3c079f1ab5ff66233574d8c5eff421698fe6b741 angie Mon Aug 18 11:51:58 2014 -0700 Revert "Checking in changes to make 'spectrum' (aka 'useScore') actually work on any pair of color/altColor settings. It used to be that only shadesOfGray, shadesOfBrown and shadesOfSea worked, leaving most cases to be shadesOfGray. I have sat on these changes for months. I am also checking in ifdef'd out code to calc the shade on the fly, rather than relaying on track->colorShades set of precomputed 10 shades. The only reason this code is not used is that it would require changing many many places/uses of colorShades. Since I am bein laid off, it seems inappropriate to make this more dramatic change at this time." This reverts commit a4adfa326bf8bec73020ee1a8aa0cb6251ea8663. refs #13833 diff --git src/hg/hgTracks/rnaFoldTrack.c src/hg/hgTracks/rnaFoldTrack.c index d981abf..f6137ef 100644 --- src/hg/hgTracks/rnaFoldTrack.c +++ src/hg/hgTracks/rnaFoldTrack.c @@ -1,227 +1,230 @@ /* rnaStructure - stuff to handle loading and coloring of rna secondary structure predictions. */ /* 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 "rnaSecStr.h" #include "rnautil.h" void bedLoadItemBySqlResult(struct track *tg, struct sqlResult *sr, int rowOffset, ItemLoader loader) /* Generic tg->item loader. */ { char **row = NULL; struct slList *itemList = NULL, *item = NULL; if (NULL == sr) errAbort("While loading track %s, bedLoadItemSqlResult was given empty sqlResult", tg->track); while ((row = sqlNextRow(sr)) != NULL) { item = loader(row + rowOffset); slAddHead(&itemList, item); } slSort(&itemList, bedCmp); tg->items = itemList; } void scoreFilterSqlClause(struct track *tg, char *extraWhere, size_t size, int defaultFilterScore) /* Make a 'where' clause for the sql query if the scoreFilter has been set. */ { char option[128]; /* Option - score filter */ char *optionScoreVal; int optionScore = defaultFilterScore; safef(option, sizeof(option), "%s.scoreFilter", tg->track); optionScoreVal = trackDbSetting(tg->tdb, "scoreFilter"); if (optionScoreVal != NULL) optionScore = atoi(optionScoreVal); optionScore = cartUsualInt(cart, option, optionScore); safef(extraWhere, size, "score >= %d",optionScore); } void loadRnaSecStr(struct track *tg) /* Load up rnaSecStr from database table to track items. */ { struct sqlConnection *conn = hAllocConn(database); int rowOffset = 0; struct sqlResult *sr = NULL; char extraWhere[128]; scoreFilterSqlClause(tg, extraWhere, sizeof(extraWhere), 0); sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, extraWhere, &rowOffset); bedLoadItemBySqlResult(tg, sr, rowOffset, (ItemLoader)rnaSecStrLoad); sqlFreeResult(&sr); hFreeConn(&conn); } void freeRnaSecStr(struct track *tg) /* Free up rnaSecStr items. */ { rnaSecStrFreeList((struct rnaSecStr**)&tg->items); } void spreadAndColorString(struct hvGfx *hvg, int x, int y, int width, int height, Color *colorIxs, int maxShade, MgFont *font, char *text, int count, double *scores, double minScore, double maxScore) /* Draw evenly spaced letters in string. The scores array contains a * score for each letter in the text string. The score will determine * which color in the colorIxs will be used for a given * letter. ColorIxs is an array of size maxShade+1. The count param is * the number of bases to print, not length of the input line * (text) */ { char c[2] = ""; int i; int x1, x2; Color clr; for (i=0; i<count; i++, text++, scores++) { x1 = i * width / count; x2 = (i+1) * width/count; clr = colorIxs[assignBin(*scores, minScore, maxScore, maxShade+1)]; c[0] = *text; hvGfxTextCentered(hvg, x1+x, y, x2-x1, height, clr, font, c); } } void spreadAndGrayShadeString(struct hvGfx *hvg, int x, int y, int width, int height, MgFont *font, char *text, int