e685265dd1b666acaab2bc076c141c368fb4be66 hiram Thu Oct 15 11:36:17 2015 -0700 fixup gcc warnings for -Wunused-but-set-variable refs #16121 diff --git src/hg/hgTracks/loweLabTracks.c src/hg/hgTracks/loweLabTracks.c index ee9f4c2..30e0769 100644 --- src/hg/hgTracks/loweLabTracks.c +++ src/hg/hgTracks/loweLabTracks.c @@ -1,711 +1,709 @@ /* Lowe lab tracks */ /* Copyright (C) 2014 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "hash.h" #include "localmem.h" #include "linefile.h" #include "jksql.h" #include "hdb.h" #include "bed.h" #include "psl.h" #include "codeBlast.h" #include "cogs.h" #include "rnaGenes.h" #include "hgTracks.h" #include "expRatioTracks.h" #include "loweLabTracks.h" #include "rnaHybridization.h" /* Declare our color gradients and the the number of colors in them */ #define LL_EXPR_DATA_SHADES 16 Color LLshadesOfGreen[LL_EXPR_DATA_SHADES]; Color LLshadesOfRed[LL_EXPR_DATA_SHADES]; boolean LLexprBedColorsMade = FALSE; /* Have the shades of Green, Red, and Blue been allocated? */ int LLmaxRGBShade = LL_EXPR_DATA_SHADES - 1; #define LL_COG_SHADES 26 Color LLshadesOfCOGS[LL_COG_SHADES]; /**** Lowe lab additions ***/ /* RNA Hybridization additions */ #define RNA_HYBRIDIZATION_SHADES 20 Color rnaHybShadesPos[RNA_HYBRIDIZATION_SHADES]; Color rnaHybShadesNeg[RNA_HYBRIDIZATION_SHADES]; int rnaHybShadesInitialized = 0; void rnaHybShadesInit(struct hvGfx *hvg) /* Allocate the LD for positive and negative values, and error cases */ { static struct rgbColor white = {255, 255, 255}; static struct rgbColor red = {255, 0, 0}; static struct rgbColor blue = { 0, 0, 255}; hvGfxMakeColorGradient(hvg, &white, &blue, RNA_HYBRIDIZATION_SHADES, rnaHybShadesPos); hvGfxMakeColorGradient(hvg, &white, &red, RNA_HYBRIDIZATION_SHADES, rnaHybShadesNeg); rnaHybShadesInitialized = 1; } void initializeColors(struct hvGfx *hvg) { LLshadesOfCOGS['J'-'A']=hvGfxFindColorIx(hvg, 252, 204,252); LLshadesOfCOGS['A'-'A']=hvGfxFindColorIx(hvg, 252, 220,252); LLshadesOfCOGS['K'-'A']=hvGfxFindColorIx(hvg, 252, 220,236); LLshadesOfCOGS['L'-'A']=hvGfxFindColorIx(hvg, 252, 220,220); LLshadesOfCOGS['B'-'A']=hvGfxFindColorIx(hvg, 252, 220,204); LLshadesOfCOGS['D'-'A']=hvGfxFindColorIx(hvg, 252, 252,220); LLshadesOfCOGS['Y'-'A']=hvGfxFindColorIx(hvg, 252, 252,204); LLshadesOfCOGS['V'-'A']=hvGfxFindColorIx(hvg, 252, 252,188); LLshadesOfCOGS['T'-'A']=hvGfxFindColorIx(hvg, 252, 252,172); LLshadesOfCOGS['M'-'A']=hvGfxFindColorIx(hvg, 236, 252,172); LLshadesOfCOGS['N'-'A']=hvGfxFindColorIx(hvg, 220, 252,172); LLshadesOfCOGS['Z'-'A']=hvGfxFindColorIx(hvg, 204, 252,172); LLshadesOfCOGS['W'-'A']=hvGfxFindColorIx(hvg, 188, 252,172); LLshadesOfCOGS['U'-'A']=hvGfxFindColorIx(hvg, 172, 252,172); LLshadesOfCOGS['O'-'A']=hvGfxFindColorIx(hvg, 156, 252,172); LLshadesOfCOGS['C'-'A']=hvGfxFindColorIx(hvg, 188, 252,252); /* light blue 133, 233,204); */ LLshadesOfCOGS['G'-'A']=hvGfxFindColorIx(hvg, 204, 252,252); LLshadesOfCOGS['E'-'A']=hvGfxFindColorIx(hvg, 220, 252,252); LLshadesOfCOGS['F'-'A']=hvGfxFindColorIx(hvg, 220, 236,252); LLshadesOfCOGS['H'-'A']=hvGfxFindColorIx(hvg, 220, 220,252); LLshadesOfCOGS['I'-'A']=hvGfxFindColorIx(hvg, 220, 204,252); LLshadesOfCOGS['P'-'A']=hvGfxFindColorIx(hvg, 204, 204,252); LLshadesOfCOGS['Q'-'A']=hvGfxFindColorIx(hvg, 188, 204,252); LLshadesOfCOGS['R'-'A']=hvGfxFindColorIx(hvg, 224, 224,224); /* general function prediction */ LLshadesOfCOGS['S'-'A']=hvGfxFindColorIx(hvg, 204, 204,204); LLshadesOfCOGS['+'+'-'-'A']=hvGfxFindColorIx(hvg, 224, 224,224);/* no cog - same as R (general function prediction) */ } void loadBed6(struct track *tg) /* Load the items in one custom track - just move beds in * window... */ { struct bed *bed, *list = NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset; sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { bed = bedLoadN(row+rowOffset, 6); slAddHead(&list, bed); } sqlFreeResult(&sr); hFreeConn(&conn); slReverse(&list); tg->items = list; } Color gbGeneColor(struct track *tg, void *item, struct hvGfx *hvg) /* Return color to draw gene in. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char query[512]; struct bed *bed = item; struct COG *COG=NULL; char *temparray[160]; char **row; if(hTableExists(database, "COG")) { sqlSafef(query, sizeof query, "select * from COG where name = '%s'", bed->name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) COG = COGLoad(row); sqlFreeResult(&sr); hFreeConn(&conn); initializeColors(hvg); if(COG!=NULL) { chopString(COG->code, "," , temparray, 9999); if (temparray[0][0] == '-') return LLshadesOfCOGS[('+'+temparray[0][0]-'A')]; else return LLshadesOfCOGS[(temparray[0][0]-'A')]; } else return blackIndex(); } else { hFreeConn(&conn); return blackIndex(); } slFreeList(&bed); } void gbGeneMethods(struct track *tg) /* Track group for genbank gene tracks */ { tg->loadItems = loadBed6; tg->itemColor = gbGeneColor; } Color gpGeneColor(struct track *tg, void *item, struct hvGfx *hvg) /* Return color to draw gene (genePred) in. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char query[512]; struct linkedFeatures *lf = item; struct COG *COG=NULL; char *temparray[160]; char **row; if (lf == NULL) return shadesOfGray[9]; if (lf->name == NULL) return shadesOfGray[9]; if(hTableExists(database, "COG")) { sqlSafef(query, sizeof query,"select * from COG where name = '%s'", lf->name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) COG = COGLoad(row); sqlFreeResult(&sr); hFreeConn(&conn); initializeColors(hvg); if(COG!=NULL) { chopString(COG->code, "," , temparray, 9999); if (temparray[0][0] == '-') return LLshadesOfCOGS[('+'+temparray[0][0]-'A')]; else return LLshadesOfCOGS[(temparray[0][0]-'A')]; } else return shadesOfGray[9]; } else { hFreeConn(&conn); return shadesOfGray[9]; } slFreeList(&lf); } Color gpGeneNameColor(struct track *tg, void *item, struct hvGfx *hvg) /* draw name for the linked feature in blue. */ { tg->ixAltColor = 1; return MG_BLACK; } void archaeaGeneMethods(struct track *tg) /* Track group for genbank gene tracks */ { tg->itemColor = gpGeneColor; tg->itemNameColor = gpGeneNameColor; tg->loadItems = loadGenePred; } Color sargassoSeaGeneColor(struct track *tg, void *item, struct hvGfx *hvg) /* Return color to draw gene in. */ { struct bed *lf=item; if (lf->score > 990) return shadesOfGray[10]; else if (lf->score > 850) return shadesOfGray[9]; else if (lf->score > 700) return shadesOfGray[8]; else if (lf->score > 550) return shadesOfGray[7]; else if (lf->score > 450) return shadesOfGray[6]; else if (lf->score > 300) return shadesOfGray[5]; else if (lf->score > 200) return shadesOfGray[4]; else if (lf->score > 100) return shadesOfGray[3]; else return shadesOfGray[2]; } void sargassoSeaMethods(struct track *tg) /* Track group for genbank gene tracks */ { tg->loadItems = loadBed6; tg->itemColor = sargassoSeaGeneColor; } Color tigrGeneColor(struct track *tg, void *item, struct hvGfx *hvg) /* Return color to draw gene in. */ { struct bed *bed = item; if (bed->strand[0] == '+') return tg->ixColor; return tg->ixAltColor; } void tigrGeneMethods(struct track *tg) /* Track group for genbank gene tracks */ { tg->loadItems = loadBed6; tg->itemColor = tigrGeneColor; } char *llBlastPName(struct track *tg, void *item) { struct bed *bed = item; char *itemName = cloneString(bed->name); static char buf[256]; char *nameParts[2]; chopByChar(itemName,'|',nameParts,ArraySize(nameParts)); sprintf(buf, "%s", nameParts[0]); chopByChar(buf,'$',nameParts,ArraySize(nameParts)); sprintf(buf,"%s",nameParts[1]); freeMem(itemName); return buf; } void llBlastPMethods(struct track *tg) { tg->itemName = llBlastPName; } struct linkedFeatures *lfsToLf(struct linkedFeaturesSeries *lfs) /* convert a linked feature into a linked feature series */ { struct linkedFeatures *lf = NULL; struct simpleFeature *sf = NULL; AllocVar(lf); lf->name = cloneString(lfs->name); lf->start = lfs->start; lf->end = lfs->end; lf->tallStart = lfs->start; lf->tallEnd = lfs->end; lf->grayIx = lfs->grayIx; lf->orientation = lfs->orientation; lf->extra = cloneString(lfs->features->extra); AllocVar(sf); sf->start = lfs->start; sf->end = lfs->end; sf->grayIx = lfs->grayIx; lf->components = sf; return lf; } struct linkedFeatures *lfFromBed6(struct codeBlast *bed, int scoreMin, int scoreMax) /* Return a linked feature from a (full) bed. */ { struct linkedFeatures *lf; struct simpleFeature *sf; int grayIx = grayInRange(bed->score, scoreMin, scoreMax); AllocVar(lf); lf->grayIx = grayIx; lf->name = cloneString(bed->name); lf->orientation = orientFromChar(bed->strand[0]); AllocVar(sf); sf->start = bed->chromStart; sf->end = bed->chromEnd; sf->grayIx = grayIx; lf->components = sf; linkedFeaturesBoundsAndGrays(lf); lf->tallStart = bed->chromStart; lf->tallEnd = bed->chromEnd; return lf; } void loadCodeBlast(struct track *tg) /* from the bed 6+1 codeBlast table, make a linkedFeaturesSeries and load it. */ { struct linkedFeaturesSeries *lfs = NULL, *originalLfs, *codeLfs, *lfsList = NULL; struct linkedFeatures *lf; struct slName *codes = NULL, *track=NULL, *scores=NULL; -struct codeBlast *bedList; struct codeBlast *cb, *list=NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **temparray3; char *temparray[32]; char *temparray2; char **row; char *tempstring; int x; int cutoff; char cMode[64]; /*The most common names used to display method*/ char *codeNames[18] = {"within genus", "\t", "crenarchaea", "euryarchaea", "\t", "bacteria", "\t", "eukarya", "\t", "thermophile", "hyperthermophile","acidophile", "alkaliphile", "halophile", "methanogen", "strict aerobe", "strict anaerobe", "anaerobe or aerobe"}; int i; safef(cMode, sizeof(cMode), "%s.scoreFilter", tg->tdb->track); cutoff=cartUsualInt(cart, cMode,0 ); sr=hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, 0); while ((row = sqlNextRow(sr)) != NULL) { cb = codeBlastLoad(row); slAddHead(&list, cb); } sqlFreeResult(&sr); hFreeConn(&conn); slReverse(&list); if(list == NULL) return; for(cb = list; cb != NULL; cb = cb->next) { AllocVar(lfs); AllocVar(lf); lfs->name = cloneString(cb->name); lf = lfFromBed6(cb,0,1000); lf->score = cb->score; tempstring=cloneString(cb->code); chopString(tempstring, "," , temparray, ArraySize(temparray)); if(sameWord(database, "pyrFur2")) { temparray3=(char**)calloc(19*8,sizeof(char**)); for(x=0; x<19; x++) { temparray3[x]=(char *)calloc(256, sizeof(char*)); /* Fix to cloneString problem when both patricia and my track was showing at the same time */ if(temparray[x]!=NULL) { if(atoi(temparray[x])==1000) temparray3[x]="1000"; else if(atoi(temparray[x])==900) temparray3[x]="900"; else if(atoi(temparray[x])==800) temparray3[x]="800"; else if(atoi(temparray[x])==700) temparray3[x]="700"; else if(atoi(temparray[x])==600) temparray3[x]="600"; else if(atoi(temparray[x])==500) temparray3[x]="500"; else if(atoi(temparray[x])==400) temparray3[x]="400"; else if(atoi(temparray[x])==300) temparray3[x]="300"; else if(atoi(temparray[x])==200) temparray3[x]="200"; else if(atoi(temparray[x])==100) temparray3[x]="100"; else temparray3[x]="0"; } } } else { temparray3=(char**)calloc(18*8,sizeof(char**)); for(x=0; x<18; x++) { temparray3[x]=(char *)calloc(256, sizeof(char*)); /* Fix to cloneString problem when both patricia and my track was showing at the same time */ if(temparray[x]!