324e56bb2fe619534c60a35706fb7bfc188c737f max Wed Mar 25 23:26:26 2015 -0700 Removing GSAID code. BrianR said that's OK. diff --git src/hg/hgTracks/pslTrack.c src/hg/hgTracks/pslTrack.c index 732de51..e94c7f6 100644 --- src/hg/hgTracks/pslTrack.c +++ src/hg/hgTracks/pslTrack.c @@ -1,553 +1,438 @@ /* pslTrack - stuff to handle loading and display of * psl (blat format) based tracks. */ /* Copyright (C) 2013 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "hCommon.h" #include "hash.h" #include "linefile.h" #include "jksql.h" #include "hdb.h" #include "hgTracks.h" #include "psl.h" #ifndef GBROWSE #include "../gsid/gsidTable/gsidTable.h" #define SELECT_SUBJ "selectSubject" struct gsidSubj *gsidSelectedSubjList = NULL; struct gsidSeq *gsidSelectedSeqList = NULL; #endif /* GBROWSE */ int pslGrayIx(struct psl *psl, boolean isXeno, int maxShade) /* Figure out gray level for an RNA block. */ { double misFactor; double hitFactor; int res; if (isXeno) { misFactor = (psl->misMatch + psl->qNumInsert + psl->tNumInsert)*2.5; } else { misFactor = (psl->misMatch + psl->qNumInsert)*5; } misFactor /= (psl->match + psl->misMatch + psl->repMatch); hitFactor = 1.0 - misFactor; res = round(hitFactor * maxShade); if (res < 1) res = 1; if (res >= maxShade) res = maxShade-1; return res; } static void filterMrna(struct track *tg, struct linkedFeatures **pLfList) /* Apply filters if any to mRNA linked features. */ { struct linkedFeatures *lf, *next, *newList = NULL, *oldList = NULL; struct mrnaUiData *mud = tg->extraUiData; struct mrnaFilter *fil; char *type; boolean anyFilter = FALSE; unsigned colorIx = 0; boolean isExclude = FALSE; boolean andLogic = TRUE; char query[256]; struct sqlResult *sr; char **row; struct sqlConnection *conn = NULL; if (*pLfList == NULL || mud == NULL) return; /* First make a quick pass through to see if we actually have * to do the filter. */ for (fil = mud->filterList; fil != NULL; fil = fil->next) { fil->pattern = cartUsualStringClosestToHome(cart, tg->tdb,FALSE,fil->suffix, ""); if (fil->pattern[0] != 0) anyFilter = TRUE; } if (!anyFilter) return; type = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, mud->filterTypeSuffix, "red"); if (sameString(type, "exclude")) isExclude = TRUE; else if (sameString(type, "include")) isExclude = FALSE; else colorIx = getFilterColor(type, MG_BLACK); type = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, mud->logicTypeSuffix, "and"); andLogic = sameString(type, "and"); /* Make a pass though each filter, and start setting up search for * those that have some text. */ conn = hAllocConn(database); for (fil = mud->filterList; fil != NULL; fil = fil->next) { if (fil->pattern[0] != 0) // Filled above { fil->hash = newHash(10); if ((fil->mrnaTableIx = sqlFieldIndex(conn, "gbCdnaInfo", fil->table)) < 0) internalErr(); } } /* Scan tables id/name tables to build up hash of matching id's. */ for (fil = mud->filterList; fil != NULL; fil = fil->next) { struct hash *hash = fil->hash; int wordIx, wordCount; char *words[128]; if (hash != NULL) { boolean anyWild; char *dupPat = cloneString(fil->pattern); wordCount = chopLine(dupPat, words); for (wordIx=0; wordIx <wordCount; ++wordIx) { char *pattern = cloneString(words[wordIx]); /* Special case for accessions as gbCdnaInfo is very large to read into memory. */ if(sameString(fil->table, "acc")) { touppers(pattern); hashAdd(hash, pattern, NULL); freez(&pattern); continue; } /* Load