/* Multiple sequence alignments */ #ifndef eslMSA_INCLUDED #define eslMSA_INCLUDED #include "esl_config.h" #include #include "esl_alphabet.h" // digital alphabets #include "esl_bitfield.h" // large bit fields (esl_msa_MarkFragments() #include "esl_keyhash.h" // string hashes, for mapping uniq seq names #include "esl_random.h" #include "esl_randomseq.h" #include "esl_ssi.h" // indexes of large flatfiles on disk #ifdef __cplusplus // magic to make C++ compilers happy extern "C" { #endif /* The following constants define the Pfam/Rfam cutoff set we propagate * from Stockholm format msa's into HMMER and Infernal models. */ /*::cexcerpt::msa_cutoffs::begin::*/ #define eslMSA_TC1 0 #define eslMSA_TC2 1 #define eslMSA_GA1 2 #define eslMSA_GA2 3 #define eslMSA_NC1 4 #define eslMSA_NC2 5 #define eslMSA_NCUTS 6 /*::cexcerpt::msa_cutoffs::end::*/ /* Object: ESL_MSA * * A multiple sequence alignment. */ typedef struct { /* Mandatory information associated with the alignment. * (The important stuff.) */ /*::cexcerpt::msa_mandatory::begin::*/ char **aseq; /* alignment itself, [0..nseq-1][0..alen-1], \0-terminated */ char **sqname; /* sequence names [0..nseq-1][], \0-terminated */ double *wgt; /* sequence weights [0..nseq-1], default 1.0 */ int64_t alen; /* length of alignment (columns); or (if growable) -1 */ int nseq; /* number of seqs in alignment; or (if growable) blocksize */ int flags; /* flags for what info has been set */ /*::cexcerpt::msa_mandatory::end::*/ /* w/ digital alphabets, we store pre-digitized data in * ax[][], instead of the text info in aseq[][]. */ ESL_ALPHABET *abc; /* reference ptr to alphabet */ ESL_DSQ **ax; /* digitized aseqs [0..nseq-1][1..alen] */ /* Optional information that we understand, and that we might have. * (The occasionally useful stuff.) */ /*::cexcerpt::msa_optional::begin::*/ char *name; /* name of alignment, or NULL */ char *desc; /* description of alignment, or NULL */ char *acc; /* accession of alignment, or NULL */ char *au; /* "author" information, or NULL */ char *ss_cons; /* consensus sec structure, or NULL; [0..alen-1], even in digital mode */ char *sa_cons; /* consensus surface access, or NULL; [0..alen-1], even in digital mode */ char *pp_cons; /* consensus posterior prob, or NULL; [0..alen-1], even in digital mode */ char *rf; /* reference coord system, or NULL; [0..alen-1], even in digital mode */ char *mm; /* model mask, or NULL; [0..alen-1], even in digital mode */ char **sqacc; /* accession numbers for sequences i */ char **sqdesc; /* description lines for sequences i */ char **ss; /* per-seq secondary structures, or NULL (string, \0-term) */ char **sa; /* per-seq surface accessibilities, or NULL (string, \0-term) */ char **pp; /* posterior prob per residue, or NULL. (string, \0-term) */ float cutoff[eslMSA_NCUTS]; /* NC/TC/GA cutoffs propagated to Pfam/Rfam */ int cutset[eslMSA_NCUTS]; /* TRUE if a cutoff is set; else FALSE */ /*::cexcerpt::msa_optional::end::*/ /* Info needed for maintenance of the data structure * (internal stuff.) */ int sqalloc; /* # seqs currently allocated for */ int64_t *sqlen; /* individual seq lengths during parsing */ int64_t *sslen; /* individual ss lengths during parsing */ int64_t *salen; /* individual sa lengths during parsing */ int64_t *pplen; /* individual pp lengths during parsing */ int lastidx; /* last index we saw; use for guessing next */ /* Optional information, especially Stockholm markup. * (The stuff we don't understand, but we can regurgitate.) * * That is, we know what type of information it is, but it's * either (interpreted as) free-text comment, or it's Stockholm * markup with unfamiliar tags. */ char **comment; /* free text comments, or NULL */ int ncomment; /* number of comment lines */ int alloc_ncomment; /* number of comment lines alloc'ed */ char **gf_tag; /* markup tags for unparsed #=GF lines */ char **gf; /* annotations for unparsed #=GF lines */ int ngf; /* number of unparsed #=GF lines */ int alloc_ngf; /* number of gf lines alloc'ed */ char **gs_tag; /* markup tags for unparsed #=GS lines */ char ***gs; /* [0..ngs-1][0..nseq-1][free text] markup */ int ngs; /* number of #=GS tag types */ char **gc_tag; /* markup tags for unparsed #=GC lines */ char **gc; /* [0..ngc-1][0..alen-1] markup */ int ngc; /* number of #=GC tag types */ char **gr_tag; /* markup tags for unparsed #=GR lines */ char ***gr; /* [0..ngr-1][0..nseq-1][0..alen-1] markup */ int ngr; /* number of #=GR tag types */ /* Keyhashing significantly speeds up parsing of large alignments. */ ESL_KEYHASH *index; /* name ->seqidx hash table */ ESL_KEYHASH *gs_idx; /* hash of #=GS tag