=NULL) { if(atoi(temparray[x])==1000) temparray3[x]="1000"; else if(atoi(temparray[x])==900) temparray3[x]="900"; else if(atoi(temparray[x])==800) temparray3[x]="800"; else if(atoi(temparray[x])==700) temparray3[x]="700"; else if(atoi(temparray[x])==600) temparray3[x]="600"; else if(atoi(temparray[x])==500) temparray3[x]="500"; else if(atoi(temparray[x])==400) temparray3[x]="400"; else if(atoi(temparray[x])==300) temparray3[x]="300"; else if(atoi(temparray[x])==200) temparray3[x]="200"; else if(atoi(temparray[x])==100) temparray3[x]="100"; else temparray3[x]="0"; } } } lf->extra = temparray3; lfs->start = lf->start; lfs->end = lf->end; lfs->features= lf; slAddHead(&lfsList, lfs); } tg->items=lfsList; -bedList=tg->items; lfsList=NULL; if(tg->limitedVis != tvDense) { originalLfs = tg->items; if(sameWord(database, "pyrFur2")) { for (i = 0; i < 19; i++) { struct linkedFeatures *lfList = NULL; AllocVar(codeLfs); /*When doing abyssi displays differnt names at the begining*/ if(i == 0) codeLfs->name="within Pho"; else if (i==1) codeLfs->name="within Pab"; else if (i==2) codeLfs->name="\t"; else codeLfs->name = cloneString(codeNames[i-1]); codeLfs->noLine = TRUE; for (lfs = originalLfs; lfs != NULL; lfs = lfs->next) { lf = lfsToLf(lfs); if(i>2) temparray2=((char**)(lfs->features->extra))[i-0]; else temparray2=((char**)(lfs->features->extra))[i]; if (i!=2 && i!=5 && i!=7 && i!=9 && atoi(temparray2)>-9997 && atoi(temparray2)!=0 && atoi(temparray2)>=cutoff) { lf->score=atoi(temparray2); slAddHead(&lfList,lf); } } slReverse(&lfList); codeLfs->features = lfList; slAddHead(&lfsList,codeLfs); } } else { for (i = 0; i < 18; i++) { struct linkedFeatures *lfList = NULL; AllocVar(codeLfs); codeLfs->name = cloneString(codeNames[i]); codeLfs->noLine = TRUE; for (lfs = originalLfs; lfs != NULL; lfs = lfs->next) { lf = lfsToLf(lfs); temparray2=((char**)(lfs->features->extra))[i]; if (i!=1 && i!=4 && i!=6 && i!=8 && atoi(temparray2)>-9997 && atoi(temparray2)!=0 && atoi(temparray2)>=cutoff) { lf->score=atoi(temparray2); slAddHead(&lfList,lf); } } slReverse(&lfList); codeLfs->features = lfList; slAddHead(&lfsList,codeLfs); } } freeLinkedFeaturesSeries(&originalLfs); slReverse(&lfsList); tg->items=lfsList; } slFreeList(&track); slFreeList(&scores); slFreeList(&codes); codeBlastFree(&list); } Color cbGeneColor(struct track *tg, void *item, struct hvGfx *hvg) /* Return color to draw gene in. */ { struct linkedFeatures *lf=item; if (lf->score > 990) return shadesOfGray[9]; else if (lf->score > 850) return shadesOfGray[8]; else if (lf->score > 700) return shadesOfGray[7]; else if (lf->score > 550) return shadesOfGray[6]; else if (lf->score > 450) return shadesOfGray[5]; else if (lf->score > 300) return shadesOfGray[4]; else if (lf->score > 200) return shadesOfGray[3]; else if (lf->score > 100) return shadesOfGray[3]; else if (lf->score != 0) return shadesOfGray[2]; else return shadesOfGray[0]; } void codeBlastMethods(struct track *tg) { linkedFeaturesSeriesMethods(tg); tg->loadItems = loadCodeBlast; tg->mapItem = lfsMapItemName; tg->itemColor=cbGeneColor; tg->mapsSelf = TRUE; } Color rgGeneColor(struct track *tg, void *item, struct hvGfx *hvg) /* Return color to draw gene in. */ { struct rnaGenes *lf=item; makeRedGreenShades(hvg); if (lf->score ==100) return shadesOfGreen[15]; if (lf->score == 300) return shadesOfRed[15]; if (lf->score == 200) return shadesOfBlue[15]; else return shadesOfGray[9]; } void rnaGenesMethods(struct track *tg) { tg->itemColor=rgGeneColor; } void loadOperon(struct track *tg) /* Load the items in one custom track - just move beds in * window... */ { struct linkedFeatures *lfList = NULL, *lf; struct bed *bed, *list = NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset; sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { bed = bedLoadN(row+rowOffset, 15); slAddHead(&list, bed); } sqlFreeResult(&sr); hFreeConn(&conn); slReverse(&list); for (bed = list; bed != NULL; bed = bed->next) { struct simpleFeature *sf; int i; lf = lfFromBed(bed); sf = lf->components; for (i = 0; i < bed->expCount; i++) { if (sf == NULL) break; sf->grayIx = grayInRange((int)(bed->expScores[i]),0,1000); sf = sf->next; } slAddHead(&lfList,lf); } tg->items = lfList; } void tigrOperonDrawAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, double scale, MgFont *font, Color color, enum trackVisibility vis) /* Draw the operon at position. */ { struct linkedFeatures *lf = item; struct simpleFeature *sf; int heightPer = tg->heightPer; int x1,x2; int s, e; Color *shades = tg->colorShades; int midY = y + (heightPer>>1); int w; color = tg->ixColor; x1 = round((double)((int)lf->start-winStart)*scale) + xOff; x2 = round((double)((int)lf->end-winStart)*scale) + xOff; w = x2-x1; innerLine(hvg, x1, midY, w, color); if (vis == tvFull || vis == tvPack) clippedBarbs(hvg, x1, midY, w, 2, 5, lf->orientation, color, FALSE); for (sf = lf->components; sf != NULL; sf = sf->next) { s = sf->start; e = sf->end; /* shade ORF (exon) based on the grayIx value of the sf */ color = shades[sf->grayIx]; drawScaledBox(hvg, s, e, scale, xOff, y, heightPer, color ); } } void tigrOperonMethods(struct track *tg) { linkedFeaturesMethods(tg); tg->loadItems = loadOperon; tg->colorShades = shadesOfGray; tg->drawItemAt = tigrOperonDrawAt; } void loadRNAHybridization(struct track *tg) /* Load the items in one custom track - just move beds in * window... */ { struct rnaHybridization *rnaHyb, *list = NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset; int minlengthSetting = cartUsualInt(cart, "rnaHybridization.minlength", 20); int maxlengthSetting = cartUsualInt(cart, "rnaHybridization.maxlength", 20); double gcSetting = (double)cartUsualInt(cart, "rnaHybridization.gc", 50) / 100; int hideTrnaSetting = cartUsualBoolean(cart, "rnaHybridization.hideTrna", FALSE); int showKnownTargetsSetting = cartUsualBoolean(cart, "rnaHybridization.showKnownTargets", TRUE); sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { rnaHyb = rnaHybridizationLoad(row); if(rnaHyb->matchLength >= minlengthSetting && rnaHyb->matchLength <= maxlengthSetting && rnaHyb->gcContent >= gcSetting && !(hideTrnaSetting && strlen(rnaHyb->trnaTarget) > 0) && !(showKnownTargetsSetting && !rnaHyb->targetAnnotation)) slAddHead(&list, rnaHyb); } sqlFreeResult(&sr); hFreeConn(&conn); slReverse(&list); tg->items = list; } Color rnaHybColor(struct track *tg, void *item, struct hvGfx *hvg) /* Return color to draw gene in. */ { struct rnaHybridization *rh=item; int cindex = (int)(rh->gcContent * (float)(RNA_HYBRIDIZATION_SHADES - 1)); if(!rnaHybShadesInitialized) rnaHybShadesInit(hvg); if(rh->targetAnnotation) { return rnaHybShadesPos[cindex]; } else { return rnaHybShadesNeg[cindex]; } } void rnaHybridizationMethods(struct track *tg) { tg->loadItems = loadRNAHybridization; tg->itemColor = rnaHybColor; } /**** End of Lowe lab additions ****/