void bamMethods(struct track *track) /* Methods for BAM alignment files. */ { knetUdcInstall(); boolean isBamWig = cartUsualBooleanClosestToHome(cart, track->tdb, FALSE, BAMWIG_MODE, (trackDbSettingClosestToHome(track->tdb, BAMWIG_MODE) != NULL)); if (isBamWig) { bamWigMethods(track, track->tdb, 0, NULL); return; } track->canPack = TRUE; boolean isPaired = cartUsualBooleanClosestToHome(cart, track->tdb, FALSE, BAM_PAIR_ENDS_BY_NAME, (trackDbSettingClosestToHome(track->tdb, BAM_PAIR_ENDS_BY_NAME) != NULL)); char *tdbShowNames = trackDbSetting(track->tdb, BAM_SHOW_NAMES); boolean showNames = cartUsualBooleanClosestToHome(cart, track->tdb, FALSE, BAM_SHOW_NAMES, SETTING_IS_ON(tdbShowNames)); char *colorMode = cartOrTdbString(cart, track->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT); char *userTag = cartOrTdbString(cart, track->tdb, BAM_COLOR_TAG, BAM_COLOR_TAG_DEFAULT); if (sameString(colorMode, BAM_COLOR_MODE_TAG) && userTag != NULL) { if (! (isalpha(userTag[0]) && isalnum(userTag[1]) && userTag[2] == '\0')) { warn("%s: BAM tag '%s' is not valid -- must be a letter followed by a letter or number.", track->tdb->shortLabel, htmlEncode(userTag)); cartRemoveVariableClosestToHome(cart, track->tdb, FALSE, BAM_COLOR_TAG); } } addBamBaseAndIndelSettings(track->tdb); if (isPaired) { linkedFeaturesSeriesMethods(track); track->loadItems = bamPairedLoadItems; track->drawItems = bamLinkedFeaturesSeriesDraw; track->drawItemAt = bamPairedDrawAt; } else { linkedFeaturesMethods(track); track->loadItems = bamLoadItems; track->drawItems = bamLinkedFeaturesDraw; track->drawItemAt = bamDrawAt; } if (!showNames) { track->drawName = TRUE; // ironic, but this is how to suppress item labels in pack mode. track->drawLeftLabels = maybeDrawLeftLabels; } track->nextItemButtonable = track->nextExonButtonable = FALSE; track->nextPrevItem = NULL; track->nextPrevExon = NULL; if (sameString(colorMode, BAM_COLOR_MODE_GRAY)) track->colorShades = shadesOfGray; }
enum wiggleGridOptEnum wigFetchTransformFuncWithCart(struct cart *theCart, struct trackDb *tdb, char *name,char **optString) /* transformFunc - none by default **********************************/ { boolean parentLevel = isNameAtParentLevel(tdb,name); char *transformFunc; enum wiggleTransformFuncEnum ret = wiggleTransformFuncNone; char * tdbDefault = trackDbSettingClosestToHome(tdb, TRANSFORMFUNC); transformFunc = cloneString(cartOptionalStringClosestToHome(theCart, tdb, parentLevel, TRANSFORMFUNC)); if ((transformFunc == NULL) && (tdbDefault != NULL)) transformFunc = cloneString(tdbDefault); if (optString && transformFunc) *optString = cloneString(transformFunc); if (transformFunc) { ret = wiggleTransformFuncToEnum(transformFunc); freeMem(transformFunc); } return((enum wiggleGridOptEnum)ret); }
static char *pubsArticleTable(struct track *tg) /* return the name of the pubs articleTable, either * the value from the trackDb statement 'articleTable' * or the default value: <trackName>Article */ { char *articleTable = trackDbSettingClosestToHome(tg->tdb, "pubsArticleTable"); if (isEmpty(articleTable)) { char buf[256]; safef(buf, sizeof(buf), "%sArticle", tg->track); articleTable = cloneString(buf); } return articleTable; }
