987241ea99c99b93aea51bb63bdf579f927e9d2b kent Wed Oct 7 13:46:09 2015 -0700 Fixing copyright on some old essentially public domain files. diff --git src/inc/gff.h src/inc/gff.h index 03b035d..85c552f 100644 --- src/inc/gff.h +++ src/inc/gff.h @@ -1,145 +1,144 @@ -/***************************************************************************** - * Copyright (C) 2000 Jim Kent. This source code may be freely used * - * for personal, academic, and non-profit purposes. Commercial use * - * permitted only by explicit agreement with Jim Kent (jim_kent@pacbell.net) * - *****************************************************************************/ -/* gff.h Parse a GFF or GTF file. */ +/* gff.h Parse a GFF or GTF file. + * + * This file is copyright 2000 Jim Kent, but license is hereby + * granted for all use - public, private or commercial. */ + #ifndef GFF_H #define GFF_H struct gffLine /* A parsed line in a GFF file. */ { struct gffLine *next; /* Next line in file */ char *seq; /* Name of sequence. */ char *source; /* Program that made this line. Not allocated here. */ char *feature; /* Type field. (Intron, CDS, etc). Not allocated here. */ int start; /* Start of feature in sequence. Starts with 0, not 1 */ int end; /* End of feature in sequence. End is not included. */ double score; /* Score. */ char strand; /* Strand of sequence feature is on. + or - or .*/ char frame; /* Frame feature is in. 1, 2, 3, or . */ char *group; /* Group line is in. Not allocated here. Corresponds to transcript_id in GTF */ char *geneId; /* gene_id in GTF, NULL in GFF. Not allocated here. */ char *exonId; /* exon_id in GTF, NULL in GFF. Not allocated here. */ int exonNumber; /* O in GFF or if missing in GTF. Otherwise exon number. */ char *intronId; /* intron_id in GTF, NULL in GFF. Not allocated here. */ char *intronStatus; /* intron status. Not allocated here. */ char *proteinId; /* protein_id in GTF, NULL in GFF. Not allocated here. */ char *geneName; /* gene_name or NULL in GTF, NULL in GFF. Not allocated here. */ char *transcriptName; /* transcript_name or NULL in GTF, NULL in GFF. Not allocated here. */ char *geneVersion; /* gene_version or NULL or NULL in GTF, NULL in GFF. Not allocated here. */ char *transcriptVersion; /* transcript_version or NULL or NULL in GTF, NULL in GFF. Not allocated here. */ char *proteinVersion; /* protein_version or NULL or NULL in GTF, NULL in GFF. Not allocated here. */ }; struct gffGroup /* A group of lines in a GFF file (all that share the same group field). */ { struct gffGroup *next; /* Next group in file. */ char *name; /* Name of group. Not allocated here. */ char *seq; /* Name of sequence. Not allocated here. */ char *source; /* Name of source program. Not allocated here. */ /* The next three fields are only valid after call to gffGroupLines() */ int start; /* Start of feature in sequence. Starts with 0, not 1 */ int end; /* End of feature in sequence. End is not included. */ char strand; /* Strand of sequence. */ struct gffLine *lineList; /* List of lines in group. */ }; struct gffSource /* A list of sources. */ { struct gffSource *next; /* Next in list. */ char *name; /* Name, not allocated here. */ unsigned int id; /* Database ID (or just 0) */ }; struct gffFeature /* A list of types in GFF file. */ { struct gffFeature *next; /* Next in list. */ char *name; /* Name, not allocated here. */ int count; /* Number of times feature is seen */ }; struct gffSeqName /* A list of sequence. */ { struct gffSeqName *next; /* Next in list. */ char *name; /* Name, not allocated here. */ }; struct gffGeneId /* A list of genes. */ { struct gffGeneId *next; /* Next in list. */ char *name; /* Name, not allocated here. */ }; struct gffFile /* This keeps information on a fully parsed GFF file. */ { struct gffFile *next; char *fileName; /* Name of file (allocated here) */ struct hash *seqHash; /* A name only hash of the sequence. */ struct hash *sourceHash; /* A name only hash of gff sources. */ struct hash *featureHash; /* A name only hash of gff types. */ struct hash *groupHash; /* Associates group names and gffGroups. */ struct hash *geneIdHash; /* Hash of all geneIds. */ struct hash *strPool; /* hash used to allocate strings */ struct gffLine *lineList; /* List of lines - lines may be in groupList instead. */ struct gffSeqName *seqList; /* List of sequences in file. */ struct gffSource *sourceList; /* List of all sources in file. */ struct gffFeature *featureList; /* List of all types in file. */ struct gffGroup *groupList; /* A list of groups. */ struct gffGeneId *geneIdList; /* List of all gene ID's. */ bool isGtf; /* Is this a GTF file? */ bool typeKnown; /* Is 'isGtf' known? */ }; void gffGroupFree(struct gffGroup **pGroup); /* Free up a gffGroup including lineList. */ void gffGroupFreeList(struct gffGroup **pList); /* Free up a list of gffGroups. */ void gffGroupLines(struct gffFile *gff); /* Group lines of gff file together, in process mofing * gff->lineList to gffGroup->lineList. */ struct gffFile *gffRead(char *fileName); /* Create a gffFile structure from a GFF file. */ struct gffFile *gffFileNew(char *fileName); /* Create a new gffFile structure. */ void gffFileAdd(struct gffFile *gff, char *fileName, int baseOffset); /* Add file to gffFile. */ void gffFileAddRow(struct gffFile *gff, int baseOffset, char *words[], int wordCount, char *fileName, int lineIx); /* Process one row of GFF file (a non-comment line parsed by tabs normally). */ void gffFileFree(struct gffFile **pGff); /* Free up a gff file. */ int gffLineCmp(const void *va, const void *vb); /* Compare two gffLines (for use in slSort, etc.) . */ void gffOutput(struct gffLine *el, FILE *f, char sep, char lastSep); /* Print out GTF. Separate fields with sep. Follow last field with lastSep. */ boolean gffHasGtfGroup(char *line); /* Return TRUE if line has a GTF group field */ #define gffTabOut(el,f) gffOutput(el,f,'\t','\n'); /* Print out GTF as a line in a tab-separated file. */ #define gffCommaOut(el,f) gffOutput(el,f,',',','); /* Print out GTF as a comma separated list including final comma. */ #endif /* GFF_H */