/* maf.h - Multiple alignment format. */ #ifndef MAF_H #define MAF_H #ifndef COMMON_H #include "common.h" #endif #ifndef AXT_H #include "axt.h" #endif struct mafFile /* A file full of multiple alignments. */ { struct mafFile *next; int version; /* Required */ char *scoring; /* Optional (may be NULL). Name of scoring scheme. */ struct mafAli *alignments; /* Possibly empty list of alignments. */ struct lineFile *lf; /* Open line file if any. NULL except while parsing. */ }; void mafFileFree(struct mafFile **pObj); /* Free up a maf file including closing file handle if necessary. */ void mafFileFreeList(struct mafFile **pList); /* Free up a list of maf files. */ struct mafAli /* A multiple alignment. */ { struct mafAli *next; double score; /* Score. Meaning depends on mafFile.scoring. 0.0 if no scoring. */ struct mafComp *components; /* List of components of alignment */ int textSize; /* Size of text in each component. */ struct mafRegDef *regDef; /* source of region definitions (r line) */ }; void mafAliFree(struct mafAli **pObj); /* Free up a maf alignment. */ void mafAliFreeList(struct mafAli **pList); /* Free up a list of maf alignmentx. */ /* the set of syntenic relationships that the previous and * following alignments have with the current one */ #define MAF_INVERSE_STATUS 'V' #define MAF_INSERT_STATUS 'I' #define MAF_CONTIG_STATUS 'C' #define MAF_CONTIG_NESTED_STATUS 'c' #define MAF_NEW_STATUS 'N' #define MAF_NEW_NESTED_STATUS 'n' #define MAF_MAYBE_NEW_STATUS 'S' #define MAF_MAYBE_NEW_NESTED_STATUS 's' #define MAF_MISSING_STATUS 'M' #define MAF_TANDEM_STATUS 'T' struct mafComp /* A component of a multiple alignment. */ { struct mafComp *next; char *src; /* Name of sequence source. */ int srcSize; /* Size of sequence source. */ char strand; /* Strand of sequence. Either + or -*/ int start; /* Start within sequence. Zero based. If strand is - is relative to src end. */ int size; /* Size in sequence (does not include dashes). */ char *text; /* The sequence including dashes. */ char *quality; /* The quality data (same length as text, or NULL). */ char leftStatus; /* the syntenic status of the alignment before us vis a vis ourselves */ int leftLen; /* length related information for the previous alignment for the species */ char rightStatus; /* the syntenic status of the alignment after us vis a vis ourselves */ int rightLen; /* length related information for the following alignment for the species */ }; void mafCompFree(struct mafComp **pObj); /* Free up a maf component. */ void mafCompFreeList(struct mafComp **pList); /* Free up a list of maf components. */ char *mafCompGetSrcDb(struct mafComp *mc, char *buf, int bufSize); /* parse the srcDb name from the mafComp src name, return NULL if no srcDb */ char *mafCompGetSrcName(struct mafComp *mc); /* parse the src sequence name from the mafComp src name */ struct mafRegDef /* MAF region definition (r line) */ { char *type; // type of definition, one of constants below (not malloced) int size; // region size char *id; // identifiers }; extern char *mafRegDefTxUpstream; // transcription start size upstream region struct mafRegDef *mafRegDefNew(char *type, int size, char *id); /* construct a new mafRegDef object */ void mafRegDefFree(struct mafRegDef **mrdPtr); /* Free a mafRegDef object */ int mafPlusStart(struct mafComp *comp); /* Return start relative to plus strand of src. */ struct mafFile *mafOpen(char *fileName); /* Open up a .maf file for reading. Read header and * verify. Prepare for subsequent calls to mafNext(). * Prints error message and aborts if there's a problem. */ struct mafFile *mafMayOpen(char *fileName); /* Like mafOpen above, but returns NULL rather than aborting * if file does not exist. */ void mafRewind(struct mafFile *mf); /* Seek to beginning of open maf file */ struct mafAli *mafNext(struct mafFile *mafFile); /* Return next alignment in file or NULL if at end. * This will close the open file handle at end as well. */ struct mafAli *mafNextWithPos(struct mafFile *mf, off_t *retOffset); /* Return next alignment in FILE or NULL if at end. If retOffset is * non-NULL, return start offset of record in file. */ struct mafFile *mafReadAll(char *fileName); /* Read in full maf file */ void mafWriteStart(FILE *f, char *scoring); /* Write maf header and scoring scheme name (may be null) */ void mafWrite(FILE *f, struct mafAli *maf); /* Write next alignment to file. */ void mafWriteDelimiter(FILE *f, struct mafAli *maf, char delimiter); /* Write next alignment to file using delimiter instead of newline. */ void mafWriteEnd(FILE *f); /* Write end tag of maf file. */ void mafWriteAll(struct mafFile *mf, char *fileName); /* Write out full mafFile. */ struct mafComp *mafMayFindComponent(struct mafAli *maf, char *src); /* Find component of given source. Return NULL if not found. */ struct mafComp *mafMayFindComponentDb(struct mafAli *maf, char *db); /* Find component of given database or source. Return NULL if not found. */ struct mafComp *mafFindComponent(struct mafAli *maf, char *src); /* Find component of given source or die trying. */ struct mafComp *mafMayFindCompSpecies(struct mafAli *maf, char *species, char sepChar); /* Find component of given source that starts with species followed by sepChar or '\0' Return NULL if not found. */ struct mafComp *mafFindCompSpecies(struct mafAli *maf, char *species, char sepChar); /* Find component of given source that starts with species followed by sepChar or '\0' or die trying. */ struct mafComp *mafMayFindCompPrefix(struct mafAli *maf, char *pre, char *sep); /* Find component of given source that starts with pre followed by sep. Return NULL if not found. */ struct mafComp *mafFindCompPrefix(struct mafAli *maf, char *pre, char *sep); /* Find component of given source that starts with pre followed by sep or die trying. */ boolean mafMayFindAllComponents(struct mafAli *maf, struct hash *cHash); /* Check to see if all components in hash are in maf block. Return FALSE if not found. */ struct mafComp *mafMayFindComponentInHash(struct mafAli *maf, struct hash *cHash); /* Find arbitrary component of given source that matches any string in the cHash. Return NULL if not found. */ struct mafComp *mafMayFindSpeciesInHash(struct mafAli *maf, struct hash *cHash, char sepChar); /* Find arbitrary component of given who's source prefix (ended by sep) matches matches any string in the cHash. Return NULL if not found. */ void mafMoveComponentToTop(struct mafAli *maf, char *componentSource); /* Move given component to head of component list. */ struct mafAli *mafFromAxt(struct axt *pAxt, int tSize, char *tPrefix, int qSize, char *qPrefix); /* Make up a maf file from axt. Slower than mafFromAxtTemp, * but the axt and maf are independent afterwards. */ void mafFromAxtTemp(struct axt *axt, int tSize, int qSize, struct mafAli *temp); /* Make a maf out of axt, parasiting on the memory in axt. * Do *not* mafFree this temp. The memory it has in pointers * is still owned by the axt. Furthermore the next call to * this function will invalidate the previous temp value. * It's sort of a kludge, but quick to run and easy to implement. */ struct mafAli *mafSubset(struct mafAli *maf, char *componentSource, int newStart, int newEnd); /* see mafSubsetE below (called with getInitialDases = FALSE */ struct mafAli *mafSubsetE(struct mafAli *maf, char *componentSource, int newStart, int newEnd, bool getInitialDashes); /* Extract subset of maf that intersects a given range * in a component sequence. The newStart and newEnd * are given in the forward strand coordinates of the * component sequence. The componentSource is typically * something like 'mm3.chr1'. This will return NULL * if maf does not intersect range. The score field * in the returned maf will not be filled in (since * we don't know which scoring scheme to use). * If getInitialDashes is TRUE then the initial -'s * in the reference sequence are *not* removed*/ boolean mafNeedSubset(struct mafAli *maf, char *componentSource, int newStart, int newEnd); /* Return TRUE if maf only partially fits between newStart/newEnd * in given component. */ double mafScoreMultiz(struct mafAli *maf); /* Return score of a maf (calculated rather than what is * stored in the structure. */ double mafScoreRangeMultiz(struct mafAli *maf, int start, int size); /* Return score of a subset of an alignment. Parameters are: * maf - the alignment * start - the (zero based) offset to start calculating score * size - the size of the subset * The following relationship should hold: * scoreRange(maf,start,size) = * scoreRange(maf,0,start+size) - scoreRange(maf,0,start) */ void mafScoreUseSimple(); /* use a simple scoring system useful for finding mismatches */ void mafScoreUseTraditional(); /* use the tradition HOX scoring system */ double mafScoreMultizMaxCol(int species); /* Return maximum possible score for a column. */ void mafColMinMaxScore(struct mafAli *maf, double *retMin, double *retMax); /* Get min/max maf scores for a column. */ void mafFlipStrand(struct mafAli *maf); /* Reverse complement maf. */ void mafSrcDb(char *name, char *retDb, int retDbSize); /* Parse out just database part of name (up to but not including * first dot). If dot found, return entire name */ boolean mafColumnEmpty(struct mafAli *maf, int col); /* Return TRUE if the column is all '-' or '.' */ void mafStripEmptyColumns(struct mafAli *maf); /* Remove columns that are all '-' or '.' from maf. */ boolean isContigOrTandem(char status); /* is status MAF_CONTIG_STATUS or MAF_TANDEM_STATUS */ struct mafComp *mafCompClone(struct mafComp *srcComp); /* clone a mafComp */ struct mafAli *mafAliClone(struct mafAli *srcAli); /* clone a mafAli */ #endif /* MAF_H */