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

diff --git src/inc/supStitch.h src/inc/supStitch.h
index 3ef0d63..96ca7cc 100644
--- src/inc/supStitch.h
+++ src/inc/supStitch.h
@@ -1,73 +1,72 @@
-/*****************************************************************************
- * 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) *
- *****************************************************************************/
 /* supStitch stitches together a bundle of ffAli alignments that share
  * a common query and target sequence into larger alignments if possible.
  * This is commonly used when the query sequence was broken up into
  * overlapping blocks in the initial alignment, and also to look for
- * introns larger than fuzzyFinder can handle. */
+ * introns larger than fuzzyFinder can handle. 
+ *
+ * This file is copyright 2000 Jim Kent, but license is hereby
+ * granted for all use - public, private or commercial. */
+
 
 #ifndef SUPSTITCH_H
 #define SUPSTITCH_H
 
 #ifndef DNASEQ_H
 #include "dnaseq.h"
 #endif
 
 #ifndef FUZZYFIND_H
 #include "fuzzyFind.h"
 #endif
 
 #ifndef PATSPACE_H
 #include "patSpace.h"
 #endif
 
 struct ssFfItem
 /* A list of fuzzy finder alignments. */
     {
     struct ssFfItem *next;      /* Next in list. */
     struct ffAli *ff;		/* Alignment (owned by ssFfItem) */
     };
 
 void ssFfItemFree(struct ssFfItem **pEl);
 /* Free a single ssFfItem. */
 
 void ssFfItemFreeList(struct ssFfItem **pList);
 /* Free a list of ssFfItems. */
 
 struct ssBundle
 /* A bunch of alignments all with the same query sequence.  This
  * is the input to the stitcher.*/
     {
     struct ssBundle *next;	/* Next in list. */
     struct ssFfItem *ffList;    /* Item list - memory owned by bundle. */
     bioSeq *qSeq;        /* Query sequence (not owned by bundle.) */
     bioSeq *genoSeq;     /* Genomic sequence (not owned by bundle.) */
     int genoIx;                 /* Index of bac in associated PatSpace. */
     int genoContigIx;           /* Index of contig inside of seq. */
     void *data;			/* User defined data pointer. */
     boolean isProt;		/* True if it's a protein based bundle. */
     struct trans3 *t3List;	/* Sometimes set to three translated frames. */
     boolean avoidFuzzyFindKludge;	/* Temporary flag to avoid call to fuzzyFind. */
     };
 
 void ssBundleFree(struct ssBundle **pEl);
 /* Free up one ssBundle */
 
 void ssBundleFreeList(struct ssBundle **pList);
 /* Free up list of ssBundles */
 
 
 void ssStitch(struct ssBundle *bundle, enum ffStringency stringency, 
 	int minScore, int maxToReturn);
 /* Glue together mrnas in bundle as much as possible. 
  * Updates bundle->ffList with stitched together version. */
 
 struct ssBundle *ssFindBundles(struct patSpace *ps, struct dnaSeq *cSeq, 
 	char *cName, enum ffStringency stringency, boolean avoidSelfSelf);
 /* Find patSpace alignments on cSeq and bundle them together. */
 
 #endif /* SUPSTITCH_H */