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/putaInfo.c src/hg/lib/putaInfo.c
index e81a783..0ee0709 100644
--- src/hg/lib/putaInfo.c
+++ src/hg/lib/putaInfo.c
@@ -1,344 +1,347 @@
 /* putaInfo.c was originally generated by the autoSql program, which also 
  * generated putaInfo.h and putaInfo.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 "putaInfo.h"
 
 
 struct putaInfo *putaInfoLoad(char **row)
 /* Load a putaInfo from row fetched with select * from putaInfo
  * from database.  Dispose of this with putaInfoFree(). */
 {
 struct putaInfo *ret;
 
 AllocVar(ret);
 ret->blockCount = sqlUnsigned(row[9]);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 ret->strand = cloneString(row[5]);
 ret->oChrom = cloneString(row[6]);
 ret->oChromStart = sqlUnsigned(row[7]);
 ret->oChromEnd = sqlUnsigned(row[8]);
 ret->stop = sqlUnsigned(row[10]);
 sqlUnsignedArray(row[11], ret->tExons, 2);
 sqlUnsignedArray(row[12], ret->qExons, 4);
 sqlUnsignedArray(row[13], ret->qBases, 4);
 sqlUnsignedArray(row[14], ret->repeats, 2);
 {
 int sizeOne;
 sqlUnsignedDynamicArray(row[15], &ret->stops, &sizeOne);
 assert(sizeOne == ret->blockCount);
 }
 sqlDoubleArray(row[16], ret->id, 2);
 return ret;
 }
 
 struct putaInfo *putaInfoLoadAll(char *fileName) 
 /* Load all putaInfo from a whitespace-separated file.
  * Dispose of this with putaInfoFreeList(). */
 {
 struct putaInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[17];
 
 while (lineFileRow(lf, row))
     {
     el = putaInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct putaInfo *putaInfoLoadAllByChar(char *fileName, char chopper) 
 /* Load all putaInfo from a chopper separated file.
  * Dispose of this with putaInfoFreeList(). */
 {
 struct putaInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[17];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = putaInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct putaInfo *putaInfoLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all putaInfo from table that satisfy the query given.  
  * Where query is of the form 'select * from example where something=something'
  * or 'select example.* from example, anotherTable where example.something = 
  * anotherTable.something'.
  * Dispose of this with putaInfoFreeList(). */
 {
 struct putaInfo *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = putaInfoLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void putaInfoSaveToDb(struct sqlConnection *conn, struct putaInfo *el, char *tableName, int updateSize)
 /* Save putaInfo as a row to the table specified by tableName. 
  * As blob fields may be arbitrary size updateSize specifies the approx size
  * of a string that would contain the entire query. Arrays of native types are
  * converted to comma separated strings and loaded as such, User defined types are
  * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
 {
 struct dyString *update = newDyString(updateSize);
 char  *tExonsArray, *qExonsArray, *qBasesArray, *repeatsArray, *stopsArray, *idArray;
 tExonsArray = sqlUnsignedArrayToString(el->tExons, 2);
 qExonsArray = sqlUnsignedArrayToString(el->qExons, 4);
 qBasesArray = sqlUnsignedArrayToString(el->qBases, 4);
 repeatsArray = sqlUnsignedArrayToString(el->repeats, 2);
 stopsArray = sqlUnsignedArrayToString(el->stops, el->blockCount);
 idArray = sqlDoubleArrayToString(el->id, 2);
 sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s',%u,%u,%u,%u,'%s','%s','%s','%s','%s','%s')", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->oChrom,  el->oChromStart,  el->oChromEnd,  el->blockCount,  el->stop,  tExonsArray ,  qExonsArray ,  qBasesArray ,  repeatsArray ,  stopsArray ,  idArray );
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 freez(&tExonsArray);
 freez(&qExonsArray);
 freez(&qBasesArray);
 freez(&repeatsArray);
 freez(&stopsArray);
 freez(&idArray);
 }
 
 
 struct putaInfo *putaInfoCommaIn(char **pS, struct putaInfo *ret)
 /* Create a putaInfo out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new putaInfo */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 ret->strand = sqlStringComma(&s);
 ret->oChrom = sqlStringComma(&s);
 ret->oChromStart = sqlUnsignedComma(&s);
 ret->oChromEnd = sqlUnsignedComma(&s);
 ret->blockCount = sqlUnsignedComma(&s);
 ret->stop = sqlUnsignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 for (i=0; i<2; ++i)
     {
     ret->tExons[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 for (i=0; i<4; ++i)
     {
     ret->qExons[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 for (i=0; i<4; ++i)
     {
     ret->qBases[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 for (i=0; i<2; ++i)
     {
     ret->repeats[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->stops, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->stops[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 for (i=0; i<2; ++i)
     {
     ret->id[i] = sqlDoubleComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 *pS = s;
 return ret;
 }
 
 void putaInfoFree(struct putaInfo **pEl)
 /* Free a single dynamically allocated putaInfo such as created
  * with putaInfoLoad(). */
 {
 struct putaInfo *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->strand);
 freeMem(el->oChrom);
 freeMem(el->stops);
 freez(pEl);
 }
 
 void putaInfoFreeList(struct putaInfo **pList)
 /* Free a list of dynamically allocated putaInfo's */
 {
 struct putaInfo *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     putaInfoFree(&el);
     }
 *pList = NULL;
 }
 
 void putaInfoOutput(struct putaInfo *el, FILE *f, char sep, char lastSep) 
 /* Print out putaInfo.  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);
 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->oChrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->oChromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->oChromEnd);
 fputc(sep,f);
 fprintf(f, "%u", el->blockCount);
 fputc(sep,f);
 fprintf(f, "%u", el->stop);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<2; ++i)
     {
     fprintf(f, "%u", el->tExons[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<4; ++i)
     {
     fprintf(f, "%u", el->qExons[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<4; ++i)
     {
     fprintf(f, "%u", el->qBases[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<2; ++i)
     {
     fprintf(f, "%u", el->repeats[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->blockCount; ++i)
     {
     fprintf(f, "%u", el->stops[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<2; ++i)
     {
     fprintf(f, "%g", el->id[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */