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/fishClones.c src/hg/lib/fishClones.c
deleted file mode 100644
index 29f535c..0000000
--- src/hg/lib/fishClones.c
+++ /dev/null
@@ -1,278 +0,0 @@
-/* fishClones.c was originally generated by the autoSql program, which also 
- * generated fishClones.h and fishClones.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 "fishClones.h"
-
-
-struct fishClones *fishClonesLoad(char **row)
-/* Load a fishClones from row fetched with select * from fishClones
- * from database.  Dispose of this with fishClonesFree(). */
-{
-struct fishClones *ret;
-int sizeOne;
-
-AllocVar(ret);
-ret->placeCount = sqlUnsigned(row[5]);
-ret->accCount = sqlUnsigned(row[10]);
-ret->stsCount = sqlUnsigned(row[12]);
-ret->beCount = sqlUnsigned(row[14]);
-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]);
-sqlStringDynamicArray(row[6], &ret->bandStarts, &sizeOne);
-assert(sizeOne == ret->placeCount);
-sqlStringDynamicArray(row[7], &ret->bandEnds, &sizeOne);
-assert(sizeOne == ret->placeCount);
-sqlStringDynamicArray(row[8], &ret->labs, &sizeOne);
-assert(sizeOne == ret->placeCount);
-ret->placeType = cloneString(row[9]);
-sqlStringDynamicArray(row[11], &ret->accNames, &sizeOne);
-assert(sizeOne == ret->accCount);
-sqlStringDynamicArray(row[13], &ret->stsNames, &sizeOne);
-assert(sizeOne == ret->stsCount);
-sqlStringDynamicArray(row[15], &ret->beNames, &sizeOne);
-assert(sizeOne == ret->beCount);
-return ret;
-}
-
-struct fishClones *fishClonesLoadAll(char *fileName) 
-/* Load all fishClones from a tab-separated file.
- * Dispose of this with fishClonesFreeList(). */
-{
-struct fishClones *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[16];
-
-while (lineFileRow(lf, row))
-    {
-    el = fishClonesLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct fishClones *fishClonesCommaIn(char **pS, struct fishClones *ret)
-/* Create a fishClones out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new fishClones */
-{
-char *s = *pS;
-int i;
-
-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->placeCount = sqlUnsignedComma(&s);
-s = sqlEatChar(s, '{');
-AllocArray(ret->bandStarts, ret->placeCount);
-for (i=0; i<ret->placeCount; ++i)
-    {
-    ret->bandStarts[i] = sqlStringComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-s = sqlEatChar(s, '{');
-AllocArray(ret->bandEnds, ret->placeCount);
-for (i=0; i<ret->placeCount; ++i)
-    {
-    ret->bandEnds[i] = sqlStringComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-s = sqlEatChar(s, '{');
-AllocArray(ret->labs, ret->placeCount);
-for (i=0; i<ret->placeCount; ++i)
-    {
-    ret->labs[i] = sqlStringComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-ret->placeType = sqlStringComma(&s);
-ret->accCount = sqlUnsignedComma(&s);
-s = sqlEatChar(s, '{');
-AllocArray(ret->accNames, ret->accCount);
-for (i=0; i<ret->accCount; ++i)
-    {
-    ret->accNames[i] = sqlStringComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-ret->stsCount = sqlUnsignedComma(&s);
-s = sqlEatChar(s, '{');
-AllocArray(ret->stsNames, ret->stsCount);
-for (i=0; i<ret->stsCount; ++i)
-    {
-    ret->stsNames[i] = sqlStringComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-ret->beCount = sqlUnsignedComma(&s);
-s = sqlEatChar(s, '{');
-AllocArray(ret->beNames, ret->beCount);
-for (i=0; i<ret->beCount; ++i)
-    {
-    ret->beNames[i] = sqlStringComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-*pS = s;
-return ret;
-}
-
