4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/genePredToMafFrames/orgGenes.h src/hg/genePredToMafFrames/orgGenes.h
index 0b6fefc..b13b5a2 100644
--- src/hg/genePredToMafFrames/orgGenes.h
+++ src/hg/genePredToMafFrames/orgGenes.h
@@ -1,118 +1,118 @@
 /* geneBins - objects used to hold gene related data */
 
 /* Copyright (C) 2006 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #ifndef GENEBINS
 #define GENEBINS
 #include "mafFrames.h"
 struct orgGenes;
 struct mafComp;
 struct mafFrames;
 
 struct orgGenes
 /* object with genes for a given organism, indexable by range */
 {
     struct orgGenes *next;   /* next organism */
     char *srcDb;             /* gene source db */
     struct chromBins *bins;  /* map of chrom and ranges to cds exons */
     struct lm *memPool;      /* memory for exons allocated from this pool */
     char *curChrom;          /* cache of current string for allocating pool memory */
     struct gene *genes;      /* linked list of all genes */
 };
 
 struct gene
 /* A gene, one per source gene, however it maybe mapped to multiple
  * target locations */
 {
     struct gene *next;
     char *name;              /* gene name */
     char *chrom;             /* source chrom and strand */
     char strand;
     int chromSize;           /* zero until first MAF hit */
     struct cdsExon *exons;   /* list of CDS exons, in transcription order */
     int numExonFrames;       /* count of associated exonFrames objects */
     struct orgGenes *genes;  /* link back to orgGenes object */
 };
 
 struct cdsExon
 /* one CDS exon */
 {
     struct cdsExon* next; /* link for gene's exons */
     struct gene *gene;    /* gene object */
     int chromStart;       /* source chromosome range (genomic coords) */
     int chromEnd;
     char frame;                 /* frame number */
     int exonNum;                /* exon number, in transcription order */
     int cdsOff;                 /* location within CDS (after splicing) */
     struct exonFrames *frames;  /* frames associated with the exon */
 };
 
 struct exonFrames
 /* object the hold frame information for part of an exon.  A new record
  * is created if there is any discontinuity in the alignment */
 {
     struct exonFrames *next;
     struct cdsExon *exon;     /* associated exon */
     int srcStart;             /* range in src organism MAF coordinates (stand coords) */
     int srcEnd;
     char srcStrand;
     int cdsStart;             /* location within CDS (after splicing)
                                * in direction of transcription */
     int cdsEnd;
     struct mafFrames mf;      /* MAF frames object being created, this is in
                                * the target genomic coordinates */
 };
 
 struct orgGenes *orgGenesNew(char *srcDb, char *genePredFile);
 /* construct a new orgGenes object from the specified file */
 
 void orgGenesFree(struct orgGenes **genesPtr);
 /* free orgGenes object */
 
 struct binElement *orgGenesFind(struct orgGenes *genes, struct mafComp *comp,
                                 int sortDir);
 /* Return list of references to exons overlapping the specified component,
  * sorted into assending order sortDir is 1, descending if it's -1.
  * slFreeList the returned list. */
 
 struct gene* geneClone(struct gene *gene);
 /* clone a gene and it's exons.  Does not clone exonFrames.  Used when
  * spliting a gene mapped to two locations */
 
 struct cdsExon *geneGetExon(struct gene *gene, int exonNum);
 /* get an exon from a gene by it's exon number, or an error */
 
 void geneSortFramesTargetOff(struct gene *gene);
 /* sort the exonFrames in each exon into target transcription order then gene
  * offset. */
 
 void geneSortFramesOffTarget(struct gene *gene);
 /* sort the exonFrames in each exon into gene offset then target transcription
  * order */
 
 void geneCheck(struct gene *gene);
 /* sanity check a gene object */
 
 struct exonFrames *cdsExonAddFrames(struct cdsExon *exon,
                                     int qStart, int qEnd, char qStrand,
                                     char *tName, int tStart, int tEnd,
                                     char frame, char geneStrand, int cdsOff);
 /* allocate a new mafFrames object and link it exon */
 
 struct exonFrames *geneFirstExonFrames(struct gene *gene);
 /* find the first exons frames object, or error if not found */
 
 struct exonFrames *exonFramesNext(struct exonFrames *ef);
 /* get the next exonFrames object, moving on to the next exon with exonFrames
  * after the current one */
 
 void exonFramesDump(FILE *fh, struct exonFrames *ef);
 /* dump contents of an exonFrame for debugging purposes */
 
 void cdsExonDump(FILE *fh, struct cdsExon *exon);
 /* dump contents of a cdsExon for debugging purposes */
 
 void geneDump(FILE *fh, struct gene *gene);
 /* dump contents of a gene for debugging purposes */
 
 #endif