314b81670d2d1446d4da81108ac0ce2a72fc569d
markd
  Fri Jan 6 15:32:57 2017 -0800
bigTransMap hgc working

diff --git src/hg/lib/bigTransMap.c src/hg/lib/bigTransMap.c
new file mode 100644
index 0000000..8e4a491
--- /dev/null
+++ src/hg/lib/bigTransMap.c
@@ -0,0 +1,370 @@
+/* bigTransMap.c was originally generated by the autoSql program, which also 
+ * generated bigTransMap.h and bigTransMap.sql.  This module links the database and
+ * the RAM representation of objects. */
+
+#include "common.h"
+#include "linefile.h"
+#include "dystring.h"
+#include "jksql.h"
+#include "bigTransMap.h"
+
+
+
+char *bigTransMapCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,reserved,blockCount,blockSizes,chromStarts,oChromStart,oChromEnd,oStrand,oChromSize,oChromStarts,oSequence,oCDS,chromSize,match,misMatch,repMatch,nCount,seqType,srcDb,srcChrom,srcChromStart,srcChromEnd,srcScore,srcAligned,geneName,geneId,geneType,transcriptType,chainType,commonName,orgAbbrev";
+
+struct bigTransMap *bigTransMapLoad(char **row)
+/* Load a bigTransMap from row fetched with select * from bigTransMap
+ * from database.  Dispose of this with bigTransMapFree(). */
+{
+struct bigTransMap *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]);
+safecpy(ret->strand, sizeof(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->oChromStart = sqlUnsigned(row[12]);
+ret->oChromEnd = sqlUnsigned(row[13]);
+safecpy(ret->oStrand, sizeof(ret->oStrand), row[14]);
+ret->oChromSize = sqlUnsigned(row[15]);
+{
+int sizeOne;
+sqlSignedDynamicArray(row[16], &ret->oChromStarts, &sizeOne);
+assert(sizeOne == ret->blockCount);
+}
+ret->oSequence = cloneString(row[17]);
+ret->oCDS = cloneString(row[18]);
+ret->chromSize = sqlUnsigned(row[19]);
+ret->match = sqlUnsigned(row[20]);
+ret->misMatch = sqlUnsigned(row[21]);
+ret->repMatch = sqlUnsigned(row[22]);
+ret->nCount = sqlUnsigned(row[23]);
+ret->seqType = sqlUnsigned(row[24]);
+ret->srcDb = cloneString(row[25]);
+ret->srcChrom = cloneString(row[26]);
+ret->srcChromStart = sqlUnsigned(row[27]);
+ret->srcChromEnd = sqlUnsigned(row[28]);
+ret->srcScore = sqlUnsigned(row[29]);
+ret->srcAligned = sqlUnsigned(row[30]);
+ret->geneName = cloneString(row[31]);
+ret->geneId = cloneString(row[32]);
+ret->geneType = cloneString(row[33]);
+ret->transcriptType = cloneString(row[34]);
+ret->chainType = cloneString(row[35]);
+ret->commonName = cloneString(row[36]);
+ret->orgAbbrev = cloneString(row[37]);
+return ret;
+}
+
+struct bigTransMap *bigTransMapLoadAll(char *fileName) 
+/* Load all bigTransMap from a whitespace-separated file.
+ * Dispose of this with bigTransMapFreeList(). */
+{
+struct bigTransMap *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[38];
+
+while (lineFileRow(lf, row))
+    {
+    el = bigTransMapLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bigTransMap *bigTransMapLoadAllByChar(char *fileName, char chopper) 
+/* Load all bigTransMap from a chopper separated file.
+ * Dispose of this with bigTransMapFreeList(). */
+{
+struct bigTransMap *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[38];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = bigTransMapLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bigTransMap *bigTransMapCommaIn(char **pS, struct bigTransMap *ret)
+/* Create a bigTransMap out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new bigTransMap */
+{
+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->oChromStart = sqlUnsignedComma(&s);
+ret->oChromEnd = sqlUnsignedComma(&s);
+sqlFixedStringComma(&s, ret->oStrand, sizeof(ret->oStrand));
+ret->oChromSize = sqlUnsignedComma(&s);
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->oChromStarts, ret->blockCount);
+for (i=0; i<ret->blockCount; ++i)
+    {
+    ret->oChromStarts[i] = sqlSignedComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+ret->oSequence = sqlStringComma(&s);
+ret->oCDS = sqlStringComma(&s);
+ret->chromSize = sqlUnsignedComma(&s);
+ret->match = sqlUnsignedComma(&s);
+ret->misMatch = sqlUnsignedComma(&s);
+ret->repMatch = sqlUnsignedComma(&s);
+ret->nCount = sqlUnsignedComma(&s);
+ret->seqType = sqlUnsignedComma(&s);
+ret->srcDb = sqlStringComma(&s);
+ret->srcChrom = sqlStringComma(&s);
+ret->srcChromStart = sqlUnsignedComma(&s);
+ret->srcChromEnd = sqlUnsignedComma(&s);
+ret->srcScore = sqlUnsignedComma(&s);
+ret->srcAligned = sqlUnsignedComma(&s);
+ret->geneName = sqlStringComma(&s);
+ret->geneId = sqlStringComma(&s);
+ret->geneType = sqlStringComma(&s);
+ret->transcriptType = sqlStringComma(&s);
+ret->chainType = sqlStringComma(&s);
+ret->commonName = sqlStringComma(&s);
+ret->orgAbbrev = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void bigTransMapFree(struct bigTransMap **pEl)
+/* Free a single dynamically allocated bigTransMap such as created
+ * with bigTransMapLoad(). */
+{
+struct bigTransMap *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->blockSizes);
+freeMem(el->chromStarts);
+freeMem(el->oChromStarts);
+freeMem(el->oSequence);
+freeMem(el->oCDS);
+freeMem(el->srcDb);
+freeMem(el->srcChrom);
+freeMem(el->geneName);
+freeMem(el->geneId);
+freeMem(el->geneType);
+freeMem(el->transcriptType);
+freeMem(el->chainType);
+freeMem(el->commonName);
+freeMem(el->orgAbbrev);
+freez(pEl);
+}
+
+void bigTransMapFreeList(struct bigTransMap **pList)
+/* Free a list of dynamically allocated bigTransMap's */
+{
+struct bigTransMap *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    bigTransMapFree(&el);
+    }
+*pList = NULL;
+}
+
+void bigTransMapOutput(struct bigTransMap *el, FILE *f, char sep, char lastSep) 
+/* Print out bigTransMap.  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, "%u", el->oChromStart);
+fputc(sep,f);
+fprintf(f, "%u", el->oChromEnd);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->oStrand);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->oChromSize);
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->blockCount; ++i)
+    {
+    fprintf(f, "%d", el->oChromStarts[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->oSequence);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->oCDS);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->chromSize);
+fputc(sep,f);
+fprintf(f, "%u", el->match);
+fputc(sep,f);
+fprintf(f, "%u", el->misMatch);
+fputc(sep,f);
+fprintf(f, "%u", el->repMatch);
+fputc(sep,f);
+fprintf(f, "%u", el->nCount);
+fputc(sep,f);
+fprintf(f, "%u", el->seqType);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->srcDb);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->srcChrom);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->srcChromStart);
+fputc(sep,f);
+fprintf(f, "%u", el->srcChromEnd);
+fputc(sep,f);
+fprintf(f, "%u", el->srcScore);
+fputc(sep,f);
+fprintf(f, "%u", el->srcAligned);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->geneName);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->geneId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->geneType);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->transcriptType);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->chainType);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->commonName);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->orgAbbrev);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+