-void fishClonesFree(struct fishClones **pEl)
-/* Free a single dynamically allocated fishClones such as created
- * with fishClonesLoad(). */
-{
-struct fishClones *el;
-
-if ((el = *pEl) == NULL) return;
-freeMem(el->chrom);
-freeMem(el->name);
-/* All strings in bandStarts are allocated at once, so only need to free first. */
-if (el->bandStarts != NULL)
-    freeMem(el->bandStarts[0]);
-freeMem(el->bandStarts);
-/* All strings in bandEnds are allocated at once, so only need to free first. */
-if (el->bandEnds != NULL)
-    freeMem(el->bandEnds[0]);
-freeMem(el->bandEnds);
-/* All strings in labs are allocated at once, so only need to free first. */
-if (el->labs != NULL)
-    freeMem(el->labs[0]);
-freeMem(el->labs);
-freeMem(el->placeType);
-/* All strings in accNames are allocated at once, so only need to free first. */
-if (el->accNames != NULL)
-    freeMem(el->accNames[0]);
-freeMem(el->accNames);
-/* All strings in stsNames are allocated at once, so only need to free first. */
-if (el->stsNames != NULL)
-    freeMem(el->stsNames[0]);
-freeMem(el->stsNames);
-/* All strings in beNames are allocated at once, so only need to free first. */
-if (el->beNames != NULL)
-    freeMem(el->beNames[0]);
-freeMem(el->beNames);
-freez(pEl);
-}
-
-void fishClonesFreeList(struct fishClones **pList)
-/* Free a list of dynamically allocated fishClones's */
-{
-struct fishClones *el, *next;
-
-for (el = *pList; el != NULL; el = next)
-    {
-    next = el->next;
-    fishClonesFree(&el);
-    }
-*pList = NULL;
-}
-
-void fishClonesOutput(struct fishClones *el, FILE *f, char sep, char lastSep) 
-/* Print out fishClones.  Separate fields with sep. Follow last field with lastSep. */
-{
-int i;
-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);
-fprintf(f, "%u", el->placeCount);
-fputc(sep,f);
-if (sep == ',') fputc('{',f);
-for (i=0; i<el->placeCount; ++i)
-    {
-    if (sep == ',') fputc('"',f);
-    fprintf(f, "%s", el->bandStarts[i]);
-    if (sep == ',') fputc('"',f);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-fputc(sep,f);
-if (sep == ',') fputc('{',f);
-for (i=0; i<el->placeCount; ++i)
-    {
-    if (sep == ',') fputc('"',f);
-    fprintf(f, "%s", el->bandEnds[i]);
-    if (sep == ',') fputc('"',f);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-fputc(sep,f);
-if (sep == ',') fputc('{',f);
-for (i=0; i<el->placeCount; ++i)
-    {
-    if (sep == ',') fputc('"',f);
-    fprintf(f, "%s", el->labs[i]);
-    if (sep == ',') fputc('"',f);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->placeType);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%u", el->accCount);
-fputc(sep,f);
-if (sep == ',') fputc('{',f);
-for (i=0; i<el->accCount; ++i)
-    {
-    if (sep == ',') fputc('"',f);
-    fprintf(f, "%s", el->accNames[i]);
-    if (sep == ',') fputc('"',f);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-fputc(sep,f);
-fprintf(f, "%u", el->stsCount);
-fputc(sep,f);
-if (sep == ',') fputc('{',f);
-for (i=0; i<el->stsCount; ++i)
-    {
-    if (sep == ',') fputc('"',f);
-    fprintf(f, "%s", el->stsNames[i]);
-    if (sep == ',') fputc('"',f);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-fputc(sep,f);
-fprintf(f, "%u", el->beCount);
-fputc(sep,f);
-if (sep == ',') fputc('{',f);
-for (i=0; i<el->beCount; ++i)
-    {
-    if (sep == ',') fputc('"',f);
-    fprintf(f, "%s", el->beNames[i]);
-    if (sep == ',') fputc('"',f);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-fputc(lastSep,f);
-}
-