229b9f6993152bab7202c2a32f461ecaa478e140
kate
  Mon Oct 1 16:28:22 2018 -0700
Rename merge mode to cluster mode. refs #21917

diff --git src/hg/hgc/interactClick.c src/hg/hgc/interactClick.c
index 2dcbfca..0e688e7 100644
--- src/hg/hgc/interactClick.c
+++ src/hg/hgc/interactClick.c
@@ -9,33 +9,33 @@
 #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)
+                                    int start, int end, char *name, char *clusterMode, char *foot)
 /* Retrieve interact items at this position from track table */
-// TODO: Support for mergeMode
+// TODO: Support for clusterMode
 {
 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)
@@ -67,91 +67,91 @@
     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)
+                                                        char *name, char *clusterMode, 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 (!name || sameString(name, "."))
         {
         if (inter->chromStart != start || inter->chromEnd != end)
             continue;
         }
     else
         {
         char *match = inter->name;
-        if (mergeMode)
-            match = sameString(mergeMode, INTERACT_MERGE_SOURCE) ?
+        if (clusterMode)
+            match = sameString(clusterMode, INTERACT_CLUSTER_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);
+char *clusterMode = interactUiClusterMode(cart, tdb->track, tdb);
 if (file != NULL)
-    iprs = getInteractsFromFile(file, chrom, start, end, name, mergeMode, foot);
+    iprs = getInteractsFromFile(file, chrom, start, end, name, clusterMode, foot);
 else
-    iprs = getInteractsFromTable(tdb, chrom, start, end, name, mergeMode, foot);
+    iprs = getInteractsFromTable(tdb, chrom, start, end, name, clusterMode, foot);
 
-// TODO: add sort on score, or position for merged items ?
+// TODO: add sort on score, or position for clustered 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> ");
@@ -248,52 +248,52 @@
 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);
+char *clusterMode = interactUiClusterMode(cart, tdb->track, tdb);
 if (count > 1)
     {
     printf("<b>Interactions:</b> %d<p>", count);
-    if (mergeMode)
+    if (clusterMode)
         {
         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)
+    if (clusterMode)
         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)
+if (count > 1 && clusterMode)
     printf("<hr>\n");
 }