/* sampleTracks - Ryan Weber's wiggle tracks. */ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "hash.h" #include "linefile.h" #include "jksql.h" #include "hdb.h" #include "hgTracks.h" #include "sample.h" int sampleUpdateY( char *name, char *nextName, int lineHeight ) /* only increment height when name root (minus the period if * there is one) is different from previous one. *This assumes that the entries are sorted by name as they would *be if loaded by hgLoadSample*/ { int ret; char *tempstr = NULL; char *tempstr2 = NULL; tempstr = cloneString( name ); if( strstr( name, "." ) != NULL ) strtok( tempstr, "." ); tempstr2 = cloneString( nextName ); if( strstr( nextName, "." ) != NULL ) strtok( tempstr2, "." ); if( !sameString( tempstr, tempstr2 )) ret = lineHeight; else ret = 0; freeMem(tempstr); freeMem(tempstr2); return(ret); } void samplePrintYAxisLabel( struct hvGfx *hvg, int y, struct track *track, char *labelString, double min0, double max0 ) /*print a label for a horizontal y-axis line*/ { double tmp; int fontHeight = tl.fontHeight; double ymin = y - (track->heightPer / 2) + fontHeight; int itemHeight0 = track->itemHeight(track, track->items); int inWid = insideX-gfxBorder*3; tmp = -whichSampleBin( atof(labelString), min0, max0, 1000 ); tmp = (int)((double)ymin+((double)tmp)*(double)track->heightPer/1000.0+(double)track->heightPer)-fontHeight/2.0; if( !withCenterLabels ) tmp -= fontHeight; hvGfxTextRight(hvg, gfxBorder, tmp, inWid-1, itemHeight0, track->ixColor, tl.font, labelString ); } static int sampleTotalHeight(struct track *tg, enum trackVisibility vis) /* Wiggle track will use this to figure out the height they use as defined in the cart */ { struct slList *item; int lines = 0; int heightFromCart; char o1[128]; safef( o1, 128, "%s.heightPer", tg->track); heightFromCart = atoi(cartUsualString(cart, o1, "50")); tg->lineHeight = max(tl.fontHeight+1, heightFromCart); tg->heightPer = tg->lineHeight - 1; switch (vis) { case tvFull: lines = 1; for (item = tg->items; item != NULL; item = item->next) { if( item->next != NULL ) if( sampleUpdateY( tg->itemName(tg, item), tg->itemName(tg, item->next), 1 )) lines++; } tg->height = lines * tg->lineHeight; break; case tvPack: case tvSquish: errAbort("Sorry can't handle pack in sampleTotalHeight (%s)", tg->track); break; case tvDense: tg->height = tg->lineHeight; break; default: break; } return tg->height; } int consTotalHeight(struct track *tg, enum trackVisibility vis) /* Human/mouse conservation total height. */ { if( vis == tvDense ) return tg->height = tg->lineHeight = 10; else return sampleTotalHeight(tg, vis); } struct linkedFeatures *lfFromSample(struct sample *sample) /* Return a linked feature from a full sample (wiggle) track. */ { struct linkedFeatures *lf; struct simpleFeature *sf, *sfList = NULL; int grayIx = grayInRange(sample->score, 0, 1000); int start, i; unsigned *X = sample->samplePosition; int *Y = sample->sampleHeight; unsigned sampleCount = sample->sampleCount; assert(X != NULL && Y != NULL && sampleCount > 0); AllocVar(lf); lf->grayIx = grayIx; lf->name = cloneString(sample->name); lf->orientation = orientFromChar(sample->strand[0]); for (i=0; ichromStart; sf->start = start; if( Y[i] < 0 ) /*hack for negative values not loading correctly*/ sf->end = start; else if( Y[i] == 0 ) sf->end = start + 1; else sf->end = start + Y[i]; sf->grayIx = grayIx; slAddHead(&sfList, sf); } slReverse(&sfList); lf->components = sfList; linkedFeaturesBoundsAndGrays(lf); lf->start = sample->chromStart; lf->end = sample->chromEnd; return lf; } int whichSampleBin( double num, double thisMin, double thisMax, double binCount ) /* Get bin value from num. */ { return (num - thisMin) * binCount / (thisMax - thisMin); } double whichSampleNum( double bin, double thisMin, double thisMax, double binCount ) /* gets range nums. from bin values*/ { return( (thisMax - thisMin) / binCount * bin + thisMin ); } int basePositionToXAxis( int base, int seqStart, int seqEnd, int width, int xOff ) { double scale = scaleForPixels(width); double x1 = round((double)((int)base-seqStart)*scale) + xOff; return(x1); } int humMusZoomLevel( void ) { int zoom1 = 80000, zoom2 = 5000, zoom3 = 300; /* bp per data point */ int pixPerBase = (winEnd - winStart)/ tl.picWidth; if(pixPerBase >= zoom1) return(1); else if( pixPerBase >= zoom2 ) return(2); else if(pixPerBase >= zoom3) return(3); else return(0); } static void drawWiggleHorizontalLine( struct hvGfx *hvg, double where, double min0, double max0, int binCount, int y, double hFactor, int heightPer, Color lineColor ) /* Draws a blue horizontal line on a wiggle track at a specified * location based on the range and number of bins*/ { int bin; double y1; bin = -whichSampleBin( where, min0, max0, binCount); y1 = (int)((double)y+((double)bin)*hFactor+(double)heightPer); hvGfxBox(hvg, 0, y1, hvg->width, 1, lineColor); } static void wiggleLinkedFeaturesDraw(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis) /* Currently this routine is adapted from Terry's * linkedFeatureSeriesDraw() routine. * It is called for 'sample' tracks as specified in the trackDb.ra. * and it looks at the cart to decide whether to interpolate, fill blocks, * and use anti-aliasing.*/ { int i; struct linkedFeatures *lf; struct simpleFeature *sf; int y = yOff; int heightPer = tg->heightPer; int lineHeight = tg->lineHeight; int x1,x2; boolean isFull = (vis == tvFull); Color bColor = tg->ixAltColor; double scale = scaleForPixels(width); int prevX = -1; int gapPrevX = -1; double prevY = -1; double y1 = -1, y2; int ybase; int sampleX, sampleY; /* A sample in sample coordinates. * Sample X coordinate is chromosome coordinate. * Sample Y coordinate is usually 0-1000 */ int binCount = 1.0/tg->scaleRange; /* Maximum sample Y coordinate. */ int bin; /* Sample Y coordinates are first converted to * bin coordinates, and then to pixels. I'm not * totally sure why. */ int currentX, currentXEnd, currentWidth; int leftSide, rightSide; int noZoom = 1; enum wiggleOptEnum wiggleType; char *interpolate = NULL; int fill; int lineGapSize; double min0, max0; char o1[128]; /* Option 1 - linear interp */ char o2[128]; /* Option 2 - anti alias */ char o3[128]; /* Option 3 - fill */ char o4[128]; /* Option 4 - minimum vertical range cutoff of plot */ char o5[128]; /* Option 5 - maximum vertical range cutoff of plot */ char o6[128]; /* Option 6 - max gap where interpolation is still done */ char cartStr[64]; char *fillStr; double hFactor; double minRange, maxRange; double minRangeCutoff, maxRangeCutoff; Color gridColor = hvGfxFindRgb(hvg, &guidelineColor); /* for horizontal lines*/ lf=tg->items; if(lf==NULL) return; //take care of cart options safef( o1, 128,"%s.linear.interp", tg->track); safef( o2, 128, "%s.anti.alias", tg->track); safef( o3, 128,"%s.fill", tg->track); safef( o4, 128,"%s.min.cutoff", tg->track); safef( o5, 128,"%s.max.cutoff", tg->track); safef( o6, 128,"%s.interp.gap", tg->track); interpolate = cartUsualString(cart, o1, "Linear Interpolation"); wiggleType = wiggleStringToEnum(interpolate); //don't fill gcPercent track by default (but fill others) if(sameString( tg->table, "pGC") && sameString(database,"zooHuman3")) { fillStr = cartUsualString(cart, o3, "0"); } else { fillStr = cartUsualString(cart, o3, "1"); } fill = atoi(fillStr); cartSetString(cart, o3, fillStr ); //the 0.1 is so the label doesn't get truncated with integer valued user input min //display range. minRangeCutoff = max( atof(cartUsualString(cart,o4,"0.0"))-0.1, tg->minRange ); maxRangeCutoff = min( atof(cartUsualString(cart,o5,"1000.0"))+0.1, tg->maxRange); lineGapSize = atoi(cartUsualString(cart, o6, "200")); //update cart settings to reflect truncated range cutoff values cartSetString( cart, "win", "F" ); safef( cartStr, 64, "%g", minRangeCutoff ); cartSetString( cart, o4, cartStr ); safef( cartStr, 64, "%g", maxRangeCutoff ); cartSetString( cart, o5, cartStr ); heightPer = tg->heightPer+1; hFactor = (double)heightPer*tg->scaleRange; //errAbort( "min=%g, max=%g\n", minRangeCutoff, maxRangeCutoff ); if( sameString( tg->table, "zoo" ) || sameString( tg->table, "zooNew" ) ) binCount = binCount - 100; //save some space at top, between each zoo species minRange = whichSampleBin( minRangeCutoff, tg->minRange, tg->maxRange, binCount ); maxRange = whichSampleBin( maxRangeCutoff, tg->minRange, tg->maxRange, binCount ); //errAbort( "(%g,%g) cutoff=(%g,%g)\n", tg->minRange, tg->maxRange, minRangeCutoff, maxRangeCutoff ); if( sameString( tg->table, "zoo" ) || sameString( tg->table, "zooNew" ) ) { /*Always interpolate zoo track (since gaps are explicitly defined*/ lineGapSize = -1; } else if( tg->minRange == 0 && tg->maxRange == 8 ) //range for all L-score tracks { if( isFull ) { min0 = whichSampleNum( minRange, tg->minRange, tg->maxRange, binCount ); max0 = whichSampleNum( maxRange, tg->minRange, tg->maxRange, binCount ); for( i=1; i<=6; i++ ) drawWiggleHorizontalLine(hvg, (double)i, min0, max0, binCount, y, hFactor, heightPer, gridColor ); } } for(lf = tg->items; lf != NULL; lf = lf->next) { gapPrevX = -1; prevX = -1; ybase = (int)((double)y+hFactor+(double)heightPer); for (sf = lf->components; sf != NULL; sf = sf->next) { sampleX = sf->start; sampleY = sf->end - sampleX; // Stange encoding but so it is. // It is to deal with the fact that // for a BED: sf->end = sf->start + length // but in our case length = height (or y-value) // so to recover height we take // height = sf->end - sf->start. // Otherwise another sf variable would // be needed. /*mapping or sequencing gap*/ if (sampleY == 0) { bin = -whichSampleBin( (int)((maxRange - minRange)/5.0+minRange), minRange, maxRange, binCount ); y1 = (int)((double)y+((double)bin)* hFactor+(double)heightPer); if( gapPrevX >= 0 ) drawScaledBox(hvg, sampleX, gapPrevX, scale, xOff, (int)y1, (int)(.10*heightPer), shadesOfGray[2]); gapPrevX = sampleX; prevX = -1; /*connect next point with gray bar too*/ continue; } if (sampleY > maxRange) sampleY = maxRange; if (sampleY < minRange) sampleY = minRange; bin = -whichSampleBin( sampleY, minRange, maxRange, binCount ); x1 = round((double)(sampleX-winStart)*scale) + xOff; y1 = (int)((double)y+((double)bin)* hFactor+(double)heightPer); if (prevX > 0) { y2 = prevY; x2 = round((double)(prevX-winStart)*scale) + xOff; if( wiggleType == wiggleLinearInterpolation ) /*connect samples*/ { if( lineGapSize < 0 || prevX - sampleX <= lineGapSize ) /*don't interpolate over large gaps*/ { if (fill) hvGfxFillUnder(hvg, x1,y1, x2,y2, ybase, bColor); else hvGfxLine(hvg, x1,y1, x2,y2, color); } } } //if( x1 < 0 || x1 > tl.picWidth ) //printf("x1 = %d, sampleX=%d, winStart = %d\n
", x1, sampleX, winStart ); if( x1 >= 0 && x1 <= tl.picWidth ) { /* Draw the points themselves*/ drawScaledBox(hvg, sampleX, sampleX+1, scale, xOff, (int)y1-1, 3, color); if( fill ) drawScaledBox(hvg, sampleX, sampleX+1, scale, xOff, (int)y1+2, ybase-y1-2, bColor); } prevX = gapPrevX = sampleX; prevY = y1; } leftSide = max( tg->itemStart(tg,lf), winStart ); rightSide = min( tg->itemEnd(tg,lf), winEnd ); currentX = round((double)((int)leftSide-winStart)*scale) + xOff; currentXEnd = round((double)((int)rightSide-winStart)*scale) + xOff; currentWidth = currentXEnd - currentX; if( noZoom && isFull ) { mapBoxHc(hvg, lf->start, lf->end, currentX ,y, currentWidth, heightPer, tg->track, tg->mapItemName(tg, lf), tg->itemName(tg, lf)); if( lf->next != NULL ) y += sampleUpdateY( lf->name, lf->next->name, lineHeight ); else y += lineHeight; } } } struct track *sortGroupList = NULL; /* Used temporarily for sample sorting. */ int lfNamePositionCmp(const void *va, const void *vb) /* Compare based on name, then chromStart, used for sorting sample based tracks. */ { const struct linkedFeatures *a = *((struct linkedFeatures **)va); const struct linkedFeatures *b = *((struct linkedFeatures **)vb); int dif; char *tgName = NULL; if(sortGroupList != NULL) tgName = sortGroupList->shortLabel; if(tgName != NULL) { if(sameString(a->name, tgName) && differentString(b->name, tgName)) return -1; if(sameString(b->name, tgName) && differentString(a->name, tgName)) return 1; } dif = strcmp(a->name, b->name); if (dif == 0) dif = a->start - b->start; return dif; } void loadSampleIntoLinkedFeature(struct track *tg) /* Convert sample info in window to linked feature. */ { int maxWiggleTrackHeight = 2500; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset; struct sample *sample; struct linkedFeatures *lfList = NULL, *lf; char *hasDense = NULL; char *where = NULL; char query[256]; /*see if we have a summary table*/ sqlSafef(query, sizeof(query), "select name from %s where name = '%s' limit 1", tg->table, tg->shortLabel); //errAbort( "%s", query ); hasDense = sqlQuickQuery(conn, query, query, sizeof(query)); /* If we're in dense mode and have a summary table load it. */ if(tg->visibility == tvDense) { if(hasDense != NULL) { sqlSafef(query, sizeof(query), " name = '%s' ", tg->shortLabel); where = cloneString(query); } } sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, where, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { sample = sampleLoad(row + rowOffset); lf = lfFromSample(sample); slAddHead(&lfList, lf); sampleFree(&sample); } if(where != NULL) freez(&where); sqlFreeResult(&sr); hFreeConn(&conn); slReverse(&lfList); /* sort to bring items with common names to the same line but only for tracks with a summary table (with name=shortLabel) in dense mode*/ if( hasDense != NULL ) { sortGroupList = tg; /* used to put track name at top of sorted list. */ slSort(&lfList, lfNamePositionCmp); sortGroupList = NULL; } tg->items = lfList; /*turn off full mode if there are too many rows or each row is too * large. A total of maxWiggleTrackHeight is allowed for number of * rows times the rowHeight*/ if( tg->visibility == tvFull && sampleTotalHeight( tg, tvFull ) > maxWiggleTrackHeight ) { tg->limitedVisSet = TRUE; tg->limitedVis = tvDense; } } void sampleLinkedFeaturesMethods(struct track *tg) /* Fill in track methods for 'sample' tracks. */ { linkedFeaturesMethods(tg); tg->drawItems = wiggleLinkedFeaturesDraw; tg->totalHeight = sampleTotalHeight; tg->itemHeight = tgFixedItemHeight; } void sampleMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]) /* Load up methods for a generic sample type track. */ { track->scaleRange = 0.001; track->minRange = 0.0; track->maxRange = 1000.0; if (wordCount > 1) /*sample minRange maxRange*/ track->minRange = atof(words[1]); if (wordCount > 2) track->maxRange = atof(words[2]); if (wordCount > 3) track->scaleRange = atof(words[3]); track->bedSize = 9; track->subType = lfSubSample; /*make subType be "sample" (=2)*/ sampleLinkedFeaturesMethods(track); track->loadItems = loadSampleIntoLinkedFeature; } void loadHumMusL(struct track *tg) /* Load humMusL track with 2 zoom levels and one normal level. * Also used for loading the musHumL track (called Human Cons) * on the mouse browser. It decides which of 4 tables to * load based on how large of a window the user is looking at*/ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset; struct sample *sample; struct linkedFeatures *lfList = NULL, *lf; char *hasDense = NULL; char tableName[256]; int z; if(tl.picWidth == 0) errAbort("hgTracks.c::loadHumMusL() - can't have pixel width of 0"); /* Determine zoom level. */ if (!strstr(tg->table,"HMRConservation")) z = humMusZoomLevel(); else z=0; if(z == 1 ) safef(tableName, sizeof(tableName), "%s_%s", "zoom1", tg->table); else if( z == 2) safef(tableName, sizeof(tableName), "%s_%s", "zoom50", tg->table); else if(z == 3) safef(tableName, sizeof(tableName), "%s_%s", "zoom2500", tg->table); else safef(tableName, sizeof(tableName), "%s", tg->table); //printf("(%s)", tableName ); sr = hRangeQuery(conn, tableName, chromName, winStart, winEnd, NULL, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { sample = sampleLoad(row+rowOffset); lf = lfFromSample(sample); slAddHead(&lfList, lf); sampleFree(&sample); } sqlFreeResult(&sr); hFreeConn(&conn); slReverse(&lfList); /* sort to bring items with common names to the same line but only for tracks with a summary table (with name=shortLabel) in dense mode*/ if( hasDense != NULL ) { sortGroupList = tg; /* used to put track name at * top of sorted list. */ slSort(&lfList, lfNamePositionCmp); sortGroupList = NULL; } tg->items = lfList; } void humMusLMethods( struct track *tg ) /* Overide the humMusL load function to look for zoomed out tracks. */ { tg->loadItems = loadHumMusL; tg->totalHeight = consTotalHeight; } struct hash *zooSpeciesHash = NULL; void zooSpeciesHashInit() /* Function to init list of zoo species */ { char *name = NULL; char *val = NULL; if (zooSpeciesHash != NULL) return; zooSpeciesHash = hashNew(6); name = cloneString("Human"); val = cloneString("1"); hashAdd(zooSpeciesHash, name, val); cartSetBoolean( cart, "zooSpecies.Human", TRUE ); name = cloneString("Chimpanzee"); val = cloneString("2"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Baboon"); val = cloneString("3"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Orangutan"); val = cloneString("4"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Macaque"); val = cloneString("5"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Vervet"); val = cloneString("6"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Lemur"); val = cloneString("7"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Cat"); val = cloneString("8"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Dog"); val = cloneString("9"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Cow"); val = cloneString("10"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Pig"); val = cloneString("11"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Horse"); val = cloneString("12"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Rabbit"); val = cloneString("13"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Hedgehog"); val = cloneString("14"); hashAdd(zooSpeciesHash, name, val); name = cloneString("ajBat"); val = cloneString("15"); hashAdd(zooSpeciesHash, name, val); name = cloneString("cpBat"); val = cloneString("16"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Rat"); val = cloneString("17"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Mouse"); val = cloneString("18"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Platypus"); val = cloneString("19"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Opossum"); val = cloneString("20"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Dunnart"); val = cloneString("21"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Chicken"); val = cloneString("22"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Fugu"); val = cloneString("23"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Tetraodon"); val = cloneString("24"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Zebrafish"); val = cloneString("25"); hashAdd(zooSpeciesHash, name, val); } int lfZooCmp(const void *va, const void *vb) /* Compare based on name, then chromStart, used for sorting sample based tracks. */ { struct linkedFeatures *a = *((struct linkedFeatures **)va); struct linkedFeatures *b = *((struct linkedFeatures **)vb); char *aVal = hashFindVal(zooSpeciesHash, a->name); char *bVal = hashFindVal(zooSpeciesHash, b->name); int aV = atoi(aVal); int bV = atoi(bVal); return aV - bV; } void loadSampleZoo(struct track *tg) /* Convert sample info in window to linked feature. */ { int maxWiggleTrackHeight = 2500; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset; struct sample *sample; struct linkedFeatures *lfList = NULL, *lf; char *hasDense = NULL; char *where = NULL; char query[256]; char option[64]; zooSpeciesHashInit(); /*see if we have a summary table*/ sqlSafef(query, sizeof(query), "select name from %s where name = '%s' limit 1", tg->table, tg->shortLabel); //errAbort( "%s", query ); hasDense = sqlQuickQuery(conn, query, query, sizeof(query)); /* If we're in dense mode and have a summary table load it. */ if(tg->visibility == tvDense) { if(hasDense != NULL) { sqlSafef(query, sizeof(query), " name = '%s' ", tg->shortLabel); where = cloneString(query); } } sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, where, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { sample = sampleLoad(row + rowOffset); lf = lfFromSample(sample); safef( option, sizeof(option), "zooSpecies.%s", sample->name ); if( cartUsualBoolean(cart, option, TRUE )) slAddHead(&lfList, lf); sampleFree(&sample); } if(where != NULL) freez(&where); sqlFreeResult(&sr); hFreeConn(&conn); slReverse(&lfList); /* sort to bring items with common names to the same line * but only for tracks with a summary table * (with name=shortLabel) in dense mode */ if( hasDense != NULL ) { sortGroupList = tg; /* used to put track name at top of sorted list. */ slSort(&lfList, lfNamePositionCmp); sortGroupList = NULL; } /* Sort in species phylogenetic order */ slSort(&lfList, lfZooCmp); tg->items = lfList; /*turn off full mode if there are too many rows or each row is too * large. A total of maxWiggleTrackHeight is allowed for number of * rows times the rowHeight*/ if( tg->visibility == tvFull && sampleTotalHeight( tg, tvFull ) > maxWiggleTrackHeight ) { tg->limitedVisSet = TRUE; tg->limitedVis = tvDense; } } void zooMethods( struct track *tg ) /* Overide the zoo sample type load function to look for zoomed out tracks. */ { tg->loadItems = loadSampleZoo; } void loadAffyTranscriptome(struct track *tg) /* Convert sample info in window to linked feature. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset; struct sample *sample; struct linkedFeatures *lfList = NULL, *lf; char *hasDense = NULL; char *where = NULL; char query[256]; char tableName[256]; int zoom1 = 23924, zoom2 = 2991; /* bp per data point */ float pixPerBase = 0; /* Set it up so we don't have linear interpretation.. */ char *noLinearInterpString = wiggleEnumToString(wiggleNoInterpolation); cartSetString(cart, "affyTranscriptome.linear.interp", noLinearInterpString); if(tl.picWidth == 0) errAbort("hgTracks.c::loadAffyTranscriptome() - can't have pixel width of 0"); pixPerBase = (winEnd - winStart)/ tl.picWidth; /* Determine zoom level. */ if(pixPerBase >= zoom1) safef(tableName, sizeof(tableName), "%s_%s", "zoom1", tg->table); else if(pixPerBase >= zoom2) safef(tableName, sizeof(tableName), "%s_%s", "zoom2", tg->table); else safef(tableName, sizeof(tableName), "%s", tg->table); /*see if we have a summary table*/ if(hTableExists(database, tableName)) sqlSafef(query, sizeof(query), "select name from %s where name = '%s' limit 1", tableName, tg->shortLabel); else { warn("

Couldn't find table %s

", tableName); sqlSafef(query, sizeof(query), "select name from %s where name = '%s' limit 1", tg->table, tg->shortLabel); safef(tableName, sizeof(tableName), "%s", tg->table); } hasDense = sqlQuickQuery(conn, query, query, sizeof(query)); /* If we're in dense mode and have a summary table load it. */ if(tg->visibility == tvDense) { if(hasDense != NULL) { sqlSafef(query, sizeof(query), " name = '%s' ", tg->shortLabel); where = cloneString(query); } } sr = hRangeQuery(conn, tableName, chromName, winStart, winEnd, where, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { sample = sampleLoad(row+rowOffset); lf = lfFromSample(sample); slAddHead(&lfList, lf); sampleFree(&sample); } if(where != NULL) freez(&where); sqlFreeResult(&sr); hFreeConn(&conn); slReverse(&lfList); /* sort to bring items with common names to the same line but only for tracks with a summary table (with name=shortLabel) in dense mode*/ if( hasDense != NULL ) { sortGroupList = tg; /* used to put track name at top of sorted list. */ slSort(&lfList, lfNamePositionCmp); sortGroupList = NULL; } tg->items = lfList; } void affyTranscriptomeMethods(struct track *tg) /* Overide the load function to look for zoomed out tracks. */ { tg->loadItems = loadAffyTranscriptome; }