3fd4131517e0d224eb271e312c9fda6419e1872d
kate
Tue Mar 13 15:51:59 2018 -0700
1. Add support for spectrum setting. 2. Allow dot for empty field. 3. Show multiple items on details page if they overlap. 4. Some cleanup of map boxes. refs #17512
diff --git src/hg/hgc/interactClick.c src/hg/hgc/interactClick.c
index 6bab38f..fdd3d47 100644
--- src/hg/hgc/interactClick.c
+++ src/hg/hgc/interactClick.c
@@ -1,31 +1,31 @@
/* 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 "hgc.h"
#include "interact.h"
#include "interactUi.h"
static struct interact *getInteractFromTable(struct trackDb *tdb, char *item,
char *chrom, int start, int end)
-/* Retrieve this item from track table */
+/* Retrieve this item or items from track table */
{
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)
@@ -43,111 +43,104 @@
inter = interactLoad(row+offset);
slAddHead(&inters, inter);
}
slReverse(&inters);
sqlFreeResult(&sr);
hFreeConn(&conn);
return inters;
}
static struct interact *getInteractFromFile(char *file, char *item, char *chrom, int start, int end)
/* Retrieve interact BED item 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 interact *inters = NULL, *inter;
for (bb = bbList; bb != NULL; bb = bb->next)
{
char startBuf[16], endBuf[16];
char *row[32];
bigBedIntervalToRow(bb, chrom, startBuf, endBuf, row, ArraySize(row));
- struct interact *interact = interactLoad(row);
- if (interact == NULL)
+ inter = interactLoad(row);
+ if (inter == NULL)
continue;
- if (sameString(interact->name, item))
- return interact;
+ if (isEmpty(item) || sameString(inter->name, item))
+ slAddHead(&inters, inter);
}
-return NULL;
+slReverse(&inters);
+return inters;
}
-static struct interact *getInteract(struct trackDb *tdb, char *item,
+static struct interact *getInteractions(struct trackDb *tdb, char *item,
char *chrom, int start, int end)
/* Retrieve interact BED item from track */
{
-struct interact *interact = NULL;
+struct interact *inters = NULL;
char *file = trackDbSetting(tdb, "bigDataUrl");
if (file != NULL)
- interact = getInteractFromFile(file, item, chrom, start, end);
+ inters = getInteractFromFile(file, item, chrom, start, end);
else
- interact = getInteractFromTable(tdb, item, chrom, start, end);
-return interact;
+ inters = getInteractFromTable(tdb, item, chrom, start, end);
+return inters;
}
-
-void doInteractDetails(struct trackDb *tdb, char *item)
+void doInteractItemDetails(struct trackDb *tdb, struct interact *inter)
/* Details of interaction item */
{
-char *chrom = cartString(cart, "c");
-int start = cartInt(cart, "o");
-int end = cartInt(cart, "t");
-struct interact *inter = getInteract(tdb, item, chrom, start, end);
-if (inter == NULL)
- errAbort("Can't find interaction '%s'", item);
-genericHeader(tdb, item);
-
char startBuf[1024], endBuf[1024], sizeBuf[1024];
-if (isNotEmpty(inter->name) && differentString(".", inter->name))
+if (!isEmptyTextField(inter->name))
printf("<b>Interaction name:</b> %s<br>\n", inter->name);
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(" %s bp<br>\n", sizeBuf);
}
printf("<b>Score:</b> %d<br>\n", inter->score);
printf("<b>Value:</b> %0.3f<br>\n", inter->value);
-if (isNotEmpty(inter->exp) && differentString(".", inter->name))
+if (!isEmptyTextField(inter->exp))
printf("<b>Experiment:</b> %s<br>\n", inter->exp);
puts("<p>");
/* 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 *region1Label = "Source";
char *region1Chrom = inter->sourceChrom;
int region1Start = inter->sourceStart;
int region1End = inter->sourceEnd;
char *region1Name = inter->sourceName;
-if (sameString(".", 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 (sameString(".", inter->targetName))
+if (isEmptyTextField(inter->targetName))
region2Name = "";
if (!interactUiDirectional(tdb))
{
if (interactOtherChrom(inter))
{
region1Label = "This";
region2Label = "Other";
}
else
{
region1Label = "Lower";
region2Label = "Upper";
}
}
@@ -156,23 +149,43 @@
sprintLongWithCommas(endBuf, region1End);
sprintLongWithCommas(sizeBuf, region1End - region1Start);
printf("<b>%s region:</b> %s "
"<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a>",
region1Label, region1Name, region1Chrom, region1Start+1, region1End,
region1Chrom, startBuf, endBuf);
printf(" %s bp<br>\n", sizeBuf);
sprintLongWithCommas(startBuf, region2Start+1);
sprintLongWithCommas(endBuf, region2End);
sprintLongWithCommas(sizeBuf, region2End - region2Start);
printf("<b>%s region:</b> %s "
"<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a>",
region2Label, region2Name, region2Chrom, region2Start+1, region2End,
region2Chrom, startBuf, endBuf);
-printf(" %s bp<br>\n", sizeBuf);
+printf(" %s bp<hr>\n", sizeBuf);
#ifdef TODO /* TODO: get count and score stats of all interactions in window ?*/
double *scores;
AllocArray(scores, count);
#endif
}
+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");
+struct interact *inter = NULL;
+struct interact *inters = getInteractions(tdb, item, chrom, start, end);
+// consider sorting by score/value so highest scored items appear first
+int count = slCount(inters);
+if (count > 1)
+ printf("<b>Interactions:</b> %d<hr>", count);
+if (inters == NULL)
+ errAbort("Can't find interaction '%s'", item);
+genericHeader(tdb, item);
+for (inter = inters; inter; inter = inter->next)
+ doInteractItemDetails(tdb, inter);
+}
+
+