b87966ef79a5c54ed61f83bc59233f1628cd7ac7
kate
  Wed Sep 26 17:02:49 2018 -0700
More click support for merged interactions. refs #21917

diff --git src/hg/hgc/interactClick.c src/hg/hgc/interactClick.c
index 89c90b6..2dcbfca 100644
--- src/hg/hgc/interactClick.c
+++ src/hg/hgc/interactClick.c
@@ -1,286 +1,299 @@
 /* Details page for interact type tracks */
 
 /* Copyright (C) 2018 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "obscure.h"
 #include "hdb.h"
 #include "jksql.h"
 #include "hgc.h"
 
 #include "interact.h"
 #include "interactUi.h"
 
 struct interactPlusRow
     {
     /* Keep field values in string format, for url processing */
     struct interactPlusRow *next;
     struct interact *interact;
     char **row;
     };
 
 static struct interactPlusRow *getInteractsFromTable(struct trackDb *tdb, char *chrom, 
                                     int start, int end, char *name, char *mergeMode, char *foot)
 /* Retrieve interact items at this position from track table */
 // TODO: Support for mergeMode
 {
 struct sqlConnection *conn = NULL;
 struct customTrack *ct = lookupCt(tdb->track);
 char *table;
 if (ct != NULL)
     {
     conn = hAllocConn(CUSTOM_TRASH);
     table = ct->dbTableName;
     }
 else
     {
     conn = hAllocConnTrack(database, tdb);
     table = tdb->table;
     }
 if (conn == NULL)
     return NULL;
 
 struct interactPlusRow *iprs = NULL;
 char **row;
 int offset;
 struct sqlResult *sr = hRangeQuery(conn, table, chrom, start, end, NULL, &offset);
 int fieldCount = 0;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct interact *inter = interactLoadAndValidate(row+offset);
     if (!name)
         {
         if (inter->chromStart != start || inter->chromEnd != end)
             continue;
         }
     else
         {
         if (differentString(inter->name, name))
             continue;
         }
     // got one, save object and row representation
     struct interactPlusRow *ipr;
     AllocVar(ipr);
     ipr->interact = inter;
     char **fieldVals;
     if (fieldCount == 0)
         fieldCount = sqlCountColumns(sr);
     AllocArray(fieldVals, fieldCount);
     int i;
     for (i = 0; i < fieldCount; i++)
         fieldVals[i] = cloneString(row[i]);
     ipr->row = fieldVals;
     slAddHead(&iprs, ipr);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 return iprs;
 }
 
 static struct interactPlusRow *getInteractsFromFile(char *file, char *chrom, int start, int end, 
                                                         char *name, char *mergeMode, char *foot)
 /* Retrieve interact items at this position or name from big file */
 {
 struct bbiFile *bbi = bigBedFileOpen(file);
 struct lm *lm = lmInit(0);
 struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, chrom, start, end, 0, lm);
 struct interactPlusRow *iprs = NULL;
 
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
     char startBuf[16], endBuf[16];
     int maxFields = 32;
     char *row[maxFields];      // big enough ?
     int fieldCount = bigBedIntervalToRow(bb, chrom, startBuf, endBuf, row, maxFields);
     struct interact *inter = interactLoadAndValidate(row);
     if (inter == NULL)
         continue;
     if (!name)
         {
         if (inter->chromStart != start || inter->chromEnd != end)
             continue;
         }
     else
         {
         char *match = inter->name;
         if (mergeMode)
             match = sameString(mergeMode, INTERACT_MERGE_SOURCE) ?
                                                 inter->sourceName : inter->targetName;
         if (differentString(name, match))
             continue;
         }
 
     // got one, save object and row representation
     struct interactPlusRow *ipr;
     AllocVar(ipr);
     ipr->interact = inter;
     char **fieldVals;
     AllocArray(fieldVals, fieldCount);
     int i;
     for (i = 0; i < fieldCount; i++)
         fieldVals[i] = cloneString(row[i]);
     ipr->row = fieldVals;
     slAddHead(&iprs, ipr);
     }
 return iprs;
 }
 
 static struct interactPlusRow *getInteractions(struct trackDb *tdb, char *chrom, 
                                                 int start, int end, char *name, char *foot)
 /* Retrieve interact items at this position or name. 
  * Also any others with the same endpoint, if endpoint clicked on*/
 {
 struct interactPlusRow *iprs = NULL;
 char *file = trackDbSetting(tdb, "bigDataUrl");
 char *mergeMode = interactUiMergeMode(cart, tdb->track, tdb);
 if (file != NULL)
     iprs = getInteractsFromFile(file, chrom, start, end, name, mergeMode, foot);
 else
     iprs = getInteractsFromTable(tdb, chrom, start, end, name, mergeMode, foot);
 
