ea5b4301814c1df9f2a0f3b2d9e0d2f06b22635e
braney
  Tue May 24 18:37:10 2016 -0700
hgTables support , some display changes, and a better hgc
page for longTabix

diff --git src/hg/lib/longRange.c src/hg/lib/longRange.c
index 57c674c..e2d6c4a 100644
--- src/hg/lib/longRange.c
+++ src/hg/lib/longRange.c
@@ -1,55 +1,83 @@
+/*    longRange --- functions to provide UI for long range interaction
+ *         graph.   Functions to retrieve long range information from
+ *         bedTabix format.
+ */
+
+/* Copyright (C) 2016 The Regents of the University of California 
+ *  * See README in this or parent directory for licensing information. */
 
 #include "longRange.h"
 
+static char *longTabixAutoSqlString =
+"table longTabix\n"
+"\"Long Range Tabix file\"\n"
+"   (\n"
+"   string chrom;      \"Reference sequence chromosome or scaffold\"\n"
+"   uint   chromStart; \"Start position in chromosome\"\n"
+"   uint   chromEnd;   \"End position in chromosome\"\n"
+"   string interactingRegion;       \"(e.g. chrX:123-456,3.14, where chrX:123-456 is the coordinate of the mate, and 3.14 is the score of the interaction)\"\n"
+"   uint   id;      \"Unique Id\"\n"
+"   char[1] strand;    \"+ or -\"\n"
+"   )\n"
+;
+
+struct asObject *longTabixAsObj()
+// Return asObject describing fields of longTabix file
+{
+return asParseText(longTabixAutoSqlString);
+}
+
 void longRangeCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed)
 /* Complete track controls for long range interaction. */
 {
 char buffer[1024];
 safef(buffer, sizeof buffer, "%s.%s", tdb->track, LONG_HEIGHT );
 unsigned height = sqlUnsigned(cartUsualString(cart, buffer, LONG_DEFHEIGHT));
 printf("<BR><b>Track height:&nbsp;</b>");
 cgiMakeIntVar(buffer, height, 3);
 safef(buffer, sizeof buffer, "%s.%s", tdb->track, LONG_MINSCORE);
 double minScore = sqlDouble(cartUsualString(cart, buffer, LONG_DEFMINSCORE));
 printf("<BR><BR><b>Minimum score:&nbsp;</b>");
 cgiMakeDoubleVar(buffer, minScore, 0);
 }
 
 static char *getOther(struct bed *bed, unsigned *s, unsigned *e, double *score)
+/* parse the name field of longTabix to get the other location */
 {
 char *otherChrom = cloneString(bed->name);
 char *ptr = strchr(otherChrom, ':');
 if (ptr == NULL)
     errAbort("bad longTabix bed name %s\n", bed->name);
 *ptr++ = 0;
 *s = atoi(ptr);
 ptr = strchr(ptr, '-');
 if (ptr == NULL)
     errAbort("bad longTabix bed name %s\n", bed->name);
 ptr++;
 *e = atoi(ptr);
 ptr = strchr(ptr, ',');
 if (ptr == NULL)
     errAbort("bad longTabix bed name %s\n", bed->name);
 ptr++;
 *score = sqlDouble(ptr);
 
 return otherChrom;
 }
 
 struct longRange *parseLongTabix(struct bed *beds, unsigned *maxWidth, double minScore)
+/* Parse longTabix format into longRange structures */
 {
 struct longRange *longRangeList = NULL;
 for(; beds; beds=beds->next)
     {
     double score;
     unsigned otherS;
     unsigned otherE;
     char *otherChrom = getOther(beds, &otherS, &otherE, &score);
     if (score < minScore)
         continue;
 
     struct longRange *longRange;
     AllocVar(longRange);
     slAddHead(&longRangeList, longRange);