2e6b73ac1803862338f283d9b353fe2e10aa0204 braney Sun Feb 12 14:17:18 2023 -0800 rename file to be more generic since display works on chains and psls diff --git src/hg/hgTracks/chainSnakeTrack.c src/hg/hgTracks/chainSnakeTrack.c deleted file mode 100644 index 065a6ca..0000000 --- src/hg/hgTracks/chainSnakeTrack.c +++ /dev/null @@ -1,1185 +0,0 @@ -/* Copyright (C) 2014 The Regents of the University of California - * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ - -/* snakeTrack - stuff to load and display snake type tracks in browser. */ - -#include "common.h" -#include "hash.h" -#include "localmem.h" -#include "linefile.h" -#include "jksql.h" -#include "hdb.h" -#include "hgTracks.h" -#include "chainBlock.h" -#include "chainLink.h" -#include "chainDb.h" -#include "chainCart.h" -#include "errCatch.h" -#include "twoBit.h" -#include "bigWarn.h" -#include <pthread.h> -#include "trackHub.h" -#include "limits.h" -#include "snakeUi.h" -#include "bits.h" -#include "trix.h" -#include "chromAlias.h" - -#include "bigPsl.h" -#include "snake.h" - -// this is the number of pixels used by the target self-align bar -#define DUP_LINE_HEIGHT 0 -// this is the number of pixels used when displaying the insertion lengths -#define INSERT_TEXT_HEIGHT 0 - -static int snakeFeatureCmpQStart(const void *va, const void *vb) -/* sort by start position on the query sequence */ -{ -const struct snakeFeature *a = *((struct snakeFeature **)va); -const struct snakeFeature *b = *((struct snakeFeature **)vb); -int diff = a->qStart - b->qStart; - -if (diff == 0) - { - diff = a->start - b->start; - } - -return diff; -} - -// static machinery to calculate full and pack snake - -#define NUM_LEVELS 1000 - -struct level -{ -boolean init; /* has this level been initialized */ -int orientation; /* strand.. see above */ -unsigned long edge; /* the leading edge of this level */ -int adjustLevel; /* used to compress out the unused levels */ -boolean hasBlock; /* are there any blocks in this level */ - -// these fields are used to compact full snakes -unsigned *connectsToLevel; /* what levels does this level connect to */ -Bits *pixels; /* keep track of what pixels are used */ -struct snakeFeature *blocks; /* the ungapped blocks attached to this level */ -}; - -static struct level Levels[NUM_LEVELS]; /* for packing the snake, not re-entrant! */ -static int maxLevel = 0; /* deepest level */ - -/* blocks that make it through the min size filter */ -static struct snakeFeature *newList = NULL; - -static void clearLevels() -/* clear out the data structure that we use to calculate snakes */ -{ -int ii; - -for(ii=0; ii < sizeof(Levels) / sizeof(Levels[0]); ii++) - Levels[ii].init = FALSE; -maxLevel = 0; -} - -static void calcFullSnakeHelper(struct snakeFeature *list, int level) -// calculate a full snake -// updates global newList with unsorted blocks that pass the min -// size filter. -{ -struct snakeFeature *cb = list; -struct snakeFeature *proposedList = NULL; - -if (level > maxLevel) - maxLevel = level; -if (level > ArraySize(Levels)) - errAbort("too many levels"); - -if (Levels[level].init == FALSE) - { - // initialize the level if this is the first time we've seen it - Levels[level].init = TRUE; - Levels[level].orientation = list->orientation; - if (list->orientation == -1) - Levels[level].edge = LONG_MAX; // bigger than the biggest chrom - else - Levels[level].edge = 0; - } - -// now we step through the blocks and assign them to levels -struct snakeFeature *next; -struct snakeFeature *insertHead = NULL; -for(; cb; cb = next) - { - // we're going to add this block to a different list - // so keep track of the next pointer - next = cb->next; - - // if this block can't fit on this level add to the insert - // list and move on to the next block - if ((Levels[level].orientation != cb->orientation) || - ((cb->orientation == 1) && (Levels[level].edge > cb->start)) || - ((cb->orientation == -1) && (Levels[level].edge < cb->end))) - { - // add this to the list of an insert - slAddHead(&insertHead, cb); - continue; - } - - // the current block will fit on this level - // go ahead and deal with the blocks that wouldn't - if (insertHead) - { - // we had an insert, go ahead and calculate where that goes - slReverse(&insertHead); - calcFullSnakeHelper(insertHead, level + 1); - insertHead = NULL; - } - - // assign the current block to this level - cb->level = level; - - if (cb->orientation == 1) - Levels[level].edge = cb->end; - else - Levels[level].edge = cb->start; - - // add this block to the list of proposed blocks for this level - slAddHead(&proposedList, cb); - } - -// we're at the end of the list. Deal with any blocks -// that didn't fit on this level -if (insertHead) - { - slReverse(&insertHead); - int nextLevel = level + 1; - calcFullSnakeHelper(insertHead, nextLevel); - insertHead = NULL; - } - -// do we have any proposed blocks -if (proposedList == NULL) - return; - -// we parsed all the blocks in the list to see if they fit in our level -// now let's see if the list of blocks for this level is big enough -// to actually add - -struct snakeFeature *temp; -double scale = scaleForWindow(insideWidth, winStart, winEnd); -int start, end; - -// order the blocks so lowest start position is first -if (Levels[level].orientation == 1) - slReverse(&proposedList); - -start=proposedList->start; -for(temp=proposedList; temp->next; temp = temp->next) - ; -end=temp->end; - -// calculate how big the string of blocks is in screen coordinates -double apparentSize = scale * (end - start); - -if (apparentSize < 0) - errAbort("size of a list of blocks should not be less than zero"); - -// check to see if the apparent size is big enough -if (apparentSize < 1) - return; - -// transfer proposedList to new block list -for(temp=proposedList; temp; temp = next) - { - next = temp->next; - temp->next = NULL; - slAddHead(&newList, temp); - } -} - -static void freeFullLevels() -// free the connection levels and bitmaps for each level -{ -int ii; - -for(ii=0; ii <= maxLevel; ii++) - { - freez(&Levels[ii].connectsToLevel); - bitFree(&Levels[ii].pixels); - } -} - -static void initializeFullLevels(struct snakeFeature *sfList) -/* initialize levels for compact snakes */ -{ -int ii; - -for(ii=0; ii <= maxLevel; ii++) - { - Levels[ii].connectsToLevel = needMem((maxLevel+1) * sizeof(unsigned)); - Levels[ii].pixels = bitAlloc(insideWidth); - Levels[ii].blocks = NULL; - } - -struct snakeFeature *sf, *next; -int prevLevel = -1; -double scale = scaleForWindow(insideWidth, winStart, winEnd); - -for(sf=sfList; sf; sf = next) - { - next = sf->next; - - if (positiveRangeIntersection(sf->start, sf->end, winStart, winEnd)) - { - int sClp = (sf->start < winStart) ? winStart : sf->start; - sf->pixX1 = round((sClp - winStart)*scale); - int eClp = (sf->end > winEnd) ? winEnd : sf->end; - sf->pixX2 = round((eClp - winStart)*scale); - } - else - { - sf->pixX1 = sf->pixX2 = 0; - } - - bitSetRange(Levels[sf->level].pixels, sf->pixX1, sf->pixX2 - sf->pixX1); - - if (prevLevel != -1) - Levels[sf->level].connectsToLevel[prevLevel] = 1; - - if(next != NULL) - Levels[sf->level].connectsToLevel[next->level] = 1; - - prevLevel = sf->level; - - slAddHead(&Levels[sf->level].blocks, sf); - } -} - -static int highestLevelBelowUs(int level) -// is there a level below us that doesn't connect to us -{ -int newLevel; - -// find the highest level below us that we connect to -for(newLevel = level - 1; newLevel >= 0; newLevel--) - if (Levels[level].connectsToLevel[newLevel]) - break; - -// if the next level is more than one below us, we may -// be able to push our blocks to it. -if ((newLevel < 0) || (newLevel + 1 == level)) - return -1; - -return newLevel + 1; -} - -// the number of pixels we need clear on either side of the blocks we push -#define EXTRASPACE 10 - -static boolean checkBlocksOnLevel(int level, struct snakeFeature *sfList) -// is there enough pixels on this level to hold our blocks? -{ -struct snakeFeature *sf; - -for(sf=sfList; sf; sf = sf->next) - { - if (bitCountRange(Levels[level].pixels, sf->pixX1 - EXTRASPACE, (sf->pixX2 - sf->pixX1) + 2*EXTRASPACE)) - return FALSE; - } -return TRUE; -} - -static void collapseLevel(int oldLevel, int newLevel) -// push level up to higher level -{ -struct snakeFeature *sf; -struct snakeFeature *next; - -for(sf=Levels[oldLevel].blocks; sf; sf = next) - { - next = sf->next; - sf->level = newLevel; - slAddHead(&Levels[newLevel].blocks, sf); - - bitSetRange(Levels[sf->level].pixels, sf->pixX1, sf->pixX2 - sf->pixX1); - } -Levels[oldLevel].blocks = NULL; -Levels[oldLevel].pixels = bitAlloc(insideWidth); -} - -static void remapConnections(int oldLevel, int newLevel) -// if we've moved a level, we need to remap all the connections -{ -int ii, jj; - -for(ii=0; ii <= maxLevel; ii++) - { - for(jj=0; jj <= maxLevel; jj++) - { - if (Levels[ii].connectsToLevel[oldLevel]) - { - Levels[ii].connectsToLevel[oldLevel] = 0; - Levels[ii].connectsToLevel[newLevel] = 1; - } - } - } -} - -static struct snakeFeature *compactSnakes(struct snakeFeature *sfList) -// collapse levels that will fit on a higer level -{ -int ii; - -initializeFullLevels(sfList); - -// start with third level to see what can be compacted -for(ii=2; ii <= maxLevel; ii++) - { - int newLevel; - // is there a level below us that doesn't connect to us - if ((newLevel = highestLevelBelowUs(ii)) > 0) - { - int jj; - for (jj=newLevel; jj < ii; jj++) - { - if (checkBlocksOnLevel(jj, Levels[ii].blocks)) - { - collapseLevel(ii, jj); - remapConnections(ii, jj); - break; - } - } - } - } - -// reattach blocks in the levels to linkedFeature -struct snakeFeature *newList = NULL; -for(ii=0; ii <= maxLevel; ii++) - { - newList = slCat(Levels[ii].blocks, newList); - } -slSort(&newList, snakeFeatureCmpQStart); - -// figure out the new max -int newMax = 0; -for(ii=0; ii <= maxLevel; ii++) - if (Levels[ii].blocks != NULL) - newMax = ii; - -freeFullLevels(); -maxLevel = newMax; - -return newList; -} - -static void calcFullSnake(struct track *tg, void *item) -// calculate a full snake -{ -struct linkedFeatures *lf = (struct linkedFeatures *)item; - -// if there aren't any blocks, don't bother -if (lf->components == NULL) - return; - -// we use the snakeInfo field to keep track of whether we already -// calculated the height of this snake -if (lf->snakeInfo == NULL) - { - clearLevels(); - struct snakeFeature *sf; - - // this will destroy lf->components, and add to newList - calcFullSnakeHelper((struct snakeFeature *)lf->components, 0); - lf->components = (struct simpleFeature *)newList; - newList = NULL; - slSort(&lf->components, snakeFeatureCmpQStart); - - // now we're going to compress the levels that aren't used - // to do that, we need to see which blocks are on the screen, - // or connected to something on the screen - int oldMax = maxLevel; - clearLevels(); - struct snakeFeature *prev = NULL; - for(sf=(struct snakeFeature *)lf->components; sf; prev = sf, sf = sf->next) - { - if (Levels[sf->level].init == FALSE) - { - Levels[sf->level].init = TRUE; - Levels[sf->level].orientation = sf->orientation; - Levels[sf->level].hasBlock = FALSE; - } - else - { - if (Levels[sf->level].orientation != sf->orientation) - errAbort("found snakeFeature with wrong orientation"); - if ((sf->orientation == 1) && (Levels[sf->level].edge > sf->start)) - errAbort("found snakeFeature that violates edge"); - if ((sf->orientation == -1) && (Levels[sf->level].edge < sf->end)) - errAbort("found snakeFeature that violates edge"); - } - if (sf->orientation == 1) - Levels[sf->level].edge = sf->end; - else - Levels[sf->level].edge = sf->start; - if (sf->level > maxLevel) - maxLevel = sf->level; - if(positiveRangeIntersection(winStart, winEnd, sf->start, sf->end)) - { - Levels[sf->level].hasBlock = TRUE; - if (sf->next != NULL) - Levels[sf->next->level].hasBlock = TRUE; - if (prev != NULL) - Levels[prev->level].hasBlock = TRUE; - - } - } - - // now figure out how to remap the blocks - int ii; - int count = 0; - for(ii=0; ii < oldMax + 1; ii++) - { - Levels[ii].adjustLevel = count; - if ((Levels[ii].init) && (Levels[ii].hasBlock)) - count++; - } - maxLevel = count; - - // remap blocks - for(sf=(struct snakeFeature *)lf->components; sf; sf = sf->next) - sf->level = Levels[sf->level].adjustLevel; - - // now compact the snakes - lf->components = (void *)compactSnakes((struct snakeFeature *)lf->components); - struct snakeInfo *si; - AllocVar(si); - si->maxLevel = maxLevel; - lf->snakeInfo = si; - } -} - -static void calcPackSnakeHelper(struct