types */ ESL_KEYHASH *gc_idx; /* hash of #=GC tag types */ ESL_KEYHASH *gr_idx; /* hash of #=GR tag types */ off_t offset; /* disk offset to start of 1st line of this MSA's record */ } ESL_MSA; /* Flags for msa->flags */ #define eslMSA_HASWGTS (1 << 0) /* 1 if wgts were set, 0 if default 1.0's */ #define eslMSA_DIGITAL (1 << 1) /* if ax[][] is used instead of aseq[][] */ /* Declarations of the API */ /* 1. The ESL_MSA object */ extern ESL_MSA *esl_msa_Create(int nseq, int64_t alen); extern int esl_msa_Expand(ESL_MSA *msa); extern int esl_msa_Copy(const ESL_MSA *msa, ESL_MSA *new_msa); extern ESL_MSA *esl_msa_Clone(const ESL_MSA *msa); extern void esl_msa_Destroy(ESL_MSA *msa); /* 2. Digital mode MSA's */ extern int esl_msa_GuessAlphabet(const ESL_MSA *msa, int *ret_type); extern ESL_MSA *esl_msa_CreateDigital(const ESL_ALPHABET *abc, int nseq, int64_t alen); extern int esl_msa_Digitize(const ESL_ALPHABET *abc, ESL_MSA *msa, char *errmsg); extern int esl_msa_Textize(ESL_MSA *msa); extern int esl_msa_ConvertDegen2X(ESL_MSA *msa); /* 3. Setting or checking data fields in an ESL_MSA */ extern int esl_msa_SetName (ESL_MSA *msa, const char *s, esl_pos_t n); extern int esl_msa_SetDesc (ESL_MSA *msa, const char *s, esl_pos_t n); extern int esl_msa_SetAccession (ESL_MSA *msa, const char *s, esl_pos_t n); extern int esl_msa_SetAuthor (ESL_MSA *msa, const char *s, esl_pos_t n); extern int esl_msa_SetSeqName (ESL_MSA *msa, int idx, const char *s, esl_pos_t n); extern int esl_msa_SetSeqAccession (ESL_MSA *msa, int idx, const char *s, esl_pos_t n); extern int esl_msa_SetSeqDescription(ESL_MSA *msa, int idx, const char *s, esl_pos_t n); extern int esl_msa_SetDefaultWeights(ESL_MSA *msa); extern int esl_msa_FormatName (ESL_MSA *msa, const char *name, ...); extern int esl_msa_FormatDesc (ESL_MSA *msa, const char *desc, ...); extern int esl_msa_FormatAccession (ESL_MSA *msa, const char *acc, ...); extern int esl_msa_FormatAuthor (ESL_MSA *msa, const char *author, ...); extern int esl_msa_FormatSeqName (ESL_MSA *msa, int idx, const char *name, ...); extern int esl_msa_FormatSeqAccession (ESL_MSA *msa, int idx, const char *acc, ...); extern int esl_msa_FormatSeqDescription(ESL_MSA *msa, int idx, const char *desc, ...); extern int esl_msa_AddComment(ESL_MSA *msa, char *p, esl_pos_t n); extern int esl_msa_AddGF (ESL_MSA *msa, char *tag, esl_pos_t taglen, char *value, esl_pos_t vlen); extern int esl_msa_AddGS (ESL_MSA *msa, char *tag, esl_pos_t taglen, int sqidx, char *value, esl_pos_t vlen); extern int esl_msa_AppendGC (ESL_MSA *msa, char *tag, char *value); extern int esl_msa_AppendGR (ESL_MSA *msa, char *tag, int sqidx, char *value); extern int esl_msa_CheckUniqueNames(const ESL_MSA *msa); /* 4. Miscellaneous functions for manipulating MSAs */ extern int esl_msa_ReasonableRF(ESL_MSA *msa, double symfrac, int useconsseq, char *rfline); extern int esl_msa_MarkFragments (const ESL_MSA *msa, float fragthresh, ESL_BITFIELD **ret_fragassign); extern int esl_msa_MarkFragments_old(ESL_MSA *msa, double fragthresh); extern int esl_msa_SequenceSubset(const ESL_MSA *msa, const int *useme, ESL_MSA **ret_new); extern int esl_msa_ColumnSubset (ESL_MSA *msa, char *errbuf, const int *useme); extern int esl_msa_MinimGaps (ESL_MSA *msa, char *errbuf, const char *gaps, int consider_rf); extern int esl_msa_MinimGapsText(ESL_MSA *msa, char *errbuf, const char *gaps, int consider_rf, int fix_bps); extern int esl_msa_NoGaps (ESL_MSA *msa, char *errbuf, const char *gaps); extern int esl_msa_NoGapsText (ESL_MSA *msa, char *errbuf, const char *gaps, int fix_bps); extern int esl_msa_SymConvert(ESL_MSA *msa, const char *oldsyms, const char *newsyms); extern int esl_msa_Checksum(const ESL_MSA *msa, uint32_t *ret_checksum); extern int esl_msa_RemoveBrokenBasepairsFromSS(char *ss, char *errbuf, int len, const int *useme); extern int esl_msa_RemoveBrokenBasepairs(ESL_MSA *msa, char *errbuf, const int *useme); extern int esl_msa_ReverseComplement(ESL_MSA *msa); extern int esl_msa_Hash(ESL_MSA *msa); extern int esl_msa_FlushLeftInserts(ESL_MSA *msa); /* 5. Debugging, testing, development */ extern int esl_msa_Validate(const ESL_MSA *msa, char *errmsg); extern ESL_MSA *esl_msa_CreateFromString(const char *s, int fmt); extern int esl_msa_Compare (ESL_MSA *a1, ESL_MSA *a2); extern int esl_msa_CompareMandatory(ESL_MSA *a1, ESL_MSA *a2); extern int esl_msa_CompareOptional (ESL_MSA *a1, ESL_MSA *a2); extern int esl_msa_Sample(ESL_RANDOMNESS *rng, ESL_ALPHABET *abc, int max_nseq, int max_alen, ESL_MSA **ret_msa); #ifdef __cplusplus // magic to make C++ compilers happy } #endif #endif /*eslMSA_INCLUDED*/