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/hg/lib/agpFrag.c src/hg/lib/agpFrag.c
index 1708f82..1822797 100644
--- src/hg/lib/agpFrag.c
+++ src/hg/lib/agpFrag.c
@@ -1,177 +1,180 @@
 /* agpFrag.c was originally generated by the autoSql program, which also 
  * generated agpFrag.h and agpFrag.sql.  This module links the database and the RAM 
  * representation of objects. */
 
+/* Copyright (C) 2014 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #include "common.h"
 #include "jksql.h"
 #include "agpFrag.h"
 #include "linefile.h"
 
 
 void agpFragStaticLoad(char **row, struct agpFrag *ret)
 /* Load a row from agpFrag table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 ret->chrom = row[0];
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->ix = sqlSigned(row[3]);
 strcpy(ret->type, row[4]);
 ret->frag = row[5];
 ret->fragStart = sqlSigned(row[6]);
 ret->fragEnd = sqlUnsigned(row[7]);
 strcpy(ret->strand, row[8]);
 }
 
 struct agpFrag *agpFragLoad(char **row)
 /* Load a agpFrag from row fetched with select * from agpFrag
  * from database.  Dispose of this with agpFragFree(). */
 {
 struct agpFrag *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->ix = sqlSigned(row[3]);
 strcpy(ret->type, row[4]);
 ret->frag = cloneString(row[5]);
 ret->fragStart = sqlUnsigned(row[6]);
 ret->fragEnd = sqlUnsigned(row[7]);
 strcpy(ret->strand, row[8]);
 return ret;
 }
 
 struct agpFrag *agpFragCommaIn(char **pS, struct agpFrag *ret)
 /* Create a agpFrag out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new agpFrag */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->ix = sqlSignedComma(&s);
 sqlFixedStringComma(&s, ret->type, sizeof(ret->type));
 ret->frag = sqlStringComma(&s);
 ret->fragStart = sqlUnsignedComma(&s);
 ret->fragEnd = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 *pS = s;
 return ret;
 }
 
 void agpFragFree(struct agpFrag **pEl)
 /* Free a single dynamically allocated agpFrag such as created
  * with agpFragLoad(). */
 {
 struct agpFrag *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->frag);
 freez(pEl);
 }
 
 void agpFragFreeList(struct agpFrag **pList)
 /* Free a list of dynamically allocated agpFrag's */
 {
 struct agpFrag *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     agpFragFree(&el);
     }
 *pList = NULL;
 }
 
 void agpFragOutput(struct agpFrag *el, FILE *f, char sep, char lastSep) 
 /* Print out agpFrag.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart+1);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 fprintf(f, "%d", el->ix);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->type);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->frag);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->fragStart+1);
 fputc(sep,f);
 fprintf(f, "%u", el->fragEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 struct agpFrag *agpFragLoadAll(char *fileName) 
 /* Load all agpFrag from a tab-separated file.
  * Dispose of this with agpFragFreeList(). */
 {
 struct agpFrag *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[9];
 
 while (lineFileRow(lf, row))
     {
     el = agpFragLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 /* ---------------------- End autoSql generated code. ---------------------- */
 
 struct agpFrag *agpFragLoadAllNotGaps(char *fileName) 
 /* Load all agpFrag from a tab-separated file.
  * Dispose of this with agpFragFreeList(). */
 {
 struct agpFrag *list = NULL, *el=NULL;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *words[32];
 int wordCount = 0;
 
 /* Check to make sure there is something in the file. */
 wordCount = lineFileChop(lf, words);
 if (wordCount == 0)
     errAbort("%s appears to be empty", fileName);
 lineFileClose(&lf);
 
 lf = lineFileOpen(fileName, TRUE);
 while ((wordCount = lineFileChop(lf, words)) > 0)
     {
     if (wordCount < 5)
 	errAbort("Short line %d of %s", lf->lineIx, lf->fileName);
     if(words[4][0] == 'N' || words[4][0] == 'U')
 	continue;
     el = agpFragLoad(words);
 /* There is a strange thing about agp files, Jim's load functions subtract 1 off
    the chromStart and fragStart but if you're loading off of files from the
    database they have already had 1 subtracted off so I'm going to add it back
    here. */
     el->chromStart++;  
     el->fragStart++;
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }