ea980437e9a5c43edab7e228fac5cb33c2494370
aamp
  Wed Dec 29 22:48:49 2010 -0800
Changes associated with the lift of the clonePos (coverage) track to hg19
diff --git src/hg/lib/clonePos.c src/hg/lib/clonePos.c
index 75d279f..ff924b5 100644
--- src/hg/lib/clonePos.c
+++ src/hg/lib/clonePos.c
@@ -1,119 +1,159 @@
 /* clonePos.c was originally generated by the autoSql program, which also 
- * generated clonePos.h and clonePos.sql.  This module links the database and the RAM 
- * representation of objects. */
+ * generated clonePos.h and clonePos.sql.  This module links the database and
+ * the RAM representation of objects. */
 
 #include "common.h"
+#include "linefile.h"
+#include "dystring.h"
 #include "jksql.h"
 #include "clonePos.h"
 
-static char const rcsid[] = "$Id: clonePos.c,v 1.4 2005/04/13 06:25:51 markd Exp $";
+static char const rcsid[] = "$Id:$";
 
 void clonePosStaticLoad(char **row, struct clonePos *ret)
 /* Load a row from clonePos table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->name = row[0];
 ret->seqSize = sqlUnsigned(row[1]);
 ret->phase = sqlUnsigned(row[2]);
 ret->chrom = row[3];
 ret->chromStart = sqlUnsigned(row[4]);
 ret->chromEnd = sqlUnsigned(row[5]);
-strcpy(ret->stage, row[6]);
+safecpy(ret->stage, sizeof(ret->stage), row[6]);
 ret->faFile = row[7];
 }
 
 struct clonePos *clonePosLoad(char **row)
 /* Load a clonePos from row fetched with select * from clonePos
  * from database.  Dispose of this with clonePosFree(). */
 {
 struct clonePos *ret;
 
 AllocVar(ret);
 ret->name = cloneString(row[0]);
 ret->seqSize = sqlUnsigned(row[1]);
 ret->phase = sqlUnsigned(row[2]);
 ret->chrom = cloneString(row[3]);
 ret->chromStart = sqlUnsigned(row[4]);
 ret->chromEnd = sqlUnsigned(row[5]);
-strcpy(ret->stage, row[6]);
+safecpy(ret->stage, sizeof(ret->stage), row[6]);
 ret->faFile = cloneString(row[7]);
 return ret;
 }
 
+struct clonePos *clonePosLoadAll(char *fileName) 
+/* Load all clonePos from a whitespace-separated file.
+ * Dispose of this with clonePosFreeList(). */
+{
+struct clonePos *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[8];
+
+while (lineFileRow(lf, row))
+    {
+    el = clonePosLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct clonePos *clonePosLoadAllByChar(char *fileName, char chopper) 
+/* Load all clonePos from a chopper separated file.
+ * Dispose of this with clonePosFreeList(). */
+{
+struct clonePos *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[8];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = clonePosLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
 struct clonePos *clonePosCommaIn(char **pS, struct clonePos *ret)
 /* Create a clonePos out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new clonePos */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->name = sqlStringComma(&s);
 ret->seqSize = sqlUnsignedComma(&s);
 ret->phase = sqlUnsignedComma(&s);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->stage, sizeof(ret->stage));
 ret->faFile = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void clonePosFree(struct clonePos **pEl)
 /* Free a single dynamically allocated clonePos such as created
  * with clonePosLoad(). */
 {
 struct clonePos *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->name);
 freeMem(el->chrom);
 freeMem(el->faFile);
 freez(pEl);
 }
 
 void clonePosFreeList(struct clonePos **pList)
 /* Free a list of dynamically allocated clonePos's */
 {
 struct clonePos *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     clonePosFree(&el);
     }
 *pList = NULL;
 }
 
 void clonePosOutput(struct clonePos *el, FILE *f, char sep, char lastSep) 
 /* Print out clonePos.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->seqSize);
 fputc(sep,f);
 fprintf(f, "%u", el->phase);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->stage);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->faFile);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+