0aaeab5b5b0d708cd9e966b1bb7d0fb9d2b1039a
hartera
  Tue Mar 24 14:21:31 2015 -0700
Removed old code that was commented out.

diff --git src/hg/lib/ucscRetroInfo.c src/hg/lib/ucscRetroInfo.c
index bb108b8..f06c452 100644
--- src/hg/lib/ucscRetroInfo.c
+++ src/hg/lib/ucscRetroInfo.c
@@ -1,445 +1,441 @@
 /* ucscRetroInfo.c was originally generated by the autoSql program, which also 
  * generated ucscRetroInfo.h and ucscRetroInfo.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 "ucscRetroInfo.h"
 
 
 struct ucscRetroInfo *ucscRetroInfoLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all ucscRetroInfo 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 ucscRetroInfoFreeList(). */
 {
 struct ucscRetroInfo *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = ucscRetroInfoLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void ucscRetroInfoSaveToDb(struct sqlConnection *conn, struct ucscRetroInfo *el, char *tableName, int updateSize)
 /* Save ucscRetroInfo 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  *blockSizesArray, *chromStartsArray;
 blockSizesArray = sqlSignedArrayToString(el->blockSizes, el->blockCount);
 chromStartsArray = sqlSignedArrayToString(el->chromStarts, el->blockCount);
 sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s',%u,%u,%u,%d,'%s','%s',%d,%d,'%s','%s',%d,%d,'%s',%u,%u,%u,%d,%d,%u,%u,%u,%u,%u,%u,%u,%d,%u,%d,%d,%d,%d,'%s',%d,%d,'%s',%d,%d,'%s',%d,%d,'%s',%d,%d,'%s',%g,%u)", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->thickStart,  el->thickEnd,  el->reserved,  el->blockCount,  blockSizesArray ,  chromStartsArray ,  el->retroExonCount,  el->axtScore,  el->type,  el->gChrom,  el->gStart,  el->gEnd,  el->gStrand,  el->parentSpliceCount,  el->geneOverlap,  el->polyA,  el->polyAstart,  el->exonCover,  el->intronCount,  el->bestAliCount,  el->matches,  el->qSize,  el->qEnd,  el->tReps,  el->coverage,  el->label,  el->milliBad, el->alignGapCount,  el->processedIntrons,  el->conservedSpliceSites,  el->maxOverlap,  el->refSeq,  el->rStart,  el->rEnd,  el->mgc,  el->mStart,  el->mEnd,  el->kgName,  el->kStart,  el->kEnd,  el->overName,  el->overStart,  el->overExonCover,  el->overStrand,  el->posConf,  el->polyAlen);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 freez(&blockSizesArray);
 freez(&chromStartsArray);
 }
 
 
 struct ucscRetroInfo *ucscRetroInfoLoad(char **row)
 /* Load a ucscRetroInfo from row fetched with select * from ucscRetroInfo
  * from database.  Dispose of this with ucscRetroInfoFree(). */
 {
 struct ucscRetroInfo *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->retroExonCount = sqlSigned(row[12]);
 ret->axtScore = sqlSigned(row[13]);
 ret->type = cloneString(row[14]);
 ret->gChrom = cloneString(row[15]);
 ret->gStart = sqlSigned(row[16]);
 ret->gEnd = sqlSigned(row[17]);
 safecpy(ret->gStrand, sizeof(ret->gStrand), row[18]);
 ret->parentSpliceCount = sqlUnsigned(row[19]);
 ret->geneOverlap = sqlUnsigned(row[20]);
 ret->polyA = sqlUnsigned(row[21]);
 ret->polyAstart = sqlSigned(row[22]);
 ret->exonCover = sqlSigned(row[23]);
 ret->intronCount = sqlUnsigned(row[24]);
 ret->bestAliCount = sqlUnsigned(row[25]);
 ret->matches = sqlUnsigned(row[26]);
 ret->qSize = sqlUnsigned(row[27]);
 ret->qEnd = sqlUnsigned(row[28]);
 ret->tReps = sqlUnsigned(row[29]);
 ret->coverage = sqlUnsigned(row[30]);
 ret->label = sqlSigned(row[31]);
 ret->milliBad = sqlUnsigned(row[32]);
-//ret->oldScore = sqlUnsigned(row[33]);
 ret->alignGapCount = sqlSigned(row[33]);
 ret->processedIntrons = sqlSigned(row[34]);
 ret->conservedSpliceSites = sqlSigned(row[35]);
 ret->maxOverlap = sqlSigned(row[36]);
 ret->refSeq = cloneString(row[37]);
 ret->rStart = sqlSigned(row[38]);
 ret->rEnd = sqlSigned(row[39]);
 ret->mgc = cloneString(row[40]);
 ret->mStart = sqlSigned(row[41]);
 ret->mEnd = sqlSigned(row[42]);
 ret->kgName = cloneString(row[43]);
 ret->kStart = sqlSigned(row[44]);
 ret->kEnd = sqlSigned(row[45]);
 ret->overName = cloneString(row[46]);
 ret->overStart = sqlSigned(row[47]);
 ret->overExonCover = sqlSigned(row[48]);
 safecpy(ret->overStrand, sizeof(ret->overStrand), row[49]);
 ret->posConf = sqlFloat(row[50]);
 ret->polyAlen = sqlUnsigned(row[51]);
 return ret;
 }
 