struct bigBedInterval *bigBedSelectRange(struct track *track, char *chrom, int start, int end, struct lm *lm) /* Return list of intervals in range. */ { struct bigBedInterval *result = NULL; /* protect against temporary network error */ struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { struct bbiFile *bbi = fetchBbiForTrack(track); int maxItems = min(BIGBEDMAXIMUMITEMS, maximumTrackItems(track)); // do not allow it to exceed BIGBEDMAXIMUMITEMS for bigBed result = bigBedIntervalQuery(bbi, chrom, start, end, maxItems + 1, lm); if (slCount(result) > maxItems) { track->limitedVis = tvDense; track->limitedVisSet = TRUE; result = NULL; AllocArray(track->summary, insideWidth); if (bigBedSummaryArrayExtended(bbi, chrom, start, end, insideWidth, track->summary)) { char *denseCoverage = trackDbSettingClosestToHome(track->tdb, "denseCoverage"); if (denseCoverage != NULL) { double endVal = atof(denseCoverage); if (endVal <= 0) { AllocVar(track->sumAll); *track->sumAll = bbiTotalSummary(bbi); } } } else freez(&track->summary); } bbiFileClose(&bbi); track->bbiFile = NULL; } errCatchEnd(errCatch); if (errCatch->gotError) { track->networkErrMsg = cloneString(errCatch->message->string); track->drawItems = bigDrawWarning; track->totalHeight = bigWarnTotalHeight; result = NULL; } errCatchFree(&errCatch); return result; }
boolean wigFetchDoNegativeWithCart(struct cart *theCart, struct trackDb *tdb, char *name,char **optString) /* doNegative - false by default **********************************/ { boolean parentLevel = isNameAtParentLevel(tdb,name); char *doNegativeDefault = trackDbSettingClosestToHome(tdb, DONEGATIVEMODE); char *doNegative = cloneString(cartOptionalStringClosestToHome(theCart, tdb, parentLevel, DONEGATIVEMODE)); if ((doNegative == NULL) && (doNegativeDefault != NULL)) doNegative = cloneString(doNegativeDefault); if (doNegative == NULL) return FALSE; return sameString(doNegative, "1") || sameString(doNegative, "on"); }
/****** itemRgb - not on by default **************************/ boolean bedItemRgb(struct trackDb *tdb) { char *Default="Off"; /* anything different than this will turn it on */ char *tdbDefault = (char *)NULL; if (tdb) tdbDefault = trackDbSettingClosestToHome(tdb, OPT_ITEM_RGB); if (tdbDefault) { if (differentWord(Default,tdbDefault)) return TRUE; } return FALSE; } /* boolean bedItemRgb(struct trackDb *tdb) */
static void bigWigClick(struct trackDb *tdb, char *fileName) /* Display details for BigWig data tracks. */ { char *chrom = cartString(cart, "c"); /* Open BigWig file and get interval list. */ struct bbiFile *bbi = NULL; struct lm *lm = lmInit(0); struct bbiInterval *bbList = NULL; char *maxWinToQuery = trackDbSettingClosestToHome(tdb, "maxWindowToQuery"); unsigned maxWTQ = 0; if (isNotEmpty(maxWinToQuery)) maxWTQ = sqlUnsigned(maxWinToQuery); if ((maxWinToQuery == NULL) || (maxWTQ > winEnd-winStart)) { bbi = bigWigFileOpen(fileName); bbList = bigWigIntervalQuery(bbi, chrom, winStart, winEnd, lm); } char num1Buf[64], num2Buf[64]; /* big enough for 2^64 (and then some) */ sprintLongWithCommas(num1Buf, BASE_1(winStart)); sprintLongWithCommas(num2Buf, winEnd); printf("<B>Position: </B> %s:%s-%s<BR>\n", chrom, num1Buf, num2Buf ); sprintLongWithCommas(num1Buf, winEnd-winStart); printf("<B>Total Bases in view: </B> %s <BR>\n", num1Buf); if (bbList != NULL) { bbiIntervalStatsReport(bbList, tdb->table, chrom, winStart, winEnd); } else if ((bbi == NULL) && (maxWTQ <= winEnd-winStart)) { sprintLongWithCommas(num1Buf, maxWTQ); printf("<P>Zoom in to a view less than %s bases to see data summary.</P>",num1Buf); } else { printf("<P>No data overlapping current position.</P>"); } lmCleanup(&lm); bbiFileClose(&bbi); }