snakeFeature *list, int level) -// calculate a packed snake -// updates global newList with unsorted blocks that pass the min -// size filter. -{ -struct snakeFeature *cb = list; -struct snakeFeature *proposedList = NULL; - -if (level > maxLevel) - maxLevel = level; -if (level > ArraySize(Levels)) - errAbort("too many levels"); - -if (Levels[level].init == FALSE) - { - // initialize the level if this is the first time we've seen it - Levels[level].init = TRUE; - Levels[level].edge = 0; - } - -// now we step through the blocks and assign them to levels -struct snakeFeature *next; -struct snakeFeature *insertHead = NULL; -for(; cb; cb = next) - { - // we're going to add this block to a different list - // so keep track of the next pointer - next = cb->next; - - // if this block can't fit on this level add to the insert - // list and move on to the next block - if ( Levels[level].edge > cb->start) - { - // add this to the list of an insert - slAddHead(&insertHead, cb); - continue; - } - - // the current block will fit on this level - // go ahead and deal with the blocks that wouldn't - if (insertHead) - { - // we had an insert, go ahead and calculate where that goes - slReverse(&insertHead); - calcPackSnakeHelper(insertHead, level + 1); - insertHead = NULL; - } - - // assign the current block to this level - cb->level = level; - - Levels[level].edge = cb->end; - - // add this block to the list of proposed blocks for this level - slAddHead(&proposedList, cb); - } - -// we're at the end of the list. Deal with any blocks -// that didn't fit on this level -if (insertHead) - { - slReverse(&insertHead); - calcPackSnakeHelper(insertHead, level + 1); - insertHead = NULL; - } - -// do we have any proposed blocks -if (proposedList == NULL) - return; - -// we parsed all the blocks in the list to see if they fit in our level -// now let's see if the list of blocks for this level is big enough -// to actually add - -struct snakeFeature *temp; -double scale = scaleForWindow(insideWidth, winStart, winEnd); -int start, end; - -// order the blocks so lowest start position is first -slReverse(&proposedList); - -start=proposedList->start; -for(temp=proposedList; temp->next; temp = temp->next) - ; -end=temp->end; - -// calculate how big the string of blocks is in screen coordinates -double apparentSize = scale * (end - start); - -if (apparentSize < 0) - errAbort("size of a list of blocks should not be less than zero"); - -// check to see if the apparent size is big enough -if (apparentSize < 1) - return; - -// transfer proposedList to new block list -for(temp=proposedList; temp; temp = next) - { - next = temp->next; - temp->next = NULL; - slAddHead(&newList, temp); - } -} - -static void calcPackSnake(struct track *tg, void *item) -{ -struct linkedFeatures *lf = (struct linkedFeatures *)item; -if (lf->components == NULL) - return; - -// we use the snakeIfno field to keep track of whether we already -// calculated the height of this snake -if (lf->snakeInfo == NULL) - { - clearLevels(); - - // this will destroy lf->components, and add to newList - calcPackSnakeHelper((struct snakeFeature *)lf->components, 0); - lf->components = (struct simpleFeature *)newList; - newList = NULL; - - //slSort(&lf->components, snakeFeatureCmpQStart); - - struct snakeInfo *si; - AllocVar(si); - si->maxLevel = maxLevel; - lf->snakeInfo = si; - } -} - -static int snakeItemHeight(struct track *tg, void *item) -// return height of a single packed snake -{ -if ((item == NULL) || (tg->visibility == tvSquish) || (tg->visibility == tvDense)) - return 0; - -struct linkedFeatures *lf = (struct linkedFeatures *)item; -if (lf->components == NULL) - return 0; - -if (tg->visibility == tvFull) - calcFullSnake(tg, item); -else if (tg->visibility == tvPack) - calcPackSnake(tg, item); - -struct snakeInfo *si = (struct snakeInfo *)lf->snakeInfo; -int lineHeight = tg->lineHeight ; -int multiplier = 1; - -if (tg->visibility == tvFull) - multiplier = 2; -return (si->maxLevel + 1) * (multiplier * lineHeight); -} - -static int snakeHeight(struct track *tg, enum trackVisibility vis) -/* calculate height of all the snakes being displayed */ -{ -if (tg->networkErrMsg != NULL) - { - // we had a parallel load failure - tg->drawItems = bigDrawWarning; - tg->totalHeight = bigWarnTotalHeight; - return bigWarnTotalHeight(tg, vis); - } - -if (vis == tvDense) - return tg->lineHeight; - -if (vis == tvSquish) - return tg->lineHeight/2; - -int height = DUP_LINE_HEIGHT + INSERT_TEXT_HEIGHT; -struct slList *item = tg->items; - -item = tg->items; - -for (item=tg->items;item; item = item->next) - { - height += tg->itemHeight(tg, item); - } -if (height < DUP_LINE_HEIGHT + tg->lineHeight) - height = DUP_LINE_HEIGHT + tg->lineHeight; -return height; -} - - -// this is a 16 color palette with every other color being a lighter version of -// the color before it -static int snakePalette2[] = -{ -0x1f77b4, 0xaec7e8, 0xff7f0e, 0xffbb78, 0x2ca02c, 0x98df8a, 0xd62728, 0xff9896, 0x9467bd, 0xc5b0d5, 0x8c564b, 0xc49c94, 0xe377c2, 0xf7b6d2, 0x7f7f7f, 0xc7c7c7, 0xbcbd22, 0xdbdb8d, 0x17becf, 0x9edae5 -}; - - -static Color hashColor(char *name) -{ -bits32 hashVal = hashString(name); -unsigned int colorInt = snakePalette2[hashVal % (sizeof(snakePalette2)/sizeof(Color))]; - -return MAKECOLOR_32(((colorInt >> 16) & 0xff),((colorInt >> 8) & 0xff),((colorInt >> 0) & 0xff)); -} - -static void boundMapBox(struct hvGfx *hvg, int start, int end, int x, int y, int width, int height, - char *track, char *item, char *statusLine, char *directUrl, boolean withHgsid, - char *extra) -// make sure start x and end x position are on the screen -// otherwise the tracking box code gets confused -{ -if (x > insideWidth) - return; - -if (x < 0) - { - width -= -x; - x = 0; - } - -if (x + width > insideWidth) - { - width -= x + width - insideWidth; - } - -mapBoxHgcOrHgGene(hvg, start, end, x, y, width, height, - track, item, statusLine, directUrl, withHgsid, - extra); -} - -static void snakeDrawAt(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 bed item at position. */ -{ -unsigned showSnpWidth = cartOrTdbInt(cart, tg->tdb, - SNAKE_SHOW_SNP_WIDTH, SNAKE_DEFAULT_SHOW_SNP_WIDTH); -struct linkedFeatures *lf = (struct linkedFeatures *)item; - - -if (tg->visibility == tvFull) - calcFullSnake(tg, item); -else if (tg->visibility == tvPack) - calcPackSnake(tg, item); - -if (lf->components == NULL) - return; - -struct snakeFeature *sf = (struct snakeFeature *)lf->components, *prevSf = NULL; -int s = tg->itemStart(tg, item); -int sClp = (s < winStart) ? winStart : s; -int x1 = round((sClp - winStart)*scale) + xOff; -int textX = x1; -int yOff = y; -boolean withLabels = (withLeftLabels && (vis == tvFull) && !tg->drawName); -unsigned labelColor = MG_BLACK; - -// draw the labels -if (withLabels) - { - char *name = tg->itemName(tg, item); - int nameWidth = mgFontStringWidth(font, name); - int dotWidth = tl.nWidth/2; - boolean snapLeft = FALSE; - boolean drawNameInverted = FALSE; - textX -= nameWidth + dotWidth; - snapLeft = (textX < fullInsideX); - /* Special tweak for expRatio in pack mode: force all labels - * left to prevent only a subset from being placed right: */ - snapLeft |= (startsWith("expRatio", tg->tdb->type)); -#ifdef IMAGEv2_NO_LEFTLABEL_ON_FULL - if (theImgBox == NULL && snapLeft) -#else///ifndef IMAGEv2_NO_LEFTLABEL_ON_FULL - if (snapLeft) /* Snap label to the left. */ -#endif ///ndef IMAGEv2_NO_LEFTLABEL_ON_FULL - { - textX = leftLabelX; - assert(hvgSide != NULL); - hvGfxUnclip(hvgSide); - hvGfxSetClip(hvgSide, leftLabelX, yOff, fullInsideX - leftLabelX, tg->height); - if(drawNameInverted) - { - int boxStart = leftLabelX + leftLabelWidth - 2 - nameWidth; - hvGfxBox(hvgSide, boxStart, y, nameWidth+1, tg->heightPer - 1, color); - hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, tg->heightPer, - MG_WHITE, font, name); - } - else - hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, tg->heightPer, - labelColor, font, name); - hvGfxUnclip(hvgSide); - hvGfxSetClip(hvgSide, insideX, yOff, insideWidth, tg->height); - } - else - { - int pdfSlop=nameWidth/5; - hvGfxUnclip(hvg); - hvGfxSetClip(hvg, textX-1-pdfSlop, y, nameWidth+1+pdfSlop, tg->heightPer); - if(drawNameInverted) - { - hvGfxBox(hvg, textX - 1, y, nameWidth+1, tg->heightPer-1, color); - hvGfxTextRight(hvg, textX, y, nameWidth, tg->heightPer, MG_WHITE, font, name); - } - else - hvGfxTextRight(hvg, textX, y, nameWidth, tg->heightPer, labelColor, font, name); - hvGfxUnclip(hvg); - hvGfxSetClip(hvg, insideX, yOff, insideWidth, tg->height); - } - } - -// now we're going to draw the boxes - -s = sf->start; -int lastE = -1; -int lastS = -1; -int offY = y; -int lineHeight = tg->lineHeight ; -int qs, qe; -int heightPer = tg->heightPer; -int lastX = -1; -int lastQEnd = 0; -int lastLevel = -1; -int e; -qe = lastQEnd = 0; -for (sf = (struct snakeFeature *)lf->components; sf != NULL; lastQEnd = qe, prevSf = sf, sf = sf->next) - { - qs = sf->qStart; - qe = sf->qEnd; - if (vis == tvDense) - y = offY; - else if ((vis == tvPack) || (vis == tvSquish)) - y = offY + (sf->level * 1) * lineHeight; - else if (vis == tvFull) - y = offY + (sf->level * 2) * lineHeight; - s = sf->start; e = sf->end; - - int sx, ex; - if (!positiveRangeIntersection(winStart, winEnd, s, e)) - continue; - sx = round((double)((int)s-winStart)*scale) + xOff; - ex = round((double)((int)e-winStart)*scale) + xOff; - - // color by strand - static Color darkBlueColor = 0; - static Color darkRedColor = 0; - if (darkRedColor == 0) - { - //the light blue: rgb(149, 204, 252) - //the light red: rgb(232, 156, 156) - darkRedColor = hvGfxFindColorIx(hvg, 232,156,156); - darkBlueColor = hvGfxFindColorIx(hvg, 149,204,252); - } - - char *colorBy = cartOrTdbString(cart, tg->tdb, - SNAKE_COLOR_BY, SNAKE_DEFAULT_COLOR_BY); - - extern Color getChromColor(char *name, struct hvGfx *hvg); - if (sameString(colorBy, SNAKE_COLOR_BY_STRAND_VALUE)) - color = (sf->orientation == -1) ? darkRedColor : darkBlueColor; - else if (sameString(colorBy, SNAKE_COLOR_BY_CHROM_VALUE)) - color = hashColor(sf->qName); - else - color = darkBlueColor; - - int w = ex - sx; - if (w == 0) - w = 1; - assert(w > 0); - char buffer[1024]; - - if (vis == tvFull) - safef(buffer, sizeof buffer, "%d-%d",sf->qStart,sf->qEnd); - else - safef(buffer, sizeof buffer, "%s:%d-%d",sf->qName,sf->qStart,sf->qEnd); - if (sx < insideX) - { - int olap = insideX - sx; - sx = insideX; - w -= olap; - } - char qAddress[4096]; - if ((vis == tvFull) || (vis == tvPack) ) - { - safef(qAddress, sizeof qAddress, "qName=%s&qs=%d&qe=%d&qWidth=%d",sf->qName, qs, qe, winEnd - winStart); - boundMapBox(hvg, s, e, sx+1, y, w-2, heightPer, tg->track, - buffer, buffer, NULL, TRUE, qAddress); - } - hvGfxBox(hvg, sx, y, w, heightPer, color); - - // now draw the mismatches if we're at high enough resolution and have the sequence - char *twoBitString = trackDbSetting(tg->tdb, "twoBit"); - if (twoBitString && ((winBaseCount < showSnpWidth) && ((vis == tvFull) || (vis == tvPack)))) - { - static struct twoBitFile *tbf = NULL; - static char *lastTwoBitString = NULL; - static struct dnaSeq *seq = NULL; - static char *lastQName = NULL; - - // sequence for chain snakes is in 2bit files which we cache - if ((lastTwoBitString == NULL) || - differentString(lastTwoBitString, twoBitString)) - { - if (tbf != NULL) - { - lastQName = NULL; - twoBitClose(&tbf); - } - tbf = twoBitOpen(twoBitString); - } - - // we're reading in the whole chrom - if ((lastQName == NULL) || differentString(sf->qName, lastQName)) - seq = twoBitReadSeqFrag(tbf, sf->qName, 0, 0); - lastQName = sf->qName; - lastTwoBitString = twoBitString; - - char *ourDna; - ourDna = &seq->dna[sf->qStart]; - - int seqLen = sf->qEnd - sf->qStart; - toUpperN(ourDna, seqLen); - if (sf->orientation == -1) - reverseComplement(ourDna,seqLen); - - // get the reference sequence - char *refDna; - struct dnaSeq *extraSeq = hDnaFromSeq(database, chromName, sf->start, sf->end, dnaUpper); - refDna = extraSeq->dna; - int si = s; - char *ptr1 = refDna; - char *ptr2 = ourDna; - for(; si < e; si++,ptr1++,ptr2++) - { - // if mismatch! If reference is N ignore, if query is N, paint yellow - if ( (*ptr1 != *ptr2) && !((*ptr1 == 'N') || (*ptr1 == 'n'))) - { - int misX1 = round((double)((int)si-winStart)*scale) + xOff; - int misX2 = round((double)((int)(si+1)-winStart)*scale) + xOff; - int w1 = misX2 - misX1; - if (w1 < 1) - w1 = 1; - - Color boxColor = MG_RED; - if ((*ptr2 == 'N') || (*ptr2 == 'n')) - boxColor = hvGfxFindRgb(hvg, &undefinedYellowColor); - hvGfxBox(hvg, misX1, y, w1, heightPer, boxColor); - } - } - - // if we're zoomed to base level, draw sequence of mismatch - if (zoomedToBaseLevel) - { - int mysx = round((double)((int)s-winStart)*scale) + xOff; - int myex = round((double)((int)e-winStart)*scale) + xOff; - int myw = myex - mysx; - spreadAlignString(hvg, mysx, y, myw, heightPer, MG_WHITE, font, ourDna, - refDna, seqLen, TRUE, FALSE); - } - - } - sf->drawn = TRUE; - lastLevel = sf->level; - //lastX = x; - } - -if (vis != tvFull) - return; - -// now we're going to draw the lines between the blocks - -lastX = -1; -lastQEnd = 0; -lastLevel = 0; -qe = lastQEnd = 0; -prevSf = NULL; -for (sf = (struct snakeFeature *)lf->components; sf != NULL; lastQEnd = qe, prevSf = sf, sf = sf->next) - { - int y1, y2; - int sx, ex; - qs = sf->qStart; - qe = sf->qEnd; - if (lastLevel == sf->level) - { - y1 = offY + (lastLevel * 2) * lineHeight + lineHeight/2; - y2 = offY + (sf->level * 2) * lineHeight + lineHeight/2; - } - else if (lastLevel > sf->level) - { - y1 = offY + (lastLevel * 2 ) * lineHeight; - y2 = offY + (sf->level * 2 + 1) * lineHeight + lineHeight/3; - } - else - { - y1 = offY + (lastLevel * 2 + 1) * lineHeight - 1; - y2 = offY + (sf->level * 2 ) * lineHeight - lineHeight/3;; - } - s = sf->start; e = sf->end; - - sx = round((double)((int)s-winStart)*scale) + xOff; - ex = round((double)((int)e-winStart)*scale) + xOff; - color = (sf->orientation == -1) ? MG_RED : MG_BLUE; - - if (lastX != -1) - { - char buffer[1024]; -#define MG_ORANGE 0xff0082E6 - int color = MG_GRAY; - - if (lastQEnd != qs) { - long long queryInsertSize = llabs(lastQEnd - qs); - if (queryInsertSize > 100) - color = MG_ORANGE; - } - double queryGapNFrac = 0.0; - double queryGapMaskedFrac = 0.0; - - // draw the vertical orange bars if there is an insert in the other sequence - if ((winBaseCount < showSnpWidth) ) - { - if ((sf->orientation == 1) && (qs != lastQEnd) && (lastE == s)) - { - hvGfxLine(hvg, sx, y2 - lineHeight/2 , sx, y2 + lineHeight/2, MG_ORANGE); - safef(buffer, sizeof buffer, "%dbp (%.1lf%% N, %.1lf%% masked)", qs - lastQEnd, queryGapNFrac*100, queryGapMaskedFrac*100); - boundMapBox(hvg, s, e, sx, y2 - lineHeight/2, 1, lineHeight, tg->track, - "foo", buffer, NULL, TRUE, NULL); - safef(buffer, sizeof buffer, "%dbp", qs - lastQEnd); - //hvGfxTextCentered(hvg, sx - 10, y2 + lineHeight/2, 20, INSERT_TEXT_HEIGHT, MG_ORANGE, font, buffer); - } - else if ((sf->orientation == -1) && (qs != lastQEnd) && (lastS == e)) - { - hvGfxLine(hvg, ex, y2 - lineHeight/2 , ex, y2 + lineHeight/2, MG_ORANGE); - safef(buffer, sizeof buffer, "%dbp (%.1lf%% N, %.1lf%% masked)", qs - lastQEnd, queryGapNFrac*100, queryGapMaskedFrac*100); - boundMapBox(hvg, s, e, ex, y2 - lineHeight/2, 1, lineHeight, tg->track, - "foo", buffer, NULL, TRUE, NULL); - safef(buffer, sizeof buffer, "%dbp", qs - lastQEnd); - //hvGfxTextCentered(hvg, ex - 10, y2 + lineHeight/2, 20, INSERT_TEXT_HEIGHT, MG_ORANGE, font, buffer); - } - } - - // now draw the lines between blocks - if ((!((lastX == sx) && (y1 == y2))) && - (sf->drawn || ((prevSf != NULL) && (prevSf->drawn))) && - (((lastE >= winStart) && (lastE <= winEnd)) || - ((s > winStart) && (s < winEnd)))) - { - if (lastLevel == sf->level) - { - if (sf->orientation == 1) - safef(buffer, sizeof buffer, "%dbp (%dbp in ref) (%.1lf%% N, %.1lf%% masked)", qs - lastQEnd, s - lastE, queryGapNFrac*100, queryGapMaskedFrac*100); - else - safef(buffer, sizeof buffer, "%dbp (%dbp in ref) (%.1lf%% N, %.1lf%% masked)", qs - lastQEnd, lastS - e, queryGapNFrac*100, queryGapMaskedFrac*100); - if (sf->orientation == -1) - { - if (lastX != ex) - { - hvGfxLine(hvg, ex, y1, lastX, y2, color); - boundMapBox(hvg, s, e, ex, y1, lastX-ex, 1, tg->track, - "", buffer, NULL, TRUE, NULL); - if (lastQEnd != qs) { - safef(buffer, sizeof buffer, "%dbp", qs - lastQEnd); - //hvGfxTextCentered(hvg, ex, y2 + lineHeight/2, lastX-ex, INSERT_TEXT_HEIGHT, MG_ORANGE, font, buffer); - } - } - } - else - { - if (lastX != sx) - { - hvGfxLine(hvg, lastX, y1, sx, y2, color); - boundMapBox(hvg, s, e, lastX, y1, sx-lastX, 1, tg->track, - "", buffer, NULL, TRUE, NULL); - if (lastQEnd != qs) { - safef(buffer, sizeof buffer, "%dbp", qs - lastQEnd); - //hvGfxTextCentered(hvg, lastX, y2 + lineHeight/2, sx-lastX, INSERT_TEXT_HEIGHT, MG_ORANGE, font, buffer); - } - } - } - } - else if (lastLevel > sf->level) - { - hvGfxLine(hvg, lastX, y1, sx, y2, color); - hvGfxLine(hvg, sx, y2, sx, y2 - lineHeight - lineHeight/3, color); - char buffer[1024]; - safef(buffer, sizeof buffer, "%d-%d %dbp gap (%.1lf%% N, %.1lf%% masked)",prevSf->qStart,prevSf->qEnd, qs - lastQEnd, queryGapNFrac*100, queryGapMaskedFrac*100); - boundMapBox(hvg, s, e, sx, y2 - lineHeight - lineHeight/3, 2, lineHeight + lineHeight/3, tg->track, - "", buffer, NULL, TRUE, NULL); - safef(buffer, sizeof buffer, "%dbp", qs - lastQEnd); - //if (lastQEnd != qs) - //hvGfxTextCentered(hvg, sx - 10, y2 + lineHeight/2, 20, INSERT_TEXT_HEIGHT, MG_ORANGE, font, buffer); - - } - else - { - char buffer[1024]; - safef(buffer, sizeof buffer, "%d-%d %dbp gap (%.1lf%% N, %.1lf%% masked)",prevSf->qStart,prevSf->qEnd, qs - lastQEnd, queryGapNFrac*100, queryGapMaskedFrac*100); - if (sf->orientation == -1) - { - hvGfxLine(hvg, lastX-1, y1, ex, y2, color); - hvGfxLine(hvg, ex, y2, ex, y2 + lineHeight , color); - boundMapBox(hvg, s, e, ex-1, y2, 2, lineHeight , tg->track, - "", buffer, NULL, TRUE, NULL); - safef(buffer, sizeof buffer, "%dbp", qs - lastQEnd); - //if (lastQEnd != qs) - //hvGfxTextCentered(hvg, ex - 10, y2 + lineHeight, 20, INSERT_TEXT_HEIGHT, MG_ORANGE, font, buffer); - } - else - { - hvGfxLine(hvg, lastX-1, y1, sx, y2, color); - hvGfxLine(hvg, sx, y2, sx, y2 + lineHeight , color); - boundMapBox(hvg, s, e, sx-1, y2, 2, lineHeight , tg->track, - "", buffer, NULL, TRUE, NULL); - - safef(buffer, sizeof buffer, "%dbp", qs - lastQEnd); - //if (lastQEnd != qs) - //hvGfxTextCentered(hvg, sx - 10, y2 + lineHeight, 20, INSERT_TEXT_HEIGHT, MG_ORANGE, font, buffer); - } - } - } - } - if (sf->orientation == -1) - lastX = sx; - else - lastX = ex; - lastS = s; - lastE = e; - lastLevel = sf->level; - lastQEnd = qe; - } -} - -struct cartOptions - { - enum chainColorEnum chainColor; /* ChromColors, ScoreColors, NoColors */ - int scoreFilter ; /* filter chains by score if > 0 */ - }; - -static void fixItems(struct linkedFeatures *lf) -// put all chain blocks from a single query chromosome into one -// linkedFeatures structure -{ -struct linkedFeatures *firstLf, *next; -struct snakeFeature *sf, *nextSf; - -firstLf = lf; -for (;lf; lf = next) - { - next = lf->next; - if (!sameString(firstLf->name, lf->name) && (lf->components != NULL)) - { - slSort(&firstLf->components, snakeFeatureCmpQStart); - firstLf = lf; - } - for (sf = (struct snakeFeature *)lf->components; sf != NULL; sf = nextSf) - { - sf->qName = lf->name; - sf->orientation = lf->orientation; - nextSf = sf->next; - if (firstLf != lf) - { - lf->components = NULL; - slAddHead(&firstLf->components, sf); - } - } - } - -if (firstLf != NULL) - { - slSort(&firstLf->components, snakeFeatureCmpQStart); - firstLf->next = 0; - } -} - - -void snakeDrawLeftLabels() -{ -} - -static void makeSnakeFeatures(struct linkedFeatures *lf) -{ -for(; lf; lf = lf->next) - { - struct simpleFeature *sf = lf->components; - struct snakeFeature *sfList = NULL; - - for(;sf; sf = sf->next) - { - struct snakeFeature *this; - - AllocVar(this); - *(struct simpleFeature *)this = *sf; - /* - if ((lf) && lf->orientation == -1) - { - int temp; - - temp = this->qStart; - this->qStart = lf->qSize - this->qEnd; - this->qEnd = lf->qSize - temp; - } - */ - this->orientation = lf->orientation; - slAddHead(&sfList, this); - } - lf->components = (struct simpleFeature *)sfList; - } -} - -void maybeLoadSnake(struct track *track) -/* check to see if we're doing snakes and if so load the correct methods. */ -{ -boolean doSnake = cartOrTdbBoolean(cart, track->tdb, "doSnake", FALSE); -if (doSnake) - { - track->drawLeftLabels = snakeDrawLeftLabels; - track->itemHeight = snakeItemHeight; - track->totalHeight = snakeHeight; - track->drawItemAt = snakeDrawAt; - - slSort(track->items, linkedFeaturesCmpStart); - makeSnakeFeatures(track->items); - fixItems(track->items); - track->visibility = track->limitedVis = tvFull; - track->canPack = FALSE; - } -} -