6db4d4f2dcc485622fe4b22f33c796d708c6fdea kate Mon Mar 26 16:28:35 2018 -0700 Fixes to click handling. refs #17512 diff --git src/hg/hgc/interactClick.c src/hg/hgc/interactClick.c index fdd3d47..412e81a 100644 --- src/hg/hgc/interactClick.c +++ src/hg/hgc/interactClick.c @@ -1,191 +1,206 @@ /* 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 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) return NULL; -struct interact *inters = NULL, *inter; +struct interact *inters = NULL, *inter = NULL; char **row; int offset; -char where[512]; -if (isNotEmpty(item)) - sqlSafefFrag(where, sizeof(where), "name='%s'", item); -struct sqlResult *sr = hRangeQuery(conn, table, chrom, start, end, where, &offset); +struct sqlResult *sr = hRangeQuery(conn, table, chrom, start, end, NULL, &offset); while ((row = sqlNextRow(sr)) != NULL) { inter = interactLoad(row+offset); + if (inter->chromStart != start || inter->chromEnd != end) + continue; + if (isNotEmpty(item) && differentString(inter->name, item)) + continue; slAddHead(&inters, inter); } -slReverse(&inters); +slSort(&inters, interactDistanceCmp); 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; +struct interact *inters = NULL, *inter = NULL; for (bb = bbList; bb != NULL; bb = bb->next) { char startBuf[16], endBuf[16]; char *row[32]; bigBedIntervalToRow(bb, chrom, startBuf, endBuf, row, ArraySize(row)); inter = interactLoad(row); if (inter == NULL) continue; - if (isEmpty(item) || sameString(inter->name, item)) + if (inter->chromStart != start || inter->chromEnd != end) + continue; + if (isNotEmpty(item) && differentString(inter->name, item)) + continue; slAddHead(&inters, inter); } -slReverse(&inters); +slSort(&inters, interactDistanceCmp); return inters; } static struct interact *getInteractions(struct trackDb *tdb, char *item, char *chrom, int start, int end) /* Retrieve interact BED item from track */ { struct interact *inters = NULL; char *file = trackDbSetting(tdb, "bigDataUrl"); if (file != NULL) inters = getInteractFromFile(file, item, chrom, start, end); else inters = getInteractFromTable(tdb, item, chrom, start, end); return inters; } -void doInteractItemDetails(struct trackDb *tdb, struct interact *inter) +void doInteractItemDetails(struct trackDb *tdb, struct interact *inter, char *item) /* Details of interaction item */ { char startBuf[1024], endBuf[1024], sizeBuf[1024]; 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 (!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 (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"; } } sprintLongWithCommas(startBuf, region1Start + 1); 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<hr>\n", sizeBuf); +printf(" %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 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 +if (inters == NULL) + errAbort("Can't find interaction %s", item ? item : ""); 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); + { + doInteractItemDetails(tdb, inter, item); + printf("<hr>\n"); + if (count > 1 && !isEmptyTextField(inter->name) && sameString(inter->name, item)) + printf("<hr>\n"); + } }