void bigBedDrawDense(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color) /* Use big-bed summary data to quickly draw bigBed. */ { struct bbiSummaryElement *summary = tg->summary; if (summary) { char *denseCoverage = trackDbSettingClosestToHome(tg->tdb, "denseCoverage"); if (denseCoverage != NULL) { double startVal = 0, endVal = atof(denseCoverage); if (endVal <= 0) { struct bbiSummaryElement sumAll = *tg->sumAll; double mean = sumAll.sumData/sumAll.validCount; double std = calcStdFromSums(sumAll.sumData, sumAll.sumSquares, sumAll.validCount); rangeFromMinMaxMeanStd(0, sumAll.maxVal, mean, std, &startVal, &endVal); } int x; for (x=0; x<width; ++x) { if (summary[x].validCount > 0) { Color color = shadesOfGray[grayInRange(summary[x].maxVal, startVal, endVal)]; hvGfxBox(hvg, x+xOff, yOff, 1, tg->heightPer, color); } } } else { int x; for (x=0; x<width; ++x) { if (summary[x].validCount > 0) { hvGfxBox(hvg, x+xOff, yOff, 1, tg->heightPer, color); } } } } freez(&tg->summary); }
static void pubsAddExtra(struct track* tg, struct linkedFeatures* lf) /* add authorYear and title to linkedFeatures->extra */ { // no extra field if we're in dense mode if (tg->limitedVis == tvDense) { return; } char *articleTable = trackDbSettingClosestToHome(tg->tdb, "pubsArticleTable"); if(isEmpty(articleTable)) return; if (lf->extra != NULL) return; struct sqlConnection *conn = hAllocConn(database); struct pubsExtra* extra = pubsMakeExtra(tg, articleTable, conn, lf); lf->extra = extra; hFreeConn(&conn); }
enum wiggleGridOptEnum wigFetchAlwaysZeroWithCart(struct cart *theCart, struct trackDb *tdb, char *name,char **optString) /* alwaysZero - off by default **********************************/ { boolean parentLevel = isNameAtParentLevel(tdb,name); char *alwaysZero; enum wiggleAlwaysZeroEnum ret = wiggleAlwaysZeroOff; char * tdbDefault = trackDbSettingClosestToHome(tdb, ALWAYSZERO); alwaysZero = cloneString(cartOptionalStringClosestToHome(theCart, tdb, parentLevel, ALWAYSZERO)); if ((alwaysZero == NULL) && (tdbDefault != NULL)) alwaysZero = cloneString(tdbDefault); if (optString && alwaysZero) *optString = cloneString(alwaysZero); if (alwaysZero) { ret = wiggleAlwaysZeroToEnum(alwaysZero); freeMem(alwaysZero); } return((enum wiggleGridOptEnum)ret); }
void loadSimpleBed(struct track *tg) /* Load the items in one track - just move beds in * window... */ { struct bed *(*loader)(char **row); struct bed *bed, *list = NULL; char **row; int rowOffset; char *words[3]; int wordCt; char query[128]; char *setting = NULL; bool doScoreCtFilter = FALSE; int scoreFilterCt = 0; char *topTable = NULL; if (tg->bedSize <= 3) loader = bedLoad3; else if (tg->bedSize == 4) loader = bedLoad; else if (tg->bedSize == 5) loader = bedLoad5; else loader = bedLoad6; // pairedTagAlign loader is required for base coloring using sequence from seq1 & seq2 // after removing optional bin