rflen); ESL_ALLOC(nseq_end_before_rfpos, sizeof(int) * rflen); esl_vec_ISet(nseq_start_after_rfpos, rflen, 0); esl_vec_ISet(nseq_end_before_rfpos, rflen, 0); /* check for special case, when we need to update spos_ct and epos_ct */ if(srfoff_ct != NULL && erfoff_ct == NULL) esl_fatal("Internal error, get_span_ct: srfoff_ct != NULL and erfoff_ct == NULL"); if(srfoff_ct == NULL && erfoff_ct != NULL) esl_fatal("Internal error, get_span_ct: srfoff_ct == NULL and erfoff_ct != NULL"); /* determine if we should correct spos_ct and epos_ct using srfoff_ct and erfoff_ct */ do_correction = (alen == rflen && srfoff_ct != NULL) ? TRUE : FALSE; /* NOTE: if alen == rflen spos_ct and epos_ct have length rflen, just like srfoff_ct and erfoff_ct */ /* first count number of seqs that start after each position */ nseq_start_after_rfpos[rflen-1] = 0; /* initialize */ nxt_apos = (int) alen - 1; for(rfpos = rflen-2; rfpos >= 0; rfpos--) { for(apos = nxt_apos; apos > msa_rf2a_map[rfpos]; apos--) { nseq_start_after_rfpos[rfpos] += spos_ct[apos]; if(do_correction) nseq_start_after_rfpos[rfpos] += srfoff_ct[apos]; } nseq_start_after_rfpos[rfpos] += nseq_start_after_rfpos[rfpos+1]; nxt_apos = msa_rf2a_map[rfpos]; } /* count number of seqs that end before each position */ nseq_end_before_rfpos[0] = 0; /* initialize */ prv_apos = 0; for(rfpos = 1; rfpos < rflen; rfpos++) { for(apos = prv_apos; apos < msa_rf2a_map[rfpos]; apos++) { nseq_end_before_rfpos[rfpos] += epos_ct[apos]; if(do_correction) nseq_end_before_rfpos[rfpos] += erfoff_ct[apos]; } nseq_end_before_rfpos[rfpos] += nseq_end_before_rfpos[rfpos-1]; prv_apos = msa_rf2a_map[rfpos]; } /* We now know how many seqs start after each rfpos (a = nseq_start_after_rfpos[rfpos]) and * how many seqs end before each rfpos (b = nseq_end_before_rfpos[rfpos]) * so c = [nseq-(a+b)] seqs span rfpos (b/c they don't start after it AND don't end before it). * * Note: this is really confusing to me, but I've convinced myself it's true, and I think * it is only true because we know each sequence's end position must be >= its start position */ for(rfpos = 0; rfpos < rflen; rfpos++) { span_ct[rfpos] = nseq - (nseq_start_after_rfpos[rfpos] + nseq_end_before_rfpos[rfpos]); /*printf("span_ct[rfpos: %d]: %d after: %d before: %d nseq: %d\n", rfpos, span_ct[rfpos], nseq_start_after_rfpos[rfpos], nseq_end_before_rfpos[rfpos], nseq);*/ } *ret_span_ct = span_ct; free(nseq_start_after_rfpos); free(nseq_end_before_rfpos); return eslOK; ERROR: return eslEMEM; } /* Function: drawfile2sspostscript() * * Purpose: Fill a postscript data structure with >= 1 new page(s), with colors described * in an input 'draw' file, with >= 1 sets of lines of data, each set * is separated by a line with only "//". must be equal to the consensus * ps->rflen. Each line contains a single real number between 0 and 1, * these are converted into 1 of 6 CMYK colors based on their values, using * the same color scheme used for frequency of inserts. * * Return: eslOK on success. */ static int drawfile2sspostscript(const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps, float ***hc_scheme, int hc_scheme_idx, int hc_nbins) { int status; int p, pp; int rfpos, c; int orig_npage = ps->npage; ESL_FILEPARSER *efp; char *s; char *dfile = esl_opt_GetString(go, "--dfile"); float *limits; float value; int l; int bi, within_mask; char *desc = NULL; char *legheader = NULL; /* allocate for limits, but don't fill it yet */ ESL_ALLOC(limits, sizeof(float) * (hc_nbins+1)); if (esl_fileparser_Open(dfile, NULL, &efp) != eslOK) ESL_FAIL(eslFAIL, errbuf, "failed to open %s in draw_file2sspostscript\n", dfile); esl_fileparser_SetCommentChar(efp, '#'); pp = orig_npage - 1; /* Format of dfile: * For each page: * line 1: description of page (max is ps->desc_max_chars*2 chars) * line 2: header for legend (max is ps->legx_max_chars chars) * line 3: limits for color bins, must be 7 tokens, all numbers, each greater than the last * lines 4-N: single tokens, numerical values for each position, N is CLEN-3. * line N+1: single token, only:"//\n" signifying end of page. * * '#' prefixed lines are considered comments and skipped. * * Example: */ rfpos = -1; while (esl_fileparser_NextLine(efp) == eslOK) { if(rfpos == -1) { /* new page, first add a new page */ /* next 3 lines must be a specific format */ /* first line is description */ if(desc != NULL) { free(desc); desc = NULL; } while((status = esl_fileparser_GetTokenOnLine(efp, &s, NULL)) == eslOK) { if((status = esl_strcat(&desc, -1, s, -1)) != eslOK) esl_fatal("Out of memory"); if((status = esl_strcat(&desc, -1, " ", -1)) != eslOK) esl_fatal("Out of memory"); } if(strlen(desc) > (ps->desc_max_chars*2.)) esl_fatal("Error reading --dfile, description length (%d) exceeds max allowed (%d)", strlen(desc), (ps->desc_max_chars*2)); if(esl_fileparser_NextLine(efp) != eslOK) esl_fatal("Error reading --dfile, expected legend header line at line %d\n", efp->linenumber); /* second line is legend header */ if(legheader != NULL) { free(legheader); legheader = NULL; } while((status = esl_fileparser_GetTokenOnLine(efp, &s, NULL)) == eslOK) { if((status = esl_strcat(&legheader, -1, s, -1)) != eslOK) esl_fatal("Out of memory"); if((status = esl_strcat(&legheader, -1, " ", -1)) != eslOK) esl_fatal("Out of memory"); } if(strlen(legheader) > ps->legx_max_chars) esl_fatal("Error reading --dfile, legend header length (%d) exceeds max allowed (%d)", strlen(legheader), ps->legx_max_chars); if(esl_fileparser_NextLine(efp) != eslOK) esl_fatal("Error reading --dfile, expected limits line at line %d\n", efp->linenumber); /* third line is bin limits for the colors, must be 7 numbers, we read them as floats */ for(l = 0; l < hc_nbins+1; l++) { if (esl_fileparser_GetTokenOnLine(efp, &s, NULL) != eslOK) esl_fatal("Error reading --dfile, expected limits line at line %d to have %d limits (numbers) in increasing order, it doesn't", efp->linenumber, hc_nbins+1); limits[l] = atof(s); if(l > 0 && limits[l] < limits[l-1]) esl_fatal("Error reading --dfile, expected limits line at line %d with %d limits (numbers) in increasing order", efp->linenumber, hc_nbins+1); } rfpos++; /* rfpos will now be 0 */ } else if(rfpos == (ps->rflen)) { /* end of page, should be a single token, a "\\" on this line */ if (esl_fileparser_GetTokenOnLine(efp, &s, NULL) != eslOK) esl_fatal("Failed to read a final token at the end of description of page %d on line %d of drawfile %s\n", (pp - orig_npage + 1), efp->linenumber, dfile); if (strcmp(s, "//") != 0) esl_fatal("Failed to read a final \"//\" token (read %s) at the end of description of draw page %d on line %d of drawfile %s\n", s, (pp - orig_npage + 1), efp->linenumber, dfile); rfpos = -1; /* add color legend */ if((status = add_text_to_scheme_colorlegend(ps, ps->sclAA[pp], legheader, ps->legx_max_chars, errbuf)) != eslOK) return status; if((status = add_page_desc_to_sspostscript(ps, ps->npage-1, desc, errbuf)) != eslOK) return status; } else { /* a normal line, should either contain a single float or the \\ marking end of this page */ rfpos++; if(rfpos == 1) { /* add a new page, (we now have limits for legend, from if(rfpos == -1) loop above) */ if((status = add_pages_sspostscript(ps, 1, ALIMODE)) != eslOK) ESL_FAIL(status, errbuf, "memory error adding pages to the postscript object."); for(p = (ps->npage-1); p < ps->npage; p++) { ESL_ALLOC(ps->bcolAAA[p], sizeof(float *) * ps->rflen); ESL_ALLOC(ps->sclAA[p], sizeof(SchemeColorLegend_t) * 1); for(c = 0; c < ps->rflen; c++) { ESL_ALLOC(ps->bcolAAA[p][c], sizeof(float) * NCMYK); /* CMYK colors */ } } pp++; /* if first page, pp == orig_npage now */ ps->sclAA[pp] = create_scheme_colorlegend(hc_scheme_idx, hc_nbins, limits, FALSE, TRUE, TRUE, TRUE); } /* now parse the line, it should have a single number, a numerical value for a position */ if (esl_fileparser_GetTokenOnLine(efp, &s, NULL) != eslOK) esl_fatal("Failed to read value for position %d for page %d on line %d of dfile\n", rfpos, (pp - orig_npage + 1), efp->linenumber); value = atof(s); if(value < limits[0] || value > limits[hc_nbins]) esl_fatal("--dfile value %.4f out of allowed range [%.3f-%.3f] on line %d\n", value, limits[0], limits[hc_nbins], efp->linenumber, dfile); within_mask = (ps->mask != NULL && ps->mask[rfpos-1] == '1') ? TRUE : FALSE; if((status = set_scheme_values(errbuf, ps->bcolAAA[pp][rfpos-1], NCMYK, hc_scheme[hc_scheme_idx], value, ps->sclAA[pp], within_mask, &bi)) != eslOK) return status; } } if(pp == (orig_npage - 1)) { /* no new pages were read, this is an error */ esl_fatal("Failed to read a single page from drawfile %s\n", dfile); } esl_fileparser_Close(efp); free(limits); if(desc != NULL) { free(desc); desc = NULL; } if(legheader != NULL) { free(legheader); legheader = NULL; } return eslOK; ERROR: ESL_FAIL(status, errbuf, "drawfile2sspostscript(): memory allocation error."); return status; /* NEVERREACHED */ } /* Function: expertfile2sspostscript() * * Purpose: Fill a postscript data structure with >= 1 new page(s), with colors described * in an input 'expert draw' file, with >= 1 sets of lines of data, each set * is separated by a line with only "//". must be equal to the consensus * ps->rflen. Each line has at least 4 floats explaining * the CMYK values for the color to use at each position of the SS diagram, * and optionally contains an extra single character which is the nucleotide * to put at that position. * * Return: eslOK on success. */ static int expertfile2sspostscript(const ESL_GETOPTS *go, char *errbuf, SSPostscript_t *ps) { int status; int p, pp; int cpos, c; int orig_npage = ps->npage; ESL_FILEPARSER *efp; char *s; char *efile = esl_opt_GetString(go, "--efile"); if (esl_fileparser_Open(efile, NULL, &efp) != eslOK) ESL_FAIL(eslFAIL, errbuf, "failed to open %s in draw_file2sspostscript\n", efile); esl_fileparser_SetCommentChar(efp, '#'); pp = orig_npage - 1; cpos = 0; while (esl_fileparser_NextLine(efp) == eslOK) { /* example line without nucleotide markup: * 0.000 0.000 0.000 0.500 * * example line with nucleotide markup: * 0.000 0.000 0.000 0.500 A */ cpos++; if(cpos == 1) { /* add a new page */ if((status = add_pages_sspostscript(ps, 1, SIMPLEMASKMODE)) != eslOK) ESL_FAIL(status, errbuf, "memory error adding pages to the postscript object."); for(p = (ps->npage-1); p < ps->npage; p++) { ESL_ALLOC(ps->rAA[p], sizeof(char) * (ps->rflen+1)); ESL_ALLOC(ps->bcolAAA[p], sizeof(float *) * ps->rflen); for(c = 0; c < ps->rflen; c++) { ESL_ALLOC(ps->bcolAAA[p][c], sizeof(float) * NCMYK); /* CMYK colors */ } } pp++; /* if first page, pp == orig_npage now */ } if(cpos == (ps->rflen+1)) { /* should be a single token, a "\\" on this line */ if (esl_fileparser_GetTokenOnLine(efp, &s, NULL) != eslOK) esl_fatal("Failed to read a final token at the end of description of draw page %d on line %d of expertfile %s\n", (pp - orig_npage + 1), efp->linenumber, efile); if (strcmp(s, "//") != 0) esl_fatal("Failed to read a final \"//\" token (read %s) at the end of description of draw page %d on line %d of expertfile %s\n", s, (pp - orig_npage + 1), efp->linenumber, efile); cpos = 0; } else { /* get C value */ if (esl_fileparser_GetTokenOnLine(efp, &s, NULL) != eslOK) esl_fatal("Failed to read C of CMYK value on line %d of expertfile %s\n", efp->linenumber, efile); ps->bcolAAA[pp][(cpos-1)][0] = atof(s); /* get M value */ if (esl_fileparser_GetTokenOnLine(efp, &s, NULL) != eslOK) esl_fatal("Failed to read M of CMYK value on line %d of expertfile %s\n", efp->linenumber, efile); ps->bcolAAA[pp][(cpos-1)][1] = atof(s); /* get Y value */ if (esl_fileparser_GetTokenOnLine(efp, &s, NULL) != eslOK) esl_fatal("Failed to read Y of CMYK value on line %d of expertfile %s\n", efp->linenumber, efile); ps->bcolAAA[pp][(cpos-1)][2] = atof(s); /* get K value */ if (esl_fileparser_GetTokenOnLine(efp, &s, NULL) != eslOK) esl_fatal("Failed to read K of CMYK value on line %d of expertfile %s\n", efp->linenumber, efile); ps->bcolAAA[pp][(cpos-1)][3] = atof(s); /* optionally read a nucleotide value */ if (esl_fileparser_GetTokenOnLine(efp, &s, NULL) == eslOK) { if(((int) strlen(s)) != 1) esl_fatal("Read multi-character string (%s) for consensus nucleotide %d on line %d of expertfile %s\n", s, cpos, efp->linenumber, efile); ps->rAA[pp][(cpos-1)] = s[0]; } else ps->rAA[pp][(cpos-1)] = ' '; } } if(pp == (orig_npage - 1)) { /* no new pages were read, this is an error */ esl_fatal("Failed to read a single page from expertfile %s\n", efile); } esl_fileparser_Close(efp); return eslOK; ERROR: ESL_FAIL(status, errbuf, "expertfile2sspostscript(): memory allocation error."); return status; /* NEVERREACHED */ } /* is_watson_crick_bp(i,j): return TRUE if i,j form a watson crick bp, FALSE if not * is_gu_or_ug_bp(i,j): return TRUE if i,j form a G-U or U-G bp, FALSE if not */ static int is_watson_crick_bp(char i, char j) { switch (toupper(i)) { case 