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/pseudoGeneLink.c src/hg/cgilib/pseudoGeneLink.c
new file mode 100644
index 0000000..ace25d9
--- /dev/null
+++ src/hg/cgilib/pseudoGeneLink.c
@@ -0,0 +1,405 @@
+/* pseudoGeneLink.c was originally generated by the autoSql program, which also 
+ * generated pseudoGeneLink.h and pseudoGeneLink.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 "dystring.h"
+#include "jksql.h"
+#include "pseudoGeneLink.h"
+
+
+struct pseudoGeneLink *pseudoGeneLinkLoad(char **row)
+/* Load a pseudoGeneLink from row fetched with select * from pseudoGeneLink
+ * from database.  Dispose of this with pseudoGeneLinkFree(). */
+{
+struct pseudoGeneLink *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]);
+strcpy(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->trfRatio = atof(row[12]);
+ret->type = cloneString(row[13]);
+ret->axtScore = sqlSigned(row[14]);
+ret->gChrom = cloneString(row[15]);
+ret->gStart = sqlSigned(row[16]);
+ret->gEnd = sqlSigned(row[17]);
+strcpy(ret->gStrand, row[18]);
+ret->exonCount = sqlUnsigned(row[19]);
+ret->geneOverlap = sqlUnsigned(row[20]);
+ret->polyA = sqlUnsigned(row[21]);
+ret->polyAstart = sqlSigned(row[22]);
+ret->exonCover = sqlSigned(row[23]);
+ret->intronCount = sqlUnsigned(row[24]);
+ret->bestAliCount = sqlUnsigned(row[25]);
+ret->matches = sqlUnsigned(row[26]);
+ret->qSize = sqlUnsigned(row[27]);
+ret->qEnd = sqlUnsigned(row[28]);
+ret->tReps = sqlUnsigned(row[29]);
+ret->overlapRhesus = sqlSigned(row[30]);
+ret->overlapMouse = sqlSigned(row[31]);
+ret->coverage = sqlUnsigned(row[32]);
+ret->label = sqlSigned(row[33]);
+ret->milliBad = sqlUnsigned(row[34]);
+ret->oldScore = sqlUnsigned(row[35]);
+ret->oldIntronCount = sqlSigned(row[36]);
+ret->processedIntrons = sqlSigned(row[37]);
+ret->conservedSpliceSites = sqlSigned(row[38]);
+ret->maxOverlap = sqlSigned(row[39]);
+ret->refSeq = cloneString(row[40]);
+ret->rStart = sqlSigned(row[41]);
+ret->rEnd = sqlSigned(row[42]);
+ret->mgc = cloneString(row[43]);
+ret->mStart = sqlSigned(row[44]);
+ret->mEnd = sqlSigned(row[45]);
+ret->kgName = cloneString(row[46]);
+ret->kStart = sqlSigned(row[47]);
+ret->kEnd = sqlSigned(row[48]);
+ret->overName = cloneString(row[49]);
+ret->overStart = sqlSigned(row[50]);
+ret->overEnd = sqlSigned(row[51]);
+strcpy(ret->overStrand, row[52]);
+ret->overlapDog = sqlSigned(row[53]);
+ret->posConf = atof(row[54]);
+ret->polyAlen = sqlUnsigned(row[55]);
+return ret;
+}
+
+struct pseudoGeneLink *pseudoGeneLinkLoadAll(char *fileName) 
+/* Load all pseudoGeneLink from a whitespace-separated file.
+ * Dispose of this with pseudoGeneLinkFreeList(). */
+{
+struct pseudoGeneLink *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[56];
+
+while (lineFileRow(lf, row))
+    {
+    el = pseudoGeneLinkLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct pseudoGeneLink *pseudoGeneLinkLoadAllByChar(char *fileName, char chopper) 
+/* Load all pseudoGeneLink from a chopper separated file.
