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/stsInfo.c src/hg/lib/stsInfo.c
deleted file mode 100644
index 833516d..0000000
--- src/hg/lib/stsInfo.c
+++ /dev/null
@@ -1,439 +0,0 @@
-/* stsInfo.c was originally generated by the autoSql program, which also 
- * generated stsInfo.h and stsInfo.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 "jksql.h"
-#include "stsInfo.h"
-
-
-struct stsInfo *stsInfoLoad(char **row)
-/* Load a stsInfo from row fetched with select * from stsInfo
- * from database.  Dispose of this with stsInfoFree(). */
-{
-struct stsInfo *ret;
-int sizeOne;
-
-AllocVar(ret);
-ret->gbCount = sqlUnsigned(row[2]);
-ret->gdbCount = sqlUnsigned(row[4]);
-ret->nameCount = sqlUnsigned(row[6]);
-ret->otherDbstsCount = sqlUnsigned(row[9]);
-ret->otherUCSCcount = sqlUnsigned(row[16]);
-ret->mergeUCSCcount = sqlUnsigned(row[18]);
-ret->identNo = sqlUnsigned(row[0]);
-ret->name = cloneString(row[1]);
-sqlStringDynamicArray(row[3], &ret->genbank, &sizeOne);
-assert(sizeOne == ret->gbCount);
-sqlStringDynamicArray(row[5], &ret->gdb, &sizeOne);
-assert(sizeOne == ret->gdbCount);
-sqlStringDynamicArray(row[7], &ret->otherNames, &sizeOne);
-assert(sizeOne == ret->nameCount);
-ret->dbSTSid = sqlUnsigned(row[8]);
-sqlUnsignedDynamicArray(row[10], &ret->otherDbSTS, &sizeOne);
-assert(sizeOne == ret->otherDbstsCount);
-ret->leftPrimer = cloneString(row[11]);
-ret->rightPrimer = cloneString(row[12]);
-ret->distance = cloneString(row[13]);
-ret->organism = cloneString(row[14]);
-ret->sequence = sqlUnsigned(row[15]);
-/* sqlUnsignedDynamicArray(row[17], &ret->otherUCSC, &sizeOne);
-   assert(sizeOne == ret->otherUCSCcount);
-   sqlUnsignedDynamicArray(row[19], &ret->mergeUCSC, &sizeOne);
-   assert(sizeOne == ret->mergeUCSCcount); */
-ret->genethonName = cloneString(row[20]);
-ret->genethonChr = cloneString(row[21]);
-ret->genethonPos = atof(row[22]);
-ret->genethonLOD = atof(row[23]);
-ret->marshfieldName = cloneString(row[24]);
-ret->marshfieldChr = cloneString(row[25]);
-ret->marshfieldPos = atof(row[26]);
-ret->marshfieldLOD = atof(row[27]);
-ret->wiyacName = cloneString(row[28]);
-ret->wiyacChr = cloneString(row[29]);
-ret->wiyacPos = atof(row[30]);
-ret->wiyacLOD = atof(row[31]);
-ret->wirhName = cloneString(row[32]);
-ret->wirhChr = cloneString(row[33]);
-ret->wirhPos = atof(row[34]);
-ret->wirhLOD = atof(row[35]);
-ret->gm99gb4Name = cloneString(row[36]);
-ret->gm99gb4Chr = cloneString(row[37]);
-ret->gm99gb4Pos = atof(row[38]);
-ret->gm99gb4LOD = atof(row[39]);
-ret->gm99g3Name = cloneString(row[40]);
-ret->gm99g3Chr = cloneString(row[41]);
-ret->gm99g3Pos = atof(row[42]);
-ret->gm99g3LOD = atof(row[43]);
-ret->tngName = cloneString(row[44]);
-ret->tngChr = cloneString(row[45]);
-ret->tngPos = atof(row[46]);
-ret->tngLOD = atof(row[47]);
-return ret;
-}
-
-struct stsInfo *stsInfoLoadAll(char *fileName) 
-/* Load all stsInfo from a tab-separated file.
