From de763bedee23494035752c11abc5a62e26364e47 Mon Sep 17 00:00:00 2001 From: jgoecks Date: Sun, 26 Jun 2016 18:13:22 -0400 Subject: [PATCH] Initial commit to get working BBI reader into Trackster. --- client/galaxy/scripts/libs/bbi/bigwig.js | 1192 +++++++++ .../scripts/libs/bbi/jquery-ajax-native.js | 157 ++ client/galaxy/scripts/libs/bbi/jszlib.js | 2163 +++++++++++++++++ client/galaxy/scripts/libs/bbi/spans.js | 257 ++ client/galaxy/scripts/viz/bbi-data-manager.js | 60 + client/galaxy/scripts/viz/trackster/tracks.js | 32 +- static/maps/libs/bbi/bigwig.js.map | 1 + .../maps/libs/bbi/jquery-ajax-native.js.map | 1 + static/maps/libs/bbi/jszlib.js.map | 1 + static/maps/libs/bbi/spans.js.map | 1 + static/maps/viz/bbi-data-manager.js.map | 1 + static/maps/viz/trackster/tracks.js.map | 2 +- static/scripts/libs/bbi/bigwig.js | 2 + static/scripts/libs/bbi/jquery-ajax-native.js | 2 + static/scripts/libs/bbi/jszlib.js | 2 + static/scripts/libs/bbi/spans.js | 2 + static/scripts/viz/bbi-data-manager.js | 2 + static/scripts/viz/trackster/tracks.js | 4 +- 18 files changed, 3877 insertions(+), 5 deletions(-) create mode 100644 client/galaxy/scripts/libs/bbi/bigwig.js create mode 100644 client/galaxy/scripts/libs/bbi/jquery-ajax-native.js create mode 100644 client/galaxy/scripts/libs/bbi/jszlib.js create mode 100644 client/galaxy/scripts/libs/bbi/spans.js create mode 100644 client/galaxy/scripts/viz/bbi-data-manager.js create mode 100644 static/maps/libs/bbi/bigwig.js.map create mode 100644 static/maps/libs/bbi/jquery-ajax-native.js.map create mode 100644 static/maps/libs/bbi/jszlib.js.map create mode 100644 static/maps/libs/bbi/spans.js.map create mode 100644 static/maps/viz/bbi-data-manager.js.map create mode 100644 static/scripts/libs/bbi/bigwig.js create mode 100644 static/scripts/libs/bbi/jquery-ajax-native.js create mode 100644 static/scripts/libs/bbi/jszlib.js create mode 100644 static/scripts/libs/bbi/spans.js create mode 100644 static/scripts/viz/bbi-data-manager.js diff --git a/client/galaxy/scripts/libs/bbi/bigwig.js b/client/galaxy/scripts/libs/bbi/bigwig.js new file mode 100644 index 00000000000..e3b94e05deb --- /dev/null +++ b/client/galaxy/scripts/libs/bbi/bigwig.js @@ -0,0 +1,1192 @@ +// +// Author: Jeremy Goecks +// +// Modified from: +// +// Dalliance Genome Explorer +// (c) Thomas Down 2006-2010 +// +// bigwig.js: indexed binary WIG (and BED) files +// + +// Requirements: +// * jquery and ajax-native plugin for reading binary data, jquery for promises +// * spans for working working with genomic intervals +// * jszlib for decompression. +define(["libs/bbi/spans", "libs/bbi/jszlib", "libs/bbi/jquery-ajax-native"], function(spans, jszlib) { + "use strict"; + + // -- Copied from das.js -- + + function DASFeature() { + } + + function DASGroup(id) { + if (id) + this.id = id; + } + + // -- End copy -- + + // -- Copied from bin.js -- + + function readInt(ba, offset) { + return (ba[offset + 3] << 24) | (ba[offset + 2] << 16) | (ba[offset + 1] << 8) | (ba[offset]); + } + + // -- End copy -- + + // Some globals. + var Range = spans.Range; + var union = spans.union; + var intersection = spans.intersection; + + var jszlib_inflate_buffer = jszlib.inflateBuffer; + var arrayCopy = jszlib.arrayCopy; + + var BIG_WIG_MAGIC = 0x888FFC26; + var BIG_WIG_MAGIC_BE = 0x26FC8F88; + var BIG_BED_MAGIC = 0x8789F2EB; + var BIG_BED_MAGIC_BE = 0xEBF28987; + + + var BIG_WIG_TYPE_GRAPH = 1; + var BIG_WIG_TYPE_VSTEP = 2; + var BIG_WIG_TYPE_FSTEP = 3; + + var M1 = 256; + var M2 = 256*256; + var M3 = 256*256*256; + var M4 = 256*256*256*256; + + var BED_COLOR_REGEXP = new RegExp("^[0-9]+,[0-9]+,[0-9]+"); + + /** + * Read binary data from a URL using HTTP Range header. Requires jQuery and ajax-native plugin. + */ + function read(url, start, size) { + // Taken from bin.js: + // This may be necessary for Safari: + // if ((isSafari || this.opts.salt) && url.indexOf('?') < 0) { + // url = url + '?salt=' + b64_sha1('' + Date.now() + ',' + (++seed)); + // } + + var chunkSizeLimit = Math.pow(10, 6); // 1 MB + if(size > chunkSizeLimit) { + // TODO: raise error. + } + + // Read data from remote file. + return $.ajax({ + type: 'GET', + dataType: 'native', + url: url, + // Potential timeout on first request to catch mixed-content errors on Chromium. + timeout: 5000, + beforeSend: function(xhrObj) { + // (size - 1) because range is inclusive. + xhrObj.setRequestHeader("Range", "bytes=" + start + "-" + (start + (size - 1))); + }, + xhrFields: { + responseType: 'arraybuffer' + } + }); + } + + function bwg_readOffset(ba, o) { + var offset = ba[o] + ba[o+1]*M1 + ba[o+2]*M2 + ba[o+3]*M3 + ba[o+4]*M4; + return offset; + } + + function BigWig() { + } + + /** + * Read the chromosome B+ tree header. + */ + BigWig.prototype.readChromTree = function() { + var thisB = this; + this.chromsToIDs = {}; + this.idsToChroms = {}; + this.maxID = 0; + + var udo = this.unzoomedDataOffset; + var eb = (udo - this.chromTreeOffset) & 3; + udo = udo + 4 - eb; + + // Read and parse the chrom tree, return the promise so that subsequent actions can be taken. + return $.when(read(this.url, this.chromTreeOffset, udo - this.chromTreeOffset)).then(function(bpt) { + var ba = new Uint8Array(bpt); + var sa = new Int16Array(bpt); + var la = new Int32Array(bpt); + var bptMagic = la[0]; + var blockSize = la[1]; + var keySize = la[2]; + var valSize = la[3]; + var itemCount = bwg_readOffset(ba, 16); + var rootNodeOffset = 32; + + var bptReadNode = function(offset) { + var nodeType = ba[offset]; + var cnt = sa[(offset/2) + 1]; + offset += 4; + for (var n = 0; n < cnt; ++n) { + if (nodeType === 0) { + offset += keySize; + var childOffset = bwg_readOffset(ba, offset); + offset += 8; + childOffset -= thisB.chromTreeOffset; + bptReadNode(childOffset); + } else { + var key = ''; + for (var ki = 0; ki < keySize; ++ki) { + var charCode = ba[offset++]; + if (charCode !== 0) { + key += String.fromCharCode(charCode); + } + } + var chromId = (ba[offset+3]<<24) | (ba[offset+2]<<16) | (ba[offset+1]<<8) | (ba[offset+0]); + var chromSize = (ba[offset + 7]<<24) | (ba[offset+6]<<16) | (ba[offset+5]<<8) | (ba[offset+4]); + offset += 8; + + thisB.chromsToIDs[key] = chromId; + if (key.indexOf('chr') === 0) { + thisB.chromsToIDs[key.substr(3)] = chromId; + } + thisB.idsToChroms[chromId] = key; + thisB.maxID = Math.max(thisB.maxID, chromId); + } + } + }; + bptReadNode(rootNodeOffset); + }); + } + + function BigWigView(bwg, cirTreeOffset, cirTreeLength, isSummary) { + this.bwg = bwg; + this.cirTreeOffset = cirTreeOffset; + this.cirTreeLength = cirTreeLength; + this.isSummary = isSummary; + } + + + + BigWigView.prototype.readWigData = function(chrName, min, max) { + var chr = this.bwg.chromsToIDs[chrName], + rval; + if (chr === undefined) { + // Not an error because some .bwgs won't have data for all chromosomes. + rval = []; + } else { + rval = this.readWigDataById(chr, min, max); + } + + return rval; + }; + + BigWigView.prototype.readWigDataById = function(chr, min, max) { + var thisB = this, + promise = $.Deferred(); + + // Read the R-tree index header and then read data again. + if (!this.cirHeader) { + $.when(read(thisB.bwg.url, this.cirTreeOffset, 48)).then(function(result) { + thisB.cirHeader = result; + var la = new Int32Array(thisB.cirHeader); + thisB.cirBlockSize = la[1]; + $.when(thisB.readWigDataById(chr, min, max)).then(function(result) { + promise.resolve(result); + }); + }); + return promise; + } + + var blocksToFetch = []; + var outstanding = 0; + + var beforeBWG = Date.now(); + + var filter = function(chromId, fmin, fmax, toks) { + return ((chr < 0 || chromId == chr) && fmin <= max && fmax >= min); + }; + + var cirFobRecur = function(offset, level) { + if (thisB.bwg.instrument) + console.log('level=' + level + '; offset=' + offset + '; time=' + (Date.now()|0)); + + outstanding += offset.length; + + if (offset.length == 1 && offset[0] - thisB.cirTreeOffset == 48 && thisB.cachedCirRoot) { + cirFobRecur2(thisB.cachedCirRoot, 0, level); + --outstanding; + if (outstanding === 0) { + $.when(thisB.fetchFeatures(filter, blocksToFetch)).then(function(result) { + promise.resolve(result); + }); + } + return; + } + + var maxCirBlockSpan = 4 + (thisB.cirBlockSize * 32); // Upper bound on size, based on a completely full leaf node. + var spans; + for (var i = 0; i < offset.length; ++i) { + var blockSpan = new Range(offset[i], offset[i] + maxCirBlockSpan); + spans = spans ? union(spans, blockSpan) : blockSpan; + } + + var fetchRanges = spans.ranges(); + for (var r = 0; r < fetchRanges.length; ++r) { + var fr = fetchRanges[r]; + cirFobStartFetch(offset, fr, level); + } + }; + + var cirFobStartFetch = function(offset, fr, level, attempts) { + var length = fr.max() - fr.min(); + $.when(read(thisB.bwg.url, fr.min(), fr.max() - fr.min())).then(function(resultBuffer) { + for (var i = 0; i < offset.length; ++i) { + if (fr.contains(offset[i])) { + cirFobRecur2(resultBuffer, offset[i] - fr.min(), level); + + if (offset[i] - thisB.cirTreeOffset == 48 && offset[i] - fr.min() === 0) + thisB.cachedCirRoot = resultBuffer; + + --outstanding; + if (outstanding === 0) { + $.when(thisB.fetchFeatures(filter, blocksToFetch)).then(function(result) { + promise.resolve(result); + }); + } + } + } + }); + }; + + var cirFobRecur2 = function(cirBlockData, offset, level) { + var ba = new Uint8Array(cirBlockData); + var sa = new Int16Array(cirBlockData); + var la = new Int32Array(cirBlockData); + + var isLeaf = ba[offset]; + var cnt = sa[offset/2 + 1]; + offset += 4; + + if (isLeaf !== 0) { + for (var i = 0; i < cnt; ++i) { + var lo = offset/4; + var startChrom = la[lo]; + var startBase = la[lo + 1]; + var endChrom = la[lo + 2]; + var endBase = la[lo + 3]; + var blockOffset = bwg_readOffset(ba, offset+16); + var blockSize = bwg_readOffset(ba, offset+24); + if (((chr < 0 || startChrom < chr) || (startChrom == chr && startBase <= max)) && + ((chr < 0 || endChrom > chr) || (endChrom == chr && endBase >= min))) + { + blocksToFetch.push({offset: blockOffset, size: blockSize}); + } + offset += 32; + } + } else { + var recurOffsets = []; + for (var i = 0; i < cnt; ++i) { + var lo = offset/4; + var startChrom = la[lo]; + var startBase = la[lo + 1]; + var endChrom = la[lo + 2]; + var endBase = la[lo + 3]; + var blockOffset = bwg_readOffset(ba, offset+16); + if ((chr < 0 || startChrom < chr || (startChrom == chr && startBase <= max)) && + (chr < 0 || endChrom > chr || (endChrom == chr && endBase >= min))) + { + recurOffsets.push(blockOffset); + } + offset += 24; + } + if (recurOffsets.length > 0) { + cirFobRecur(recurOffsets, level + 1); + } + } + }; + + cirFobRecur([thisB.cirTreeOffset + 48], 1); + return promise; + }; + + /** + * Fetch data for a set of blocks. Returns a promise that resolves to fetched data. + */ + BigWigView.prototype.fetchFeatures = function(filter, blocksToFetch) { + var thisB = this, + promise = $.Deferred(); + + blocksToFetch.sort(function(b0, b1) { + return (b0.offset|0) - (b1.offset|0); + }); + + if (blocksToFetch.length === 0) { + return []; + } else { + var features = []; + var createFeature = function(chr, fmin, fmax, opts) { + if (!opts) { + opts = {}; + } + + var f = new DASFeature(); + f._chromId = chr; + f.segment = thisB.bwg.idsToChroms[chr]; + f.min = fmin; + f.max = fmax; + f.type = thisB.bwg.type; + + for (var k in opts) { + f[k] = opts[k]; + } + + features.push(f); + }; + + // Recursive function to read blocks of data. + var tramp = function() { + if (blocksToFetch.length === 0) { + var afterBWG = Date.now(); + // dlog('BWG fetch took ' + (afterBWG - beforeBWG) + 'ms'); + return promise.resolve(features); + } + else { + var block = blocksToFetch[0]; + if (block.data) { + thisB.parseFeatures(block.data, createFeature, filter); + blocksToFetch.splice(0, 1); + tramp(); + } + else { + var fetchStart = block.offset; + var fetchSize = block.size; + var bi = 1; + while (bi < blocksToFetch.length && blocksToFetch[bi].offset == (fetchStart + fetchSize)) { + fetchSize += blocksToFetch[bi].size; + ++bi; + } + + $.when(read(thisB.bwg.url, fetchStart, fetchSize)).then(function(result) { + var offset = 0; + var bi = 0; + while (offset < fetchSize) { + var fb = blocksToFetch[bi]; + + var data; + if (thisB.bwg.uncompressBufSize > 0) { + data = jszlib_inflate_buffer(result, offset + 2, fb.size - 2); + } else { + var tmp = new Uint8Array(fb.size); // FIXME is this really the best we can do? + arrayCopy(new Uint8Array(result, offset, fb.size), 0, tmp, 0, fb.size); + data = tmp.buffer; + } + fb.data = data; + + offset += fb.size; + ++bi; + } + tramp(); + }); + } + } + }; + tramp(); + } + + return promise; + }; + + BigWigView.prototype.parseFeatures = function(data, createFeature, filter) { + var ba = new Uint8Array(data); + + if (this.isSummary) { + var sa = new Int16Array(data); + var la = new Int32Array(data); + var fa = new Float32Array(data); + + var itemCount = data.byteLength/32; + for (var i = 0; i < itemCount; ++i) { + var chromId = la[(i*8)]; + var start = la[(i*8)+1]; + var end = la[(i*8)+2]; + var validCnt = la[(i*8)+3]; + var minVal = fa[(i*8)+4]; + var maxVal = fa[(i*8)+5]; + var sumData = fa[(i*8)+6]; + var sumSqData = fa[(i*8)+7]; + + if (filter(chromId, start + 1, end)) { + var summaryOpts = {type: 'bigwig', score: sumData/validCnt, maxScore: maxVal}; + if (this.bwg.type == 'bigbed') { + summaryOpts.type = 'density'; + } + createFeature(chromId, start + 1, end, summaryOpts); + } + } + } + else if (this.bwg.type == 'bigwig') { + var sa = new Int16Array(data); + var la = new Int32Array(data); + var fa = new Float32Array(data); + + var chromId = la[0]; + var blockStart = la[1]; + var blockEnd = la[2]; + var itemStep = la[3]; + var itemSpan = la[4]; + var blockType = ba[20]; + var itemCount = sa[11]; + + if (blockType == BIG_WIG_TYPE_FSTEP) { + for (var i = 0; i < itemCount; ++i) { + var score = fa[i + 6]; + var fmin = blockStart + (i*itemStep) + 1, fmax = blockStart + (i*itemStep) + itemSpan; + if (filter(chromId, fmin, fmax)) + createFeature(chromId, fmin, fmax, {score: score}); + } + } else if (blockType == BIG_WIG_TYPE_VSTEP) { + for (var i = 0; i < itemCount; ++i) { + var start = la[(i*2) + 6] + 1; + var end = start + itemSpan - 1; + var score = fa[(i*2) + 7]; + if (filter(chromId, start, end)) + createFeature(chromId, start, end, {score: score}); + } + } else if (blockType == BIG_WIG_TYPE_GRAPH) { + for (var i = 0; i < itemCount; ++i) { + var start = la[(i*3) + 6] + 1; + var end = la[(i*3) + 7]; + var score = fa[(i*3) + 8]; + if (start > end) { + start = end; + } + if (filter(chromId, start, end)) + createFeature(chromId, start, end, {score: score}); + } + } else { + console.log('Currently not handling bwgType=' + blockType); + } + } else if (this.bwg.type == 'bigbed') { + var offset = 0; + var dfc = this.bwg.definedFieldCount; + var schema = this.bwg.schema; + + while (offset < ba.length) { + var chromId = (ba[offset+3]<<24) | (ba[offset+2]<<16) | (ba[offset+1]<<8) | (ba[offset+0]); + var start = (ba[offset+7]<<24) | (ba[offset+6]<<16) | (ba[offset+5]<<8) | (ba[offset+4]); + var end = (ba[offset+11]<<24) | (ba[offset+10]<<16) | (ba[offset+9]<<8) | (ba[offset+8]); + offset += 12; + var rest = ''; + while (true) { + var ch = ba[offset++]; + if (ch != 0) { + rest += String.fromCharCode(ch); + } else { + break; + } + } + + var featureOpts = {}; + + var bedColumns; + if (rest.length > 0) { + bedColumns = rest.split('\t'); + } else { + bedColumns = []; + } + if (bedColumns.length > 0 && dfc > 3) { + featureOpts.label = bedColumns[0]; + } + if (bedColumns.length > 1 && dfc > 4) { + var score = parseInt(bedColumns[1]); + if (!isNaN(score)) + featureOpts.score = score; + } + if (bedColumns.length > 2 && dfc > 5) { + featureOpts.orientation = bedColumns[2]; + } + if (bedColumns.length > 5 && dfc > 8) { + var color = bedColumns[5]; + if (BED_COLOR_REGEXP.test(color)) { + featureOpts.itemRgb = 'rgb(' + color + ')'; + } + } + + if (bedColumns.length > dfc-3 && schema) { + for (var col = dfc - 3; col < bedColumns.length; ++col) { + featureOpts[schema.fields[col+3].name] = bedColumns[col]; + } + } + + if (filter(chromId, start + 1, end, bedColumns)) { + if (dfc < 12) { + createFeature(chromId, start + 1, end, featureOpts); + } else { + // TODO: add block starts, sizes, thick start, thick end to feature. + var thickStart = bedColumns[3]|0; + var thickEnd = bedColumns[4]|0; + var blockCount = bedColumns[6]|0; + var blockSizes = bedColumns[7].split(','); + var blockStarts = bedColumns[8].split(','); + + if (featureOpts.exonFrames) { + var exonFrames = featureOpts.exonFrames.split(','); + featureOpts.exonFrames = undefined; + } + + featureOpts.type = 'transcript' + var grp = new DASGroup(); + for (var k in featureOpts) { + grp[k] = featureOpts[k]; + } + grp.id = bedColumns[0]; + grp.segment = this.bwg.idsToChroms[chromId]; + grp.min = start + 1; + grp.max = end; + grp.notes = []; + featureOpts.groups = [grp]; + + // Moving towards using bigGenePred model, but will + // still support old Dalliance-style BED12+gene-name for the + // foreseeable future. + if (bedColumns.length > 9) { + var geneId = featureOpts.geneName || bedColumns[9]; + var geneName = geneId; + if (bedColumns.length > 10) { + geneName = bedColumns[10]; + } + if (featureOpts.geneName2) + geneName = featureOpts.geneName2; + + var gg = $.extend({}, grp); + gg.id = geneId; + gg.label = geneName; + gg.type = 'gene'; + featureOpts.groups.push(gg); + } + + var spanList = []; + for (var b = 0; b < blockCount; ++b) { + var bmin = (blockStarts[b]|0) + start; + var bmax = bmin + (blockSizes[b]|0); + var span = new Range(bmin, bmax); + spanList.push(span); + } + var spans = union(spanList); + + var tsList = spans.ranges(); + for (var s = 0; s < tsList.length; ++s) { + var ts = tsList[s]; + createFeature(chromId, ts.min() + 1, ts.max(), featureOpts); + } + + if (thickEnd > thickStart) { + var codingRegion = (featureOpts.orientation == '+') ? + new