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/stsInfo.c src/hg/cgilib/stsInfo.c
new file mode 100644
index 0000000..833516d
--- /dev/null
+++ src/hg/cgilib/stsInfo.c
@@ -0,0 +1,439 @@
+/* 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);
+}
+