a44421a79fb36cc2036fe116b97ea3bc9590cd0c
braney
  Fri Dec 2 09:34:39 2011 -0800
removed rcsid (#295)
diff --git src/hg/lib/bed12wSeq.c src/hg/lib/bed12wSeq.c
index 0473a83..1d6f813 100644
--- src/hg/lib/bed12wSeq.c
+++ src/hg/lib/bed12wSeq.c
@@ -1,294 +1,293 @@
 /* bed12wSeq.c was originally generated by the autoSql program, which also 
  * generated bed12wSeq.h and bed12wSeq.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 "bed12wSeq.h"
 
-static char const rcsid[] = "$Id: bed12wSeq.c,v 1.1 2009/09/24 21:26:51 braney Exp $";
 
 struct bed12wSeq *bed12wSeqLoad(char **row)
 /* Load a bed12wSeq from row fetched with select * from bed12wSeq
  * from database.  Dispose of this with bed12wSeqFree(). */
 {
 struct bed12wSeq *ret;
 
 AllocVar(ret);
 ret->blockCount = sqlSigned(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]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->thickStart = sqlUnsigned(row[6]);
 ret->thickEnd = sqlUnsigned(row[7]);
 ret->reserved = sqlUnsigned(row[8]);
 {
 int sizeOne;
 sqlSignedDynamicArray(row[10], &ret->blockSizes, &sizeOne);
 assert(sizeOne == ret->blockCount);
 }
 {
 int sizeOne;
 sqlSignedDynamicArray(row[11], &ret->chromStarts, &sizeOne);
 assert(sizeOne == ret->blockCount);
 }
 ret->seq1 = cloneString(row[12]);
 ret->seq2 = cloneString(row[13]);
 return ret;
 }
 
 struct bed12wSeq *bed12wSeqLoadAll(char *fileName) 
 /* Load all bed12wSeq from a whitespace-separated file.
  * Dispose of this with bed12wSeqFreeList(). */
 {
 struct bed12wSeq *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[14];
 
 while (lineFileRow(lf, row))
     {
     el = bed12wSeqLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct bed12wSeq *bed12wSeqLoadAllByChar(char *fileName, char chopper) 
 /* Load all bed12wSeq from a chopper separated file.
  * Dispose of this with bed12wSeqFreeList(). */
 {
 struct bed12wSeq *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[14];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = bed12wSeqLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct bed12wSeq *bed12wSeqLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all bed12wSeq 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 bed12wSeqFreeList(). */
 {
 struct bed12wSeq *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = bed12wSeqLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void bed12wSeqSaveToDb(struct sqlConnection *conn, struct bed12wSeq *el, char *tableName, int updateSize)
 /* Save bed12wSeq 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. Note that strings must be escaped to allow insertion into the database.
  * For example "autosql's features include" --> "autosql\'s features include" 
  * If worried about this use bed12wSeqSaveToDbEscaped() */
 {
 struct dyString *update = newDyString(updateSize);
 char  *blockSizesArray, *chromStartsArray;
 blockSizesArray = sqlSignedArrayToString(el->blockSizes, el->blockCount);
 chromStartsArray = sqlSignedArrayToString(el->chromStarts, el->blockCount);
 dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s',%u,%u,%u,%d,'%s','%s','%s','%s')", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->thickStart,  el->thickEnd,  el->reserved,  el->blockCount,  blockSizesArray ,  chromStartsArray ,  el->seq1,  el->seq2);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 freez(&blockSizesArray);
 freez(&chromStartsArray);
 }
 
 void bed12wSeqSaveToDbEscaped(struct sqlConnection *conn, struct bed12wSeq *el, char *tableName, int updateSize)
 /* Save bed12wSeq 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. Automatically 
  * escapes all simple strings (not arrays of string) but may be slower than bed12wSeqSaveToDb().
  * For example automatically copies and converts: 
  * "autosql's features include" --> "autosql\'s features include" 
  * before inserting into database. */ 
 {
 struct dyString *update = newDyString(updateSize);
 char  *chrom, *name, *strand, *blockSizesArray, *chromStartsArray, *seq1, *seq2;
 chrom = sqlEscapeString(el->chrom);
 name = sqlEscapeString(el->name);
 strand = sqlEscapeString(el->strand);
 seq1 = sqlEscapeString(el->seq1);
 seq2 = sqlEscapeString(el->seq2);
 
 blockSizesArray = sqlSignedArrayToString(el->blockSizes, el->blockCount);
 chromStartsArray = sqlSignedArrayToString(el->chromStarts, el->blockCount);
 dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s',%u,%u,%u,%d,'%s','%s','%s','%s')", 
 	tableName,  chrom,  el->chromStart,  el->chromEnd,  name,  el->score,  strand,  el->thickStart,  el->thickEnd,  el->reserved,  el->blockCount,  blockSizesArray ,  chromStartsArray ,  seq1,  seq2);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 freez(&chrom);
 freez(&name);
 freez(&strand);
 freez(&blockSizesArray);
 freez(&chromStartsArray);
 freez(&seq1);
 freez(&seq2);
 }
 
 struct bed12wSeq *bed12wSeqCommaIn(char **pS, struct bed12wSeq *ret)
 /* Create a bed12wSeq out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new bed12wSeq */
 {
 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);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->thickStart = sqlUnsignedComma(&s);
 ret->thickEnd = sqlUnsignedComma(&s);
 ret->reserved = sqlUnsignedComma(&s);
 ret->blockCount = sqlSignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->blockSizes, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->blockSizes[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->chromStarts, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->chromStarts[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 ret->seq1 = sqlStringComma(&s);
 ret->seq2 = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void bed12wSeqFree(struct bed12wSeq **pEl)
 /* Free a single dynamically allocated bed12wSeq such as created
  * with bed12wSeqLoad(). */
 {
 struct bed12wSeq *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->blockSizes);
 freeMem(el->chromStarts);
 freeMem(el->seq1);
 freeMem(el->seq2);
 freez(pEl);
 }
 
 void bed12wSeqFreeList(struct bed12wSeq **pList)
 /* Free a list of dynamically allocated bed12wSeq's */
 {
 struct bed12wSeq *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     bed12wSeqFree(&el);
     }
 *pList = NULL;
 }
 
 void bed12wSeqOutput(struct bed12wSeq *el, FILE *f, char sep, char lastSep) 
 /* Print out bed12wSeq.  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);
 fprintf(f, "%u", el->thickStart);
 fputc(sep,f);
 fprintf(f, "%u", el->thickEnd);
 fputc(sep,f);
 fprintf(f, "%u", el->reserved);
 fputc(sep,f);
 fprintf(f, "%d", el->blockCount);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->blockCount; ++i)
     {
     fprintf(f, "%d", el->blockSizes[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, "%d", el->chromStarts[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->seq1);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->seq2);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */