e70152e44cc66cc599ff6b699eb8adc07f3e656a kent Sat May 24 21:09:34 2014 -0700 Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment. diff --git src/hg/hgTracks/transcriptome.c src/hg/hgTracks/transcriptome.c index 448a89e..ab5a190 100644 --- src/hg/hgTracks/transcriptome.c +++ src/hg/hgTracks/transcriptome.c @@ -1,195 +1,198 @@ /* transcriptome - stuff to handle loading and coloring of the affymetrix transcriptome tracks. These are sets of wiggle tracks representing probes tiled through non-repetitive portions of the human genome at 5 bp resolution. Also included are transfrags tracks which are bed tracks indicating what is thought to be expressed. */ +/* Copyright (C) 2012 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + #include "common.h" #include "jksql.h" #include "hdb.h" #include "hgTracks.h" #include "bed.h" #include "wigCommon.h" static Color affyTransfragColor(struct track *tg, void *item, struct hvGfx *hvg) /* Color for an affyTransfrag item. Different colors are returned depending on score. 0 - Passes all filters 1 - Overlaps a pseudogene 2 - Overlaps a blat hit 3 - Overlaps both a pseudogene and a blat hit. */ { static Color cleanCol = MG_WHITE; static Color blatCol = MG_WHITE; static Color pseudoCol = MG_WHITE; struct bed *bed = item; /* If first time through make the colors. */ if(cleanCol == MG_WHITE) { cleanCol = tg->ixColor; blatCol = hvGfxFindColorIx(hvg, 100, 100, 160); pseudoCol = hvGfxFindColorIx(hvg, 190, 190, 230); } switch(bed->score) { case 0 : return cleanCol; case 1 : return pseudoCol; case 2 : return blatCol; case 3 : return pseudoCol; default: errAbort("Don't recognize score for transfrag %s", bed->name); }; return tg->ixColor; } static struct slList *affyTransfragLoader(char **row) /* Wrapper around bedLoad5 to conform to ItemLoader type. */ { return (struct slList *)bedLoad5(row); } static void affyTransfragsLoad(struct track *tg) /* Load the items from the chromosome range indicated. Filter as necessary to remove things the user has requested not to see. Score indicates the status of a transfrag: 0 - Passes all filters 1 - Overlaps a pseudogene 2 - Overlaps a blat hit 3 - Overlaps both a pseudogene and a blat hit. */ { struct bed *bed = NULL, *bedNext = NULL, *bedList = NULL; boolean skipPseudos = cartUsualBoolean(cart, "affyTransfrags.skipPseudos", TRUE); boolean skipDups = cartUsualBoolean(cart, "affyTransfrags.skipDups", FALSE); /* Use simple bed loader to do database work. */ bedLoadItem(tg, tg->table, affyTransfragLoader); /* Now filter based on options. */ for(bed = tg->items; bed != NULL; bed = bedNext) { bedNext = bed->next; if((bed->score == 1 || bed->score == 3) && skipPseudos) bedFree(&bed); else if((bed->score == 2 || bed->score == 3) && skipDups) bedFree(&bed); else { slAddHead(&bedList, bed); } } slReverse(&bedList); tg->items = bedList; } void affyTransfragsMethods(struct track *tg) /* Substitute a new load method that filters based on score. Also add a new itemColor() method that draws transfrags that overlap dups and pseudoGenes in a different color. */ { tg->itemColor = affyTransfragColor; tg->loadItems = affyTransfragsLoad; } static Color affyTxnPhase2ItemColor(struct track *tg, void *item, struct hvGfx *hvg) /* Color for an affyTransfrag item. Different colors are returned depending on name. 0 - Passes all filters 1 - Overlaps a pseudogene 2 - Overlaps a blat hit 3 - Overlaps both a pseudogene and a blat hit. */ { static Color cleanCol = MG_WHITE; static Color blatCol = MG_WHITE; static Color pseudoCol = MG_WHITE; struct bed *bed = item; /* If first time through make the colors. */ if(cleanCol == MG_WHITE) { cleanCol = tg->ixColor; blatCol = hvGfxFindColorIx(hvg, 100, 100, 160); pseudoCol = hvGfxFindColorIx(hvg, 190, 190, 230); } switch(bed->name[0]) { case '0' : return cleanCol; case '1' : return pseudoCol; case '2' : return blatCol; case '3' : return pseudoCol; default: errAbort("Don't recognize score for transfrag %s", bed->name); }; return tg->ixColor; } static void affyTxnPhase2BedDrawLeftLabels(struct track *track, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, int height, boolean withCenterLabels, MgFont *font, Color color, enum trackVisibility vis) /* Draw the left label. Simple as we draw the name centered in the track height no matter what. */ { int fontHeight = mgFontLineHeight(font); int tHeight = track->height; int centerLabel = (tHeight/2)-(fontHeight/2); /* vertical center of track. */ Color labelColor = (track->labelColor ? track->labelColor : track->ixColor); /* If dense do nothing and return. */ if(track->limitedVis == tvHide) return; /* Add the center label if necessary and draw track name on left side centered vertically. */ if (withCenterLabels) yOff += fontHeight; hvGfxSetClip(hvg, leftLabelX, yOff, leftLabelWidth, tHeight); hvGfxTextRight(hvg, leftLabelX, yOff+centerLabel, leftLabelWidth-1, track->lineHeight, labelColor, font, track->shortLabel); hvGfxUnclip(hvg); } static char *affyTxnP2ItemName(struct track *track, void *item) /* Don't have names for tese items. */ { return ""; } static void affyTxnPhase2MapItem(struct track *tg, struct hvGfx *hvg, void *item, char *itemName, char *mapItemName, int start, int end, int x, int y, int width, int height) /* Don't map anything. */ { } void affyTxnPhase2Methods(struct track *track) /* Methods for dealing with a composite transcriptome tracks. */ { if (track->subtracks == NULL && stringIn("bed", track->tdb->type)) { track->itemName = affyTxnP2ItemName; track->drawLeftLabels = affyTxnPhase2BedDrawLeftLabels; track->itemColor = affyTxnPhase2ItemColor; track->mapsSelf = TRUE; track->mapItem = affyTxnPhase2MapItem; } }