Range(thickStart, thickEnd + 3) : + new Range(thickStart - 3, thickEnd); + // +/- 3 to account for stop codon + + var tl = intersection(spans, codingRegion); + if (tl) { + featureOpts.type = 'translation'; + var tlList = tl.ranges(); + var readingFrame = 0; + + var tlOffset = 0; + while (tlList[0].min() > tsList[tlOffset].max()) + tlOffset++; + + for (var s = 0; s < tlList.length; ++s) { + // Record reading frame for every exon + var index = s; + if (featureOpts.orientation == '-') + index = tlList.length - s - 1; + var ts = tlList[index]; + featureOpts.readframe = readingFrame; + if (exonFrames) { + var brf = parseInt(exonFrames[index + tlOffset]); + if (typeof(brf) === 'number' && brf >= 0 && brf <= 2) { + featureOpts.readframe = brf; + featureOpts.readframeExplicit = true; + } + } + var length = ts.max() - ts.min(); + readingFrame = (readingFrame + length) % 3; + createFeature(chromId, ts.min() + 1, ts.max(), featureOpts); + } + } + } + } + } + } + } else { + throw Error("Don't know what to do with " + this.bwg.type); + } + } + + // + // nasty cut/paste, should roll back in! + // + + BigWigView.prototype.getFirstAdjacent = function(chrName, pos, dir, callback) { + var chr = this.bwg.chromsToIDs[chrName]; + if (chr === undefined) { + // Not an error because some .bwgs won't have data for all chromosomes. + return callback([]); + } else { + this.getFirstAdjacentById(chr, pos, dir, callback); + } + } + + BigWigView.prototype.getFirstAdjacentById = function(chr, pos, dir, callback) { + var thisB = this; + if (!this.cirHeader) { + this.bwg.data.slice(this.cirTreeOffset, 48).fetch(function(result) { + thisB.cirHeader = result; + var la = new Int32Array(thisB.cirHeader); + thisB.cirBlockSize = la[1]; + thisB.getFirstAdjacentById(chr, pos, dir, callback); + }); + return; + } + + var blockToFetch = null; + var bestBlockChr = -1; + var bestBlockOffset = -1; + + var outstanding = 0; + + var beforeBWG = Date.now(); + + var cirFobRecur = function(offset, level) { + outstanding += offset.length; + + var maxCirBlockSpan = 4 + (thisB.cirBlockSize * 32); // Upper bound on size, based on a completely full leaf node. + var spans; + for (var i = 0; i < offset.length; ++i) { + var blockSpan = new Range(offset[i], offset[i] + maxCirBlockSpan); + spans = spans ? union(spans, blockSpan) : blockSpan; + } + + var fetchRanges = spans.ranges(); + for (var r = 0; r < fetchRanges.length; ++r) { + var fr = fetchRanges[r]; + cirFobStartFetch(offset, fr, level); + } + } + + var cirFobStartFetch = function(offset, fr, level, attempts) { + var length = fr.max() - fr.min(); + thisB.bwg.data.slice(fr.min(), fr.max() - fr.min()).fetch(function(resultBuffer) { + for (var i = 0; i < offset.length; ++i) { + if (fr.contains(offset[i])) { + cirFobRecur2(resultBuffer, offset[i] - fr.min(), level); + --outstanding; + if (outstanding == 0) { + if (!blockToFetch) { + if (dir > 0 && (chr != 0 || pos > 0)) { + return thisB.getFirstAdjacentById(0, 0, dir, callback); + } else if (dir < 0 && (chr != thisB.bwg.maxID || pos < 1000000000)) { + return thisB.getFirstAdjacentById(thisB.bwg.maxID, 1000000000, dir, callback); + } + return callback([]); + } + + thisB.fetchFeatures(function(chrx, fmin, fmax, toks) { + return (dir < 0 && (chrx < chr || fmax < pos)) || (dir > 0 && (chrx > chr || fmin > pos)); + }, [blockToFetch], function(features) { + var bestFeature = null; + var bestChr = -1; + var bestPos = -1; + for (var fi = 0; fi < features.length; ++fi) { + var f = features[fi]; + var chrx = f._chromId, fmin = f.min, fmax = f.max; + if (bestFeature == null || ((dir < 0) && (chrx > bestChr || fmax > bestPos)) || ((dir > 0) && (chrx < bestChr || fmin < bestPos))) { + bestFeature = f; + bestPos = (dir < 0) ? fmax : fmin; + bestChr = chrx; + } + } + + if (bestFeature != null) + return callback([bestFeature]); + else + return callback([]); + }); + } + } + } + }); + } + + var cirFobRecur2 = function(cirBlockData, offset, level) { + var ba = new Uint8Array(cirBlockData); + var sa = new Int16Array(cirBlockData); + var la = new Int32Array(cirBlockData); + + var isLeaf = ba[offset]; + var cnt = sa[offset/2 + 1]; + offset += 4; + + if (isLeaf != 0) { + for (var i = 0; i < cnt; ++i) { + var lo = offset/4; + var startChrom = la[lo]; + var startBase = la[lo + 1]; + var endChrom = la[lo + 2]; + var endBase = la[lo + 3]; + var blockOffset = bwg_readOffset(ba, offset+16); + var blockSize = bwg_readOffset(ba, offset+24); + if ((dir < 0 && ((startChrom < chr || (startChrom == chr && startBase <= pos)))) || + (dir > 0 && ((endChrom > chr || (endChrom == chr && endBase >= pos))))) + { + // console.log('Got an interesting block: startBase=' + startChrom + ':' + startBase + '; endBase=' + endChrom + ':' + endBase + '; offset=' + blockOffset + '; size=' + blockSize); + if (/_random/.exec(thisB.bwg.idsToChroms[startChrom])) { + // dlog('skipping random: ' + thisB.bwg.idsToChroms[startChrom]); + } else if (blockToFetch == null || ((dir < 0) && (endChrom > bestBlockChr || (endChrom == bestBlockChr && endBase > bestBlockOffset)) || + (dir > 0) && (startChrom < bestBlockChr || (startChrom == bestBlockChr && startBase < bestBlockOffset)))) + { + // dlog('best is: startBase=' + startChrom + ':' + startBase + '; endBase=' + endChrom + ':' + endBase + '; offset=' + blockOffset + '; size=' + blockSize); + blockToFetch = {offset: blockOffset, size: blockSize}; + bestBlockOffset = (dir < 0) ? endBase : startBase; + bestBlockChr = (dir < 0) ? endChrom : startChrom; + } + } + offset += 32; + } + } else { + var bestRecur = -1; + var bestPos = -1; + var bestChr = -1; + for (var i = 0; i < cnt; ++i) { + var lo = offset/4; + var startChrom = la[lo]; + var startBase = la[lo + 1]; + var endChrom = la[lo + 2]; + var endBase = la[lo + 3]; + var blockOffset = (la[lo + 4]<<32) | (la[lo + 5]); + if ((dir < 0 && ((startChrom < chr || (startChrom == chr && startBase <= pos)) && + (endChrom >= chr))) || + (dir > 0 && ((endChrom > chr || (endChrom == chr && endBase >= pos)) && + (startChrom <= chr)))) + { + if (bestRecur < 0 || endBase > bestPos) { + bestRecur = blockOffset; + bestPos = (dir < 0) ? endBase : startBase; + bestChr = (dir < 0) ? endChrom : startChrom; + } + } + offset += 24; + } + if (bestRecur >= 0) { + cirFobRecur([bestRecur], level + 1); + } + } + }; + + + cirFobRecur([thisB.cirTreeOffset + 48], 1); + } + + /** + * Automatically choose a zoom level and return data from that level. + */ + BigWig.prototype.readWigData = function(chrName, min, max) { + // Maximum number of data points to return when reading a bigwig. This is used + // to choose the appropriate level. One data point ~= 25-65 bytes. + // FIXME: For targeted sequencing, data points returned is going to be much lower, + // so this will need to be tuned appropriately. + var MAX_DATA_POINTS = 25000; + + var range = max - min, + view; + // If no zooming needed or available (common in bigbed), use unzoomed view. + if (range <= MAX_DATA_POINTS || this.zoomLevels.length === 0) { + view = this.getUnzoomedView(); + console.log("zoomLevel unzoomed"); + } + else { + // Find reasonable zoom level. Reduction is the # of bases represented + // by each data point at that level. + for (var i = 0; i < this.zoomLevels.length; i++) { + if (range/this.zoomLevels[i].reduction < MAX_DATA_POINTS) { + view = this.getZoomedView(i); + console.log("zoomLevel", i); + break; + } + } + } + + return view.readWigData(chrName, min, max); + } + + BigWig.prototype.getUnzoomedView = function() { + if (!this.unzoomedView) { + var cirLen = 4000; + var nzl = this.zoomLevels[0]; + if (nzl) { + cirLen = this.zoomLevels[0].dataOffset - this.unzoomedIndexOffset; + } + this.unzoomedView = new BigWigView(this, this.unzoomedIndexOffset, cirLen, false); + } + return this.unzoomedView; + } + + BigWig.prototype.getZoomedView = function(z) { + var zh = this.zoomLevels[z]; + if (!zh.view) { + zh.view = new BigWigView(this, zh.indexOffset, /* this.zoomLevels[z + 1].dataOffset - zh.indexOffset */ 4000, true); + } + return zh.view; + } + + /** + * Create a BigWig object using a URL to a bigwig/bigbed file. Returns a promise + * that resolves to the object when it's available. + */ + function makeBwg(url) { + var promise = $.Deferred(), + bwg = new BigWig(); + bwg.url = url; + + // Read and parse bigwig header, including chrom tree. + $.when(read(bwg.url, 0, 512)).then(function(result) { + if (!result) { + return promise.resolve(null, "Couldn't fetch file"); + } + + var header = result; + var ba = new Uint8Array(header); + var sa = new Int16Array(header); + var la = new Int32Array(header); + var magic = ba[0] + (M1 * ba[1]) + (M2 * ba[2]) + (M3 * ba[3]); + if (magic == BIG_WIG_MAGIC) { + bwg.type = 'bigwig'; + } else if (magic == BIG_BED_MAGIC) { + bwg.type = 'bigbed'; + } else if (magic == BIG_WIG_MAGIC_BE || magic == BIG_BED_MAGIC_BE) { + return promise.resolve(null, "Currently don't support big-endian BBI files"); + + } else { + return promise.resolve(null, "Not a supported format, magic=0x" + magic.toString(16)); + + } + + bwg.version = sa[2]; // 4 + bwg.numZoomLevels = sa[3]; // 6 + bwg.chromTreeOffset = bwg_readOffset(ba, 8); + bwg.unzoomedDataOffset = bwg_readOffset(ba, 16); + bwg.unzoomedIndexOffset = bwg_readOffset(ba, 24); + bwg.fieldCount = sa[16]; // 32 + bwg.definedFieldCount = sa[17]; // 34 + bwg.asOffset = bwg_readOffset(ba, 36); + bwg.totalSummaryOffset = bwg_readOffset(ba, 44); + bwg.uncompressBufSize = la[13]; // 52 + bwg.extHeaderOffset = bwg_readOffset(ba, 56); + + bwg.zoomLevels = []; + for (var zl = 0; zl < bwg.numZoomLevels; ++zl) { + var zlReduction = la[zl*6 + 16] + var zlData = bwg_readOffset(ba, zl*24 + 72); + var zlIndex = bwg_readOffset(ba, zl*24 + 80); + bwg.zoomLevels.push({reduction: zlReduction, dataOffset: zlData, indexOffset: zlIndex}); + } + + $.when(bwg.readChromTree()).then(function() { + bwg.getAutoSQL(function(as) { + bwg.schema = as; + return promise.resolve(bwg); + }); + }); + }); + + return promise; + } + + + BigWig.prototype._tsFetch = function(zoom, chr, min, max, callback) { + var bwg = this; + if (zoom >= this.zoomLevels.length - 1) { + if (!this.topLevelReductionCache) { + this.getZoomedView(this.zoomLevels.length - 1).readWigDataById(-1, 0, 300000000, function(feats) { + bwg.topLevelReductionCache = feats; + return bwg._tsFetch(zoom, chr, min, max, callback); + }); + } else { + var f = []; + var c = this.topLevelReductionCache; + for (var fi = 0; fi < c.length; ++fi) { + if (c[fi]._chromId == chr) { + f.push(c[fi]); + } + } + return callback(f); + } + } else { + var view; + if (zoom < 0) { + view = this.getUnzoomedView(); + } else { + view = this.getZoomedView(zoom); + } + return view.readWigDataById(chr, min, max, callback); + } + } + + BigWig.prototype.thresholdSearch = function(chrName, referencePoint, dir, threshold, callback) { + dir = (dir<0) ? -1 : 1; + var bwg = this; + var initialChr = this.chromsToIDs[chrName]; + var candidates = [{chrOrd: 0, chr: initialChr, zoom: bwg.zoomLevels.length - 4, min: 0, max: 300000000, fromRef: true}] + for (var i = 1; i <= this.maxID + 1; ++i) { + var chrId = (initialChr + (dir*i)) % (this.maxID + 1); + if (chrId < 0) + chrId += (this.maxID + 1); + candidates.push({chrOrd: i, chr: chrId, zoom: bwg.zoomLevels.length - 1, min: 0, max: 300000000}) + } + + function fbThresholdSearchRecur() { + if (candidates.length == 0) { + return callback(null); + } + candidates.sort(function(c1, c2) { + var d = c1.zoom - c2.zoom; + if (d != 0) + return d; + + d = c1.chrOrd - c2.chrOrd; + if (d != 0) + return d; + else + return c1.min - c2.min * dir; + }); + + var candidate = candidates.splice(0, 1)[0]; + bwg._tsFetch(candidate.zoom, candidate.chr, candidate.min, candidate.max, function(feats) { + var rp = dir > 0 ? 