'A': switch (toupper(j)) { case 'U': return TRUE; break; case 'T': return TRUE; break; default: break; } break; case 'C': switch (toupper(j)) { case 'G': return TRUE; break; default: break; } break; case 'G': switch (toupper(j)) { case 'C': return TRUE; break; default: break; } break; case 'U': switch (toupper(j)) { case 'A': return TRUE; break; default: break; } break; case 'T': switch (toupper(j)) { case 'A': return TRUE; break; default: break; } break; default: break; } return FALSE; } static int is_gu_or_ug_bp(char i, char j) { switch (toupper(i)) { case 'G': switch (toupper(j)) { case 'U': return TRUE; break; case 'T': return TRUE; break; default: break; } break; case 'U': switch (toupper(j)) { case 'G': return TRUE; break; default: break; } break; case 'T': switch (toupper(j)) { case 'G': return TRUE; break; default: break; } break; default: break; } return FALSE; } /* Function: get_consensus_seqs_from_abc_ct() * Date: EPN, Wed Apr 7 07:39:57 2010 * * Given an abc_ct array: * [0..apos..alen-1][0..abc->K]: per position count of * each symbol in alphabet over all seqs. * * Determine the consensus sequence for the msa that abc_ct * corresponds to, one nucleotide per nongap RF position, the * most informative IUPAC nucleotide (including ambiguous nucleotides) * that represents >= fraction of the sequences in the msa * that have a nongap at that position. * * Alternatively, if --majrule is enabled, define consensus nucleotide * as the most common nucleotide at each position. Uppercase * if frequency >= 0.5 of nongap nts, else it is lowercase. * * ps - the postscript object * errbuf - informative error message, returned upon failure * abc_ct - count of nucleotides per alignment position (see above) * abc - the alphabet * cthresh - consensus nucleotide must explain >= fraction * of nucleotides in msa (ex: if cthresh = 0.8, and * A=0.6, C=0.01, G=0.25, U=0.14, consensus nucleotide = R (A|G)) * ret_cseq - RETURN: the consensus sequence [0..rflen-1] * * Returns eslOK on success. */ typedef struct nt2sort_s { double ntfreq; /* frequency of this nucleotide */ int ntidx; /* index of this nucleotide in alphabet (ex: 1 for 'C' in eslRNA) */ } nt2sort_t; int compare_by_ntfreq(const void *a_void, const void *b_void) { nt2sort_t *a, *b; a = (nt2sort_t *) a_void; b = (nt2sort_t *) b_void; if (a->ntfreq > b->ntfreq) return -1; else if (a->ntfreq < b->ntfreq) return 1; else return 0; } /* Function: get_consensus_nucleotide() * Date: EPN, Wed Apr 7 07:39:57 2010 * * Given a useme array: * [0..i..abc->K]: TRUE if nucleotide i is used, FALSE if not * Return the consensus nucleotide - the least ambiguous iupac * nucleotide that represents all TRUEs. For ex: [1,0,1,0] --> R * If is TRUE, return 'T' instead of 'U' when appropriate. * * Returns the consensus nucleotide. * * Degeneracies: * R = A|G * Y = C|U * M = A|C * K = G|U * S = C|G * W = A|U * H = A|C|U * B = C|G|U * V = A|C|G * D = A|G|U */ int get_consensus_nucleotide(int *useme, int K) { /* You brute! */ if((! useme[0]) && (! useme[1]) && (! useme[2]) && ( useme[3])) { return 'U'; } /* 0001 */ if((! useme[0]) && (! useme[1]) && ( useme[2]) && (! useme[3])) { return 'G'; } /* 0010 */ if((! useme[0]) && ( useme[1]) && (! useme[2]) && (! useme[3])) { return 'C'; } /* 0100 */ if(( useme[0]) && (! useme[1]) && (! useme[2]) && (! useme[3])) { return 'A'; } /* 1000 */ if(( useme[0]) && ( useme[1]) && ( useme[2]) && ( useme[3])) { return 'N'; } /* 1111 */ if((! useme[0]) && ( useme[1]) && ( useme[2]) && ( useme[3])) { return 'B'; } /* 0111 */ if(( useme[0]) && (! useme[1]) && ( useme[2]) && ( useme[3])) { return 'D'; } /* 1011 */ if(( useme[0]) && ( useme[1]) && ( useme[2]) && (! useme[3])) { return 'V'; } /* 1110 */ if(( useme[0]) && ( useme[1]) && (! useme[2]) && ( useme[3])) { return 'H'; } /* 1101 */ if((! useme[0]) && (! useme[1]) && ( useme[2]) && ( useme[3])) { return 'K'; } /* 0011 */ if((! useme[0]) && ( useme[1]) && ( useme[2]) && (! useme[3])) { return 'S'; } /* 0110 */ if(( useme[0]) && ( useme[1]) && (! useme[2]) && (! useme[3])) { return 'M'; } /* 1100 */ if((! useme[0]) && ( useme[1]) && (! useme[2]) && ( useme[3])) { return 'Y'; } /* 0101 */ if(( useme[0]) && (! useme[1]) && (! useme[2]) && ( useme[3])) { return 'W'; } /* 1001 */ if(( useme[0]) && (! useme[1]) && ( useme[2]) && (! useme[3])) { return 'R'; } /* 1010 */ if((! useme[0]) && (! useme[1]) && (! useme[2]) && (! useme[3])) { return '-'; } /* 0000 */ esl_fatal("coding error in consensus_nucleotide"); return ' '; /* NEVERREACHED */ } int get_consensus_seqs_from_abc_ct(const ESL_GETOPTS *go, SSPostscript_t *ps, char *errbuf, double **abc_ct, ESL_ALPHABET *abc, int64_t msa_alen) { int status; /* the Easel return status */ char *cseq_maj = NULL; /* the consensus sequence string based on majority rule that we're building */ char *cseq_amb = NULL; /* the consensus sequence string including ambiguities that we're building */ int rfpos, apos; /* counter over nongap RF, alignment positions */ float nongap_freq; /* for current position, fraction of nongap nucleotides from abc_ct */ float covered; /* fraction of nongap nucleotides currently covered while * calculating the consensus nucleotide */ int *nt_is_used; /* [0..a..abc->K-1] TRUE if nucleotide a is included for * current consensus nucleotide, FALSE if not */ nt2sort_t *sorted_ntfreq; /* [0..abc->K-1] sorted array of nt2sort structures */ int sorted_idx; /* index in sorted_ntfreq */ int a; /* counter over nucleotides in abc */ float cthresh = esl_opt_GetReal(go, "--cthresh"); float athresh = esl_opt_GetReal(go, "--athresh"); /* allocate and initialize */ ESL_ALLOC(cseq_maj, sizeof(char) * (ps->rflen+1)); ESL_ALLOC(cseq_amb, sizeof(char) * (ps->rflen+1)); cseq_maj[ps->rflen] = '\0'; cseq_amb[ps->rflen] = '\0'; ESL_ALLOC(sorted_ntfreq, sizeof(nt2sort_t) * (abc->K)); ESL_ALLOC(nt_is_used, sizeof(int) * (abc->K)); rfpos = 0; for(apos = 0; apos < msa_alen; apos++) { if(esl_abc_CIsResidue(abc, ps->msa->rf[apos])) { nongap_freq = esl_vec_DSum(abc_ct[apos], abc->K); if(esl_DCompare(nongap_freq, 0., eslSMALLX1) == eslOK) { /* all nucleotides are gaps */ cseq_maj[rfpos] = cseq_amb[rfpos] = '-'; } else { /* at least one sequence has a nongap at rfpos, calculate the consensus nucleotide */ for(a = 0; a < abc->K; a++) { sorted_ntfreq[a].ntfreq = abc_ct[apos][a] / nongap_freq; sorted_ntfreq[a].ntidx = a; } /* quicksort */ qsort(sorted_ntfreq, abc->K, sizeof(nt2sort_t), compare_by_ntfreq); covered = 0.; esl_vec_ISet(nt_is_used, abc->K, FALSE); sorted_idx = 0; /* determine majority rule nucleotide */ cseq_maj[rfpos] = (sorted_ntfreq[sorted_idx].ntfreq >= cthresh) ? toupper(abc->sym[sorted_ntfreq[sorted_idx].ntidx]) : tolower(abc->sym[sorted_ntfreq[sorted_idx].ntidx]); /* determine ambiguous nucleotide that covers > --athresh fraction of seqs */ while(covered < athresh) { nt_is_used[sorted_ntfreq[sorted_idx].ntidx] = TRUE; covered += sorted_ntfreq[sorted_idx].ntfreq; /*printf("RF: %4d SIDX: %d AIDX: %d FREQ: %.3f COVERED: %.3f\n", rfpos, sorted_idx, sorted_ntfreq[sorted_idx].ntidx, sorted_ntfreq[sorted_idx].ntfreq, covered);*/ sorted_idx++; } cseq_amb[rfpos] = get_consensus_nucleotide(nt_is_used, abc->K); } rfpos++; } } /* printf("\n"); */ ps->msa_cseq_maj = cseq_maj; ps->msa_cseq_amb = cseq_amb; free(sorted_ntfreq); free(nt_is_used); return eslOK; ERROR: ESL_FAIL(eslEMEM, errbuf, "Ran out of memory in get_consensus_seqs_from_abc_ct."); return eslEMEM; /* NEVERREACHED */ } /* Function: compare_two_cmyk_colors() * Date: EPN, Fri Apr 23 05:47:54 2010 * * Given four CMYK values defining a color * and four CMYK values defining a color , check if * and are the same color. Return TRUE if they * are and FALSE if not. * * acol_C - first CMYK value for color (Cyan) * acol_M - second CMYK value for color (Magenta) * acol_Y - third CMYK value for color (Yellow) * acol_K - fourth CMYK value for color (Key) * bcol_C - first CMYK value for color (Cyan) * bcol_M - second CMYK value for color (Magenta) * bcol_Y - third CMYK value for color (Yellow) * bcol_K - fourth CMYK value for color (Key) * * Returns TRUE if colors a and b are identical, FALSE if not. */ int compare_two_cmyk_colors(float acol_C, float acol_M, float acol_Y, float acol_K, float bcol_C, float bcol_M, float bcol_Y, float bcol_K) { if(esl_FCompare(acol_C, bcol_C, eslSMALLX1) != eslOK) return FALSE; if(esl_FCompare(acol_M, bcol_M, eslSMALLX1) != eslOK) return FALSE; if(esl_FCompare(acol_Y, bcol_Y, eslSMALLX1) != eslOK) return FALSE; if(esl_FCompare(acol_K, bcol_K, eslSMALLX1) != eslOK) return FALSE; return TRUE; } /* Function: define_outline_procedures() * Date: EPN, Sun May 2 10:36:32 2010 * * Given an open output postscript file, define * the three procedures for drawing outlines of * cells. * * Returns void. */ void define_outline_procedure(FILE *fp) { fprintf(fp, "\n/%s %% stack: x y cellsize linewidth (empty)\n", OUTLINE_PROCEDURE); fprintf(fp, "{\n");; fprintf(fp, " 0. 0. 0. 1. setcmykcolor\n");/* set linewidth as top value on stack */ fprintf(fp, " setlinewidth\n"); /* set linewidth as top value on stack */ fprintf(fp, " /cellsize exch def\n"); /* push /cellsize onto stack, invert top 2 els, and define cellsize */ fprintf(fp, " newpath moveto\n"); /* move to x, y, which are now on top of stack */ fprintf(fp, " currentlinewidth 2. div currentlinewidth 2. div rmoveto\n"); fprintf(fp, " 0 cellsize currentlinewidth sub rlineto\n"); fprintf(fp, " cellsize currentlinewidth sub 0 rlineto\n"); fprintf(fp, " 0 cellsize currentlinewidth sub -1 mul rlineto\n"); fprintf(fp, " closepath stroke\n"); fprintf(fp, "} def\n\n"); /* Old definitions, kept here for reference, note these