-// TODO: add sort on score in interacts in ipr
+// TODO: add sort on score, or position for merged items ?
 //slSort(&inters, bedCmpScore);
 //slReverse(&inters);
 return iprs;
 }
 
 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);
     sprintLongWithCommas(endBuf, inter->chromEnd);
     sprintLongWithCommas(sizeBuf, inter->chromEnd - inter->chromStart);
     printf("<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a>", 
                 inter->chrom, inter->chromStart, inter->chromEnd,
                 inter->chrom, startBuf, endBuf);
     printf("&nbsp;&nbsp;%s bp<br>\n", sizeBuf);
     }
 printf("<br>");
 char *region1Label = "Source";
 char *region1Chrom = inter->sourceChrom;
 int region1Start = inter->sourceStart;
 int region1End = inter->sourceEnd;
 char *region1Name = inter->sourceName;
 if (isEmptyTextField(inter->sourceName))
     region1Name = "";
 
 char *region2Label = "Target";
 char *region2Chrom = inter->targetChrom;
 int region2Start = inter->targetStart;
 int region2End = inter->targetEnd;
 char *region2Name = inter->targetName;
 if (isEmptyTextField(inter->targetName))
     region2Name = "";
 
 if (!interactUiDirectional(tdb))
     {
     if (interactOtherChrom(inter))
         {
         region1Label = "This";
         region2Label = "Other";
         }
     else
         {
         region1Label = "Lower";
         region2Label = "Upper";
         }
     }
 // format and print
 sprintLongWithCommas(startBuf, region1Start + 1);
 sprintLongWithCommas(endBuf, region1End);
 sprintLongWithCommas(sizeBuf, region1End - region1Start);
 printf("<b>%s region:</b> %s&nbsp;&nbsp;"
                 "<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a> %s",
                 region1Label, region1Name, region1Chrom, region1Start+1, region1End,
-                region1Chrom, startBuf, endBuf, inter->sourceStrand[0] == '.' ? "" : inter->sourceStrand);
+                region1Chrom, startBuf, endBuf, 
+                inter->sourceStrand[0] == '.' ? "" : inter->sourceStrand);
 printf("&nbsp;&nbsp;%s bp<br>\n", sizeBuf);
 
 sprintLongWithCommas(startBuf, region2Start+1);
 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);
+                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); 
     }
 
 #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)
 /* Details of interaction item */
 {
 struct interact *inter = ipr->interact;
 struct slPair *fields = getFields(tdb, ipr->row);
 printCustomUrlWithFields(tdb, item, item, 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);
 }
 
 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 = cartOptionalString(cart, "foot");
 struct interactPlusRow *iprs = getInteractions(tdb, chrom, start, end, item, foot);
 if (iprs == NULL)
     errAbort("Can't find interaction %s", item ? item : "");
 int count = slCount(iprs);
 char *mergeMode = interactUiMergeMode(cart, tdb->track, tdb);
 if (count > 1)
     {
     printf("<b>Interactions:</b> %d<p>", count);
-    if (!mergeMode)
+    if (mergeMode)
+        {
+        char startBuf[1024], endBuf[1024], sizeBuf[1024];
+        sprintLongWithCommas(startBuf, start + 1);
+        sprintLongWithCommas(endBuf, end);
+        sprintLongWithCommas(sizeBuf, end - start);
+        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);
     printf("</p>");
     }
 genericHeader(tdb, item);
 static struct interactPlusRow *ipr = NULL;
 for (ipr = iprs; ipr != NULL; ipr = ipr->next)
     {
     if (count > 1)
         printf("<hr>\n");
     if (mergeMode)
         doInteractRegionDetails(tdb, ipr->interact);
     else
         doInteractItemDetails(tdb, ipr, item, count > 1);
     if (count > 1 && !isEmptyTextField(ipr->interact->name) && sameString(ipr->interact->name, item))
         printf("<hr>\n");
     }
 if (count > 1 && mergeMode)
     printf("<hr>\n");
 }