b8180d9f6d41dc708a2f249ba892cbca311e7a06 jcasper Mon Feb 27 11:38:55 2023 -0800 Adding transparency support for colors refs #30569 diff --git src/hg/hgTracks/cgapSageTrack.c src/hg/hgTracks/cgapSageTrack.c index af90c1b..a102ab5 100644 --- src/hg/hgTracks/cgapSageTrack.c +++ src/hg/hgTracks/cgapSageTrack.c @@ -1,315 +1,315 @@ /* cgapSageTrack - module for CGAP SAGE track. */ /* 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 "hCommon.h" #include "cgapSage/cgapSage.h" #include "cgapSage/cgapSageLib.h" static int grayIxForCgap(double tpm) /* Return a grayIx based on the score. */ { int val = (int)ceil(tpm); return grayInRange(val, 0, 150); } static struct hash *libTissueHash(struct sqlConnection *conn) /* Read two columns of a table and hash em up. */ { struct hash *ret = newHash(9); struct sqlResult *sr = NULL; char query[49]; char **row; sqlSafef(query, sizeof query, "select libId,tissue from cgapSageLib"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) hashAdd(ret, row[0], cloneString(row[1])); sqlFreeResult(&sr); return ret; } struct cgapSageTpmHashEl /* A convenience struct for computing means. */ { double total; long freqTotal; long libTotals; int count; }; static boolean keepThisLib(char *tissue, char *libId) /* Tissue filtering code checks cart. */ { char *tissueHl = cartUsualString(cart, "cgapSage.tissueHl", "All"); if (!tissue) errAbort("NULL tissue or libId passed into keepThisLib()"); if (sameString(tissueHl, "All") || sameString(tissue, tissueHl)) return TRUE; return FALSE; } static struct hash *combineCgapSages(struct cgapSage *tag, struct hash *libHash, struct hash *libTotHash) /* Go through the each lib for a tag and combine it's score using a hash for */ /* repeated tissues. */ { struct hash *tpmHash = newHash(5); int i; for (i = 0; i < tag->numLibs; i++) { char libId[16]; char *libName; int libTotTags = 0; struct cgapSageTpmHashEl *tpm; safef(libId, sizeof(libId), "%d", tag->libIds[i]); libName = hashMustFindVal(libHash, libId); tpm = hashFindVal(tpmHash, libName); libTotTags = hashIntVal(libTotHash, libId); if (keepThisLib(libName, libId)) { if (tpm) { tpm->count++; tpm->freqTotal += tag->freqs[i]; tpm->total += tag->tagTpms[i]; tpm->libTotals += libTotTags; } else { AllocVar(tpm); tpm->count = 1; tpm->total = tag->tagTpms[i]; tpm->freqTotal = tag->freqs[i]; tpm->libTotals = libTotTags; hashAdd(tpmHash, libName, tpm); } } } return tpmHash; } static struct linkedFeatures *skeletonLf(struct cgapSage *tag) /* Fill in everything except the name and score. */ { struct linkedFeatures *lf; struct simpleFeature *sf; AllocVar(lf); AllocVar(sf); lf->start = sf->start = tag->chromStart; lf->end = sf->end = tag->chromEnd; lf->tallStart = tag->thickStart; lf->tallEnd = tag->thickEnd; lf->orientation = orientFromChar(tag->strand[0]); lf->components = sf; return lf; } static void addSimpleFeature(struct linkedFeatures *lf) /* Make a dumb simpleFeature out of a single linkedFeatures. */ { struct simpleFeature *sf; AllocVar(sf); sf->start = lf->start; sf->end = lf->end; sf->grayIx = lf->grayIx; lf->components = sf; } static char *cgapSageMapItemName(struct track *tg, void *item) /* Use what's in the ->extra for the name. */ { struct linkedFeatures *lf = item; return (char *)lf->extra; } static void cgapSageMapItem(struct track *tg, struct hvGfx *hvg, void *item, char *itemName, char *mapItemName, int start, int end, int x, int y, int width, int height) { struct linkedFeatures *lf = item; mapBoxHgcOrHgGene(hvg, start, end, x, y, width, height, tg->track, itemName, NULL, NULL, TRUE, (char *)lf->extra); } int cgapLinkedFeaturesCmp(const void *va, const void *vb) /* Compare to sort based on chrom,chromStart. */ { const struct linkedFeatures *a = *((struct linkedFeatures **)va); const struct linkedFeatures *b = *((struct linkedFeatures **)vb); return (int)b->score - (int)a->score; } static struct linkedFeatures *cgapSageToLinkedFeatures(struct cgapSage *tag, struct hash *libHash, struct hash *libTotHash, enum trackVisibility vis) /* Convert a single CGAP tag to a list of linkedFeatures. */ { struct linkedFeatures *libList = NULL; struct linkedFeatures *skel = skeletonLf(tag); int i; if (vis == tvDense) /* Just use the skeleton one. */ { int tagTotal = 0; int freqTotal = 0; int libsUsed = 0; for (i = 0; i < tag->numLibs; i++) { char libId[16]; char *libName; safef(libId, sizeof(libId), "%d", tag->libIds[i]); libName = hashMustFindVal(libHash, libId); if (keepThisLib(libName, libId)) { int libTotal = hashIntVal(libTotHash, libId); tagTotal += libTotal; freqTotal += tag->freqs[i]; libsUsed++; } } if (libsUsed > 0) { skel->name = cloneString("whatever"); skel->score = (float)((double)freqTotal * (1000000/tagTotal)); skel->grayIx = grayIxForCgap(skel->score); addSimpleFeature(skel); libList = skel; } } else if (vis == tvPack) { /* If it's pack mode, average tissues into one linkedFeature. */ struct hash *tpmHash = combineCgapSages(tag, libHash, libTotHash); struct hashEl *tpmList = hashElListHash(tpmHash); struct hashEl *tpmEl; slSort(&tpmList, slNameCmp); for (tpmEl = tpmList; tpmEl != NULL; tpmEl = tpmEl->next) { struct linkedFeatures *tiss = CloneVar(skel); struct cgapSageTpmHashEl *tpm = (struct cgapSageTpmHashEl *)tpmEl->val; char link[256]; char *encTissName = NULL; double score = 0; int len = strlen(tpmEl->name) + 32; tiss->name = needMem(len); safef(tiss->name, len, "%s (%d)", tpmEl->name, tpm->count); encTissName = cgiEncode(tpmEl->name); safef(link, sizeof(link), "i=%s&tiss=%s", tag->name, encTissName); score = (double)tpm->freqTotal*(1000000/(double)tpm->libTotals); tiss->score = (float)score; tiss->grayIx = grayIxForCgap(score); tiss->extra = cloneString(link); freeMem(encTissName); addSimpleFeature(tiss); slAddHead(&libList, tiss); } hashElFreeList(&tpmList); freeHashAndVals(&tpmHash); } else /* full mode */ { for (i = 0; i < tag->numLibs; i++) { char libId[16]; char *libName; char link[256]; struct linkedFeatures *lf; safef(libId, sizeof(libId), "%d", tag->libIds[i]); libName = hashMustFindVal(libHash, libId); if (keepThisLib(libName, libId)) { lf = CloneVar(skel); lf->name = cloneString(libName); safef(link, sizeof(link), "i=%s&lib=%s", tag->name, libId); lf->score = (float)tag->tagTpms[i]; lf->grayIx = grayIxForCgap(tag->tagTpms[i]); lf->extra = cloneString(link); addSimpleFeature(lf); slAddHead(&libList, lf); } } } slSort(&libList, cgapLinkedFeaturesCmp); slReverse(&libList); return libList; } struct hash *getTotTagsHashFromTable(struct sqlConnection *conn) /* Load the cgapSageLib table for the db then call getTotTagsHash. */ { char query[1024]; sqlSafef(query, sizeof query, "select * from cgapSageLib"); struct cgapSageLib *libs = cgapSageLibLoadByQuery(conn, query); struct hash *libTotHash = getTotTagsHash(libs); cgapSageLibFreeList(&libs); return libTotHash; } void cgapSageLoadItems(struct track *tg) /* This function loads the beds in the current window into a linkedFeatures list. */ /* Each bed entry may turn into multiple linkedFeatures because one is made for */ /* each library at a given tag (bed). */ { struct linkedFeatures *itemList = NULL; struct sqlConnection *conn = hAllocConn(database); struct hash *libHash = libTissueHash(conn); struct hash *libTotHash = getTotTagsHashFromTable(conn); struct sqlResult *sr = NULL; char **row; int rowOffset; sr = hOrderedRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset); if ((winEnd - winStart) > CGAP_SAGE_DENSE_GOVERNOR) tg->visibility = tvDense; while ((row = sqlNextRow(sr)) != NULL) { struct cgapSage *tag = cgapSageLoad(row+rowOffset); struct linkedFeatures *oneLfList = cgapSageToLinkedFeatures(tag, libHash, libTotHash, tg->visibility); itemList = slCat(oneLfList, itemList); } slReverse(&itemList); sqlFreeResult(&sr); hFreeConn(&conn); tg->items = itemList; } /***** All the drawing/color-related stuff. ******/ static Color cgapShadesOfRed[10+1]; /* This will go from white to darker red. */ static Color cgapSageItemColor(struct track *tg, void *item, struct hvGfx *hvg) /* Return color to draw CGAP SAGE item */ { struct linkedFeatures *thisItem = item; return cgapShadesOfRed[thisItem->grayIx]; } void cgapSageDrawItems(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis) /* Initialize the colors, then do the normal drawing. */ { -static struct rgbColor lowerColor = {205, 191, 191}; -static struct rgbColor cgapRed = {205, 0, 0}; +static struct rgbColor lowerColor = {205, 191, 191, 255}; +static struct rgbColor cgapRed = {205, 0, 0, 255}; hvGfxMakeColorGradient(hvg, &lowerColor, &cgapRed, 10, cgapShadesOfRed); genericDrawItems(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis); } void cgapSageMethods(struct track *tg) /* Make track for simple repeats. */ { linkedFeaturesMethods(tg); tg->loadItems = cgapSageLoadItems; tg->itemColor = cgapSageItemColor; tg->drawItems = cgapSageDrawItems; tg->mapItemName = cgapSageMapItemName; tg->mapItem = cgapSageMapItem; }