68684c7c01875a771889d1fd03354f58bae34427
braney
  Tue Oct 31 15:01:59 2023 -0700
rename bedCollect to chainArrangeCollect in response to code review

diff --git src/hg/lib/chainArrange.c src/hg/lib/chainArrange.c
new file mode 100644
index 0000000..95d22eb
--- /dev/null
+++ src/hg/lib/chainArrange.c
@@ -0,0 +1,184 @@
+/* chainArrange.c was originally generated by the autoSql program, which also 
+ * generated chainArrange.h and chainArrange.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 "chainArrange.h"
+
+
+
+char *chainArrangeCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,source,querySize,label";
+
+void chainArrangeStaticLoad(char **row, struct chainArrange *ret)
+/* Load a row from chainArrange table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->chrom = row[0];
+ret->chromStart = sqlUnsigned(row[1]);
+ret->chromEnd = sqlUnsigned(row[2]);
+ret->name = 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]);
+ret->source = row[9];
+ret->querySize = sqlUnsigned(row[10]);
+ret->label = row[11];
+}
+
+struct chainArrange *chainArrangeLoad(char **row)
+/* Load a chainArrange from row fetched with select * from chainArrange
+ * from database.  Dispose of this with chainArrangeFree(). */
+{
+struct chainArrange *ret;
+
+AllocVar(ret);
+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]);
+ret->source = cloneString(row[9]);
+ret->querySize = sqlUnsigned(row[10]);
+ret->label = cloneString(row[11]);
+return ret;
+}
+
+struct chainArrange *chainArrangeLoadAll(char *fileName) 
+/* Load all chainArrange from a whitespace-separated file.
+ * Dispose of this with chainArrangeFreeList(). */
+{
+struct chainArrange *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[12];
+
+while (lineFileRow(lf, row))
+    {
+    el = chainArrangeLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct chainArrange *chainArrangeLoadAllByChar(char *fileName, char chopper) 
+/* Load all chainArrange from a chopper separated file.
+ * Dispose of this with chainArrangeFreeList(). */
+{
+struct chainArrange *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[12];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = chainArrangeLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct chainArrange *chainArrangeCommaIn(char **pS, struct chainArrange *ret)
+/* Create a chainArrange out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new chainArrange */
+{
+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->source = sqlStringComma(&s);
+ret->querySize = sqlUnsignedComma(&s);
+ret->label = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void chainArrangeFree(struct chainArrange **pEl)
+/* Free a single dynamically allocated chainArrange such as created
+ * with chainArrangeLoad(). */
+{
+struct chainArrange *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->source);
+freeMem(el->label);
+freez(pEl);
+}
+
+void chainArrangeFreeList(struct chainArrange **pList)
+/* Free a list of dynamically allocated chainArrange's */
+{
+struct chainArrange *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    chainArrangeFree(&el);
+    }
+*pList = NULL;
+}
+
+void chainArrangeOutput(struct chainArrange *el, FILE *f, char sep, char lastSep) 
+/* Print out chainArrange.  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);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->source);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->querySize);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->label);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+