- * Dispose of this with stsInfoFreeList(). */
-{
-struct stsInfo *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[48];
-
-while (lineFileRow(lf, row))
-    {
-    el = stsInfoLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct stsInfo *stsInfoCommaIn(char **pS, struct stsInfo *ret)
-/* Create a stsInfo out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new stsInfo */
-{
-char *s = *pS;
-int i;
-
-if (ret == NULL)
-    AllocVar(ret);
-ret->identNo = sqlUnsignedComma(&s);
-ret->name = sqlStringComma(&s);
-ret->gbCount = sqlUnsignedComma(&s);
-s = sqlEatChar(s, '{');
-AllocArray(ret->genbank, ret->gbCount);
-for (i=0; i<ret->gbCount; ++i)
-    {
-    ret->genbank[i] = sqlStringComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-ret->gdbCount = sqlUnsignedComma(&s);
-s = sqlEatChar(s, '{');
-AllocArray(ret->gdb, ret->gdbCount);
-for (i=0; i<ret->gdbCount; ++i)
-    {
-    ret->gdb[i] = sqlStringComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-ret->nameCount = sqlUnsignedComma(&s);
-s = sqlEatChar(s, '{');
-AllocArray(ret->otherNames, ret->nameCount);
-for (i=0; i<ret->nameCount; ++i)
-    {
-    ret->otherNames[i] = sqlStringComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-ret->dbSTSid = sqlUnsignedComma(&s);
-ret->otherDbstsCount = sqlUnsignedComma(&s);
-s = sqlEatChar(s, '{');
-AllocArray(ret->otherDbSTS, ret->otherDbstsCount);
-for (i=0; i<ret->otherDbstsCount; ++i)
-    {
-    ret->otherDbSTS[i] = sqlUnsignedComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-ret->leftPrimer = sqlStringComma(&s);
-ret->rightPrimer = sqlStringComma(&s);
-ret->distance = sqlStringComma(&s);
-ret->organism = sqlStringComma(&s);
-ret->sequence = sqlUnsignedComma(&s);
-ret->otherUCSCcount = sqlUnsignedComma(&s);
-s = sqlEatChar(s, '{');
-AllocArray(ret->otherUCSC, ret->otherUCSCcount);
-for (i=0; i<ret->otherUCSCcount; ++i)
-    {
-    ret->otherUCSC[i] = sqlUnsignedComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-ret->mergeUCSCcount = sqlUnsignedComma(&s);
-s = sqlEatChar(s, '{');
-AllocArray(ret->mergeUCSC, ret->mergeUCSCcount);
-for (i=0; i<ret->mergeUCSCcount; ++i)
-    {
-    ret->mergeUCSC[i] = sqlUnsignedComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-ret->genethonName = sqlStringComma(&s);
-ret->genethonChr = sqlStringComma(&s);
-ret->genethonPos = sqlSignedComma(&s);
-ret->genethonLOD = sqlSignedComma(&s);
-ret->marshfieldName = sqlStringComma(&s);
-ret->marshfieldChr = sqlStringComma(&s);
-ret->marshfieldPos = sqlSignedComma(&s);
-ret->marshfieldLOD = sqlSignedComma(&s);
-ret->wiyacName = sqlStringComma(&s);
-ret->wiyacChr = sqlStringComma(&s);
-ret->wiyacPos = sqlSignedComma(&s);
-ret->wiyacLOD = sqlSignedComma(&s);
-ret->wirhName = sqlStringComma(&s);
-ret->wirhChr = sqlStringComma(&s);
-ret->wirhPos = sqlSignedComma(&s);
-ret->wirhLOD = sqlSignedComma(&s);
-ret->gm99gb4Name = sqlStringComma(&s);
-ret->gm99gb4Chr = sqlStringComma(&s);
-ret->gm99gb4Pos = sqlSignedComma(&s);
-ret->gm99gb4LOD = sqlSignedComma(&s);
-ret->gm99g3Name = sqlStringComma(&s);
-ret->gm99g3Chr = sqlStringComma(&s);
-ret->gm99g3Pos = sqlSignedComma(&s);
-ret->gm99g3LOD = sqlSignedComma(&s);
-ret->tngName = sqlStringComma(&s);
-ret->tngChr = sqlStringComma(&s);
-ret->tngPos = sqlSignedComma(&s);
-ret->tngLOD = sqlSignedComma(&s);
-*pS = s;
-return ret;
-}
-
-void stsInfoFree(struct stsInfo **pEl)
-/* Free a single dynamically allocated stsInfo such as created
- * with stsInfoLoad(). */
-{
-struct stsInfo *el;
-
-if ((el = *pEl) == NULL) return;
-freeMem(el->name);
-/* All strings in genbank are allocated at once, so only need to free first. */
-if (el->genbank != NULL)
-    freeMem(el->genbank[0]);
-freeMem(el->genbank);
-/* All strings in gdb are allocated at once, so only need to free first. */
-if (el->gdb != NULL)
-    freeMem(el->gdb[0]);
-freeMem(el->gdb);
-/* All strings in otherNames are allocated at once, so only need to free first. */
-if (el->otherNames != NULL)
-    freeMem(el->otherNames[0]);
-freeMem(el->otherNames);
-freeMem(el->otherDbSTS);
-freeMem(el->leftPrimer);
-freeMem(el->rightPrimer);
-freeMem(el->distance);
-freeMem(el->organism);
-freeMem(el->otherUCSC);
-freeMem(el->mergeUCSC);
-freeMem(el->genethonName);
-freeMem(el->genethonChr);
-freeMem(el->marshfieldName);
-freeMem(el->marshfieldChr);
-freeMem(el->wiyacName);
-freeMem(el->wiyacChr);
-freeMem(el->wirhName);
-freeMem(el->wirhChr);
