e70152e44cc66cc599ff6b699eb8adc07f3e656a kent Sat May 24 21:09:34 2014 -0700 Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment. diff --git src/hg/inc/ggMrnaAli.h src/hg/inc/ggMrnaAli.h index 79f5cd0..877bddf 100644 --- src/hg/inc/ggMrnaAli.h +++ src/hg/inc/ggMrnaAli.h @@ -1,185 +1,188 @@ /* ggMrnaAli.h was originally generated by the autoSql program, which also * generated ggMrnaAli.c and ggMrnaAli.sql. This header links the database and * the RAM representation of objects. */ +/* Copyright (C) 2013 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + #ifndef GGMRNAALI_H #define GGMRNAALI_H #ifndef JKSQL_H #include "jksql.h" #endif #ifndef PSL_H #include "psl.h" #endif #ifndef DNASEQ_H #include "dnaseq.h" #endif struct ggMrnaBlock /* A single block of an mRNA alignment. */ { struct ggMrnaBlock *next; /* Next in singly linked list. */ int qStart; /* Start of block in query */ int qEnd; /* End of block in query */ int tStart; /* Start of block in target */ int tEnd; /* End of block in target */ }; void ggMrnaBlockStaticLoad(char **row, struct ggMrnaBlock *ret); /* Load a row from ggMrnaBlock table into ret. The contents of ret will * be replaced at the next call to this function. */ struct ggMrnaBlock *ggMrnaBlockLoad(char **row); /* Load a ggMrnaBlock from row fetched with select * from ggMrnaBlock * from database. Dispose of this with ggMrnaBlockFree(). */ struct ggMrnaBlock *ggMrnaBlockLoadAll(char *fileName); /* Load all ggMrnaBlock from a tab-separated file. * Dispose of this with ggMrnaBlockFreeList(). */ struct ggMrnaBlock *ggMrnaBlockLoadByQuery(struct sqlConnection *conn, char *query); /* Load all ggMrnaBlock from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with ggMrnaBlockFreeList(). */ void ggMrnaBlockSaveToDb(struct sqlConnection *conn, struct ggMrnaBlock *el, char *tableName, int updateSize); /* Save ggMrnaBlock as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */ struct ggMrnaBlock *ggMrnaBlockCommaIn(char **pS, struct ggMrnaBlock *ret); /* Create a ggMrnaBlock out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new ggMrnaBlock */ void ggMrnaBlockFree(struct ggMrnaBlock **pEl); /* Free a single dynamically allocated ggMrnaBlock such as created * with ggMrnaBlockLoad(). */ void ggMrnaBlockFreeList(struct ggMrnaBlock **pList); /* Free a list of dynamically allocated ggMrnaBlock's */ void ggMrnaBlockOutput(struct ggMrnaBlock *el, FILE *f, char sep, char lastSep); /* Print out ggMrnaBlock. Separate fields with sep. Follow last field with lastSep. */ #define ggMrnaBlockTabOut(el,f) ggMrnaBlockOutput(el,f,'\t','\n'); /* Print out ggMrnaBlock as a line in a tab-separated file. */ #define ggMrnaBlockCommaOut(el,f) ggMrnaBlockOutput(el,f,',',','); /* Print out ggMrnaBlock as a comma separated list including final comma. */ struct ggMrnaAli /* An mRNA alignment, little richer data format than psl */ { struct ggMrnaAli *next; /* Next in singly linked list. */ char *tName; /* target that this alignment it to */ int tStart; /* start in target sequence */ int tEnd; /* end in target sequence */ char strand[4]; /* + or - depending on which strand alignment is to */ char *qName; /* name (accession) of mRNA */ int qStart; /* start of alignment in query */ int qEnd; /* end of alignment in query */ unsigned baseCount; /* number of bases in query */ short orientation; /* 1 or -1 orientation query appears to be in given biological evidence (i.e. splice site) 0 indicates no evidence. This could disagree with strand if est submitted rc'd for