column, this loader assumes seq1 and seq2 are in // row[6] and row[7] respectively of the sql result. if ((setting = trackDbSetting(tg->tdb, BASE_COLOR_USE_SEQUENCE)) && sameString(setting, "seq1Seq2")) loader = bedLoadPairedTagAlign; /* limit to a specified count of top scoring items. * If this is selected, it overrides selecting item by specified score */ if ((setting = trackDbSettingClosestToHome(tg->tdb, "filterTopScorers")) != NULL) { wordCt = chopLine(cloneString(setting), words); if (wordCt >= 3) { doScoreCtFilter = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE, "filterTopScorersOn",sameString(words[0], "on")); scoreFilterCt = cartUsualIntClosestToHome(cart, tg->tdb, FALSE, "filterTopScorersCt", atoi(words[1])); topTable = words[2]; /* if there are not too many rows in the table then can define */ /* top table as the track or subtrack table */ if (sameWord(topTable, "self")) topTable = cloneString(tg->table); } } /* Get list of items */ if (tg->isBigBed) { // avoid opening an unneeded db connection for bigBed; required not to use mysql for parallel fetch tracks char *scoreFilter = cartOrTdbString(cart, tg->tdb, "scoreFilter", NULL); struct lm *lm = lmInit(0); struct bigBedInterval *bb, *bbList = bigBedSelectRange(tg, chromName, winStart, winEnd, lm); char *bedRow[32]; char startBuf[16], endBuf[16]; int minScore = 0; if (scoreFilter) minScore = atoi(scoreFilter); for (bb = bbList; bb != NULL; bb = bb->next) { bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow)); bed = loader(bedRow); if (scoreFilter == NULL || bed->score >= minScore) slAddHead(&list, bed); } lmCleanup(&lm); } else { struct sqlConnection *conn = hAllocConnTrack(database, tg->tdb); struct sqlResult *sr = NULL; /* limit to items above a specified score */ char *scoreFilterClause = getScoreFilterClause(cart, tg->tdb,NULL); if (doScoreCtFilter && (topTable != NULL) && hTableExists(database, topTable)) { sqlSafef(query, sizeof(query),"select * from %s order by score desc limit %d", topTable, scoreFilterCt); sr = sqlGetResult(conn, query); rowOffset = hOffsetPastBin(database, hDefaultChrom(database), topTable); } else if(scoreFilterClause != NULL && tg->bedSize >= 5) { sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, scoreFilterClause, &rowOffset); } else { sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset); } freeMem(scoreFilterClause); while ((row = sqlNextRow(sr)) != NULL) { bed = loader(row+rowOffset); slAddHead(&list, bed); } sqlFreeResult(&sr); hFreeConn(&conn); } if (doScoreCtFilter) { /* filter out items not in this window */ struct bed *newList = bedFilterListInRange(list, NULL, chromName, winStart, winEnd); list = newList; } slReverse(&list); tg->items = list; }
void bamDrawAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, double scale, MgFont *font, Color color, enum trackVisibility vis) /* Draw a single bam linkedFeatures item. Borrows a lot from linkedFeaturesDrawAt, * but cuts a lot of unneeded features (like coding region) and adds a couple * additional sources of color. */ { struct linkedFeatures *lf = item; struct simpleFeature *sf; int heightPer = tg->heightPer; int x1 = round((double)((int)lf->start-winStart)*scale) + xOff; int x2 = round((double)((int)lf->end-winStart)*scale) + xOff; int w = x2-x1; int midY = y + (heightPer>>1); char *exonArrowsDense = trackDbSettingClosestToHome(tg->tdb, "exonArrowsDense"); boolean exonArrowsEvenWhenDense = (exonArrowsDense != NULL && SETTING_IS_ON(exonArrowsDense)); boolean exonArrows = (tg->exonArrows && (vis != tvDense || exonArrowsEvenWhenDense)); struct dnaSeq *mrnaSeq = NULL; enum baseColorDrawOpt drawOpt = baseColorDrawOff; boolean indelShowDoubleInsert, indelShowQueryInsert, indelShowPolyA; struct psl *psl = (struct psl *)(lf->original); char *colorMode = cartOrTdbString(cart, tg->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT); char *grayMode = cartOrTdbString(cart, tg->tdb, BAM_GRAY_MODE, BAM_GRAY_MODE_DEFAULT); bool baseQualMode = (sameString(colorMode, BAM_COLOR_MODE_GRAY) && sameString(grayMode, BAM_GRAY_MODE_BASE_QUAL)); char *qSeq = lf->extra; if (vis != tvDense && isNotEmpty(qSeq) && !sameString(qSeq, "*")) { drawOpt = baseColorDrawSetup(hvg, tg, lf, &mrnaSeq, &psl); if (drawOpt > baseColorDrawOff) exonArrows = FALSE; } static Color darkBlueColor = 0; static Color darkRedColor = 0; if (darkRedColor == 0) { darkRedColor = hvGfxFindColorIx(hvg, 100,0,0); darkBlueColor = hvGfxFindColorIx(hvg, 0,0,100); } if (sameString(colorMode, BAM_COLOR_MODE_STRAND)) color = (lf->orientation < 0) ? darkRedColor : darkBlueColor; else if (lf->filterColor != 0) { // In bamTrack, lf->filterColor is an RGBA value color = lf->filterColor; } else if (tg->colorShades) color = tg->colorShades[lf->grayIx]; else color = tg->ixColor; indelEnabled(cart, tg->tdb, basesPerPixel, &indelShowDoubleInsert, &indelShowQueryInsert, &indelShowPolyA); if (!indelShowDoubleInsert) innerLine(hvg, x1, midY, w, color); for (sf = lf->components; sf != NULL; sf = sf->next) { int s = sf->start, e = sf->end; if (e <= s || e < winStart || s > winEnd) continue; if (baseQualMode) color = tg->colorShades[sf->grayIx]; baseColorDrawItem(tg, lf, sf->grayIx, hvg, xOff, y, scale, font, s, e, heightPer, zoomedToCodonLevel, mrnaSeq, sf, psl, drawOpt, MAXPIXELS, winStart, color); if (tg->exonArrowsAlways || (exonArrows && (sf->start <= winStart || sf->start == lf->start) && (sf->end >= winEnd || sf->end == lf->end))) { Color barbColor = hvGfxContrastingColor(hvg, color); x1 = round((double)((int)s-winStart)*scale) + xOff; x2 = round((double)((int)e-winStart)*scale) + xOff; w = x2-x1; clippedBarbs(hvg, x1+1, midY, x2-x1-2, tl.barbHeight, tl.barbSpacing, lf->orientation, barbColor, TRUE); } } if (indelShowDoubleInsert && psl) { int intronGap = 0; if (vis != tvDense) intronGap = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "intronGap", "0")); lfDrawSpecialGaps(lf, intronGap, TRUE, 0, tg, hvg, xOff, y, scale, color, color, vis); } if (vis != tvDense) { /* If highlighting differences between aligned sequence and genome when * zoomed way out, this must be done in a separate pass after exons are * drawn so that exons sharing the pixel don't overdraw differences. */ if ((indelShowQueryInsert || indelShowPolyA) && psl) baseColorOverdrawQInsert(tg, lf, hvg, xOff, y, scale, heightPer, mrnaSeq, psl, winStart, drawOpt, indelShowQueryInsert, indelShowPolyA); baseColorOverdrawDiff(tg, lf, hvg, xOff, y, scale, heightPer, mrnaSeq, psl, winStart, drawOpt); baseColorDrawCleanup(lf, &mrnaSeq, &psl); } }