533112afe2a2005e80cdb1f82904ea65032d4302
braney
  Sat Oct 2 11:37:34 2021 -0700
split hg/lib into two separate libaries, one only used by the cgis

diff --git src/hg/lib/bigTransMap.c src/hg/lib/bigTransMap.c
deleted file mode 100644
index 4a0c28a..0000000
--- src/hg/lib/bigTransMap.c
+++ /dev/null
@@ -1,384 +0,0 @@
-/* bigTransMap.c was originally generated by the autoSql program, which also 
- * generated bigTransMap.h and bigTransMap.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 "bigTransMap.h"
-
-
-
-char *bigTransMapCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,reserved,blockCount,blockSizes,chromStarts,oChromStart,oChromEnd,oStrand,oChromSize,oChromStarts,oSequence,oCDS,chromSize,match,misMatch,repMatch,nCount,seqType,srcDb,srcTransId,srcChrom,srcChromStart,srcChromEnd,srcIdent,srcAligned,geneName,geneId,geneType,transcriptType,chainType,commonName,scientificName,orgAbbrev";
-
-struct bigTransMap *bigTransMapLoad(char **row)
-/* Load a bigTransMap from row fetched with select * from bigTransMap
- * from database.  Dispose of this with bigTransMapFree(). */
-{
-struct bigTransMap *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->oChromStart = sqlUnsigned(row[12]);
-ret->oChromEnd = sqlUnsigned(row[13]);
-safecpy(ret->oStrand, sizeof(ret->oStrand), row[14]);
-ret->oChromSize = sqlUnsigned(row[15]);
-{
-int sizeOne;
-sqlSignedDynamicArray(row[16], &ret->oChromStarts, &sizeOne);
-assert(sizeOne == ret->blockCount);
-}
-ret->oSequence = cloneString(row[17]);
-ret->oCDS = cloneString(row[18]);
-ret->chromSize = sqlUnsigned(row[19]);
-ret->match = sqlUnsigned(row[20]);
-ret->misMatch = sqlUnsigned(row[21]);
-ret->repMatch = sqlUnsigned(row[22]);
-ret->nCount = sqlUnsigned(row[23]);
-ret->seqType = sqlUnsigned(row[24]);
-ret->srcDb = cloneString(row[25]);
-ret->srcTransId = cloneString(row[26]);
-ret->srcChrom = cloneString(row[27]);
-ret->srcChromStart = sqlUnsigned(row[28]);
-ret->srcChromEnd = sqlUnsigned(row[29]);
-ret->srcIdent = sqlUnsigned(row[30]);
-ret->srcAligned = sqlUnsigned(row[31]);
-ret->geneName = cloneString(row[32]);
-ret->geneId = cloneString(row[33]);
-ret->geneType = cloneString(row[34]);
-ret->transcriptType = cloneString(row[35]);
-ret->chainType = cloneString(row[36]);
-ret->commonName = cloneString(row[37]);
-ret->scientificName = cloneString(row[38]);
-ret->orgAbbrev = cloneString(row[39]);
-return ret;
-}
-
-struct bigTransMap *bigTransMapLoadAll(char *fileName) 
-/* Load all bigTransMap from a whitespace-separated file.
- * Dispose of this with bigTransMapFreeList(). */
-{
-struct bigTransMap *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[40];
-
-while (lineFileRow(lf, row))
-    {
-    el = bigTransMapLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct bigTransMap *bigTransMapLoadAllByChar(char *fileName, char chopper) 
-/* Load all bigTransMap from a chopper separated file.