0 : 300000000; + if (candidate.fromRef) + rp = referencePoint; + + for (var fi = 0; fi < feats.length; ++fi) { + var f = feats[fi]; + var score; + if (f.maxScore != undefined) + score = f.maxScore; + else + score = f.score; + + if (dir > 0) { + if (score > threshold) { + if (candidate.zoom < 0) { + if (f.min > rp) + return callback(f); + } else if (f.max > rp) { + candidates.push({chr: candidate.chr, chrOrd: candidate.chrOrd, zoom: candidate.zoom - 2, min: f.min, max: f.max, fromRef: candidate.fromRef}); + } + } + } else { + if (score > threshold) { + if (candidate.zoom < 0) { + if (f.max < rp) + return callback(f); + } else if (f.min < rp) { + candidates.push({chr: candidate.chr, chrOrd: candidate.chrOrd, zoom: candidate.zoom - 2, min: f.min, max: f.max, fromRef: candidate.fromRef}); + } + } + } + } + fbThresholdSearchRecur(); + }); + } + + fbThresholdSearchRecur(); + } + + BigWig.prototype.getAutoSQL = function(callback) { + var thisB = this; + if (!this.asOffset) + return callback(null); + + $.when(read(this.url, this.asOffset, 2048)).then(function(result) { + var ba = new Uint8Array(result); + var s = ''; + for (var i = 0; i < ba.length; ++i) { + if (ba[i] == 0) + break; + s += String.fromCharCode(ba[i]); + } + + /* + * Quick'n'dirty attempt to parse autoSql format. + * See: http://www.linuxjournal.com/files/linuxjournal.com/linuxjournal/articles/059/5949/5949l2.html + */ + + var header_re = /(\w+)\s+(\w+)\s+("([^"]+)")?\s+\(\s*/; + var field_re = /([\w\[\]]+)\s+(\w+)\s*;\s*("([^"]+)")?\s*/g; + + var headerMatch = header_re.exec(s); + if (headerMatch) { + var as = { + declType: headerMatch[1], + name: headerMatch[2], + comment: headerMatch[4], + + fields: [] + }; + + s = s.substring(headerMatch[0]); + for (var m = field_re.exec(s); m != null; m = field_re.exec(s)) { + as.fields.push({type: m[1], + name: m[2], + comment: m[4]}); + } + + return callback(as); + } + }); + }; + + BigWig.prototype.getExtraIndices = function(callback) { + var thisB = this; + if (this.version < 4 || this.extHeaderOffset == 0 || this.type != 'bigbed') { + return callback(null); + } else { + this.data.slice(this.extHeaderOffset, 64).fetch(function(result) { + if (!result) { + return callback(null, "Couldn't fetch extension header"); + } + + var ba = new Uint8Array(result); + var sa = new Int16Array(result); + var la = new Int32Array(result); + + var extHeaderSize = sa[0]; + var extraIndexCount = sa[1]; + var extraIndexListOffset = bwg_readOffset(ba, 4); + + if (extraIndexCount == 0) { + return callback(null); + } + + // FIXME 20byte records only make sense for single-field indices. + // Right now, these seem to be the only things around, but the format + // is actually more general. + thisB.data.slice(extraIndexListOffset, extraIndexCount * 20).fetch(function(eil) { + if (!eil) { + return callback(null, "Couldn't fetch index info"); + } + + var ba = new Uint8Array(eil); + var sa = new Int16Array(eil); + var la = new Int32Array(eil); + + var indices = []; + for (var ii = 0; ii < extraIndexCount; ++ii) { + var eiType = sa[ii*10]; + var eiFieldCount = sa[ii*10 + 1]; + var eiOffset = bwg_readOffset(ba, ii*20 + 4); + var eiField = sa[ii*10 + 8] + var index = new BBIExtraIndex(thisB, eiType, eiFieldCount, eiOffset, eiField); + indices.push(index); + } + callback(indices); + }); + }); + } + } + + function BBIExtraIndex(bbi, type, fieldCount, offset, field) { + this.bbi = bbi; + this.type = type; + this.fieldCount = fieldCount; + this.offset = offset; + this.field = field; + } + + BBIExtraIndex.prototype.lookup = function(name, callback) { + var thisB = this; + + this.bbi.data.slice(this.offset, 32).fetch(function(bpt) { + var ba = new Uint8Array(bpt); + var sa = new Int16Array(bpt); + var la = new Int32Array(bpt); + var bptMagic = la[0]; + var blockSize = la[1]; + var keySize = la[2]; + var valSize = la[3]; + var itemCount = bwg_readOffset(ba, 16); + var rootNodeOffset = 32; + + function bptReadNode(nodeOffset) { + thisB.bbi.data.slice(nodeOffset, 4 + (blockSize * (keySize + valSize))).fetch(function(node) { + var ba = new Uint8Array(node); + var sa = new Uint16Array(node); + var la = new Uint32Array(node); + + var nodeType = ba[0]; + var cnt = sa[1]; + + var offset = 4; + if (nodeType == 0) { + var lastChildOffset = null; + for (var n = 0; n < cnt; ++n) { + var key = ''; + for (var ki = 0; ki < keySize; ++ki) { + var charCode = ba[offset++]; + if (charCode != 0) { + key += String.fromCharCode(charCode); + } + } + + var childOffset = bwg_readOffset(ba, offset); + offset += 8; + + if (name.localeCompare(key) < 0 && lastChildOffset) { + bptReadNode(lastChildOffset); + return; + } + lastChildOffset = childOffset; + } + bptReadNode(lastChildOffset); + } else { + for (var n = 0; n < cnt; ++n) { + var key = ''; + for (var ki = 0; ki < keySize; ++ki) { + var charCode = ba[offset++]; + if (charCode != 0) { + key += String.fromCharCode(charCode); + } + } + + // Specific for EI case. + if (key == name) { + var start = bwg_readOffset(ba, offset); + var length = readInt(ba, offset + 8); + + return thisB.bbi.getUnzoomedView().fetchFeatures( + function(chr, min, max, toks) { + if (toks && toks.length > thisB.field - 3) + return toks[thisB.field - 3] == name; + }, + [{offset: start, size: length}], + callback); + } + offset += valSize; + } + return callback([]); + } + }); + } + + bptReadNode(thisB.offset + rootNodeOffset); + }); + } + + return { + makeBwg: makeBwg + }; +}); diff --git a/client/galaxy/scripts/libs/bbi/jquery-ajax-native.js b/client/galaxy/scripts/libs/bbi/jquery-ajax-native.js new file mode 100644 index 00000000000..557027072f9 --- /dev/null +++ b/client/galaxy/scripts/libs/bbi/jquery-ajax-native.js @@ -0,0 +1,157 @@ +// jQuery Ajax Native Plugin + +// (c) 2015 Tarik Zakaria Benmerar, Acigna Inc. +// jQuery Ajax Native Plugin may be freely distributed under the MIT license. +(function (root, factory) { + if (typeof define === 'function' && define.amd) { + // AMD. Register as an anonymous module. + define(['jquery'], factory); + } else if (typeof exports === 'object') { + // Node. Does not work with strict CommonJS, but + // only CommonJS-like environments that support module.exports, + // like Node. + module.exports = factory(require('jquery')); + } else { + // Browser globals (root is window) + factory(root.jQuery); + } +}(this, function ( $ ) { + var ajaxSettings = $.ajaxSettings; + ajaxSettings.responseFields.native = 'responseNative'; + ajaxSettings.converters[ '* native' ] = true; + var support = {}, + xhrId = 0, + xhrSuccessStatus = { + // file protocol always yields status code 0, assume 200 + 0: 200, + // Support: IE9 + // #1450: sometimes IE returns 1223 when it should be 204 + 1223: 204 + }, + xhrCallbacks = {}, + xhrSupported = jQuery.ajaxSettings.xhr(); + // Support: IE9 + // Open requests must be manually aborted on unload (#5280) + if ( window.ActiveXObject ) { + $( window ).on( "unload", function() { + for ( var key in xhrCallbacks ) { + xhrCallbacks[ key ](); + } + }); + } + support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported ); + support.ajax = xhrSupported = !!xhrSupported; + + //Native Data Type Ajax Transport + $.ajaxTransport('native', function ( options ) { + var callback; + // Cross domain only allowed if supported through XMLHttpRequest + if ( support.cors || xhrSupported && !options.crossDomain ) { + return { + send: function( headers, complete ) { + var i, + xhr = options.xhr(), + id = ++xhrId, + responses = {}; + + xhr.open( options.type, options.url, options.async, options.username, options.password ); + + // Apply custom fields if provided + if ( options.xhrFields ) { + for ( i in options.xhrFields ) { + xhr[ i ] = options.xhrFields[ i ]; + } + } + + // Override mime type if needed + if ( options.mimeType && xhr.overrideMimeType ) { + xhr.overrideMimeType( options.mimeType ); + } + + // X-Requested-With header + // For cross-domain requests, seeing as conditions for a preflight are + // akin to a jigsaw puzzle, we simply never set it to be sure. + // (it can always be set on a per-request basis or even using ajaxSetup) + // For same-domain requests, won't change header if already provided. + if ( !options.crossDomain && !headers["X-Requested-With"] ) { + headers["X-Requested-With"] = "XMLHttpRequest"; + } + + // Set headers + for ( i in headers ) { + xhr.setRequestHeader( i, headers[ i ] ); + } + + // Callback + callback = function( type ) { + return function() { + if ( callback ) { + delete xhrCallbacks[ id ]; + callback = xhr.onload = xhr.onerror = null; + + if ( type === "abort" ) { + xhr.abort(); + } else if ( type === "error" ) { + complete( + // file: protocol always yields status 0; see #8605, #14207 + xhr.status, + xhr.statusText + ); + } else { + // The native response associated with the responseType + // Stored in the xhr.response attribute (XHR2 Spec) + if ( xhr.response ) { + responses.native = xhr.response; + } + + complete( + xhrSuccessStatus[ xhr.status ] || xhr.status, + xhr.statusText, + responses, + xhr.getAllResponseHeaders() + ); + } + } + }; + }; + + // Listen to events + xhr.onload = callback(); + xhr.onerror = callback("error"); + + // Create the abort callback + callback = xhrCallbacks[ id ] = callback("abort"); + + try { + // Do send the request (this may raise an exception) + xhr.send( options.hasContent && options.data || null ); + } catch ( e ) { + // #14683: Only rethrow if this hasn't been notified as an error yet + if ( callback ) { + throw e; + } + } + }, + + abort: function() { + if ( callback ) { + callback(); + } + } + }; + } + }); + + + //$.getNative wrapper + $.getNative = function ( url, callback ) { + return $.ajax({ + dataType: 'native', + url: url, + xhrFields: { + responseType: 'arraybuffer' + }, + success: callback + }); + } +})); diff --git a/client/galaxy/scripts/libs/bbi/jszlib.js b/client/galaxy/scripts/libs/bbi/jszlib.js new file mode 100644 index 00000000000..1274c479e9b --- /dev/null +++ b/client/galaxy/scripts/libs/bbi/jszlib.js @@ -0,0 +1,2163 @@ +/* -*- mode: javascript; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +// +// Javascript ZLib +// By Thomas Down 2010-2011 +// +// Based very heavily on portions of jzlib (by ymnk@jcraft.com), who in +// turn credits Jean-loup Gailly and Mark Adler for the original zlib code. +// +// inflate.js: ZLib inflate code +// + +// +// Shared constants +// + +define([],function() { + +var MAX_WBITS=15; // 32K LZ77 window +var DEF_WBITS=MAX_WBITS; +var MAX_MEM_LEVEL=9; +var MANY=1440; +var BMAX = 15; + +// preset dictionary flag in zlib header +var PRESET_DICT=0x20; + +var Z_NO_FLUSH=0; +var Z_PARTIAL_FLUSH=1; +var Z_SYNC_FLUSH=2; +var Z_FULL_FLUSH=3; +var Z_FINISH=4; + +var Z_DEFLATED=8; + +var Z_OK=0; +var Z_STREAM_END=1; +var Z_NEED_DICT=2; +var Z_ERRNO=-1; +var Z_STREAM_ERROR=-2; +var Z_DATA_ERROR=-3; +var Z_MEM_ERROR=-4; +var Z_BUF_ERROR=-5; +var Z_VERSION_ERROR=-6; + +var METHOD=0; // waiting for method byte +var FLAG=1; // waiting for flag byte +var DICT4=2; // four dictionary check bytes to go +var DICT3=3; // three dictionary check bytes to go +var DICT2=4; // two dictionary check bytes to go +var DICT1=5; // one dictionary check byte to go +var DICT0=6; // waiting for inflateSetDictionary +var BLOCKS=7; // decompressing blocks +var CHECK4=8; // four check bytes to go +var CHECK3=9; // three check bytes to go +var CHECK2=10; // two check bytes to go +var CHECK1=11; // one check byte to go +var DONE=12; // finished check, done +var BAD=13; // got an error--stay here + +var inflate_mask = [0x00000000, 0x00000001, 0x00000003, 0x00000007, 0x0000000f, 0x0000001f, 0x0000003f, 0x0000007f, 0x000000ff, 0x000001ff, 0x000003ff, 0x000007ff, 0x00000fff, 0x00001fff, 0x00003fff, 0x00007fff, 0x0000ffff]; + +var IB_TYPE=0; // get type bits (3, including end bit) +var IB_LENS=1; // get lengths for stored +var IB_STORED=2;// processing stored block +var IB_TABLE=3; // get table lengths +var IB_BTREE=4; // get bit lengths tree for a dynamic block +var IB_DTREE=5; // get length, distance trees for a dynamic block +var IB_CODES=6; // processing fixed or dynamic block +var IB_DRY=7; // output remaining window bytes +var IB_DONE=8; // finished last