e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/lib/annoAssembly.c src/lib/annoAssembly.c
index 45cee66..0de6657 100644
--- src/lib/annoAssembly.c
+++ src/lib/annoAssembly.c
@@ -1,56 +1,59 @@
 /* annoAssembly -- basic metadata about an assembly for the annoGrator framework. */
 
+/* Copyright (C) 2013 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #include "annoAssembly.h"
 #include "obscure.h"
 #include "twoBit.h"
 
 struct annoAssembly *annoAssemblyNew(char *name, char *twoBitPath)
 /* Return an annoAssembly with open twoBitFile. */
 {
 struct annoAssembly *aa;
 AllocVar(aa);
 aa->name = cloneString(name);
 aa->tbf = twoBitOpen(twoBitPath);
 aa->twoBitPath = cloneString(twoBitPath);
 return aa;
 }
 
 struct slName *annoAssemblySeqNames(struct annoAssembly *aa)
 /* Return a list of sequence names in this assembly. */
 {
 struct slName *seqNames = twoBitSeqNames(aa->twoBitPath);
 slSort(&seqNames, slNameCmp);
 return seqNames;
 }
 
 uint annoAssemblySeqSize(struct annoAssembly *aa, char *seqName)
 /* Return the number of bases in seq which must be in aa's twoBitFile. */
 {
 if (aa->seqSizes == NULL)
     aa->seqSizes = hashNew(digitsBaseTwo(aa->tbf->seqCount));
 struct hashEl *hel = hashLookup(aa->seqSizes, seqName);
 uint seqSize;
 if (hel != NULL)
     seqSize = (uint)(hel->val - NULL);
 else
     {
     seqSize = (uint)twoBitSeqSize(aa->tbf, seqName);
     char *pt = NULL;
     hashAdd(aa->seqSizes, seqName, pt + seqSize);
     }
 return seqSize;
 }
 
 void annoAssemblyClose(struct annoAssembly **pAa)
 /* Close aa's twoBitFile and free mem. */
 {
 if (*pAa == NULL)
     return;
 struct annoAssembly *aa = *pAa;
 freeMem(aa->name);
 freeMem(aa->twoBitPath);
 twoBitClose(&(aa->tbf));
 hashFree(&(aa->seqSizes));
 freez(pAa);
 }