 struct ucscRetroInfo *ucscRetroInfoLoadAll(char *fileName) 
 /* Load all ucscRetroInfo from a whitespace-separated file.
  * Dispose of this with ucscRetroInfoFreeList(). */
 {
 struct ucscRetroInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[52];
 
 while (lineFileRow(lf, row))
     {
     el = ucscRetroInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct ucscRetroInfo *ucscRetroInfoLoadAllByChar(char *fileName, char chopper) 
 /* Load all ucscRetroInfo from a chopper separated file.
  * Dispose of this with ucscRetroInfoFreeList(). */
 {
 struct ucscRetroInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[52];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = ucscRetroInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct ucscRetroInfo *ucscRetroInfoCommaIn(char **pS, struct ucscRetroInfo *ret)
 /* Create a ucscRetroInfo out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new ucscRetroInfo */
 {
 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->retroExonCount = sqlSignedComma(&s);
 ret->axtScore = sqlSignedComma(&s);
 ret->type = sqlStringComma(&s);
 ret->gChrom = sqlStringComma(&s);
 ret->gStart = sqlSignedComma(&s);
 ret->gEnd = sqlSignedComma(&s);
 sqlFixedStringComma(&s, ret->gStrand, sizeof(ret->gStrand));
 ret->parentSpliceCount = sqlUnsignedComma(&s);
 ret->geneOverlap = sqlUnsignedComma(&s);
 ret->polyA = sqlUnsignedComma(&s);
 ret->polyAstart = sqlSignedComma(&s);
 ret->exonCover = sqlSignedComma(&s);
 ret->intronCount = sqlUnsignedComma(&s);
 ret->bestAliCount = sqlUnsignedComma(&s);
 ret->matches = sqlUnsignedComma(&s);
 ret->qSize = sqlUnsignedComma(&s);
 ret->qEnd = sqlUnsignedComma(&s);
 ret->tReps = sqlUnsignedComma(&s);
 ret->coverage = sqlUnsignedComma(&s);
 ret->label = sqlSignedComma(&s);
 ret->milliBad = sqlUnsignedComma(&s);
-//ret->oldScore = sqlUnsignedComma(&s);
 ret->alignGapCount = sqlSignedComma(&s);
 ret->processedIntrons = sqlSignedComma(&s);
 ret->conservedSpliceSites = sqlSignedComma(&s);
 ret->maxOverlap = sqlSignedComma(&s);
 ret->refSeq = sqlStringComma(&s);
 ret->rStart = sqlSignedComma(&s);
 ret->rEnd = sqlSignedComma(&s);
 ret->mgc = sqlStringComma(&s);
 ret->mStart = sqlSignedComma(&s);
 ret->mEnd = sqlSignedComma(&s);
 ret->kgName = sqlStringComma(&s);
 ret->kStart = sqlSignedComma(&s);
 ret->kEnd = sqlSignedComma(&s);
 ret->overName = sqlStringComma(&s);
 ret->overStart = sqlSignedComma(&s);
 ret->overExonCover = sqlSignedComma(&s);
 sqlFixedStringComma(&s, ret->overStrand, sizeof(ret->overStrand));
 ret->posConf = sqlFloatComma(&s);
 ret->polyAlen = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void ucscRetroInfoFree(struct ucscRetroInfo **pEl)
 /* Free a single dynamically allocated ucscRetroInfo such as created
  * with ucscRetroInfoLoad(). */
 {
 struct ucscRetroInfo *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->blockSizes);
 freeMem(el->chromStarts);
 freeMem(el->type);
 freeMem(el->gChrom);
 freeMem(el->refSeq);
 freeMem(el->mgc);
 freeMem(el->kgName);
 freeMem(el->overName);
 freez(pEl);
 }
 
 void ucscRetroInfoFreeList(struct ucscRetroInfo **pList)
 /* Free a list of dynamically allocated ucscRetroInfo's */
 {
 struct ucscRetroInfo *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     ucscRetroInfoFree(&el);
     }
 *pList = NULL;
 }
 
 void ucscRetroInfoOutput(struct ucscRetroInfo *el, FILE *f, char sep, char lastSep) 
 /* Print out ucscRetroInfo.  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);
 fprintf(f, "%d", el->retroExonCount);
 fputc(sep,f);
 fprintf(f, "%d", el->axtScore);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->type);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->gChrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->gStart);
 fputc(sep,f);
 fprintf(f, "%d", el->gEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->gStrand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->parentSpliceCount);
 fputc(sep,f);
 fprintf(f, "%u", el->geneOverlap);
 fputc(sep,f);
 fprintf(f, "%u", el->polyA);
 fputc(sep,f);
 fprintf(f, "%d", el->polyAstart);
 fputc(sep,f);
 fprintf(f, "%d", el->exonCover);
 fputc(sep,f);
 fprintf(f, "%u", el->intronCount);
 fputc(sep,f);
 fprintf(f, "%u", el->bestAliCount);
 fputc(sep,f);
 fprintf(f, "%u", el->matches);
 fputc(sep,f);
 fprintf(f, "%u", el->qSize);
 fputc(sep,f);
 fprintf(f, "%u", el->qEnd);
 fputc(sep,f);
 fprintf(f, "%u", el->tReps);
 fputc(sep,f);
 fprintf(f, "%u", el->coverage);
 fputc(sep,f);
 fprintf(f, "%d", el->label);
 fputc(sep,f);
 fprintf(f, "%u", el->milliBad);
 fputc(sep,f);
-//fprintf(f, "%u", el->oldScore);
-//fputc(sep,f);
 fprintf(f, "%d", el->alignGapCount);
 fputc(sep,f);
 fprintf(f, "%d", el->processedIntrons);
 fputc(sep,f);
 fprintf(f, "%d", el->conservedSpliceSites);
 fputc(sep,f);
 fprintf(f, "%d", el->maxOverlap);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->refSeq);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->rStart);
 fputc(sep,f);
 fprintf(f, "%d", el->rEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->mgc);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->mStart);
 fputc(sep,f);
 fprintf(f, "%d", el->mEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->kgName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->kStart);
 fputc(sep,f);
 fprintf(f, "%d", el->kEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->overName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->overStart);
 fputc(sep,f);
 fprintf(f, "%d", el->overExonCover);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->overStrand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->posConf);
 fputc(sep,f);
 fprintf(f, "%u", el->polyAlen);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 struct ucscRetroInfo *ucscRetroInfoQuery(struct sqlConnection *conn,
                                        char *table, char *mappedId)
 /* load a single retro object for an mapped id from a table,
  * or error if not found */
 {
 return sqlQueryObjs(conn, (sqlLoadFunc)ucscRetroInfoLoad,
                     sqlQuerySingle,
                     "SELECT * FROM %s WHERE name = \"%s\"",
                     table, mappedId);
 }