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/plasEndPairs.c src/hg/lib/plasEndPairs.c
index 846a906..92fac4c 100644
--- src/hg/lib/plasEndPairs.c
+++ src/hg/lib/plasEndPairs.c
@@ -1,217 +1,220 @@
 /* plasEndPairs.c was originally generated by the autoSql program, which also 
  * generated plasEndPairs.h and plasEndPairs.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 "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "plasEndPairs.h"
 
 
 struct plasEndPairs *plasEndPairsLoad(char **row)
 /* Load a plasEndPairs from row fetched with select * from plasEndPairs
  * from database.  Dispose of this with plasEndPairsFree(). */
 {
 struct plasEndPairs *ret;
 int sizeOne;
 
 AllocVar(ret);
 ret->lfCount = sqlUnsigned(row[8]);
 ret->bin = sqlSigned(row[0]);
 ret->chrom = cloneString(row[1]);
 ret->chromStart = sqlUnsigned(row[2]);
 ret->chromEnd = sqlUnsigned(row[3]);
 ret->name = cloneString(row[4]);
 ret->score = sqlUnsigned(row[5]);
 strcpy(ret->strand, row[6]);
 ret->pslTable = cloneString(row[7]);
 sqlUnsignedDynamicArray(row[9], &ret->lfStarts, &sizeOne);
 assert(sizeOne == ret->lfCount);
 sqlUnsignedDynamicArray(row[10], &ret->lfSizes, &sizeOne);
 assert(sizeOne == ret->lfCount);
 sqlStringDynamicArray(row[11], &ret->lfNames, &sizeOne);
 assert(sizeOne == ret->lfCount);
 return ret;
 }
 
 struct plasEndPairs *plasEndPairsLoadAll(char *fileName) 
 /* Load all plasEndPairs from a tab-separated file.
  * Dispose of this with plasEndPairsFreeList(). */
 {
 struct plasEndPairs *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileRow(lf, row))
     {
     el = plasEndPairsLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct plasEndPairs *plasEndPairsLoadWhere(struct sqlConnection *conn, char *table, char *where)
 /* Load all plasEndPairs from table that satisfy where clause. The
  * where clause may be NULL in which case whole table is loaded
  * Dispose of this with plasEndPairsFreeList(). */
 {
 struct plasEndPairs *list = NULL, *el;
 struct dyString *query = dyStringNew(256);
 struct sqlResult *sr;
 char **row;
 
 sqlDyStringPrintf(query, "select * from %s", table);
 if (where != NULL)
     dyStringPrintf(query, " where %s", where);
 sr = sqlGetResult(conn, query->string);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = plasEndPairsLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 dyStringFree(&query);
 return list;
 }
 
 struct plasEndPairs *plasEndPairsCommaIn(char **pS, struct plasEndPairs *ret)
 /* Create a plasEndPairs out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new plasEndPairs */
 {
 char *s = *pS;
 int i;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->bin = sqlSignedComma(&s);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->pslTable = sqlStringComma(&s);
 ret->lfCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->lfStarts, ret->lfCount);
 for (i=0; i<ret->lfCount; ++i)
     {
     ret->lfStarts[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->lfSizes, ret->lfCount);
 for (i=0; i<ret->lfCount; ++i)
     {
     ret->lfSizes[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->lfNames, ret->lfCount);
 for (i=0; i<ret->lfCount; ++i)
     {
     ret->lfNames[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 *pS = s;
 return ret;
 }
 
 void plasEndPairsFree(struct plasEndPairs **pEl)
 /* Free a single dynamically allocated plasEndPairs such as created
  * with plasEndPairsLoad(). */
 {
 struct plasEndPairs *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->pslTable);
 freeMem(el->lfStarts);
 freeMem(el->lfSizes);
 /* All strings in lfNames are allocated at once, so only need to free first. */
 if (el->lfNames != NULL)
     freeMem(el->lfNames[0]);
 freeMem(el->lfNames);
 freez(pEl);
 }
 
 void plasEndPairsFreeList(struct plasEndPairs **pList)
 /* Free a list of dynamically allocated plasEndPairs's */
 {
 struct plasEndPairs *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     plasEndPairsFree(&el);
     }
 *pList = NULL;
 }
 
 void plasEndPairsOutput(struct plasEndPairs *el, FILE *f, char sep, char lastSep) 
 /* Print out plasEndPairs.  Separate fields with sep. Follow last field with lastSep. */
 {
 int i;
 fprintf(f, "%d", el->bin);
 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->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->score);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->pslTable);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->lfCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->lfCount; ++i)
     {
     fprintf(f, "%u", el->lfStarts[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->lfCount; ++i)
     {
     fprintf(f, "%u", el->lfSizes[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->lfCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->lfNames[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(lastSep,f);
 }