-freeMem(el->gm99gb4Name);
-freeMem(el->gm99gb4Chr);
-freeMem(el->gm99g3Name);
-freeMem(el->gm99g3Chr);
-freeMem(el->tngName);
-freeMem(el->tngChr);
-freez(pEl);
-}
-
-void stsInfoFreeList(struct stsInfo **pList)
-/* Free a list of dynamically allocated stsInfo's */
-{
-struct stsInfo *el, *next;
-
-for (el = *pList; el != NULL; el = next)
-    {
-    next = el->next;
-    stsInfoFree(&el);
-    }
-*pList = NULL;
-}
-
-void stsInfoOutput(struct stsInfo *el, FILE *f, char sep, char lastSep) 
-/* Print out stsInfo.  Separate fields with sep. Follow last field with lastSep. */
-{
-int i;
-fprintf(f, "%u", el->identNo);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->name);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%u", el->gbCount);
-fputc(sep,f);
-if (sep == ',') fputc('{',f);
-for (i=0; i<el->gbCount; ++i)
-    {
-    if (sep == ',') fputc('"',f);
-    fprintf(f, "%s", el->genbank[i]);
-    if (sep == ',') fputc('"',f);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-fputc(sep,f);
-fprintf(f, "%u", el->gdbCount);
-fputc(sep,f);
-if (sep == ',') fputc('{',f);
-for (i=0; i<el->gdbCount; ++i)
-    {
-    if (sep == ',') fputc('"',f);
-    fprintf(f, "%s", el->gdb[i]);
-    if (sep == ',') fputc('"',f);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-fputc(sep,f);
-fprintf(f, "%u", el->nameCount);
-fputc(sep,f);
-if (sep == ',') fputc('{',f);
-for (i=0; i<el->nameCount; ++i)
-    {
-    if (sep == ',') fputc('"',f);
-    fprintf(f, "%s", el->otherNames[i]);
-    if (sep == ',') fputc('"',f);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-fputc(sep,f);
-fprintf(f, "%u", el->dbSTSid);
-fputc(sep,f);
-fprintf(f, "%u", el->otherDbstsCount);
-fputc(sep,f);
-if (sep == ',') fputc('{',f);
-for (i=0; i<el->otherDbstsCount; ++i)
-    {
-    fprintf(f, "%u", el->otherDbSTS[i]);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->leftPrimer);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->rightPrimer);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->distance);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->organism);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%u", el->sequence);
-fputc(sep,f);
-fprintf(f, "%u", el->otherUCSCcount);
-fputc(sep,f);
-if (sep == ',') fputc('{',f);
-for (i=0; i<el->otherUCSCcount; ++i)
-    {
-    fprintf(f, "%u", el->otherUCSC[i]);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-fputc(sep,f);
-fprintf(f, "%u", el->mergeUCSCcount);
-fputc(sep,f);
-if (sep == ',') fputc('{',f);
-for (i=0; i<el->mergeUCSCcount; ++i)
-    {
-    fprintf(f, "%u", el->mergeUCSC[i]);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->genethonName);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->genethonChr);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%f", el->genethonPos);
-fputc(sep,f);
-fprintf(f, "%f", el->genethonLOD);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->marshfieldName);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->marshfieldChr);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%f", el->marshfieldPos);
-fputc(sep,f);
-fprintf(f, "%f", el->marshfieldLOD);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->wiyacName);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->wiyacChr);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%f", el->wiyacPos);
-fputc(sep,f);
-fprintf(f, "%f", el->wiyacLOD);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->wirhName);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->wirhChr);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%f", el->wirhPos);
-fputc(sep,f);
-fprintf(f, "%f", el->wirhLOD);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->gm99gb4Name);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->gm99gb4Chr);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%f", el->gm99gb4Pos);
-fputc(sep,f);
-fprintf(f, "%f", el->gm99gb4LOD);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->gm99g3Name);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->gm99g3Chr);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%f", el->gm99g3Pos);
-fputc(sep,f);
-fprintf(f, "%f", el->gm99g3LOD);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->tngName);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->tngChr);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%f", el->tngPos);
-fputc(sep,f);
-fprintf(f, "%f", el->tngLOD);
-fputc(lastSep,f);
-}
-