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/pslWQueryID.c src/hg/lib/pslWQueryID.c
index 02ed9b8..3c39594 100644
--- src/hg/lib/pslWQueryID.c
+++ src/hg/lib/pslWQueryID.c
@@ -1,248 +1,251 @@
 /* pslWQueryID.c was originally generated by the autoSql program, which also 
  * generated pslWQueryID.h and pslWQueryID.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 "pslWQueryID.h"
 
 
 struct pslWQueryID *pslWQueryIDLoad(char **row)
 /* Load a pslWQueryID from row fetched with select * from pslWQueryID
  * from database.  Dispose of this with pslWQueryIDFree(). */
 {
 struct pslWQueryID *ret;
 int sizeOne,i;
 char *s;
 
 AllocVar(ret);
 ret->blockCount = sqlUnsigned(row[17]);
 ret->matches = sqlUnsigned(row[0]);
 ret->misMatches = sqlUnsigned(row[1]);
 ret->repMatches = sqlUnsigned(row[2]);
 ret->nCount = sqlUnsigned(row[3]);
 ret->qNumInsert = sqlUnsigned(row[4]);
 ret->qBaseInsert = sqlUnsigned(row[5]);
 ret->tNumInsert = sqlUnsigned(row[6]);
 ret->tBaseInsert = sqlUnsigned(row[7]);
 strcpy(ret->strand, row[8]);
 ret->qName = cloneString(row[9]);
 ret->qSize = sqlUnsigned(row[10]);
 ret->qStart = sqlUnsigned(row[11]);
 ret->qEnd = sqlUnsigned(row[12]);
 ret->tName = cloneString(row[13]);
 ret->tSize = sqlUnsigned(row[14]);
 ret->tStart = sqlUnsigned(row[15]);
 ret->tEnd = sqlUnsigned(row[16]);
 sqlUnsignedDynamicArray(row[18], &ret->blockSizes, &sizeOne);
 assert(sizeOne == ret->blockCount);
 sqlUnsignedDynamicArray(row[19], &ret->qStarts, &sizeOne);
 assert(sizeOne == ret->blockCount);
 sqlUnsignedDynamicArray(row[20], &ret->tStarts, &sizeOne);
 assert(sizeOne == ret->blockCount);
 ret->queryID = cloneString(row[21]);
 return ret;
 }
 
 struct pslWQueryID *pslWQueryIDLoadAll(char *fileName) 
 /* Load all pslWQueryID from a whitespace-separated file.
  * Dispose of this with pslWQueryIDFreeList(). */
 {
 struct pslWQueryID *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[22];
 
 while (lineFileRow(lf, row))
     {
     el = pslWQueryIDLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct pslWQueryID *pslWQueryIDLoadAllByChar(char *fileName, char chopper) 
 /* Load all pslWQueryID from a chopper separated file.
  * Dispose of this with pslWQueryIDFreeList(). */
 {
 struct pslWQueryID *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[22];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = pslWQueryIDLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct pslWQueryID *pslWQueryIDCommaIn(char **pS, struct pslWQueryID *ret)
 /* Create a pslWQueryID out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new pslWQueryID */
 {
 char *s = *pS;
 int i;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->matches = sqlUnsignedComma(&s);
 ret->misMatches = sqlUnsignedComma(&s);
 ret->repMatches = sqlUnsignedComma(&s);
 ret->nCount = sqlUnsignedComma(&s);
 ret->qNumInsert = sqlUnsignedComma(&s);
 ret->qBaseInsert = sqlUnsignedComma(&s);
 ret->tNumInsert = sqlUnsignedComma(&s);
 ret->tBaseInsert = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->qName = sqlStringComma(&s);
 ret->qSize = sqlUnsignedComma(&s);
 ret->qStart = sqlUnsignedComma(&s);
 ret->qEnd = sqlUnsignedComma(&s);
 ret->tName = sqlStringComma(&s);
 ret->tSize = sqlUnsignedComma(&s);
 ret->tStart = sqlUnsignedComma(&s);
 ret->tEnd = sqlUnsignedComma(&s);
 ret->blockCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->blockSizes, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->blockSizes[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->qStarts, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->qStarts[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->tStarts, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->tStarts[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->queryID = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void pslWQueryIDFree(struct pslWQueryID **pEl)
 /* Free a single dynamically allocated pslWQueryID such as created
  * with pslWQueryIDLoad(). */
 {
 struct pslWQueryID *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->qName);
 freeMem(el->tName);
 freeMem(el->blockSizes);
 freeMem(el->qStarts);
 freeMem(el->tStarts);
 freeMem(el->queryID);
 freez(pEl);
 }
 
 void pslWQueryIDFreeList(struct pslWQueryID **pList)
 /* Free a list of dynamically allocated pslWQueryID's */
 {
 struct pslWQueryID *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     pslWQueryIDFree(&el);
     }
 *pList = NULL;
 }
 
 void pslWQueryIDOutput(struct pslWQueryID *el, FILE *f, char sep, char lastSep) 
 /* Print out pslWQueryID.  Separate fields with sep. Follow last field with lastSep. */
 {
 int i;
 fprintf(f, "%u", el->matches);
 fputc(sep,f);
 fprintf(f, "%u", el->misMatches);
 fputc(sep,f);
 fprintf(f, "%u", el->repMatches);
 fputc(sep,f);
 fprintf(f, "%u", el->nCount);
 fputc(sep,f);
 fprintf(f, "%u", el->qNumInsert);
 fputc(sep,f);
 fprintf(f, "%u", el->qBaseInsert);
 fputc(sep,f);
 fprintf(f, "%u", el->tNumInsert);
 fputc(sep,f);
 fprintf(f, "%u", el->tBaseInsert);
 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->qName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->qSize);
 fputc(sep,f);
 fprintf(f, "%u", el->qStart);
 fputc(sep,f);
 fprintf(f, "%u", el->qEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->tSize);
 fputc(sep,f);
 fprintf(f, "%u", el->tStart);
 fputc(sep,f);
 fprintf(f, "%u", el->tEnd);
 fputc(sep,f);
 fprintf(f, "%u", el->blockCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->blockCount; ++i)
     {
     fprintf(f, "%u", el->blockSizes[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->blockCount; ++i)
     {
     fprintf(f, "%u", el->qStarts[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->blockCount; ++i)
     {
     fprintf(f, "%u", el->tStarts[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->queryID);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */