95ac3b9a9a4696a6ff59dc4dc8cb057b6a43c898
kate
  Fri Aug 23 16:10:24 2019 -0700
Add multi-region link for all regions in interact cluster. refs #24037

diff --git src/hg/hgc/interactClick.c src/hg/hgc/interactClick.c
index e12f974..3b3483f 100644
--- src/hg/hgc/interactClick.c
+++ src/hg/hgc/interactClick.c
@@ -144,96 +144,145 @@
             if (differentString(name, inter->sourceName) && differentString(name, inter->targetName))
                 continue;
             }
         }
     minStart = inter->chromStart <  minStart ? inter->chromStart : minStart;
     maxEnd = inter->chromEnd > maxEnd ? inter->chromEnd : maxEnd;
     slAddHead(&filtered, ipr);
     }
 
 *retStart = minStart;
 *retEnd = maxEnd;
 // consider sorting on score or position
 return filtered;
 }
 
-static char *makeInteractRegionFile(struct interact *inter)
+static char *makeInteractRegionFile(char *name, struct interact *inters)
 /* Create bed file in trash directory with end coordinates for multi-region mode */
 {
 struct tempName mrTn;
 trashDirFile(&mrTn, "hgt", "custRgn_interact", ".bed");
 FILE *f = fopen(mrTn.forCgi, "w");
 if (f == NULL)
     errAbort("can't create temp file %s", mrTn.forCgi);
 char regionInfo[1024];
 // TODO: check chrom bounds
 int padding = 200;
 //cartSetBoolean(cart, "emAltHighlight", TRUE);
 
 safef(regionInfo, sizeof regionInfo, "#padding %d\n", padding);
 mustWrite(f, regionInfo, strlen(regionInfo));
 //warn("%s", regionInfo);
 
-safef(regionInfo, sizeof regionInfo, "#shortDesc %s\n", inter->name);
+safef(regionInfo, sizeof regionInfo, "#shortDesc %s\n", name);
 mustWrite(f, regionInfo, strlen(regionInfo));
 //warn("%s", regionInfo);
-char *region1Chrom = inter->sourceChrom, *region2Chrom = inter->targetChrom;
-int region1Start = inter->sourceStart, region1End = inter->sourceEnd;
-int region2Start = inter->targetStart, region2End = inter->targetEnd;
-if (sameString(inter->sourceChrom, inter->targetChrom))
-    {
-    if (inter->sourceStart > inter->targetStart)
-        {
-        region1Start = inter->targetStart;
-        region1End = inter->targetEnd;
-        region2Start = inter->sourceStart;
-        region2End = inter->sourceEnd;
-        }
+
+struct interact *inter = NULL;
+struct bed *region, *regions = NULL;
+struct hash *uniqRegions = hashNew(0);
+for (inter = inters; inter != NULL; inter = inter->next)
+    {
+    char buf[256];
+    //safef(buf, sizeof buf, "%s:%d-%d", region1->chrom, region1->chromStart, region1->chromEnd);
+    safef(buf, sizeof buf, "%s:%d-%d", inter->sourceChrom, inter->sourceStart, inter->sourceEnd);
+    if (!hashLookup(uniqRegions, buf))
+        {
+        hashAdd(uniqRegions, cloneString(buf), NULL);
+        AllocVar(region);
+        region->chrom = inter->sourceChrom;
+        region->chromStart = inter->sourceStart;
+        region->chromEnd = inter->sourceEnd;
+        slAddHead(&regions, region);
         }
-else
-    {
-    if (sameString(inter->chrom, inter->targetChrom))
-        {
-        region1Chrom = inter->targetChrom;
-        region1Start = inter->targetStart;
-        region1End = inter->targetEnd;
-        region2Chrom = inter->sourceChrom;
-        region2Start = inter->sourceStart;
-        region2End = inter->sourceEnd;
+    //safef(buf, sizeof buf, "%s:%d-%d", region2->chrom, region2->chromStart, region2->chromEnd);
+    safef(buf, sizeof buf, "%s:%d-%d", inter->targetChrom, inter->targetStart, inter->targetEnd);
+    if (!hashLookup(uniqRegions, buf))
+        {
+        hashAdd(uniqRegions, cloneString(buf), NULL);
+        AllocVar(region);
+        region->chrom = inter->chrom;
+        region->chromStart = inter->targetStart;
+        region->chromEnd = inter->targetEnd;
+        slAddHead(&regions, region);
         }
     }
-safef(regionInfo, sizeof regionInfo, "%s\t%d\t%d\n"
-           "%s\t%d\t%d\n",
-                region1Chrom, region1Start, region1End,
-                region2Chrom, region2Start, region2End);
+slSort(&regions, bedCmp);
+for (region = regions; region != NULL; region = region->next)
+    {
+    safef(regionInfo, sizeof regionInfo, "%s\t%d\t%d\n",
+                    region->chrom, region->chromStart, region->chromEnd);
     mustWrite(f, regionInfo, strlen(regionInfo));
     //warn("%s", regionInfo);
+    }
 fclose(f);
 
 // create SHA1 file; used to see if file has changed
 unsigned char hash[SHA_DIGEST_LENGTH];
 SHA1((const unsigned char *)regionInfo, strlen(regionInfo), hash);
 char newSha1[(SHA_DIGEST_LENGTH + 1) * 2];
 hexBinaryString(hash, SHA_DIGEST_LENGTH, newSha1, (SHA_DIGEST_LENGTH + 1) * 2);
 char sha1File[1024];
 safef(sha1File, sizeof sha1File, "%s.sha1", mrTn.forCgi);
 f = mustOpen(sha1File, "w");
 mustWrite(f, newSha1, strlen(newSha1));
 carefulClose(&f);
 return cloneString(mrTn.forCgi);
 }
 
+static void multiRegionLink(char *name, struct interact *inters)
+// Print link to multi-region view of ends if appropriate 
+// (or provide a link to remove if already in this mode) 
+{
+if (inters->next == NULL && interactEndsOverlap(inters))
+    return;
+char *virtShortDesc = cartOptionalString(cart, "virtShortDesc");
+boolean isVirtMode = cartUsualBoolean(cart, "virtMode", FALSE);
+//warn("virtShortDesc: %s, name: %s", virtShortDesc, name);
+if (isVirtMode && virtShortDesc && sameString(virtShortDesc, name))
+    {
+    printf("<br>Show interaction%s in "
+                "<a href='hgTracks?"
+                    "virtMode=0&"
+                    "virtModeType=default'>"
+                " normal browser view</a> (exit multi-region view)",
+                        inters->next != NULL ? "s" : "");
+    }
+else
+    {
+    char *regionFile = makeInteractRegionFile(name, inters);
+    //warn("regionFile: %s", regionFile);
+    printf("<br>Show interaction ends in "
+            "<a href='hgTracks?"
+                "virtMode=1&"
+                "virtModeType=customUrl&"
+                "virtWinFull=on&"
+                "virtShortDesc=%s&"
+                "multiRegionsBedUrl=%s'>"
+            " multi-region browser view </a>(custom region mode)",
+                    name, cgiEncode(regionFile));
+    if (isVirtMode)
+        printf(" or "
+                "<a href='hgTracks?"
+                    "virtMode=0&"
+                    "virtModeType=default'>"
+                " normal browser view</a>");
+    }
+printf("&nbsp;&nbsp;&nbsp;");
+printf("<a href=\"../goldenPath/help/multiRegionHelp.html\" target=_blank>(Help)</a>\n");
+}
+
 void doInteractRegionDetails(struct trackDb *tdb, struct interact *inter)
 {
     /* print info for both regions */
 /* Use different labels:
         1) directional (source/target)
         2) non-directional same chrom (lower/upper)
         3) non-directional other chrom (this/other)
 */
 char startBuf[1024], endBuf[1024], sizeBuf[1024];
 printf("<b>Interaction region:</b> ");
 if (interactOtherChrom(inter))
     printf("across chromosomes<br>");
 else
     {
     sprintLongWithCommas(startBuf, inter->chromStart+1);
@@ -289,124 +338,112 @@
 sprintLongWithCommas(endBuf, region2End);
 sprintLongWithCommas(sizeBuf, region2End - region2Start);
 printf("<b>%s region:</b> %s&nbsp;&nbsp;"
                 "<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a> %s",
                 region2Label, region2Name, region2Chrom, region2Start+1, region2End,
                 region2Chrom, startBuf, endBuf, 
                 inter->targetStrand[0] == '.' ? "" : inter->targetStrand);
 printf("&nbsp;&nbsp;%s bp<br>\n", sizeBuf);
 int distance = interactRegionDistance(inter);
 if (distance > 0)
     {
     // same chrom
     sprintLongWithCommas(sizeBuf, distance);
     printf("<b>Distance between midpoints:</b> %s bp<br>\n", sizeBuf); 
     }
-
-// print link to multi-region view of ends if appropriate 
-// (or provide a link to remove if already in this mode) 
-
-if (trackDbSettingOn(tdb, "interactMultiRegion") && !interactEndsOverlap(inter))
-    {
-    char *virtShortDesc = cartOptionalString(cart, "virtShortDesc");
-    //warn("virtShortDesc: %s", virtShortDesc);
-    if (virtShortDesc && sameString(virtShortDesc, inter->name))
-        {
-        printf("<br><a target='_blank' "
-                    "href='hgTracks?"
-                        "virtMode=0&"
-                        "virtModeType=default'>"
-                    "Show interaction in normal browser view (exit multi-region view)</a>");
-        }
-    else
-        {
-        char *regionFile = makeInteractRegionFile(inter);
-        //warn("regionFile: %s", regionFile);
-        printf("<br><a target='_blank' "
-                "href='hgTracks?"
-                    "virtMode=1&"
-                    "virtModeType=customUrl&"
-                    "virtWinFull=on&"
-                    "virtShortDesc=%s&"
-                    "multiRegionsBedUrl=%s'>"
-                "Show both ends of interaction in multi-region browser view (custom region mode)</a>",
-                        inter->name, cgiEncode(regionFile));
-        }
-    printf("&nbsp;&nbsp;&nbsp;");
-    printf("<a href=\"../goldenPath/help/multiRegionHelp.html\" target=_blank>(Help)</a>\n");
-    }
-
-#ifdef TODO /* TODO: get count and score stats of all interactions in window ?*/
-double *scores;
-AllocArray(scores, count);
-#endif
 }
 
