a28db878858e0398a84afa488da7061e29b0918d
braney
  Wed Aug 20 16:37:22 2014 -0700
first cut at genePredToBigGenePred  refs #13681
diff --git src/hg/lib/bigGenePred.c src/hg/lib/bigGenePred.c
new file mode 100644
index 0000000..2f72c19
--- /dev/null
+++ src/hg/lib/bigGenePred.c
@@ -0,0 +1,284 @@
+/* bigGenePred.c was originally generated by the autoSql program, which also 
+ * generated bigGenePred.h and bigGenePred.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 "bigGenePred.h"
+
+
+
+char *bigGenePredCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,chromStarts,name2,cdsStartStat,cdsEndStat,exonFrames,type,geneName,geneName2,geneType";
+
+struct bigGenePred *bigGenePredLoad(char **row)
+/* Load a bigGenePred from row fetched with select * from bigGenePred
+ * from database.  Dispose of this with bigGenePredFree(). */
+{
+struct bigGenePred *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->itemRgb = sqlUnsigned(row[8]);
+{
+int sizeOne;
+sqlUnsignedDynamicArray(row[10], &ret->blockSizes, &sizeOne);
+assert(sizeOne == ret->blockCount);
+}
+{
+int sizeOne;
+sqlUnsignedDynamicArray(row[11], &ret->chromStarts, &sizeOne);
+assert(sizeOne == ret->blockCount);
+}
+ret->name2 = cloneString(row[12]);
+ret->cdsStartStat = parseCdsStat(row[13]);
+ret->cdsEndStat = parseCdsStat(row[14]);
+{
+int sizeOne;
+sqlSignedDynamicArray(row[15], &ret->exonFrames, &sizeOne);
+assert(sizeOne == ret->blockCount);
+}
+ret->type = cloneString(row[16]);
+ret->geneName = cloneString(row[17]);
+ret->geneName2 = cloneString(row[18]);
+ret->geneType = cloneString(row[19]);
+return ret;
+}
+
+struct bigGenePred *bigGenePredLoadAll(char *fileName) 
+/* Load all bigGenePred from a whitespace-separated file.
+ * Dispose of this with bigGenePredFreeList(). */
+{
+struct bigGenePred *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[20];
+
+while (lineFileRow(lf, row))
+    {
+    el = bigGenePredLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bigGenePred *bigGenePredLoadAllByChar(char *fileName, char chopper) 
+/* Load all bigGenePred from a chopper separated file.
+ * Dispose of this with bigGenePredFreeList(). */
+{
+struct bigGenePred *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[20];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = bigGenePredLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+#ifdef NOTNOW
+struct bigGenePred *bigGenePredCommaIn(char **pS, struct bigGenePred *ret)
+/* Create a bigGenePred out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new bigGenePred */
+{
+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->itemRgb = 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->name2 = sqlStringComma(&s);
+ret->cdsStartStat = parseCdsStat(&s);
+ret->cdsEndStat = parseCdsStat(&s);
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->exonFrames, ret->blockCount);
+for (i=0; i<ret->blockCount; ++i)
+    {
+    ret->exonFrames[i] = sqlSignedComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+ret->type = sqlStringComma(&s);
+ret->geneName = sqlStringComma(&s);
+ret->geneName2 = sqlStringComma(&s);
+ret->geneType = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+#endif
+
+void bigGenePredFree(struct bigGenePred **pEl)
+/* Free a single dynamically allocated bigGenePred such as created
+ * with bigGenePredLoad(). */
+{
+struct bigGenePred *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->blockSizes);
+freeMem(el->chromStarts);
+freeMem(el->name2);
+freeMem(el->exonFrames);
+freeMem(el->type);
+freeMem(el->geneName);
+freeMem(el->geneName2);
+freeMem(el->geneType);
+freez(pEl);
+}
+
+void bigGenePredFreeList(struct bigGenePred **pList)
+/* Free a list of dynamically allocated bigGenePred's */
+{
+struct bigGenePred *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    bigGenePredFree(&el);
+    }
+*pList = NULL;
+}
+
+void bigGenePredOutput(struct bigGenePred *el, FILE *f, char sep, char lastSep) 
+/* Print out bigGenePred.  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->itemRgb);
+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);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->name2);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", genePredCdsStatStr(el->cdsStartStat));
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", genePredCdsStatStr(el->cdsEndStat));
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->blockCount; ++i)
+    {
+    fprintf(f, "%d", el->exonFrames[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->type);
+if (sep == ',') fputc('"',f);
+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->geneName2);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->geneType);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+