987241ea99c99b93aea51bb63bdf579f927e9d2b
kent
  Wed Oct 7 13:46:09 2015 -0700
Fixing copyright on some old essentially public domain files.

diff --git src/inc/hgGene.h src/inc/hgGene.h
index ba9752b..3031b7d 100644
--- src/inc/hgGene.h
+++ src/inc/hgGene.h
@@ -1,129 +1,128 @@
-/*****************************************************************************
- * 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) *
- *****************************************************************************/
 /* hgGene.h was originally generated by the autoSql program, which also 
  * generated hgGene.c and hgGene.sql.  This header links the database and the RAM 
- * representation of objects. */
+ * representation of objects. 
+ *
+ * This file is copyright 2000 Jim Kent, but license is hereby
+ * granted for all use - public, private or commercial. */
+
 
 struct geneFinder
 /* A gene finding program. */
     {
     struct geneFinder *next;  /* Next in singly linked list. */
     unsigned id;	/* Unique ID */
     char *name;	/* Name of gene finder */
     };
 
 void geneFinderStaticLoad(char **row, struct geneFinder *ret);
 /* Load a row from geneFinder table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 
 struct geneFinder *geneFinderLoad(char **row);
 /* Load a geneFinder from row fetched with select * from geneFinder
  * from database.  Dispose of this with geneFinderFree(). */
 
 struct geneFinder *geneFinderCommaIn(char **pS);
 /* Create a geneFinder out of a comma separated string. */
 
 void geneFinderFree(struct geneFinder **pEl);
 /* Free a single dynamically allocated geneFinder such as created
  * with geneFinderLoad(). */
 
 void geneFinderFreeList(struct geneFinder **pList);
 /* Free a list of dynamically allocated geneFinder's */
 
 void geneFinderOutput(struct geneFinder *el, FILE *f, char sep, char lastSep);
 /* Print out geneFinder.  Separate fields with sep. Follow last field with lastSep. */
 
 #define geneFinderTabOut(el,f) geneFinderOutput(el,f,'\t','\n');
 /* Print out geneFinder as a line in a tab-separated file. */
 
 #define geneFinderCommaOut(el,f) geneFinderOutput(el,f,',',',');
 /* Print out geneFinder as a comma separated list including final comma. */
 
 struct hgGene
 /* A gene prediction */
     {
     struct hgGene *next;  /* Next in singly linked list. */
     unsigned id;	/* Unique ID */
     char *name;	/* Name of gene */
     unsigned geneFinder;	/* Program that made prediction */
     unsigned startBac;	/* Bac this starts in */
     unsigned startPos;	/* Position within bac where starts */
     unsigned endBac;	/* Bac this ends in */
     unsigned endPos;	/* Position withing bac where ends */
     signed char orientation;	/* Orientation relative to start bac */
     unsigned transcriptCount;	/* Number of transcripts */
     unsigned *transcripts;	/* Array of transcripts */
     };
 
 struct hgGene *hgGeneLoad(char **row);
 /* Load a hgGene from row fetched with select * from hgGene
  * from database.  Dispose of this with hgGeneFree(). */
 
 struct hgGene *hgGeneCommaIn(char **pS);
 /* Create a hgGene out of a comma separated string. */
 
 void hgGeneFree(struct hgGene **pEl);
 /* Free a single dynamically allocated hgGene such as created
  * with hgGeneLoad(). */
 
 void hgGeneFreeList(struct hgGene **pList);
 /* Free a list of dynamically allocated hgGene's */
 
 void hgGeneOutput(struct hgGene *el, FILE *f, char sep, char lastSep);
 /* Print out hgGene.  Separate fields with sep. Follow last field with lastSep. */
 
 #define hgGeneTabOut(el,f) hgGeneOutput(el,f,'\t','\n');
 /* Print out hgGene as a line in a tab-separated file. */
 
 #define hgGeneCommaOut(el,f) hgGeneOutput(el,f,',',',');
 /* Print out hgGene as a comma separated list including final comma. */
 
 struct hgTranscript
 /* A transcript prediction */
     {
     struct hgTranscript *next;  /* Next in singly linked list. */
     unsigned id;	/* Unique ID */
     char *name;	/* Name of transcript */
     unsigned hgGene;	/* Gene this is in */
     unsigned startBac;	/* Bac this starts in */
     unsigned startPos;	/* Position within bac where starts */
     unsigned endBac;	/* Bac this ends in */
     unsigned endPos;	/* Position withing bac where ends */
     unsigned cdsStartBac;	/* Start of coding region. */
     unsigned cdsStartPos;	/* Start of coding region. */
     unsigned cdsEndBac;	/* End of coding region. */
     unsigned cdsEndPos;	/* End of coding region. */
     signed char orientation;	/* Orientation relative to start bac */
     unsigned exonCount;	/* Number of exons */
     unsigned *exonStartBacs;	/* Exon start positions */
     unsigned *exonStartPos;	/* Exon start positions */
     unsigned *exonEndBacs;	/* Exon start positions */
     unsigned *exonEndPos;	/* Exon start positions */
     };
 
 struct hgTranscript *hgTranscriptLoad(char **row);
 /* Load a hgTranscript from row fetched with select * from hgTranscript
  * from database.  Dispose of this with hgTranscriptFree(). */
 
 struct hgTranscript *hgTranscriptCommaIn(char **pS);
 /* Create a hgTranscript out of a comma separated string. */
 
 void hgTranscriptFree(struct hgTranscript **pEl);
 /* Free a single dynamically allocated hgTranscript such as created
  * with hgTranscriptLoad(). */
 
 void hgTranscriptFreeList(struct hgTranscript **pList);
 /* Free a list of dynamically allocated hgTranscript's */
 
 void hgTranscriptOutput(struct hgTranscript *el, FILE *f, char sep, char lastSep);
 /* Print out hgTranscript.  Separate fields with sep. Follow last field with lastSep. */
 
 #define hgTranscriptTabOut(el,f) hgTranscriptOutput(el,f,'\t','\n');
 /* Print out hgTranscript as a line in a tab-separated file. */
 
 #define hgTranscriptCommaOut(el,f) hgTranscriptOutput(el,f,',',',');
 /* Print out hgTranscript as a comma separated list including final comma. */