up entire table looking for matches. */ if (lastChar(pattern) != '*') { int len = strlen(pattern)+1; pattern = needMoreMem(pattern, len, len+1); pattern[len-1] = '*'; } anyWild = (strchr(pattern, '*') != NULL || strchr(pattern, '?') != NULL); sqlSafef(query, sizeof query, "select id,name from %s", fil->table); touppers(pattern); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { boolean gotMatch; touppers(row[1]); if (anyWild) gotMatch = wildMatch(pattern, row[1]); else gotMatch = sameString(pattern, row[1]); if (gotMatch) { hashAdd(hash, row[0], NULL); } } sqlFreeResult(&sr); freez(&pattern); } freez(&dupPat); } } /* Scan through linked features coloring and or including/excluding ones that * match filter. */ for (lf = *pLfList; lf != NULL; lf = next) { boolean passed = andLogic; next = lf->next; sqlSafef(query, sizeof query, "select * from gbCdnaInfo where acc = '%s'", lf->name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { for (fil = mud->filterList; fil != NULL; fil = fil->next) { if (fil->hash != NULL) { if (hashLookup(fil->hash, row[fil->mrnaTableIx]) == NULL) { if (andLogic) passed = FALSE; } else { if (!andLogic) passed = TRUE; } } } } sqlFreeResult(&sr); if (passed ^ isExclude) { slAddHead(&newList, lf); if (colorIx != 0) lf->filterColor = colorIx; } else { slAddHead(&oldList, lf); } } slReverse(&newList); slReverse(&oldList); if (colorIx > 0) { /* Draw stuff that passes filter first in full mode, last in dense. */ if (tg->visibility == tvDense) { newList = slCat(oldList, newList); } else { newList = slCat(newList, oldList); } } *pLfList = newList; tg->limitedVisSet = FALSE; /* Need to recalculate this after filtering. */ /* Free up hashes, etc. */ for (fil = mud->filterList; fil != NULL; fil = fil->next) { hashFree(&fil->hash); } hFreeConn(&conn); } struct simpleFeature *sfFromPslX(struct psl *psl,int grayIx, int sizeMul) { struct simpleFeature *sf = NULL, *sfList = NULL; unsigned *starts = psl->tStarts; unsigned *qStarts = psl->qStarts; unsigned *sizes = psl->blockSizes; int i, blockCount = psl->blockCount; boolean rcTarget = (psl->strand[1] == '-'); for (i=0; i<blockCount; ++i) { AllocVar(sf); sf->start = sf->end = starts[i]; sf->end += sizes[i]*sizeMul; sf->qStart = sf->qEnd = qStarts[i]; sf->qEnd += sizes[i]; if (rcTarget) { int s, e; s = psl->tSize - sf->end; e = psl->tSize - sf->start; sf->start = s; sf->end = e; } sf->grayIx = grayIx; slAddHead(&sfList, sf); } return(sfList); } struct linkedFeatures *lfFromPslx(struct psl *psl, int sizeMul, boolean isXeno, boolean nameGetsPos, struct track *tg) /* Create a linked feature item from pslx. Pass in sizeMul=1 for DNA, * sizeMul=3 for protein. * Don't free psl afterwards! */ { int grayIx = pslGrayIx(psl, isXeno, maxShade); struct linkedFeatures *lf; boolean rcTarget = (psl->strand[1] == '-'); AllocVar(lf); lf->score = (psl->match - psl->misMatch - psl->repMatch); lf->grayIx = grayIx; if (nameGetsPos) { char buf[256]; safef(buf, sizeof(buf), "%s:%d-%d %s:%d-%d", psl->qName, psl->qStart, psl->qEnd, psl->tName, psl->tStart, psl->tEnd); lf->extra = cloneString(buf); int len = strlen(psl->qName) + 32; lf->name = needMem(len); safef(lf->name, len, "%s %s %dk", psl->qName, psl->strand, psl->qStart/1000); } else lf->name = cloneString(psl->qName); lf->orientation = orientFromChar(psl->strand[0]); if (rcTarget) lf->orientation = -lf->orientation; lf->components = sfFromPslX(psl, grayIx, sizeMul); lf->start = lf->tallStart = psl->tStart; lf->end = lf->tallEnd = psl->tEnd; /* Hang on to psl for use in drawing phase (this is why caller must not free psl!): */ lf->original = psl; return lf; } struct linkedFeatures *lfFromPsl(struct psl *psl, boolean isXeno) /* Create a linked feature item from psl. * Don't free psl afterwards! */ { return lfFromPslx(psl, 1, isXeno, FALSE, NULL); } -#ifndef GBROWSE -boolean gsidSelectedSubjListLoaded = FALSE; - -void initializeGsidSubjList() -{ -struct gsidSubj *subj; -struct lineFile *lf; - -char *line; -int lineSize; - -char *subjListFileName; - -if (hIsGisaidServer()) - { - subjListFileName = cartOptionalString(cart, gisaidSubjList); - } -else - { - subjListFileName = cartOptionalString(cart, gsidSubjList); - } -if (subjListFileName) - { - lf = lineFileOpen(subjListFileName, TRUE); - - while (lineFileNext(lf, &line, &lineSize)) - { - AllocVar(subj); - subj->subjId = cloneString(line); - slAddHead(&gsidSelectedSubjList, subj); - } - slReverse(&gsidSelectedSubjList); - lineFileClose(&lf); - gsidSelectedSubjListLoaded = TRUE; - } -} - -/* special processing for GSID entries */ -/* check if the entry belongs to a subject that is selected */ -boolean isSelected(char *seqId) -{ -char query[256]; -struct sqlResult *sr; -char **row; -char *subjId, *testSubjId; -struct sqlConnection *conn; -struct gsidSubj *subj; - -if (!gsidSelectedSubjListLoaded) initializeGsidSubjList(); - -conn= hAllocConn(database); - -if (hIsGsidServer()) - { - sqlSafef(query, sizeof query, "select subjId from gsIdXref where dnaSeqId='%s'", seqId); - } -else - { - sqlSafef(query, sizeof query, "select subjId from gisaidXref where dnaSeqId='%s'", seqId); - } -sr = sqlMustGetResult(conn, query); -row = sqlNextRow(sr); -if (row != NULL) - { - subjId = row[0]; - - /* scan thru subj ID list */ - subj = gsidSelectedSubjList; - while (subj != NULL) - { - testSubjId = subj->subjId; - if (sameWord(subjId, testSubjId)) - { - sqlFreeResult(&sr); - hFreeConn(&conn); - return(TRUE); - } - subj = subj->next; - } - } -sqlFreeResult(&sr); -hFreeConn(&conn); -return(FALSE); -} - -boolean gsidCheckSelected(struct track *tg) -{ -char *setting; -char *subjListFileName; - -/* check subject only if the selectSubject is set to on in trackDb for this track */ -setting = trackDbSetting(tg->tdb, SELECT_SUBJ); -if (isNotEmpty(setting)) - { - if (sameString(setting, "on")) - { - /* return TRUE only if the user has selected the subjects */ - if (hIsGisaidServer()) - { - subjListFileName = strdup(gisaidSubjList); - } - else - { - subjListFileName = gsidSubjList; - } - if (cartOptionalString(cart, subjListFileName)) - { - return(TRUE); - } - } - } -return(FALSE); -} -#endif /* GBROWSE */ - static void connectedLfFromPslsInRange(struct sqlConnection *conn, struct track *tg, int start, int end, char *chromName, boolean isXeno, boolean nameGetsPos, int sizeMul) /* Return linked features from range of table after have * already connected to database.. */ { struct sqlResult *sr = NULL; char **row; int rowOffset; char *optionChrStr; struct linkedFeatures *lfList = NULL, *lf; char optionChr[128]; /* Option - chromosome filter */ char extraWhere[128]; safef( optionChr, sizeof(optionChr), "%s.chromFilter", tg->track); optionChrStr = cartUsualString(cart, optionChr, "All"); if (startsWith("chr",optionChrStr)) { safef(extraWhere, sizeof(extraWhere), "qName = \"%s\"",optionChrStr); sr = hRangeQuery(conn, tg->table, chromName, start, end, extraWhere, &rowOffset); } else { safef(extraWhere, sizeof(extraWhere), " "); sr = hRangeQuery(conn, tg->table, chromName, start, end, NULL, &rowOffset); } if (sqlCountColumns(sr) < 21+rowOffset) errAbort("trackDb has incorrect table type for track \"%s\"", tg->track); while ((row = sqlNextRow(sr)) != NULL) { struct psl *psl = pslLoad(row+rowOffset); lf = lfFromPslx(psl, sizeMul, isXeno, nameGetsPos, tg); #ifndef GBROWSE /* if this is a GSID track, check if we need to check for inclusion of the item */ if (hIsGsidServer() && gsidCheckSelected(tg)) { if (isSelected(lf->name)) slAddHead(&lfList, lf); } else #endif /* GBROWSE */ slAddHead(&lfList, lf); // Don't free psl - may be used by baseColor code (and freeing is slow) } slReverse(&lfList); if (tg->visibility != tvDense) slSort(&lfList, linkedFeaturesCmpStart); if (tg->extraUiData) filterMrna(tg, &lfList); tg->items = lfList; sqlFreeResult(&sr); } static void lfFromPslsInRange(struct track *tg, int start, int end, char *chromName, boolean isXeno, boolean nameGetsPos, int sizeMul) /* Return linked features from range of table. */ { struct sqlConnection *conn = hAllocConn(database); connectedLfFromPslsInRange(conn, tg, start, end, chromName, isXeno, nameGetsPos, sizeMul); hFreeConn(&conn); } static void loadXenoPslWithPos(struct track *tg) /* load up all of the psls from correct table into tg->items item list*/ { lfFromPslsInRange(tg, winStart,winEnd, chromName, TRUE, TRUE, 1); } void pslChromMethods(struct track *tg, char *colorChromDefault) /* Fill in custom parts of xeno psl <otherdb> track */ { char option[128]; /* Option - rainbow chromosome color */ char *optionStr ; safef( option, sizeof(option), "%s.color", tg->track); optionStr = cartUsualString(cart, option, colorChromDefault); tg->mapItemName = lfMapNameFromExtra; if( sameString( optionStr, "on" )) /*use chromosome coloring*/ tg->itemColor = lfChromColor; else tg->itemColor = NULL; tg->loadItems = loadXenoPslWithPos; } void loadPsl(struct track *tg) /* load up all of the psls from correct table into tg->items item list*/ { lfFromPslsInRange(tg, winStart,winEnd, chromName, FALSE, FALSE, 1); } void loadProteinPsl(struct track *tg) /* load up all of the psls from correct table into tg->items item list*/ { lfFromPslsInRange(tg, winStart,winEnd, chromName, TRUE, FALSE, 3); } void loadXenoPsl(struct track *tg) /* load up all of the psls from correct table into tg->items item list*/ { lfFromPslsInRange(tg, winStart,winEnd, chromName, TRUE, FALSE, 1); } void pslMethods(struct track *track, struct trackDb *tdb, int argc, char *argv[]) /* Load up psl type methods. */ { char *subType = "."; if (argc >= 2) subType = argv[1]; linkedFeaturesMethods(track); if (!tdb->useScore) track->colorShades = NULL; if (sameString(subType, "protein")) { track->subType = lfSubXeno; track->loadItems = loadProteinPsl; } else if (sameString(subType, "xeno")) { track->subType = lfSubXeno; track->loadItems = loadXenoPsl; if (argc >= 3) { pslChromMethods(track, trackDbSettingOrDefault(tdb, "colorChromDefault", "on")); } } else if (sameString(subType, "version")) { track->mapItemName = refGeneMapName; track->loadItems = loadPsl; } else track->loadItems = loadPsl; if (sameString(subType, "est")) track->drawItems = linkedFeaturesAverageDense; }