example */ int hasIntrons; /* TRUE if intron present, FALSE otherwise */ short milliScore; /* Score 0-1000 */ short blockCount; /* Number of blocks. */ struct ggMrnaBlock *blocks; /* Dynamically allocated array. */ char *sourceType; /* Not allocated here. Typically "refSeq", "mrna" etc. */ }; struct ggMrnaAli *ggMrnaAliLoad(char **row); /* Load a ggMrnaAli from row fetched with select * from ggMrnaAli * from database. Dispose of this with ggMrnaAliFree(). */ struct ggMrnaAli *ggMrnaAliLoadAll(char *fileName); /* Load all ggMrnaAli from a tab-separated file. * Dispose of this with ggMrnaAliFreeList(). */ struct ggMrnaAli *ggMrnaAliLoadByQuery(struct sqlConnection *conn, char *query); /* Load all ggMrnaAli from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with ggMrnaAliFreeList(). */ void ggMrnaAliSaveToDb(struct sqlConnection *conn, struct ggMrnaAli *el, char *tableName, int updateSize); /* Save ggMrnaAli as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */ struct ggMrnaAli *ggMrnaAliCommaIn(char **pS, struct ggMrnaAli *ret); /* Create a ggMrnaAli out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new ggMrnaAli */ void ggMrnaAliFree(struct ggMrnaAli **pEl); /* Free a single dynamically allocated ggMrnaAli such as created * with ggMrnaAliLoad(). */ void ggMrnaAliFreeList(struct ggMrnaAli **pList); /* Free a list of dynamically allocated ggMrnaAli's */ void ggMrnaAliOutput(struct ggMrnaAli *el, FILE *f, char sep, char lastSep); /* Print out ggMrnaAli. Separate fields with sep. Follow last field with lastSep. */ #define ggMrnaAliTabOut(el,f) ggMrnaAliOutput(el,f,'\t','\n'); /* Print out ggMrnaAli as a line in a tab-separated file. */ #define ggMrnaAliCommaOut(el,f) ggMrnaAliOutput(el,f,',',','); /* Print out ggMrnaAli as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ struct maRef /* Holds a reference to a ma */ { struct maRef *next; /* Next in list. */ struct ggMrnaAli *ma; /* Cdna alignment info. */ }; struct ggMrnaInput /* This holds the input for the core clustering algorithm. */ { char *tName; /* name of target sequence, i.e. chrom */ unsigned int tStart, tEnd; /* coordinates that tSeq cooresponds to */ char strand[3]; /* + or -, should always be plus for chromsome */ struct dnaSeq *genoSeq; /* target sequences. */ struct ggMrnaAli *maList; /* List of alignments. */ }; struct ggMrnaAli *pslToGgMrnaAli(struct psl *psl, char *chrom, unsigned int chromStart, unsigned int chromEnd, struct dnaSeq *genoSeq); /* Convert from psl format of alignment to ma format. chrom, chromStart, and chromEnd correspond to where genoseq comes from */ struct ggMrnaAli *pslListToGgMrnaAliList(struct psl *pslList, char *chrom, unsigned int chromStart, unsigned int chromEnd, struct dnaSeq *genoSeq, int maxGap); /* create a ggMrnaAli list from a psl list merging gaps below size maxGap */ boolean ggMrnaAliMergeBlocks(struct ggMrnaAli *ma, int maxGap); /* merge blocks that look to be separated by small amounts of sequencing noise only. */ int cmpGgMrnaAliTargetStart(const void *va, const void *vb); /* Compare two ggMrnaAli based on their strand, tEnd. */ void ggMrnaAliBedOut(struct ggMrnaAli *ma, FILE *f); /* write out the target blocks in simple bed format, one bed per block */ void ggMrnaAliBed12Out(struct ggMrnaAli *ma, FILE *f); /* Write out the target blocks as a linked feature bed format. */ struct ggMrnaInput *ggMrnaInputFromAlignments(struct ggMrnaAli *maList, struct dnaSeq *genoSeq); /* wrap a ggMrnaInput around some alignments */ #endif /* GGMRNAALI_H */