+ * Dispose of this with pseudoGeneLinkFreeList(). */
+{
+struct pseudoGeneLink *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[56];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = pseudoGeneLinkLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct pseudoGeneLink *pseudoGeneLinkCommaIn(char **pS, struct pseudoGeneLink *ret)
+/* Create a pseudoGeneLink out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new pseudoGeneLink */
+{
+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->trfRatio = sqlFloatComma(&s);
+ret->type = sqlStringComma(&s);
+ret->axtScore = sqlSignedComma(&s);
+ret->gChrom = sqlStringComma(&s);
+ret->gStart = sqlSignedComma(&s);
+ret->gEnd = sqlSignedComma(&s);
+sqlFixedStringComma(&s, ret->gStrand, sizeof(ret->gStrand));
+ret->exonCount = sqlUnsignedComma(&s);
+ret->geneOverlap = sqlUnsignedComma(&s);
+ret->polyA = sqlUnsignedComma(&s);
+ret->polyAstart = sqlSignedComma(&s);
+ret->exonCover = sqlSignedComma(&s);
+ret->intronCount = sqlUnsignedComma(&s);
+ret->bestAliCount = sqlUnsignedComma(&s);
+ret->matches = sqlUnsignedComma(&s);
+ret->qSize = sqlUnsignedComma(&s);
+ret->qEnd = sqlUnsignedComma(&s);
+ret->tReps = sqlUnsignedComma(&s);
+ret->overlapRhesus = sqlSignedComma(&s);
+ret->overlapMouse = sqlSignedComma(&s);
+ret->coverage = sqlUnsignedComma(&s);
+ret->label = sqlSignedComma(&s);
+ret->milliBad = sqlUnsignedComma(&s);
+ret->oldScore = sqlUnsignedComma(&s);
+ret->oldIntronCount = sqlSignedComma(&s);
+ret->processedIntrons = sqlSignedComma(&s);
+ret->conservedSpliceSites = sqlSignedComma(&s);
+ret->maxOverlap = sqlSignedComma(&s);
+ret->refSeq = sqlStringComma(&s);
+ret->rStart = sqlSignedComma(&s);
+ret->rEnd = sqlSignedComma(&s);
+ret->mgc = sqlStringComma(&s);
+ret->mStart = sqlSignedComma(&s);
+ret->mEnd = sqlSignedComma(&s);
+ret->kgName = sqlStringComma(&s);
+ret->kStart = sqlSignedComma(&s);
+ret->kEnd = sqlSignedComma(&s);
+ret->overName = sqlStringComma(&s);
+ret->overStart = sqlSignedComma(&s);
+ret->overEnd = sqlSignedComma(&s);
+sqlFixedStringComma(&s, ret->overStrand, sizeof(ret->overStrand));
+ret->overlapDog = sqlSignedComma(&s);
+ret->posConf = sqlFloatComma(&s);
+ret->polyAlen = sqlUnsignedComma(&s);
+*pS = s;
+return ret;
+}
+
+void pseudoGeneLinkFree(struct pseudoGeneLink **pEl)
+/* Free a single dynamically allocated pseudoGeneLink such as created
+ * with pseudoGeneLinkLoad(). */
+{
+struct pseudoGeneLink *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->blockSizes);
+freeMem(el->chromStarts);
+freeMem(el->type);
+freeMem(el->gChrom);
+freeMem(el->refSeq);
+freeMem(el->mgc);
+freeMem(el->kgName);
+freeMem(el->overName);
+freez(pEl);
+}
+
+void pseudoGeneLinkFreeList(struct pseudoGeneLink **pList)
+/* Free a list of dynamically allocated pseudoGeneLink's */
+{
+struct pseudoGeneLink *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    pseudoGeneLinkFree(&el);
+    }
+*pList = NULL;
+}
+
+void pseudoGeneLinkOutput(struct pseudoGeneLink *el, FILE *f, char sep, char lastSep) 
+/* Print out pseudoGeneLink.  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, "%g", el->trfRatio);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->type);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%d", el->axtScore);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->gChrom);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%d", el->gStart);
+fputc(sep,f);
+fprintf(f, "%d", el->gEnd);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->gStrand);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->exonCount);
+fputc(sep,f);
+fprintf(f, "%u", el->geneOverlap);
+fputc(sep,f);
+fprintf(f, "%u", el->polyA);
+fputc(sep,f);
+fprintf(f, "%d", el->polyAstart);
+fputc(sep,f);
+fprintf(f, "%d", el->exonCover);
+fputc(sep,f);
+fprintf(f, "%u", el->intronCount);
+fputc(sep,f);
+fprintf(f, "%u", el->bestAliCount);
+fputc(sep,f);
+fprintf(f, "%u", el->matches);
+fputc(sep,f);
+fprintf(f, "%u", el->qSize);
+fputc(sep,f);
+fprintf(f, "%u", el->qEnd);
+fputc(sep,f);
+fprintf(f, "%u", el->tReps);
+fputc(sep,f);
+fprintf(f, "%d", el->overlapRhesus);
+fputc(sep,f);
+fprintf(f, "%d", el->overlapMouse);
+fputc(sep,f);
+fprintf(f, "%u", el->coverage);
+fputc(sep,f);
+fprintf(f, "%d", el->label);
+fputc(sep,f);
+fprintf(f, "%u", el->milliBad);
+fputc(sep,f);
+fprintf(f, "%u", el->oldScore);
+fputc(sep,f);
+fprintf(f, "%d", el->oldIntronCount);
+fputc(sep,f);
+fprintf(f, "%d", el->processedIntrons);
+fputc(sep,f);
+fprintf(f, "%d", el->conservedSpliceSites);
+fputc(sep,f);
+fprintf(f, "%d", el->maxOverlap);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->refSeq);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%d", el->rStart);
+fputc(sep,f);
+fprintf(f, "%d", el->rEnd);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->mgc);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%d", el->mStart);
+fputc(sep,f);
+fprintf(f, "%d", el->mEnd);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->kgName);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%d", el->kStart);
+fputc(sep,f);
+fprintf(f, "%d", el->kEnd);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->overName);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%d", el->overStart);
+fputc(sep,f);
+fprintf(f, "%d", el->overEnd);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->overStrand);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%d", el->overlapDog);
+fputc(sep,f);
+fprintf(f, "%g", el->posConf);
+fputc(sep,f);
+fprintf(f, "%u", el->polyAlen);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+