 void doInteractItemDetails(struct trackDb *tdb, struct interactPlusRow *ipr, char *item, 
-                                boolean isMultiple)
+                                boolean isMultiple, boolean doMultiRegion)
 /* Details of interaction item */
 {
 struct interact *inter = ipr->interact;
 struct slPair *fields = getFields(tdb, ipr->row);
 printCustomUrlWithFields(tdb, inter->name, inter->name, TRUE, fields);
 if (!isEmptyTextField(inter->name))
     printf("<b>Interaction:</b> %s<br>\n", inter->name);
 printf("<b>Score:</b> %d<br>\n", inter->score);
 printf("<b>Value:</b> %0.3f<br>\n", inter->value);
 if (!isEmptyTextField(inter->exp))
     printf("<b>Experiment:</b> %s<br>\n", inter->exp);
 puts("<p>");
 if (!isMultiple)
+    {
     doInteractRegionDetails(tdb, inter);
+    if (doMultiRegion)
+        multiRegionLink(inter->name, inter);
+    }
+}
+
+static struct interact *iprsToInters(struct interactPlusRow *iprs)
+/* Create list of interacts from interactPlusRows */
+{
+struct interactPlusRow *ipr;
+struct interact *inters = NULL;
+for (ipr = iprs; ipr != NULL; ipr = ipr->next)
+    slAddHead(&inters, ipr->interact);
+return inters;
 }
 
 void doInteractDetails(struct trackDb *tdb, char *item)
 /* Details of interaction items */
 {
 char *chrom = cartString(cart, "c");
 int start = cartInt(cart, "o");
 int end = cartInt(cart, "t");
 char *foot = cgiOptionalString("foot");
+boolean doMultiRegion = trackDbSettingOn(tdb, "interactMultiRegion");
 int minStart, maxEnd;
 struct interactPlusRow *iprs = getInteractions(tdb, chrom, start, end, item, foot, &minStart, &maxEnd);
 start = minStart;
 end = maxEnd;
 if (iprs == NULL)
     errAbort("Can't find interaction %s", item ? item : "");
 int count = slCount(iprs);
 char *clusterMode = interactUiClusterMode(cart, tdb->track, tdb);
 if (count > 1 || clusterMode)
     {
     printf("<b>Interactions:</b> %d<p>", count);
+    struct interact *inters = iprsToInters(iprs);
     if (clusterMode || foot)
         {
         char startBuf[1024], endBuf[1024], sizeBuf[1024];
         sprintLongWithCommas(startBuf, start + 1);
         sprintLongWithCommas(endBuf, end);
         sprintLongWithCommas(sizeBuf, end - start + 1);
         printf("<b>%s interactions region:</b> &nbsp;&nbsp;"
                         "<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a> ",
                         item, chrom, start+1, end, chrom, startBuf, endBuf);
         printf("&nbsp;&nbsp;%s bp<br>\n", sizeBuf);
         }
     else
         {
-        doInteractRegionDetails(tdb, iprs->interact);
+        // overlapping items, same start/end/name
+        doInteractRegionDetails(tdb, inters);
         }
+    if (doMultiRegion)
+        multiRegionLink(item, inters);
     printf("</p>");
     }
 
-genericHeader(tdb, item);
+//genericHeader(tdb, item);
 static struct interactPlusRow *ipr = NULL;
 for (ipr = iprs; ipr != NULL; ipr = ipr->next)
     {
     if (count > 1)
         printf("<hr>\n");
-    doInteractItemDetails(tdb, ipr, item, count > 1);
+    doInteractItemDetails(tdb, ipr, item, count > 1, doMultiRegion);
     if (foot || (clusterMode && count > 1))
-        doInteractRegionDetails(tdb, ipr->interact);
+        {
+        struct interact *inter = ipr->interact;
+        // just one interact (we have these in list for handling clusters earlier)
+        inter->next = NULL;
+        doInteractRegionDetails(tdb, inter);
+        if (doMultiRegion)
+            multiRegionLink(inter->name, inter);
+        }
     if (count > 1 && !isEmptyTextField(ipr->interact->name) && sameString(ipr->interact->name, item))
         printf("<hr>\n");
     }
 }