7ae4a70c26c3414a34b262329b2f7febe831923c
hiram
  Thu Jul 18 10:26:34 2013 -0700
checking in Robert's code refs #9741
diff --git src/hg/lib/rmskJoined.c src/hg/lib/rmskJoined.c
new file mode 100644
index 0000000..b02947e
--- /dev/null
+++ src/hg/lib/rmskJoined.c
@@ -0,0 +1,218 @@
+/* rmskJoined.c was originally generated by the autoSql program, which also 
+ * generated rmskJoined.h and rmskJoined.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 "rmskJoined.h"
+
+
+struct rmskJoined *rmskJoinedLoad(char **row)
+/* Load a rmskJoined from row fetched with select * from rmskJoined
+ * from database.  Dispose of this with rmskJoinedFree(). */
+{
+struct rmskJoined *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->alignStart = sqlUnsigned(row[6]);
+ret->alignEnd = 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->blockRelStarts, &sizeOne);
+assert(sizeOne == ret->blockCount);
+}
+ret->id = cloneString(row[12]);
+ret->description = cloneString(row[13]);
+return ret;
+}
+
+struct rmskJoined *rmskJoinedLoadAll(char *fileName) 
+/* Load all rmskJoined from a whitespace-separated file.
+ * Dispose of this with rmskJoinedFreeList(). */
+{
+struct rmskJoined *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[14];
+
+while (lineFileRow(lf, row))
+    {
+    el = rmskJoinedLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct rmskJoined *rmskJoinedLoadAllByChar(char *fileName, char chopper) 
+/* Load all rmskJoined from a chopper separated file.
+ * Dispose of this with rmskJoinedFreeList(). */
+{
+struct rmskJoined *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[14];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = rmskJoinedLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct rmskJoined *rmskJoinedCommaIn(char **pS, struct rmskJoined *ret)
+/* Create a rmskJoined out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new rmskJoined */
+{
+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->alignStart = sqlUnsignedComma(&s);
+ret->alignEnd = 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->blockRelStarts, ret->blockCount);
+for (i=0; i<ret->blockCount; ++i)
+    {
+    ret->blockRelStarts[i] = sqlSignedComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+ret->id = sqlStringComma(&s);
+ret->description = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void rmskJoinedFree(struct rmskJoined **pEl)
+/* Free a single dynamically allocated rmskJoined such as created
+ * with rmskJoinedLoad(). */
+{
+struct rmskJoined *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->blockSizes);
+freeMem(el->blockRelStarts);
+freeMem(el->id);
+freeMem(el->description);
+freez(pEl);
+}
+
+void rmskJoinedFreeList(struct rmskJoined **pList)
+/* Free a list of dynamically allocated rmskJoined's */
+{
+struct rmskJoined *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    rmskJoinedFree(&el);
+    }
+*pList = NULL;
+}
+
+void rmskJoinedOutput(struct rmskJoined *el, FILE *f, char sep, char lastSep) 
+/* Print out rmskJoined.  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->alignStart);
+fputc(sep,f);
+fprintf(f, "%u", el->alignEnd);
+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->blockRelStarts[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->id);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->description);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+