cc6dfb2327a38c758277142df7d35c03d92b0c0f kate Wed Aug 15 13:51:16 2018 -0700 List multiple items on details page if they overlap. refs #21917 diff --git src/hg/hgc/interactClick.c src/hg/hgc/interactClick.c index e175468..f8ebdbb 100644 --- src/hg/hgc/interactClick.c +++ src/hg/hgc/interactClick.c @@ -1,207 +1,213 @@ /* 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 */ +static struct interact *getInteractFromTable(struct trackDb *tdb, char *chrom, int start, int end) +/* Retrieve interact items at this position 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 = NULL; char **row; int offset; struct sqlResult *sr = hRangeQuery(conn, table, chrom, start, end, NULL, &offset); while ((row = sqlNextRow(sr)) != NULL) { inter = interactLoadAndValidate(row+offset); if (inter->chromStart != start || inter->chromEnd != end) continue; - if (isNotEmpty(item) && differentString(inter->name, item)) - continue; slAddHead(&inters, inter); } -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 */ +static struct interact *getInteractFromFile(char *file, char *chrom, int start, int end) +/* Retrieve interact items at this position 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 = 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 = interactLoadAndValidate(row); if (inter == NULL) continue; if (inter->chromStart != start || inter->chromEnd != end) continue; - if (isNotEmpty(item) && differentString(inter->name, item)) - continue; slAddHead(&inters, inter); } -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 */ +static struct interact *getInteractions(struct trackDb *tdb, char *chrom, int start, int end) +/* Retrieve interact items at this position */ { struct interact *inters = NULL; char *file = trackDbSetting(tdb, "bigDataUrl"); if (file != NULL) - inters = getInteractFromFile(file, item, chrom, start, end); + inters = getInteractFromFile(file, chrom, start, end); else - inters = getInteractFromTable(tdb, item, chrom, start, end); + inters = getInteractFromTable(tdb, chrom, start, end); +slSort(&inters, bedCmpScore); +slReverse(&inters); return inters; } -void doInteractItemDetails(struct trackDb *tdb, struct interact *inter, char *item) -/* Details of interaction item */ +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]; -if (!isEmptyTextField(inter->name)) - printf("Interaction name: %s
\n", inter->name); printf("Interaction region: "); if (interactOtherChrom(inter)) printf("across chromosomes
"); else { sprintLongWithCommas(startBuf, inter->chromStart+1); sprintLongWithCommas(endBuf, inter->chromEnd); sprintLongWithCommas(sizeBuf, inter->chromEnd - inter->chromStart); printf("%s:%s-%s", inter->chrom, inter->chromStart, inter->chromEnd, inter->chrom, startBuf, endBuf); printf("  %s bp
\n", sizeBuf); } -printf("Score: %d
\n", inter->score); -printf("Value: %0.3f
\n", inter->value); -if (!isEmptyTextField(inter->exp)) - printf("Experiment: %s
\n", inter->exp); -puts("

"); - -/* 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) -*/ +printf("
"); 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("%s region: %s  " "%s:%s-%s %s", region1Label, region1Name, region1Chrom, region1Start+1, region1End, region1Chrom, startBuf, endBuf, inter->sourceStrand[0] == '.' ? "" : inter->sourceStrand); printf("  %s bp
\n", sizeBuf); sprintLongWithCommas(startBuf, region2Start+1); sprintLongWithCommas(endBuf, region2End); sprintLongWithCommas(sizeBuf, region2End - region2Start); printf("%s region: %s  " "%s:%s-%s %s", region2Label, region2Name, region2Chrom, region2Start+1, region2End, region2Chrom, startBuf, endBuf, inter->targetStrand[0] == '.' ? "" : inter->targetStrand); printf("  %s bp
\n", sizeBuf); int distance = interactRegionDistance(inter); if (distance > 0) { // same chrom sprintLongWithCommas(sizeBuf, distance); printf("Distance between midpoints: %s bp
\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 interact *inter, char *item, boolean isMultiple) +/* Details of interaction item */ +{ +if (!isEmptyTextField(inter->name)) + printf("Interaction name: %s
\n", inter->name); + + +printf("Score: %d
\n", inter->score); +printf("Value: %0.3f
\n", inter->value); +if (!isEmptyTextField(inter->exp)) + printf("Experiment: %s
\n", inter->exp); +puts("

"); +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"); struct interact *inter = NULL; -struct interact *inters = getInteractions(tdb, item, chrom, start, end); +struct interact *inters = getInteractions(tdb, chrom, start, end); if (inters == NULL) errAbort("Can't find interaction %s", item ? item : ""); int count = slCount(inters); if (count > 1) - printf("Interactions: %d

", count); + { + printf("Interactions at this position: %d

", count); + doInteractRegionDetails(tdb, inters); + printf("

"); + } genericHeader(tdb, item); for (inter = inters; inter; inter = inter->next) { - doInteractItemDetails(tdb, inter, item); + if (count > 1) printf("
\n"); + doInteractItemDetails(tdb, inter, item, count > 1); if (count > 1 && !isEmptyTextField(inter->name) && sameString(inter->name, item)) printf("
\n"); } }