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

diff --git src/inc/oldGff.h src/inc/oldGff.h
index 550e9cc..f7fd351 100644
--- src/inc/oldGff.h
+++ src/inc/oldGff.h
@@ -1,103 +1,102 @@
-/*****************************************************************************
- * 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) *
- *****************************************************************************/
 /* oldGff.h - This reads a *special* type of .GFF file.  
  * Some of the routines herein expect the gff file to include
  * both DNA and gene/intron/exon info.  They expect the
- * genes to be named by the group field. */
+ * genes to be named by the group field. 
+ *
+ * This file is copyright 2000 Jim Kent, but license is hereby
+ * granted for all use - public, private or commercial. */
+
 #ifndef OLDGFF_H
 #define OLDGFF_H
 
 struct gff
 /* This is the structure that holds info on a gff file.
  */
     {
     char fileName[256];
     FILE *file;
     long fileSize;
     char buf[256];
     int bufSize;
     int bytesInBuf;
     int readIx;
     int lineNumber;
     struct lm *memPool;
     char *dna;
     long dnaSize;
     char dnaName[128];
     struct gffGene *genes;
     };
 
 /* An intron or exon - just an offset into a DNA array. */
 struct gffSegment
     {
     struct gffSegment *next;	/* This must be first field! */
     long start, end;
     int frame;
     };
 typedef struct gffSegment GffIntron;
 typedef struct gffSegment GffExon;
 
 struct gffGene
 /* At the end of a GFF file are a number of genes, each of which 
  * is a list of exons/introns. */
     {
     struct gffGene *next;	/* This must be first field! */
     long start, end;
     int frame;
     char strand;	/* + or - */
     char name[64];
     GffExon *exons;
     GffIntron *introns;
     DNA *dna;
     long dnaSize;
     };
 
 
 boolean gffOpen(struct gff *gff, char *fileName);
 /* Initialize gff structure and open file for it. */
 
 boolean gffOpenAndRead(struct gff *gff, char *fileName);
 /* Open up gff file and read everything in it. */
 
 void gffClose(struct gff *gff);
 /* Close down gff structure. */
 
 boolean gffReadDna(struct gff *gff);
 /* Read all the DNA in a file. */
 
 struct gffGene *gffFindGene(struct gff *gff, char *geneName);
 /* Find gene with given name.  Case sensitive. */
 
 struct gffGene *gffFindGeneIgnoreCase(struct gff *gff, char *geneName);
 /* Find gene with given name.  Not case sensitive. */
 
 void gffPrintInfo(struct gff *gff, FILE *out);
 /* Print summary info about file. */
 
 boolean gffReadGenes(struct gff *gff);
 /* Read all the gene (as opposed to base) info in file. */
 
 struct gffGene *gffDupeGene(struct gff *gff, struct gffGene *oldGene);
 /* Make a duplicate of gene (with it's own DNA). gffFreeGene it when done. */
 
 struct gffGene *gffDupeGeneAndSurrounds(struct gff *gff, struct gffGene *oldGene,
     int leftExtra, int rightExtra);
 /* Make a duplicate of gene with extra DNA around coding region. 
  * gffFreeGene it when done. */
 
 struct gffGene *gffGeneWithOwnDna(struct gff *gff, char *geneName);
 /* Find gene with given name.  Case sensitive. */
 
 void gffFreeGene(struct gffGene **pGene);
 /* Free a gene returned with dupeGene or geneWithOwnDna. 
  * (You don't want to free the ones returned by findGene,
  * they are still owned by the gff.)
  */
 
 struct dnaSeq *gffReadDnaSeq(char *fileName);
 /* Open gff file and read DNA sequence from it. */
 
 #endif /* GFF_H */