only work with OUTLINE_LINEWIDTH of 1.0 */ /* //printing basic box outline fprintf(fp, "\n/%s %% stack: x y => ---\n", OUTLINE_MAX_PROCEDURE); fprintf(fp, "{ %.2f setlinewidth\n", OUTLINE_LINEWIDTH_MAX); fprintf(fp, " newpath moveto\n"); fprintf(fp, " %.2f %.2f rmoveto\n", OUTLINE_LINEWIDTH_MAX / 2., OUTLINE_LINEWIDTH_MAX / 2.); fprintf(fp, " 0 %.2f rlineto %.2f 0 rlineto 0 %.2f rlineto\n", CELLSIZE - OUTLINE_LINEWIDTH_MAX, CELLSIZE - OUTLINE_LINEWIDTH_MAX, -1 * (CELLSIZE - OUTLINE_LINEWIDTH_MAX)); fprintf(fp, " closepath gsave stroke grestore \n"); fprintf(fp, "} def\n\n"); //printing a double-line outline fprintf(fp, "\n/%s %% stack: x y => ---\n", OUTLINE_MAX_PROCEDURE); fprintf(fp, "{ %s\n", OUTLINE_MIN_PROCEDURE); fprintf(fp, " %.2f %.2f rmoveto\n", OUTLINE_LINEWIDTH * 2., OUTLINE_LINEWIDTH * 2.); fprintf(fp, " 0 %.2f rlineto %.2f 0 rlineto 0 %.2f rlineto\n", CELLSIZE - (5. * OUTLINE_LINEWIDTH), CELLSIZE - (5. * OUTLINE_LINEWIDTH), -1 * (CELLSIZE - (5. * OUTLINE_LINEWIDTH))); fprintf(fp, " closepath gsave stroke grestore \n"); fprintf(fp, "} def\n\n"); //drawing corners only for the outline fprintf(fp, "\n/outlinemin %% stack: x y => ---\n"); fprintf(fp, "{ newpath moveto\n"); fprintf(fp, " %.2f 0 rmoveto 0 %.2f rlineto closepath gsave stroke\n", OUTLINE_LINEWIDTH/2, CELLSIZE / 4.); fprintf(fp, " grestore 0 %.2f rmoveto 0 %.2f rlineto closepath gsave stroke\n", 3 * CELLSIZE / 4., CELLSIZE / 4. ); fprintf(fp, " grestore %.2f %.2f rmoveto %.2f 0 rlineto closepath gsave stroke\n", -1 * OUTLINE_LINEWIDTH / 2., 3 * OUTLINE_LINEWIDTH / 2., CELLSIZE / 4.); fprintf(fp, " grestore %.2f 0 rmoveto %.2f 0 rlineto closepath gsave stroke\n", 3 * CELLSIZE / 4., CELLSIZE / 4. ); fprintf(fp, " grestore %.2f %.2f rmoveto 0 %.2f rlineto closepath gsave stroke\n", 3 * OUTLINE_LINEWIDTH / 2., -3 * OUTLINE_LINEWIDTH/2, CELLSIZE / 4.); fprintf(fp, " grestore 0 %.2f rmoveto 0 %.2f rlineto closepath gsave stroke\n", -3 * CELLSIZE / 4., CELLSIZE / 4.); fprintf(fp, " grestore %.2f %.2f rmoveto %.2f 0 rlineto closepath gsave stroke\n", -3 * OUTLINE_LINEWIDTH / 2., OUTLINE_LINEWIDTH / 2., CELLSIZE / 4.); fprintf(fp, " grestore %.2f 0 rmoveto %.2f 0 rlineto closepath gsave stroke\n", -3 * CELLSIZE / 4., CELLSIZE / 4.); fprintf(fp, "} def\n"); //drawing corners plus a dash in the middle of each side for the outline fprintf(fp, "/outlinemid %% stack: x y => ---\n"); fprintf(fp, "{ \n"); fprintf(fp, " outlinemin\n"); fprintf(fp, " grestore %.2f %.2f rmoveto 0 %.2f rlineto closepath gsave stroke\n", OUTLINE_LINEWIDTH / 2., CELLSIZE / 4. + OUTLINE_LINEWIDTH / 2., CELLSIZE / 4.); fprintf(fp, " grestore %.2f %.2f rmoveto 0 %.2f rlineto closepath gsave stroke\n", CELLSIZE / 4. + OUTLINE_LINEWIDTH / 2., CELLSIZE / 2. + OUTLINE_LINEWIDTH / 2., CELLSIZE / 4.); fprintf(fp, " grestore %.2f %.2f rmoveto 0 %.2f rlineto closepath gsave stroke\n", CELLSIZE / 2. + OUTLINE_LINEWIDTH / 2., -1 * (CELLSIZE / 2. + OUTLINE_LINEWIDTH / 2.), CELLSIZE / 4.); fprintf(fp, " grestore %.2f %.2f rmoveto 0 %.2f rlineto closepath gsave stroke\n", -1 * (CELLSIZE / 2. + OUTLINE_LINEWIDTH / 2.), -1 * CELLSIZE / 4. + OUTLINE_LINEWIDTH / 2., CELLSIZE / 4.); fprintf(fp, " gsave\n"); fprintf(fp, "} def\n"); */ return; }