- * Dispose of this with bigTransMapFreeList(). */
-{
-struct bigTransMap *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[40];
-
-while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
-    {
-    el = bigTransMapLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct bigTransMap *bigTransMapCommaIn(char **pS, struct bigTransMap *ret)
-/* Create a bigTransMap out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new bigTransMap */
-{
-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->oChromStart = sqlUnsignedComma(&s);
-ret->oChromEnd = sqlUnsignedComma(&s);
-sqlFixedStringComma(&s, ret->oStrand, sizeof(ret->oStrand));
-ret->oChromSize = sqlUnsignedComma(&s);
-{
-int i;
-s = sqlEatChar(s, '{');
-AllocArray(ret->oChromStarts, ret->blockCount);
-for (i=0; i<ret->blockCount; ++i)
-    {
-    ret->oChromStarts[i] = sqlSignedComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-}
-ret->oSequence = sqlStringComma(&s);
-ret->oCDS = sqlStringComma(&s);
-ret->chromSize = sqlUnsignedComma(&s);
-ret->match = sqlUnsignedComma(&s);
-ret->misMatch = sqlUnsignedComma(&s);
-ret->repMatch = sqlUnsignedComma(&s);
-ret->nCount = sqlUnsignedComma(&s);
-ret->seqType = sqlUnsignedComma(&s);
-ret->srcDb = sqlStringComma(&s);
-ret->srcTransId = sqlStringComma(&s);
-ret->srcChrom = sqlStringComma(&s);
-ret->srcChromStart = sqlUnsignedComma(&s);
-ret->srcChromEnd = sqlUnsignedComma(&s);
-ret->srcIdent = sqlUnsignedComma(&s);
-ret->srcAligned = sqlUnsignedComma(&s);
-ret->geneName = sqlStringComma(&s);
-ret->geneId = sqlStringComma(&s);
-ret->geneType = sqlStringComma(&s);
-ret->transcriptType = sqlStringComma(&s);
-ret->chainType = sqlStringComma(&s);
-ret->commonName = sqlStringComma(&s);
-ret->scientificName = sqlStringComma(&s);
-ret->orgAbbrev = sqlStringComma(&s);
-*pS = s;
-return ret;
-}
-
-void bigTransMapFree(struct bigTransMap **pEl)
-/* Free a single dynamically allocated bigTransMap such as created
- * with bigTransMapLoad(). */
-{
-struct bigTransMap *el;
-
-if ((el = *pEl) == NULL) return;
-freeMem(el->chrom);
-freeMem(el->name);
-freeMem(el->blockSizes);
-freeMem(el->chromStarts);
-freeMem(el->oChromStarts);
-freeMem(el->oSequence);
-freeMem(el->oCDS);
-freeMem(el->srcDb);
-freeMem(el->srcTransId);
-freeMem(el->srcChrom);
-freeMem(el->geneName);
-freeMem(el->geneId);
-freeMem(el->geneType);
-freeMem(el->transcriptType);
-freeMem(el->chainType);
-freeMem(el->commonName);
-freeMem(el->scientificName);
-freeMem(el->orgAbbrev);
-freez(pEl);
-}
-
-void bigTransMapFreeList(struct bigTransMap **pList)
-/* Free a list of dynamically allocated bigTransMap's */
-{
-struct bigTransMap *el, *next;
-
-for (el = *pList; el != NULL; el = next)
-    {
-    next = el->next;
-    bigTransMapFree(&el);
-    }
-*pList = NULL;
-}
-
-void bigTransMapOutput(struct bigTransMap *el, FILE *f, char sep, char lastSep) 
-/* Print out bigTransMap.  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, "%u", el->oChromStart);
-fputc(sep,f);
-fprintf(f, "%u", el->oChromEnd);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->oStrand);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%u", el->oChromSize);
-fputc(sep,f);
-{
-int i;
-if (sep == ',') fputc('{',f);
-for (i=0; i<el->blockCount; ++i)
-    {
-    fprintf(f, "%d", el->oChromStarts[i]);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-}
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->oSequence);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->oCDS);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%u", el->chromSize);
-fputc(sep,f);
-fprintf(f, "%u", el->match);
-fputc(sep,f);
-fprintf(f, "%u", el->misMatch);
-fputc(sep,f);
-fprintf(f, "%u", el->repMatch);
-fputc(sep,f);
-fprintf(f, "%u", el->nCount);
-fputc(sep,f);
-fprintf(f, "%u", el->seqType);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->srcDb);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->srcTransId);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->srcChrom);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%u", el->srcChromStart);
-fputc(sep,f);
-fprintf(f, "%u", el->srcChromEnd);
-fputc(sep,f);
-fprintf(f, "%u", el->srcIdent);
-fputc(sep,f);
-fprintf(f, "%u", el->srcAligned);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->geneName);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->geneId);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->geneType);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->transcriptType);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->chainType);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->commonName);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->scientificName);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->orgAbbrev);
-if (sep == ',') fputc('"',f);
-fputc(lastSep,f);
-}
-
-/* -------------------------------- End autoSql Generated Code -------------------------------- */
-