/* bigRmskTrack - A comprehensive RepeatMasker visualization track * handler for bigRmsk file ( BED9+5 ) track hubs. * Based on previous visualization work with table * supported rmskJoined tracks. * * * Written by Robert Hubley 10/2021 * * Modifications: * 6/6/22 : Added doLeftLabels functionality to Full/Pack modes * */ /* Copyright (C) 2014 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 "bigRmskUi.h" /* Track Development Notes: * * Summary of concerns: * 1. tg->loadItems: * Should be responsible for loading data "items". * In our case they will be bigRmskRecords. * 2. tg->totalHeight: * Should be responsible for layout calculations * that determine the totalHeight of the track at the * current scale and/or visual style ( 'pack', 'full' etc. ) * NOTE: This doesn't include the track center label (if present) * 3. tg->preDrawItems: * Not sure the use case for this. * 4. tg->drawItems: * Pretty self explanatory. * 5. tg->drawLeftLabels: * Draw labels to left of track (if desired). * * Detailed track flow: * mainMain: * cartHtmlShell ... doMiddle() * * hgTrack: * doMiddle() ### called by mainMain ### * tracksDisplay() * doTrackForm() * remoteParallelLoad() * Call track->loadItems() * -------------or-------------- * Call track->loadItems() * * printTrackInitJavascript() * makeActiveImage() * doLeftLabels() * trackPlusLabelHeight() * Call subtrack->totalHeight() * doCenterLabels() * Call track->totalHeight() * doPreDrawItems() * doDrawitems() * Call track->drawItems() * Call track->totalHeight() * Call track->drawLeftLabels() * doTrackMap() * Call subtrack->totalHeight() */ /* Structure to hold repeat class names/colors */ struct classRecord { struct classes *next; // just in case we want to use it as a slList char *className; int layoutLevel; Color color; }; /* The primary "item" record used by this track */ struct bigRmskRecord { struct bigRmskRecord *next; /* Next in singly linked list. */ char *chrom; /* Reference sequence chromosome or scaffold */ unsigned chromStart; /* Start position of feature in chromosome */ unsigned chromEnd; /* End position feature in chromosome */ char *name; /* Annotation name [ typically TE family identifier ] */ unsigned score; /* Score from 0-1000 */ char strand[2]; /* + or - */ unsigned alignStart; /* Start position of aligned portion of feature */ unsigned alignEnd; /* End position of aligned portion of feature */ unsigned reserved; /* Used as itemRgb */ int blockCount; /* Number of blocks */ int *blockSizes; /* Comma separated list of block sizes */ int *blockRelStarts; /* Start positions rel. to chromStart or -1 for unaligned blocks */ unsigned id; /* ID to bed used in URL to link back */ char *description; /* Long description of item for the details page */ unsigned visualStart; /* For use by layout routines -- calc visual start (in bp coord)*/ unsigned visualEnd; /* For use by layout routines -- calc visual end (in bp coord)*/ int layoutLevel; /* For use by layout routines -- layout row */ int leftLabel; /* For use by visualization routines -- left side labels */ }; /* Datastructure for graph-based layout */ struct Graph { // the number of nodes in the graph int n; // an array of edges for each node, size n^2 // access: g->edges[(i * n) + j] int *edges; // an array of degrees for each node // access: g->degrees[i] int *degrees; }; /* DETAIL_VIEW_MAX_SCALE: The size ( window bp ) at which the * detailed view of repeats is turned allowed, otherwise it reverts * back to the original UCSC glyph. I chose not to make this a function of * data density so that switching between views could be more predictable. */ #define DETAIL_VIEW_MAX_SCALE 45000 /* MAX_UNALIGNED_PIXEL_LEN: The maximum size of unaligned sequence * to draw before switching to the unscaled view: ie. "----/###/---" * This is measured in pixels *not* base pairs due to the * mixture of scaled ( lines ) and unscaled ( text ) glyph * components. */ #define MAX_UNALIGNED_PIXEL_LEN 150 /* LABEL_PADDING: The amount of space to reserve to the left * of the label (in px). */ #define LABEL_PADDING 20 /* MINHEIGHT: The minimum height for a track row. */ #define MINHEIGHT 24 /* MAX_PACK_ITEMS: The maximum number of items to show in pack mode. Over * this value and the track switches to dense mode. */ #define MAX_PACK_ITEMS 500 /* MIN_VISIBLE_EXT_PIXELS: Minimum unextended region to show (in pixels). If * under this value the vertical and horizontal arms are completely omitted. */ #define MIN_VISIBLE_EXT_PIXELS 4 /* Hash of the repeatItems ( tg->items ) for this track. * This is used to hold display names for the lines of * the track, the line heights, and class colors. */ static struct hash *classHashBR = NULL; // Repeat Classes: Display names static char *rptClassNames[] = { "SINE", "LINE", "LTR", "DNA", "Simple", "Low Complexity", "Satellite", "RNA", "Other", "Unknown", }; // Repeat Classes: Data names static char *rptClasses[] = { "SINE", "LINE", "LTR", "DNA", "Simple_repeat", "Low_complexity", "Satellite", "RNA", "Other", "Unknown", }; /* Repeat class to color mappings. * - Currently borrowed from snakePalette. * * NOTE: If these are changed, do not forget to update the * help table in joinedRmskTrack.html */ static Color rmskJoinedClassColors[] = { // Current // Previously 0xff1f77b4, // SINE - blue // SINE - red 0xffff7f0e, // LINE - orange // LINE - lime 0xff2ca02c, // LTR - green // LTR - maroon 0xffd62728, // DNA - red // DNA - fuchsia 0xff9467bd, // Simple - purple // Simple - yellow 0xff8c564b, // LowComplex - brown // LowComplex - olive 0xffe377c2, // Satellite - pink // Satellite - blue 0xff7f7f7f, // RNA - grey // RNA - green 0xffbcbd22, // Other - lime // Other - teal 0xff17becf, // Unknown - aqua // Unknown - aqua }; static int cmpStartEnd(const void *va, const void *vb) /* Sort repeats by alignStart (thickStart) ascending and alignEnd * (thickEnd) descending. ie. sort by position (longest first) */ { struct bigRmskRecord *a = *((struct bigRmskRecord **) va); struct bigRmskRecord *b = *((struct bigRmskRecord **) vb); unsigned startDiff = (a->alignStart - b->alignStart); if ( startDiff != 0 ) return (startDiff); return (b->alignEnd - a->alignEnd); } static void getVisualExtentsInBP(struct bigRmskRecord *rm, float pixelsPerBase, unsigned *pStart, unsigned *pEnd, bool showUnalignedExtents, bool showLabels) /* Calculate the glyph visual extents in genome coordinate * space ( ie. bp ) * * It is not straightforward to determine the extent * of this track's glyph due to the mixture of graphic * text elements within the glyph. */ { int start; int end; char lenLabel[20]; // Start position is anchored by the alignment start // coordinates. Then we subtract from that space for // the label. if ( showLabels ) { start = rm->alignStart - (int) ((mgFontStringWidth(tl.font, rm->name) + LABEL_PADDING) / pixelsPerBase); // Fix for redmine #29473 if ( start < 0 ) start = 0; } else { start = rm->alignStart; } // Now subtract out space for the unaligned sequence // bar starting off the graphics portion of the glyph. if ( showUnalignedExtents ) { if ((rm->blockSizes[0] * pixelsPerBase) > MAX_UNALIGNED_PIXEL_LEN) { // Unaligned sequence bar needs length label -- account for that. safef(lenLabel, sizeof(lenLabel), "%d", rm->blockSizes[0]); start -= (int) (MAX_UNALIGNED_PIXEL_LEN / pixelsPerBase) + (int) ((mgFontStringWidth(tl.font, lenLabel) + LABEL_PADDING) / pixelsPerBase); } else { start -= rm->blockSizes[0]; } } end = rm->alignEnd; if ( showUnalignedExtents ) { if ((rm->blockSizes[rm->blockCount - 1] * pixelsPerBase) > MAX_UNALIGNED_PIXEL_LEN) { safef(lenLabel, sizeof(lenLabel), "%d", rm->blockSizes[rm->blockCount - 1]); end += (int) (MAX_UNALIGNED_PIXEL_LEN / pixelsPerBase) + (int) ((mgFontStringWidth(tl.font, lenLabel) + LABEL_PADDING) / pixelsPerBase); } else { end += rm->blockSizes[rm->blockCount - 1]; } } *pStart = start; *pEnd = end; } bool overlap(struct bigRmskRecord *a, struct bigRmskRecord *b, int tolerance) /* Determine if two glyphs will overlap */ { return ((a->visualStart - tolerance) <= b->visualEnd) && ((a->visualEnd + tolerance) >= b->visualStart); } struct Graph *newGraph(struct bigRmskRecord **recs, int n) /* Create a new layout graph */ { struct Graph *g = malloc(sizeof(struct Graph)); g->n = n; g->edges = malloc((n * n) * sizeof(int)); g->degrees = malloc((n) * sizeof(int)); for (int i = 0; i < n; i++) { g->degrees[i] = 0; for (int j = 0; j < n; j++) { g->edges[i * n + j] = -1; } } // all vs all comparison of all nodes to check for overlap for (int idxA = 0; idxA < n; idxA++) { struct bigRmskRecord annA = *recs[idxA]; for (int idxB = 0; idxB < n; idxB++) { struct bigRmskRecord annB = *recs[idxB]; if (idxA == idxB) continue; if (overlap(&annA, &annB, 0)) { g->edges[(idxA * n) + g->degrees[idxA]] = idxB; g->degrees[idxA]++; } } } return (g); } void removeIdx(int idx, int *arr, int nElements) /* Remove entry in list by overwriting element at position idx and * shifting all remaining elements down by one position. * Support routine for detailedLayout(). */ { for (int i = idx; i < nElements - 1; i++) { arr[i] = arr[i + 1]; } arr[nElements - 1] = -1; } void swap(int *xp, int *yp) /* Swap elements in a list. Support routine * for detailedLayout() */ { int temp = *xp; *xp = *yp; *yp = temp; } void sortRemainingByWidth(int *remaining, struct bigRmskRecord **recs, int n) { int i, j, maxIdx; struct bigRmskRecord *a, *b; for (i = 0; i < n - 1; i++) { maxIdx = i; for (j = i + 1; j < n; j++) { a = recs[remaining[j]]; b = recs[remaining[maxIdx]]; if ((a->alignEnd - a->alignStart) > (b->alignEnd - b->alignStart)) maxIdx = j; } swap(&remaining[maxIdx], &remaining[i]); } } void detailedLayout(struct bigRmskRecord *firstRec, double pixelsPerBase) { /* * Compute a non-overlapping layout for a list of annotations * * We define a graph in which each annotation is represented as a node. * Nodes share an edge if the annotations they represent horizontally overlap. * * In each iteration, this algorithm picks the first available node and then * greedily grows an independent set. The nodes in each independent set are * assigned a unique color/row. Once a node is assigned a color, it is permanently * removed from further consideration. * * For book keeping, we keep two lists: a list of remaining uncolored node * indices, and a boolean list that describes whether or not a node is available * during the current iteration. * * This layout routine was written by Jack Roddy */ int nRecs = slCount(firstRec); struct bigRmskRecord **recs = malloc(nRecs * sizeof(struct bigRmskRecord *)); struct bigRmskRecord *rec = firstRec; boolean showUnalignedExtents = cartUsualBoolean(cart, BIGRMSK_SHOW_UNALIGNED_EXTENTS, BIGRMSK_SHOW_UNALIGNED_EXTENTS_DEFAULT); boolean showLabels = cartUsualBoolean(cart, BIGRMSK_SHOW_LABELS, BIGRMSK_SHOW_LABELS_DEFAULT); int n = 0; while (rec != NULL) { getVisualExtentsInBP(rec, pixelsPerBase, &(rec->visualStart),&(rec->visualEnd), showUnalignedExtents, showLabels); recs[n++] = rec; rec = rec->next; } struct Graph *g = newGraph(recs, n); int nextColor = 0; int nRemaining = n; int *remaining = malloc(sizeof(int) * n); bool *available = malloc(sizeof(bool) * n); for (int i = 0; i < n; i++) { remaining[i] = i; available[i] = TRUE; } sortRemainingByWidth(remaining, recs, n); while (nRemaining > 0) { // at the start of every iteration, set everything remaining to available for (int i = 0; i < nRemaining; i++) { available[remaining[i]] = TRUE; } // for every remaining node for (int i = 0; i < nRemaining; i++) { // find the index in the rec array int uIdx = remaining[i]; if (available[uIdx]) { // if node u is available, assign a color/row recs[uIdx]->layoutLevel = nextColor; int *uEdges = &(g->edges[uIdx * n]); int uDegree = g->degrees[uIdx]; // iterate across u's edges and set them to unavailable for this iteration for (int j = 0; j < uDegree; j++) { int vIdx = uEdges[j]; available[vIdx] = FALSE; } // u is unavailable since we just placed it available[uIdx] = FALSE; // remove uIdx from remaining removeIdx(i, remaining, nRemaining); nRemaining--; i--; } } nextColor++; } free(remaining); free(available); free(recs); } void bigRmskLayoutItems(struct track *tg) { /* After the items have been loaded and before any rendering occurs, * this function delegates the layout based on the current visualization * type. * * I am not sure how permissible it is to access winStart/winEnd/insideWidth * as globals. This seems to be the pattern that I see used in other tracks * but it makes me uncomfortable. */ int baseWidth = winEnd - winStart; double pixelsPerBase = scaleForPixels(insideWidth); struct bigRmskRecord *items = tg->items; boolean showLabels = cartUsualBoolean(cart, BIGRMSK_SHOW_LABELS, BIGRMSK_SHOW_LABELS_DEFAULT); boolean origPackViz = cartUsualBoolean(cart, BIGRMSK_ORIG_PACKVIZ, BIGRMSK_ORIG_PACKVIZ_DEFAULT); if ((tg->visibility == tvSquish) || (tg->visibility == tvDense)) showLabels = FALSE; if (tg->visibility == tvFull && baseWidth <= DETAIL_VIEW_MAX_SCALE) { // Perform the most detailed glyph layout aka "Full" mode. detailedLayout(items, pixelsPerBase); } else { // Either class based or single row...dense char class[256]; struct classRecord *cr; if ( origPackViz ) { // Original "pack" visualization displays greyscale box annotations // for each "unjoined" feature on a repeat class specific row. while (items) { struct bigRmskRecord *rr = items; items = items->next; // Extract the class from the annotation name // - Simplify repClass for lookup: strip trailing '?', // simplify *RNA to RNA: char *poundPtr = index(rr->name, '#'); if (poundPtr) { safecpy(class, sizeof(class), poundPtr + 1); char *slashPtr = index(class, '/'); if (slashPtr) *slashPtr = '\0'; } else { safecpy(class, sizeof(class), "Unknown"); } char *p = &(class[strlen(class) - 1]); if (*p == '?') *p = '\0'; if (endsWith(class, "RNA")) safecpy(class, sizeof(class), "RNA"); cr = hashFindVal(classHashBR, class); if (cr == NULL) cr = hashFindVal(classHashBR, "Other"); rr->layoutLevel = cr->layoutLevel; } } else { // New "pack" visualization are joined features with labels. slSort(&items, cmpStartEnd); // If you slSort you reset the linked list and it's head. tg->items = items; int inLevel = 0; while (items) { struct bigRmskRecord *rr = items; items = items->next; if ( rr->layoutLevel < 0 ) { unsigned rrChromStart, rrChromEnd; getVisualExtentsInBP(rr, pixelsPerBase, &rrChromStart, &rrChromEnd, 0, showLabels); rr->layoutLevel = inLevel; struct bigRmskRecord *rm = NULL; unsigned rmChromStart, rmChromEnd; rm = items; while (rm) { if ( rm->layoutLevel < 0 ) { getVisualExtentsInBP(rm, pixelsPerBase, &rmChromStart, &rmChromEnd, 0, showLabels); if (rmChromStart > rrChromEnd) { rm->layoutLevel = inLevel; rrChromEnd = rmChromEnd; } } rm = rm->next; } // while ( rm ) inLevel++; } // if ( rr->layoutLevel... } // while ( items ) } // if(... } } static void bigRmskLoadItems(struct track *tg) /* * Loading is done first given the region the display is currently centered on. * This function is responsible for fetching the data *and* defining the number * of "items" that will be displayed. An item represents a row of the track. * Therefore, while this is a "loading" function it also needs to perform enough * of the layout to determine how many "items" to generate. */ { int i; if ( classHashBR == NULL ) { struct classRecord *cr; int numClasses = ArraySize(rptClasses); classHashBR = newHash(6); for (i = 0; i < numClasses; ++i) { AllocVar(cr); cr->className = rptClassNames[i]; cr->layoutLevel = i; unsigned int colorInt = rmskJoinedClassColors[i]; cr->color = MAKECOLOR_32(((colorInt >> 16) & 0xff),((colorInt >> 8) & 0xff),((colorInt >> 0) & 0xff)); hashAdd(classHashBR, rptClasses[i], cr); } } struct bigRmskRecord *detailList = NULL; if (tg->isBigBed) { struct bbiFile *bbi = fetchBbiForTrack(tg); if (bbi->fieldCount < 14) errAbort("track %s has a bigBed being read as a bed14 that has %d columns.", tg->track, bbi->fieldCount); struct lm *lm = lmInit(0); struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, chromName, winStart, winEnd, 0, lm); char *bedRow[bbi->fieldCount]; /* One might ask, "Why didn't you use a linkedFeature set here?" Good question! I am not using a standard encoding of blockStarts as would be expected by a BED12 validator, and therefore I must use BED9+ and handle the blocks myself. */ char startBuf[16], endBuf[16]; char *filterString = cartUsualString(cart, BIGRMSK_NAME_FILTER, BIGRMSK_NAME_FILTER_DEFAULT); boolean isFilterRegexp = cartUsualBoolean(cart, BIGRMSK_REGEXP_FILTER, BIGRMSK_REGEXP_FILTER_DEFAULT); regex_t regEx; if (isFilterRegexp) regcomp(®Ex, filterString, REG_NOSUB); for (bb = bbList; bb != NULL; bb = bb->next) { bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow)); if ( (isFilterRegexp && (regexec(®Ex,bedRow[3], 0, NULL,0 ) == 0)) || (!isFilterRegexp && wildMatch(filterString, bedRow[3])) ) { struct bigRmskRecord *rm = NULL; AllocVar(rm); rm->next = NULL; rm->chrom = cloneString(bedRow[0]); rm->chromStart = sqlUnsigned(bedRow[1]); rm->chromEnd = sqlUnsigned(bedRow[2]); rm->name = cloneString(bedRow[3]); rm->score = sqlUnsigned(bedRow[4]); safef(rm->strand, sizeof(rm->strand), "%s", bedRow[5]); rm->alignStart = sqlUnsigned(bedRow[6]); rm->alignEnd = sqlUnsigned(bedRow[7]); // RGB is unused? bedRow[8] rm->blockCount = sqlUnsigned(bedRow[9]); { int sizeOne; sqlSignedDynamicArray(bedRow[10], &rm->blockSizes, &sizeOne); assert(sizeOne == rm->blockCount); } { int sizeOne; sqlSignedDynamicArray(bedRow[11], &rm->blockRelStarts, &sizeOne); assert(sizeOne == rm->blockCount); } rm->id = sqlUnsigned(bedRow[12]); rm->description = cloneString(bedRow[13]); rm->layoutLevel = -1; // Indicates layout has not been calculated. rm->leftLabel = 0; // Flag for labels that need to be leftLabeled slAddHead(&detailList, rm); } } // for(bb = bbList... bbiFileClose(&bbi); lmCleanup(&lm); } // if (tg->isBigBed... //Could also...have DB loader here in the future. tg->items = detailList; // Man, I went back and forth on this one. I *wish* there was // an API for layout in between the loadItems() and totalHeight() // stubs. The totalHeight() method is called multiple times which // isn't ideal for layout operations since the layout logic needs // to detect if it needs to really re-layout the data (expensive). // For now, this is the only way to be assured that it gets called // once for real changes in the visual appearance. bigRmskLayoutItems(tg); } int bigRmskItemHeight(struct track *tg, void *item) { enum trackVisibility vis = tg->visibility; if (vis == tvDense) tg->heightPer = tl.fontHeight; else if (vis == tvPack) tg->heightPer = tl.fontHeight; else if (vis == tvSquish) tg->heightPer = tl.fontHeight/2; else if (vis == tvFull ) { if ( winBaseCount <= DETAIL_VIEW_MAX_SCALE) tg->heightPer = max(tl.fontHeight, MINHEIGHT); else tg->heightPer = tl.fontHeight; } tg->lineHeight = tg->heightPer + 1; return(tg->heightPer); } int bigRmskTotalHeight(struct track *tg, enum trackVisibility vis) { boolean origPackViz = cartUsualBoolean(cart, BIGRMSK_ORIG_PACKVIZ, BIGRMSK_ORIG_PACKVIZ_DEFAULT); // Ensure that lineHeight is set correctly bigRmskItemHeight(tg, (void *)NULL); int count = slCount(tg->items); if ( count > MAX_PACK_ITEMS || vis == tvDense ) { tg->height = tg->lineHeight; return(tg->height); } else { // Count the layout depth struct bigRmskRecord *cr; int numLevels = 0; for ( cr = tg->items; cr != NULL; cr = cr->next ) { if ( cr->layoutLevel > numLevels ) numLevels = cr->layoutLevel; } numLevels++; if (tg->limitedVis == tvFull && winBaseCount <= DETAIL_VIEW_MAX_SCALE) { tg->height = numLevels * max(tg->lineHeight, MINHEIGHT); } else { if ( origPackViz ) { // Original class-per-line track int numClasses = ArraySize(rptClasses); tg->height = numClasses * tg->lineHeight; } else { // Color pack track tg->height = numLevels * tg->lineHeight; } } return(tg->height); } } static void drawDenseGlyphs(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont * font, Color color, enum trackVisibility vis) /* draw 'dense' mode track */ { int x1, x2, w; int baseWidth = seqEnd - seqStart; int heightPer = tg->heightPer; struct classRecord *ri; Color col; struct bigRmskRecord *cr; for (cr = tg->items; cr != NULL; cr = cr->next) { // Break apart the name and get the class of the // repeat. char class[256]; // Simplify repClass for lookup: strip trailing '?', // simplify *RNA to RNA: char *poundPtr = index(cr->name, '#'); if (poundPtr) { safecpy(class, sizeof(class), poundPtr + 1); char *slashPtr = index(class, '/'); if (slashPtr) *slashPtr = '\0'; } else { safecpy(class, sizeof(class), "Unknown"); } char *p = &(class[strlen(class) - 1]); if (*p == '?') *p = '\0'; if (endsWith(class, "RNA")) safecpy(class, sizeof(class), "RNA"); // Lookup the class to get the color scheme ri = hashFindVal(classHashBR, class); if (ri == NULL) ri = hashFindVal(classHashBR, "Other"); col = ri->color; int idx = 0; for (idx = 0; idx < cr->blockCount; idx++) { if (cr->blockRelStarts[idx] >= 0) { int blockStart = cr->chromStart + cr->blockRelStarts[idx]; int blockEnd = cr->chromStart + cr->blockRelStarts[idx] + cr->blockSizes[idx]; x1 = roundingScale(blockStart - winStart, width, baseWidth) + xOff; x1 = max(x1, 0); x2 = roundingScale(blockEnd - winStart, width, baseWidth) + xOff; w = x2 - x1; if (w <= 0) w = 1; hvGfxBox(hvg, x1, yOff, w, heightPer, col); } } } } static void drawOrigPackGlyphs(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont * font, Color color, enum trackVisibility vis) /* Do grayscale representation spread out individual class-specific rows */ { int y = yOff; int percId; int grayLevel; Color col; int x1, x2, w; int baseWidth = seqEnd - seqStart; int heightPer = tg->heightPer; // Added per ticket #29469 char idStr[80]; char statusLine[128]; // bugfix ticket #28644 int trackHeight = bigRmskTotalHeight(tg, vis); hvGfxSetClip(hvg, xOff, yOff, width, trackHeight); struct bigRmskRecord *cr; for (cr = tg->items; cr != NULL; cr = cr->next) { percId = 1000 - cr->score; grayLevel = grayInRange(percId, 500, 1000); col = shadesOfGray[grayLevel]; // Get id for click handler sprintf(idStr,"%d",cr->id); int idx = 0; for (idx = 0; idx < cr->blockCount; idx++) { if (cr->blockRelStarts[idx] >= 0) { int blockStart = cr->chromStart + cr->blockRelStarts[idx]; int blockEnd = cr->chromStart + cr->blockRelStarts[idx] + cr->blockSizes[idx]; x1 = roundingScale(blockStart - winStart, width, baseWidth) + xOff; x1 = max(x1, 0); x2 = roundingScale(blockEnd - winStart, width, baseWidth) + xOff; y = yOff + (cr->layoutLevel * tg->lineHeight); w = x2 - x1; if (w <= 0) w = 1; hvGfxBox(hvg, x1, y, w, heightPer, col); // feature change ticket #29469 safef(statusLine, sizeof(statusLine), "%s", cr->name); mapBoxHc(hvg, cr->alignStart, cr->alignEnd, x1, y, w, heightPer, tg->track, idStr, statusLine); } } }//for (cr = ri->itemData... } static void drawPackGlyphs(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont * font, Color color, enum trackVisibility vis) /* Do color representation packed closely */ { boolean showLabels = cartUsualBoolean(cart, BIGRMSK_SHOW_LABELS, BIGRMSK_SHOW_LABELS_DEFAULT); if ( vis == tvSquish ) showLabels = FALSE; int y = yOff; Color col; Color black = hvGfxFindColorIx(hvg, 0, 0, 0); int x1, x2, w; int baseWidth = seqEnd - seqStart; int heightPer = tg->heightPer; struct bigRmskRecord *cr; struct classRecord *ri; int fontHeight = mgFontLineHeight(font); // Added per ticket #29469 char idStr[80]; char statusLine[128]; // bugfix ticket #28644 int trackHeight = bigRmskTotalHeight(tg, vis); hvGfxSetClip(hvg, xOff, yOff, width, trackHeight); for (cr = tg->items; cr != NULL; cr = cr->next) { // Break apart the name and get the class of the // repeat. char family[256]; char class[256]; // Simplify repClass for lookup: strip trailing '?', // simplify *RNA to RNA: char *poundPtr = index(cr->name, '#'); if (poundPtr) { safecpy(family, sizeof(family), cr->name); poundPtr = index(family, '#'); *poundPtr = '\0'; safecpy(class, sizeof(class), poundPtr + 1); char *slashPtr = index(class, '/'); if (slashPtr) *slashPtr = '\0'; } else { safecpy(family, sizeof(family), 0); safecpy(class, sizeof(class), "Unknown"); } char *p = &(class[strlen(class) - 1]); if (*p == '?') *p = '\0'; if (endsWith(class, "RNA")) safecpy(class, sizeof(class), "RNA"); // Lookup the class to get the color scheme ri = hashFindVal(classHashBR, class); if (ri == NULL) ri = hashFindVal(classHashBR, "Other"); col = ri->color; if ( showLabels ) { int stringWidth = mgFontStringWidth(font, family) + LABEL_PADDING; x1 = roundingScale(cr->alignStart - winStart, width, baseWidth); // Remove labels that overlap the window and use leftLabel instead if ( x1-stringWidth > 0 ) { y = yOff + (cr->layoutLevel * tg->lineHeight); hvGfxTextCentered(hvg, x1 + xOff - stringWidth, heightPer - fontHeight + y, stringWidth, fontHeight, MG_BLACK, font, family); cr->leftLabel = 0; }else { x1 = roundingScale(cr->alignEnd - winStart, width, baseWidth); if ( x1 > 0 ) cr->leftLabel = 1; } } // Get id for click handler sprintf(idStr,"%d",cr->id); int idx = 0; int prevBlockEnd = -1; for (idx = 0; idx < cr->blockCount; idx++) { if (cr->blockRelStarts[idx] >= 0) { int blockStart = cr->chromStart + cr->blockRelStarts[idx]; int blockEnd = cr->chromStart + cr->blockRelStarts[idx] + cr->blockSizes[idx]; x1 = roundingScale(blockStart - winStart, width, baseWidth) + xOff; x1 = max(x1, 0); x2 = roundingScale(blockEnd - winStart, width, baseWidth) + xOff; y = yOff + (cr->layoutLevel * tg->lineHeight); w = x2 - x1; if (w <= 0) w = 1; hvGfxBox(hvg, x1, y, w, heightPer, col); // feature change ticket #29469 safef(statusLine, sizeof(statusLine), "%s", cr->name); mapBoxHc(hvg, cr->alignStart, cr->alignEnd, x1, y, w, heightPer, tg->track, idStr, statusLine); int midY = y + (heightPer>>1); int dir = 0; if (cr->strand[0] == '+') dir = 1; else if (cr->strand[0] == '-') dir = -1; Color textColor = hvGfxContrastingColor(hvg, col); clippedBarbs(hvg, x1, midY, w, tl.barbHeight, tl.barbSpacing, dir, textColor, TRUE); if ( prevBlockEnd > 0 ) { int px1 = roundingScale(prevBlockEnd - winStart, width, baseWidth) + xOff; px1 = max(px1, 0); hvGfxLine(hvg, px1, midY, x1, midY, black); } prevBlockEnd = blockEnd; } } }//for (cr = ri->itemData... } static void bigRmskFreeItems(struct track *tg) /* Free up rmskJoinedMasker items. */ { slFreeList(&tg->items); } static char * bigRmskItemName(struct track *tg, void *item) // This is really not necessary...but placed it here anyway... { return ""; } static void drawDashedHorizLine(struct hvGfx *hvg, int x1, int x2, int y, int dashLen, int gapLen, Color lineColor) // ie. - - - - - - - - - - - - - - - - { int cx1 = x1; int cx2; while (1) { cx2 = cx1 + dashLen; if (cx2 > x2) cx2 = x2; hvGfxLine(hvg, cx1, y, cx2, y, lineColor); cx1 += (dashLen + gapLen); if (cx1 > x2) break; } } static void drawDashedHorizLineWHash(struct hvGfx *hvg, int x1, int x2, int y, int dashLen, int gapLen, Color lineColor, int unalignedLen) // ie. - - - - - - -\234\- - - - - - - - - { int cx1 = x1; int cx2; char lenLabel[20]; safef(lenLabel, sizeof(lenLabel), "%d", unalignedLen); MgFont *font = tl.font; int fontHeight = tl.fontHeight; int stringWidth = mgFontStringWidth(font, lenLabel) + LABEL_PADDING; int glyphWidth = x2 - x1; if (glyphWidth < stringWidth + 6 + (2 * dashLen)) stringWidth = 0; int midX = ((glyphWidth) / 2) + x1; int startHash = midX - (stringWidth * 0.5); int midPointDrawn = 0; /* * Degrade Gracefully: * Too little space to draw dashes or even * hash marks, give up. */ if (glyphWidth < 6 + dashLen) { hvGfxLine(hvg, x1, y, x2, y, lineColor); return; } if (glyphWidth < 6 + (2 * dashLen)) { midX -= 3; hvGfxLine(hvg, x1, y, midX, y, lineColor); hvGfxLine(hvg, midX, y - 3, midX + 3, y + 3, lineColor); hvGfxLine(hvg, midX + 3, y - 3, midX + 6, y + 3, lineColor); hvGfxLine(hvg, midX + 6, y, x2, y, lineColor); return; } while (1) { cx2 = cx1 + dashLen; if (cx2 > x2) cx2 = x2; if (!midPointDrawn && cx2 > startHash) { // Draw double slashes "\\" instead of dash hvGfxLine(hvg, cx1, y - 3, cx1 + 3, y + 3, lineColor); if (stringWidth) { hvGfxTextCentered(hvg, cx1 + 3, y - (fontHeight/2), stringWidth, fontHeight, MG_BLACK, font, lenLabel); cx1 += stringWidth; } hvGfxLine(hvg, cx1 + 3, y - 3, cx1 + 6, y + 3, lineColor); cx1 += 6; midPointDrawn = 1; } else { // Draw a dash hvGfxLine(hvg, cx1, y, cx2, y, lineColor); cx1 += dashLen; } if (!midPointDrawn && cx1 + gapLen > midX) { // Draw double slashes "\\" instead of gap hvGfxLine(hvg, cx1, y - 3, cx1 + 3, y + 3, lineColor); if (stringWidth) { hvGfxTextCentered(hvg, cx1 + 3, y - 3, stringWidth, fontHeight, MG_BLACK, font, lenLabel); cx1 += stringWidth; } hvGfxLine(hvg, cx1 + 3, y - 3, cx1 + 6, y + 3, lineColor); cx1 += 6; midPointDrawn = 1; } else { cx1 += gapLen; } if (cx1 > x2) break; } } static void drawNormalBox(struct hvGfx *hvg, int x1, int y1, int width, int height, Color fillColor, Color outlineColor) { struct gfxPoly *poly = gfxPolyNew(); // RMH: Fixed 8/4/22 : One-off error in height/width to x/y calcs int y2 = y1 + height - 1; int x2 = x1 + width - 1; /* * 1,5--------------2 * | | * | | * | | * 4--------------3 */ gfxPolyAddPoint(poly, x1, y1); gfxPolyAddPoint(poly, x2, y1); gfxPolyAddPoint(poly, x2, y2); gfxPolyAddPoint(poly, x1, y2); gfxPolyAddPoint(poly, x1, y1); hvGfxDrawPoly(hvg, poly, fillColor, TRUE); hvGfxDrawPoly(hvg, poly, outlineColor, FALSE); gfxPolyFree(&poly); } static void drawBoxWChevrons(struct hvGfx *hvg, int x1, int y1, int width, int height, Color fillColor, Color outlineColor, char strand) { drawNormalBox(hvg, x1, y1, width, height, fillColor, outlineColor); static Color white = 0xffffffff; int dir = (strand == '+' ? 1 : -1); int midY = y1 + ((height) >> 1); clippedBarbs(hvg, x1 + 1, midY, width - 2, ((height >> 1) - 2), 5, dir, white, TRUE); } static void drawRMGlyph(struct hvGfx *hvg, int y, int heightPer, int width, int baseWidth, int xOff, struct bigRmskRecord *rm, enum trackVisibility vis, boolean showUnalignedExtents, boolean showLabels) /* * Draw a detailed RepeatMasker annotation glyph given * a single bigRmskRecord structure. * * A couple of caveats about the use of the bigRmskRecord * structure to hold a RepeatMasker annotation. * * chromStart/chromEnd: These represent genomic coordinates * that mark the extents of graphics * annotation on the genome. I.e * aligned blocks + unaligned consensus * blocks. The code below may not * draw to these extents in some cases. * * score: This represents the average divergence of the * individual aligned blocks. It is a percentage * * 100. Ie. 23.11 % is encoded as the integer 2311. * * blockRelStarts: Two types of blocks are interwoven in this * format. Aligned and unaligned blocks. Aligned * blocks will have a value >= 0 representing the * relative position from chromStart for this * start of this block. A value of -1 for chromStart * is indicative of unaligned block and starts from * the end of the last aligned block on the chromosome * or from chromStart if it's the first block in the list. * * name: Stores the id#class/family * * rgb: Unused at this time * * description: Unused but the intention would be to store * the RepeatMasker *.out lines which make up * all the aligned sections of this joined * annotation. * * blockSizes: As you would expect. * * Here is an example: * ie. * A forward strand RM annotation from chr1:186-196 * which is aligned to a 100 bp repeat from 75-84 * in the consensus would be represented as: * * chromStart: 111 * chromEnd: 212 * blockRelStarts: -1, 75, -1 * blockSizes: 75, 10, 16 * */ { int idx; int lx1, lx2; int cx1, cx2; int end; char lenLabel[20]; int w; struct classRecord *ri; // heightPer is the God given height of a single // track item...respect your overlord. int alignedBlockHeight = heightPer * 0.5; int alignedBlockOffset = heightPer - alignedBlockHeight; int unalignedBlockHeight = heightPer * 0.75; int unalignedBlockOffset = heightPer - unalignedBlockHeight; float pixelsPerBase = (float)width / (float)baseWidth; Color black = hvGfxFindColorIx(hvg, 0, 0, 0); Color fillColor = shadesOfGray[5]; Color outlineColor = rmskJoinedClassColors[0]; // Break apart the name and get the class of the // repeat. char class[256]; // Simplify repClass for lookup: strip trailing '?', // simplify *RNA to RNA: char *poundPtr = index(rm->name, '#'); if (poundPtr) { safecpy(class, sizeof(class), poundPtr + 1); char *slashPtr = index(class, '/'); if (slashPtr) *slashPtr = '\0'; } else { safecpy(class, sizeof(class), "Unknown"); } char *p = &(class[strlen(class) - 1]); if (*p == '?') *p = '\0'; if (endsWith(class, "RNA")) safecpy(class, sizeof(class), "RNA"); // Lookup the class to get the color scheme ri = hashFindVal(classHashBR, class); if (ri == NULL) ri = hashFindVal(classHashBR, "Other"); // Pick the fill color based on the divergence int percId = 1000 - rm->score; int grayLevel = grayInRange(percId, 500, 1000); fillColor = shadesOfGray[grayLevel]; outlineColor = ri->color; // Draw from left to right for (idx = 0; idx < rm->blockCount; idx++) { int fragGStart = rm->blockRelStarts[idx]; // Assumptions about blockCount // - first aligned block = 1, the block 0 is // the unaligned consensus either 5' or 3' of // this block. // - The last aligned block is blockCount - 1; if (fragGStart > -1) { // Aligned Block int fragSize = rm->blockSizes[idx]; fragGStart += rm->chromStart; int fragGEnd = fragGStart + fragSize; lx1 = roundingScale(fragGStart - winStart, width, baseWidth) + xOff; lx1 = max(lx1, 0); lx2 = roundingScale(fragGEnd - winStart, width, baseWidth) + xOff; w = lx2 - lx1; if (w <= 0) w = 1; if (idx == 1 && rm->blockCount == 3) { // One and only one aligned block drawBoxWChevrons(hvg, lx1, y + alignedBlockOffset, w, alignedBlockHeight, fillColor, outlineColor, rm->strand[0]); } else if (idx == 1) { // First block if (rm->strand[0] == '-') { // First block on negative strand is the point block drawBoxWChevrons(hvg, lx1, y + alignedBlockOffset, w, alignedBlockHeight, fillColor, outlineColor, rm->strand[0]); } else { // First block on the positive strand is the tail block drawBoxWChevrons(hvg, lx1, y + alignedBlockOffset, w, alignedBlockHeight, fillColor, outlineColor, rm->strand[0]); } } else if (idx == (rm->blockCount - 2)) { // Last block if (rm->strand[0] == '-') { // Last block on the negative strand is the tail block drawBoxWChevrons(hvg, lx1, y + alignedBlockOffset, w, alignedBlockHeight, fillColor, outlineColor, rm->strand[0]); } else { // Last block on the positive strand is the poitn block drawBoxWChevrons(hvg, lx1, y + alignedBlockOffset, w, alignedBlockHeight, fillColor, outlineColor, rm->strand[0]); } } else { // Intermediate aligned blocks are drawn as rectangles drawBoxWChevrons(hvg, lx1, y + alignedBlockOffset, w, alignedBlockHeight, fillColor, outlineColor, rm->strand[0]); } } else { // Unaligned Block int relStart = 0; if (idx == 0) { // Start with the assumption that we don't show // unaligned extentions. lx1 = roundingScale(rm->chromStart + rm->blockRelStarts[idx + 1] - winStart, width, baseWidth) + xOff; if ( showUnalignedExtents ) { /* * Unaligned sequence at the start of an annotation * Draw as: * |------------- or |------//------ * | | * >>>>>>> >>>>>>>> */ lx2 = roundingScale(rm->chromStart + rm->blockRelStarts[idx + 1] - winStart, width, baseWidth) + xOff; if ((rm->blockSizes[idx] * pixelsPerBase) > MAX_UNALIGNED_PIXEL_LEN) { lx1 = roundingScale(rm->chromStart + (rm->blockRelStarts[idx + 1] - (int) (MAX_UNALIGNED_PIXEL_LEN / pixelsPerBase)) - winStart, width, baseWidth) + xOff; // Line Across drawDashedHorizLineWHash(hvg, lx1, lx2, y + unalignedBlockOffset, 5, 5, black, rm->blockSizes[idx]); // Line down to box hvGfxLine(hvg, lx2, y + alignedBlockOffset, lx2, y + unalignedBlockOffset, black); // extension cap "|---" hvGfxLine(hvg, lx1, y + unalignedBlockOffset - 3, lx1, y + unalignedBlockOffset + 3, black); } else { lx1 = roundingScale(rm->chromStart - winStart, width, baseWidth) + xOff; // Only display extension if the resolution is high enough to // fully see the extension line and cap distinctly: eg. "|--" if ( lx2-lx1 >= MIN_VISIBLE_EXT_PIXELS) { // Line Across drawDashedHorizLine(hvg, lx1, lx2, y + unalignedBlockOffset, 5, 5, black); // Line down to box hvGfxLine(hvg, lx2, y + alignedBlockOffset, lx2, y + unalignedBlockOffset, black); // extension cap "|---" hvGfxLine(hvg, lx1, y + unalignedBlockOffset - 3, lx1, y + unalignedBlockOffset + 3, black); } } } if ( showLabels ) { MgFont *font = tl.font; int fontHeight = tl.fontHeight; int stringWidth = mgFontStringWidth(font, rm->name) + LABEL_PADDING; if ( lx1-stringWidth-xOff >= -(LABEL_PADDING/2) ) { hvGfxTextCentered(hvg, lx1 - stringWidth, heightPer - fontHeight + y, stringWidth, fontHeight, MG_BLACK, font, rm->name); rm->leftLabel = 0; }else { end = rm->alignEnd; if ( showUnalignedExtents ) { if ((rm->blockSizes[rm->blockCount - 1] * pixelsPerBase) > MAX_UNALIGNED_PIXEL_LEN) { safef(lenLabel, sizeof(lenLabel), "%d", rm->blockSizes[rm->blockCount - 1]); end += (int) (MAX_UNALIGNED_PIXEL_LEN / pixelsPerBase) + (int) ((mgFontStringWidth(tl.font, lenLabel) + LABEL_PADDING) / pixelsPerBase); } else { end += rm->blockSizes[rm->blockCount - 1]; } } // RMH: Should be no need to scale this. Both numbers are // in bp coordinates. //int endx = roundingScale(rm->visualEnd - winStart, // width, baseWidth); //if ( endx > 0 ) if ( rm->visualEnd >= winStart ) rm->leftLabel = 1; } } } else if (idx == (rm->blockCount - 1)) { if ( showUnalignedExtents ) { /* * Unaligned sequence at the end of an annotation * Draw as: * -------------| or ------//------| * | | * >>>>> >>>>>>> */ lx1 = roundingScale(rm->chromStart + rm->blockRelStarts[idx - 1] + rm->blockSizes[idx - 1] - winStart, width, baseWidth) + xOff; if ((rm->blockSizes[idx] * pixelsPerBase) > MAX_UNALIGNED_PIXEL_LEN) { lx2 = roundingScale(rm->chromStart + rm->blockRelStarts[idx - 1] + rm->blockSizes[idx - 1] + (int)(MAX_UNALIGNED_PIXEL_LEN / pixelsPerBase) - winStart, width, baseWidth) + xOff; // Line Across drawDashedHorizLineWHash(hvg, lx1, lx2, y + unalignedBlockOffset, 5, 5, black, rm->blockSizes[idx]); // Line down to box hvGfxLine(hvg, lx1, y + alignedBlockOffset, lx1, y + unalignedBlockOffset, black); // Cap "--|" hvGfxLine(hvg, lx2, y + unalignedBlockOffset - 3, lx2, y + unalignedBlockOffset + 3, black); } else { lx2 = roundingScale(rm->chromStart + rm->blockRelStarts[idx - 1] + rm->blockSizes[idx - 1] + rm->blockSizes[idx] - winStart, width, baseWidth) + xOff; if ( lx2-lx1 >= MIN_VISIBLE_EXT_PIXELS) { // Line Across drawDashedHorizLine(hvg, lx1, lx2, y + unalignedBlockOffset, 5, 5, black); // Line down to box hvGfxLine(hvg, lx1, y + alignedBlockOffset, lx1, y + unalignedBlockOffset, black); // Cap "--|" hvGfxLine(hvg, lx2, y + unalignedBlockOffset - 3, lx2, y + unalignedBlockOffset + 3, black); } } } } else { /* * Middle Unaligned * Draw unaligned sequence between aligned fragments * as: ......... * / \ * >>>>> >>>>>> * * or: * ............. * \ / * >>>>> >>>>>> * * Also use ....//.... to indicate not to scale if * necessary. * */ int alignedGapSize = rm->blockRelStarts[idx + 1] - (rm->blockRelStarts[idx - 1] + rm->blockSizes[idx - 1]); int unaSize = rm->blockSizes[idx]; int alignedOverlapSize = unaSize - alignedGapSize; if (unaSize < 0) { relStart = rm->blockRelStarts[idx - 1] + rm->blockSizes[idx - 1] - (alignedOverlapSize / 2); if (abs(unaSize) > rm->blockSizes[idx - 1]) unaSize = -rm->blockSizes[idx - 1]; lx1 = roundingScale(rm->chromStart + rm->blockRelStarts[idx - 1] + rm->blockSizes[idx - 1] + unaSize - winStart, width, baseWidth) + xOff; lx1 = max(lx1, 0); lx2 = roundingScale(rm->chromStart + rm->blockRelStarts[idx + 1] - winStart, width, baseWidth) + xOff; int midPoint = ((lx2 - lx1) / 2) + lx1; // Block Intersection Line hvGfxLine(hvg, lx1, y + alignedBlockOffset, lx1, y + alignedBlockOffset + alignedBlockHeight, black); // Line Up hvGfxLine(hvg, lx1, y + alignedBlockOffset, midPoint, y + unalignedBlockOffset, black); // Line Down hvGfxLine(hvg, lx2, y + alignedBlockOffset, midPoint, y + unalignedBlockOffset, black); } else if (alignedOverlapSize > 0 && ((alignedOverlapSize * 0.5) > (0.3 * rm->blockSizes[idx - 1]) || (alignedOverlapSize * 0.5) > (0.3 * rm->blockSizes[idx + 1]))) { // Need to shorten unaligned length int smallOverlapLen = 0; smallOverlapLen = (0.3 * rm->blockSizes[idx - 1]); if (smallOverlapLen > (0.3 * rm->blockSizes[idx + 1])) smallOverlapLen = (0.3 * rm->blockSizes[idx + 1]); unaSize = (smallOverlapLen * 2) + alignedGapSize; relStart = rm->blockRelStarts[idx - 1] + rm->blockSizes[idx - 1] - smallOverlapLen; lx1 = roundingScale(relStart + rm->chromStart - winStart, width, baseWidth) + xOff; lx1 = max(lx1, 0); lx2 = roundingScale(relStart + rm->chromStart + unaSize - winStart, width, baseWidth) + xOff; // Line Up cx1 = roundingScale(rm->chromStart + rm->blockRelStarts[idx - 1] + rm->blockSizes[idx - 1] - winStart, width, baseWidth) + xOff; hvGfxLine(hvg, cx1, y + alignedBlockOffset, lx1, y + unalignedBlockOffset, black); // Line Across drawDashedHorizLineWHash(hvg, lx1, lx2, y + unalignedBlockOffset, 5, 5, black, rm->blockSizes[idx]); // Line Down cx2 = roundingScale(rm->chromStart + rm->blockRelStarts[idx + 1] - winStart, width, baseWidth) + xOff; hvGfxLine(hvg, cx2, y + alignedBlockOffset, lx2, y + unalignedBlockOffset, black); } else { // Adequate to display full length relStart = rm->blockRelStarts[idx - 1] + rm->blockSizes[idx - 1] - (alignedOverlapSize / 2); lx1 = roundingScale(relStart + rm->chromStart - winStart, width, baseWidth) + xOff; lx1 = max(lx1, 0); lx2 = roundingScale(relStart + rm->chromStart + unaSize - winStart, width, baseWidth) + xOff; // Line Up int cx1 = roundingScale(rm->chromStart + rm->blockRelStarts[idx - 1] + rm->blockSizes[idx - 1] - winStart, width, baseWidth) + xOff; hvGfxLine(hvg, cx1, y + alignedBlockOffset, lx1, y + unalignedBlockOffset, black); drawDashedHorizLine(hvg, lx1, lx2, y + unalignedBlockOffset, 5, 5, black); // Line Down cx2 = roundingScale(rm->chromStart + rm->blockRelStarts[idx + 1] - winStart, width, baseWidth) + xOff; hvGfxLine(hvg, cx2, y + alignedBlockOffset, lx2, y + unalignedBlockOffset, black); } } } // if ( fragStart .. else { } // for(idx=.. } static void bigRmskDrawItems(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont * font, Color color, enum trackVisibility vis) /* Main callback for displaying this track in the viewport * of the browser. */ { int baseWidth = seqEnd - seqStart; /* * Its unclear to me why heightPer is not updated to the * value set in bigRmskItemHeight() at the time this callback * is invoked. Getting the correct value myself. * was: * int heightPer = tg->heightPer; */ int heightPer = bigRmskItemHeight(tg, NULL); struct bigRmskRecord *rm; boolean showUnalignedExtents = cartUsualBoolean(cart, BIGRMSK_SHOW_UNALIGNED_EXTENTS, BIGRMSK_SHOW_UNALIGNED_EXTENTS_DEFAULT); boolean showLabels = cartUsualBoolean(cart, BIGRMSK_SHOW_LABELS, BIGRMSK_SHOW_LABELS_DEFAULT); boolean origPackViz = cartUsualBoolean(cart, BIGRMSK_ORIG_PACKVIZ, BIGRMSK_ORIG_PACKVIZ_DEFAULT); // If we are in full view mode and the scale is sufficient, // display the detailed visualization. if (vis == tvFull && baseWidth <= DETAIL_VIEW_MAX_SCALE) { int level; for (rm = tg->items; rm != NULL; rm = rm->next) { level = yOff + (rm->layoutLevel * tg->lineHeight); drawRMGlyph(hvg, level, heightPer, width, baseWidth, xOff, rm, vis, showUnalignedExtents, showLabels ); char statusLine[128]; int ss1 = roundingScale(rm->alignStart - winStart, width, baseWidth) + xOff; safef(statusLine, sizeof(statusLine), "%s", rm->name); int x1 = roundingScale(rm->alignStart - winStart, width, baseWidth) + xOff; x1 = max(x1, 0); int x2 = roundingScale(rm->alignEnd - winStart, width, baseWidth) + xOff; int w = x2 - x1; if (w <= 0) w = 1; char idStr[80]; sprintf(idStr,"%d",rm->id); mapBoxHc(hvg, rm->alignStart, rm->alignEnd, ss1, level, w, heightPer, tg->track, idStr, statusLine); } } else { // Experiment with further context sensitivity int count = slCount(tg->items); if ( count > MAX_PACK_ITEMS || vis == tvDense ) { // Draw the single line view drawDenseGlyphs(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis); } else { if ( origPackViz ) // Draw the stereotypical class view drawOrigPackGlyphs(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis); else // Draw new pack view drawPackGlyphs(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis); } } } void bigRmskLeftLabels(struct track *tg, 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 labels on the left margin */ { boolean origPackViz = cartUsualBoolean(cart, BIGRMSK_ORIG_PACKVIZ, BIGRMSK_ORIG_PACKVIZ_DEFAULT); Color labelColor = tg->labelColor; labelColor = maybeDarkerLabels(tg, hvg, labelColor); int heightPer = bigRmskItemHeight(tg, NULL); int titleFontHeight = tl.fontHeight; int labelFontHeight = mgFontLineHeight(font); int yOffAfterTitle = yOff + titleFontHeight; int fontOffset = heightPer - labelFontHeight; int y = yOffAfterTitle; if (vis == tvDense) { hvGfxTextRight(hvg, xOff, y, width - 1, heightPer, labelColor, font, "Repeats"); } else if ( vis == tvPack && origPackViz ) { int i; int numClasses = ArraySize(rptClasses); for (i = 0; i < numClasses; ++i) { hvGfxTextRight(hvg, xOff, y + fontOffset, width - 1, heightPer, labelColor, font, rptClassNames[i]); y += heightPer; } } else { struct bigRmskRecord *cr; int highestLevel = 0; for (cr = tg->items; cr != NULL; cr = cr->next) { if ( cr->layoutLevel > highestLevel ) highestLevel = cr->layoutLevel; if ( cr->leftLabel ) { // Break apart the name and get the class of the // repeat. char family[256]; // Simplify repClass for lookup: strip trailing '?', // simplify *RNA to RNA: safecpy(family, sizeof(family), cr->name); // RMH: For now allow the full name to show in left column. // If this ends up being too wide we can make it an option // to only show the identifier as was originally coded: //char *poundPtr = index(cr->name, '#'); //if (poundPtr) // { // poundPtr = index(family, '#'); // *poundPtr = '\0'; // } y = yOffAfterTitle + (cr->layoutLevel * tg->lineHeight) + fontOffset; hvGfxSetClip(hvgSide, leftLabelX, y, insideWidth, tg->height); hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, heightPer-fontOffset, color, font, family); hvGfxUnclip(hvgSide); } } } } void bigRmskMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]) { bigBedMethods(track, tdb, wordCount, words); track->loadItems = bigRmskLoadItems; track->totalHeight = bigRmskTotalHeight; track->drawItems = bigRmskDrawItems; track->drawLeftLabels = bigRmskLeftLabels; track->freeItems = bigRmskFreeItems; track->colorShades = shadesOfGray; track->itemName = bigRmskItemName; track->mapItemName = bigRmskItemName; track->itemHeight = bigRmskItemHeight; track->itemStart = tgItemNoStart; track->itemEnd = tgItemNoEnd; track->mapsSelf = TRUE; track->canPack = TRUE; }