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

diff --git src/inc/trans3.h src/inc/trans3.h
index 61f0f0c..6188225 100644
--- src/inc/trans3.h
+++ src/inc/trans3.h
@@ -1,59 +1,58 @@
-/*****************************************************************************
- * 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) *
- *****************************************************************************/
 /* trans3 - a sequence and three translated reading frames. 
  * In the gfServer/gfClient system these are found in a
  * t3Hash that has as values lists of trans3.  These reflect
  * the fragments of the genome actually loaded in memory
- * to perform the alignment. */
+ * to perform the alignment. 
+ *
+ * This file is copyright 2000 Jim Kent, but license is hereby
+ * granted for all use - public, private or commercial. */
+
 
 #ifndef TRANS3_H
 #define TRANS3_H
 
 #ifndef DNASEQ_H
 #include "dnaseq.h"
 #endif
 
 #ifndef HASH_H
 #include "hash.h"
 #endif
 
 struct trans3
 /* A sequence and three translations of it. */
      {
      struct trans3 *next;		/* Next in list. */
      char *name;			/* Name (not allocated here) */
      struct dnaSeq *seq;		/* Untranslated sequence.  Not allocated here. */
      aaSeq *trans[3];			/* Translated sequences.  Allocated here*/
      int start,end;			/* Start/end of sequence in a larger context. */
      int nibSize;			/* Size of nib file this is embedded in. */
      boolean isRc;			/* Has been reverse complemented? */
      };
 
 struct trans3 *trans3New(struct dnaSeq *seq);
 /* Create a new set of translated sequences. */
 
 void trans3Free(struct trans3 **pT3);
 /* Free a trans3 structure. */
 
 void trans3FreeList(struct trans3 **pList);
 /* Free a list of dynamically allocated trans3's */
 
 struct trans3 *trans3Find(struct hash *t3Hash, char *name, int start, int end);
 /* Find trans3 in hash which corresponds to sequence of given name and includes
  * bases between start and end. */
 
 void trans3Offset(struct trans3 *t3List, AA *aa, int *retOffset, int *retFrame);
 /* Figure out offset of peptide in context of larger sequences. */
 
 int trans3GenoPos(char *pt, bioSeq *seq, struct trans3 *t3List, boolean isEnd);
 /* Convert from position in one of three translated frames in
  * t3List to genomic offset. If t3List is NULL then just use seq
  * instead. */
 
 int trans3Frame(char *pt, struct trans3 *t3List);
 /* Figure out which frame pt is in or 0 if no frame. */
 
 #endif /* TRANS3_H */