count, double *scores, double minScore, double maxScore) /* Draw evenly spaced letters in string and gray shade letters according to scores. */ { spreadAndColorString(hvg, x, y, width, height, shadesOfGray+2, maxShade-2, font, text, count, scores, minScore, maxScore); } void spreadRnaFoldAnno(struct hvGfx *hvg, int x, int y, int width, int height, Color color, MgFont *font, struct rnaSecStr *item) /* Draw parenthesis structure which defines rna secondary structure. */ { char *fold = cloneString(item->secStr); double *scores = CloneArray(item->conf, item->size); if (*item->strand == '-') { reverseFold(fold); reverseDoubles(scores, item->size); } spreadAndGrayShadeString(hvg, x, y, width, height, font, fold, item->size, scores, 0.0, 1.0); freeMem(fold); freeMem(scores); } void drawCharBox(struct hvGfx *hvg, int x, int y, int width, int height, Color color, char *s, char c) /* s defines a string which spans width. Draw a box in intervals * corresponding to positions where s has letter c */ { double charWidth = ((double)width)/strlen(s); int i = 0, begin = 0, length = 0; for (;*s;s++,i++) { if (*s == c) { if (!length) begin = i; length++; } /* Draw box if at end of interval or at end of string */ if (*s != c || !*(s+1) ) if (length) { int x1 = x + (int) begin *charWidth; int w = (int) length*charWidth; hvGfxBox(hvg, x1, y, w, height, color); length = 0; } } } void colorSingleStranded(struct hvGfx *hvg, int x, int y, int width, int height, Color color, struct rnaSecStr *item) { char *fold = cloneString(item->secStr); if (*item->strand == '-') reverseFold(fold); drawCharBox(hvg, x, y, width, height, color, fold, '.'); freeMem(fold); } void rnaSecStrDrawAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, double scale, MgFont *font, Color color, enum trackVisibility vis) /* Draw a single simple rnaSecStr item at position. */ { struct rnaSecStr *rnaSecStr = item; int heightPer = tg->heightPer; int x1 = round((double)((int)rnaSecStr->chromStart-winStart)*scale) + xOff; int x2 = round((double)((int)rnaSecStr->chromEnd-winStart)*scale) + xOff; int w; struct trackDb *tdb = tg->tdb; int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMin", "0")); int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMax", "1000")); if (tg->itemColor != NULL) color = tg->itemColor(tg, rnaSecStr, hvg); else - color = colorBySpectrumOrDefault(hvg,tg,grayInRange(rnaSecStr->score,scoreMin,scoreMax),color); + { + if (tg->colorShades) + color = tg->colorShades[grayInRange(rnaSecStr->score, scoreMin, scoreMax)]; + } w = x2-x1; if (w < 1) w = 1; if (color) { if (zoomedToBaseLevel) spreadRnaFoldAnno(hvg, x1, y, w, heightPer, color, font, rnaSecStr); else { hvGfxBox(hvg, x1, y, w, heightPer, color); colorSingleStranded(hvg, x1, y, w, heightPer, lighterColor(hvg, color), rnaSecStr); if (tg->subType == lfWithBarbs || tg->exonArrows) { int dir = 0; if (rnaSecStr->strand[0] == '+') dir = 1; else if (rnaSecStr->strand[0] == '-') dir = -1; if (dir != 0 && w > 2) { int midY = y + (heightPer>>1); Color textColor = hvGfxContrastingColor(hvg, color); clippedBarbs(hvg, x1, midY, w, 2, 5, dir, textColor, TRUE); } } } if (tg->drawName && vis != tvSquish) { char *s = tg->itemName(tg, rnaSecStr); w = x2-x1; if (w > mgFontStringWidth(font, s)) { Color textColor = hvGfxContrastingColor(hvg, color); hvGfxTextCentered(hvg, x1, y, w, heightPer, textColor, font, s); } mapBoxHc(hvg, rnaSecStr->chromStart, rnaSecStr->chromEnd, x1, y, x2 - x1, heightPer, tg->track, tg->mapItemName(tg, rnaSecStr), NULL); } } } void rnaSecStrMethods(struct track *tg) /* Make track which visualizes RNA secondary structure annotation. */ { tg->loadItems = loadRnaSecStr; tg->freeItems = freeRnaSecStr; tg->drawItemAt = rnaSecStrDrawAt; }