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/cgilib/fishClones.c src/hg/cgilib/fishClones.c
new file mode 100644
index 0000000..29f535c
--- /dev/null
+++ src/hg/cgilib/fishClones.c
@@ -0,0 +1,278 @@
+/* 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);
+}
+