block, done +var IB_BAD=9; // ot a data error--stuck here + +var fixed_bl = 9; +var fixed_bd = 5; + +var fixed_tl = [ + 96,7,256, 0,8,80, 0,8,16, 84,8,115, + 82,7,31, 0,8,112, 0,8,48, 0,9,192, + 80,7,10, 0,8,96, 0,8,32, 0,9,160, + 0,8,0, 0,8,128, 0,8,64, 0,9,224, + 80,7,6, 0,8,88, 0,8,24, 0,9,144, + 83,7,59, 0,8,120, 0,8,56, 0,9,208, + 81,7,17, 0,8,104, 0,8,40, 0,9,176, + 0,8,8, 0,8,136, 0,8,72, 0,9,240, + 80,7,4, 0,8,84, 0,8,20, 85,8,227, + 83,7,43, 0,8,116, 0,8,52, 0,9,200, + 81,7,13, 0,8,100, 0,8,36, 0,9,168, + 0,8,4, 0,8,132, 0,8,68, 0,9,232, + 80,7,8, 0,8,92, 0,8,28, 0,9,152, + 84,7,83, 0,8,124, 0,8,60, 0,9,216, + 82,7,23, 0,8,108, 0,8,44, 0,9,184, + 0,8,12, 0,8,140, 0,8,76, 0,9,248, + 80,7,3, 0,8,82, 0,8,18, 85,8,163, + 83,7,35, 0,8,114, 0,8,50, 0,9,196, + 81,7,11, 0,8,98, 0,8,34, 0,9,164, + 0,8,2, 0,8,130, 0,8,66, 0,9,228, + 80,7,7, 0,8,90, 0,8,26, 0,9,148, + 84,7,67, 0,8,122, 0,8,58, 0,9,212, + 82,7,19, 0,8,106, 0,8,42, 0,9,180, + 0,8,10, 0,8,138, 0,8,74, 0,9,244, + 80,7,5, 0,8,86, 0,8,22, 192,8,0, + 83,7,51, 0,8,118, 0,8,54, 0,9,204, + 81,7,15, 0,8,102, 0,8,38, 0,9,172, + 0,8,6, 0,8,134, 0,8,70, 0,9,236, + 80,7,9, 0,8,94, 0,8,30, 0,9,156, + 84,7,99, 0,8,126, 0,8,62, 0,9,220, + 82,7,27, 0,8,110, 0,8,46, 0,9,188, + 0,8,14, 0,8,142, 0,8,78, 0,9,252, + 96,7,256, 0,8,81, 0,8,17, 85,8,131, + 82,7,31, 0,8,113, 0,8,49, 0,9,194, + 80,7,10, 0,8,97, 0,8,33, 0,9,162, + 0,8,1, 0,8,129, 0,8,65, 0,9,226, + 80,7,6, 0,8,89, 0,8,25, 0,9,146, + 83,7,59, 0,8,121, 0,8,57, 0,9,210, + 81,7,17, 0,8,105, 0,8,41, 0,9,178, + 0,8,9, 0,8,137, 0,8,73, 0,9,242, + 80,7,4, 0,8,85, 0,8,21, 80,8,258, + 83,7,43, 0,8,117, 0,8,53, 0,9,202, + 81,7,13, 0,8,101, 0,8,37, 0,9,170, + 0,8,5, 0,8,133, 0,8,69, 0,9,234, + 80,7,8, 0,8,93, 0,8,29, 0,9,154, + 84,7,83, 0,8,125, 0,8,61, 0,9,218, + 82,7,23, 0,8,109, 0,8,45, 0,9,186, + 0,8,13, 0,8,141, 0,8,77, 0,9,250, + 80,7,3, 0,8,83, 0,8,19, 85,8,195, + 83,7,35, 0,8,115, 0,8,51, 0,9,198, + 81,7,11, 0,8,99, 0,8,35, 0,9,166, + 0,8,3, 0,8,131, 0,8,67, 0,9,230, + 80,7,7, 0,8,91, 0,8,27, 0,9,150, + 84,7,67, 0,8,123, 0,8,59, 0,9,214, + 82,7,19, 0,8,107, 0,8,43, 0,9,182, + 0,8,11, 0,8,139, 0,8,75, 0,9,246, + 80,7,5, 0,8,87, 0,8,23, 192,8,0, + 83,7,51, 0,8,119, 0,8,55, 0,9,206, + 81,7,15, 0,8,103, 0,8,39, 0,9,174, + 0,8,7, 0,8,135, 0,8,71, 0,9,238, + 80,7,9, 0,8,95, 0,8,31, 0,9,158, + 84,7,99, 0,8,127, 0,8,63, 0,9,222, + 82,7,27, 0,8,111, 0,8,47, 0,9,190, + 0,8,15, 0,8,143, 0,8,79, 0,9,254, + 96,7,256, 0,8,80, 0,8,16, 84,8,115, + 82,7,31, 0,8,112, 0,8,48, 0,9,193, + + 80,7,10, 0,8,96, 0,8,32, 0,9,161, + 0,8,0, 0,8,128, 0,8,64, 0,9,225, + 80,7,6, 0,8,88, 0,8,24, 0,9,145, + 83,7,59, 0,8,120, 0,8,56, 0,9,209, + 81,7,17, 0,8,104, 0,8,40, 0,9,177, + 0,8,8, 0,8,136, 0,8,72, 0,9,241, + 80,7,4, 0,8,84, 0,8,20, 85,8,227, + 83,7,43, 0,8,116, 0,8,52, 0,9,201, + 81,7,13, 0,8,100, 0,8,36, 0,9,169, + 0,8,4, 0,8,132, 0,8,68, 0,9,233, + 80,7,8, 0,8,92, 0,8,28, 0,9,153, + 84,7,83, 0,8,124, 0,8,60, 0,9,217, + 82,7,23, 0,8,108, 0,8,44, 0,9,185, + 0,8,12, 0,8,140, 0,8,76, 0,9,249, + 80,7,3, 0,8,82, 0,8,18, 85,8,163, + 83,7,35, 0,8,114, 0,8,50, 0,9,197, + 81,7,11, 0,8,98, 0,8,34, 0,9,165, + 0,8,2, 0,8,130, 0,8,66, 0,9,229, + 80,7,7, 0,8,90, 0,8,26, 0,9,149, + 84,7,67, 0,8,122, 0,8,58, 0,9,213, + 82,7,19, 0,8,106, 0,8,42, 0,9,181, + 0,8,10, 0,8,138, 0,8,74, 0,9,245, + 80,7,5, 0,8,86, 0,8,22, 192,8,0, + 83,7,51, 0,8,118, 0,8,54, 0,9,205, + 81,7,15, 0,8,102, 0,8,38, 0,9,173, + 0,8,6, 0,8,134, 0,8,70, 0,9,237, + 80,7,9, 0,8,94, 0,8,30, 0,9,157, + 84,7,99, 0,8,126, 0,8,62, 0,9,221, + 82,7,27, 0,8,110, 0,8,46, 0,9,189, + 0,8,14, 0,8,142, 0,8,78, 0,9,253, + 96,7,256, 0,8,81, 0,8,17, 85,8,131, + 82,7,31, 0,8,113, 0,8,49, 0,9,195, + 80,7,10, 0,8,97, 0,8,33, 0,9,163, + 0,8,1, 0,8,129, 0,8,65, 0,9,227, + 80,7,6, 0,8,89, 0,8,25, 0,9,147, + 83,7,59, 0,8,121, 0,8,57, 0,9,211, + 81,7,17, 0,8,105, 0,8,41, 0,9,179, + 0,8,9, 0,8,137, 0,8,73, 0,9,243, + 80,7,4, 0,8,85, 0,8,21, 80,8,258, + 83,7,43, 0,8,117, 0,8,53, 0,9,203, + 81,7,13, 0,8,101, 0,8,37, 0,9,171, + 0,8,5, 0,8,133, 0,8,69, 0,9,235, + 80,7,8, 0,8,93, 0,8,29, 0,9,155, + 84,7,83, 0,8,125, 0,8,61, 0,9,219, + 82,7,23, 0,8,109, 0,8,45, 0,9,187, + 0,8,13, 0,8,141, 0,8,77, 0,9,251, + 80,7,3, 0,8,83, 0,8,19, 85,8,195, + 83,7,35, 0,8,115, 0,8,51, 0,9,199, + 81,7,11, 0,8,99, 0,8,35, 0,9,167, + 0,8,3, 0,8,131, 0,8,67, 0,9,231, + 80,7,7, 0,8,91, 0,8,27, 0,9,151, + 84,7,67, 0,8,123, 0,8,59, 0,9,215, + 82,7,19, 0,8,107, 0,8,43, 0,9,183, + 0,8,11, 0,8,139, 0,8,75, 0,9,247, + 80,7,5, 0,8,87, 0,8,23, 192,8,0, + 83,7,51, 0,8,119, 0,8,55, 0,9,207, + 81,7,15, 0,8,103, 0,8,39, 0,9,175, + 0,8,7, 0,8,135, 0,8,71, 0,9,239, + 80,7,9, 0,8,95, 0,8,31, 0,9,159, + 84,7,99, 0,8,127, 0,8,63, 0,9,223, + 82,7,27, 0,8,111, 0,8,47, 0,9,191, + 0,8,15, 0,8,143, 0,8,79, 0,9,255 +]; +var fixed_td = [ + 80,5,1, 87,5,257, 83,5,17, 91,5,4097, + 81,5,5, 89,5,1025, 85,5,65, 93,5,16385, + 80,5,3, 88,5,513, 84,5,33, 92,5,8193, + 82,5,9, 90,5,2049, 86,5,129, 192,5,24577, + 80,5,2, 87,5,385, 83,5,25, 91,5,6145, + 81,5,7, 89,5,1537, 85,5,97, 93,5,24577, + 80,5,4, 88,5,769, 84,5,49, 92,5,12289, + 82,5,13, 90,5,3073, 86,5,193, 192,5,24577 +]; + + // Tables for deflate from PKZIP's appnote.txt. + var cplens = [ // Copy lengths for literal codes 257..285 + 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17, 19, 23, 27, 31, + 35, 43, 51, 59, 67, 83, 99, 115, 131, 163, 195, 227, 258, 0, 0 + ]; + + // see note #13 above about 258 + var cplext = [ // Extra bits for literal codes 257..285 + 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, + 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 0, 112, 112 // 112==invalid + ]; + + var cpdist = [ // Copy offsets for distance codes 0..29 + 1, 2, 3, 4, 5, 7, 9, 13, 17, 25, 33, 49, 65, 97, 129, 193, + 257, 385, 513, 769, 1025, 1537, 2049, 3073, 4097, 6145, + 8193, 12289, 16385, 24577 + ]; + + var cpdext = [ // Extra bits for distance codes + 0, 0, 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6, + 7, 7, 8, 8, 9, 9, 10, 10, 11, 11, + 12, 12, 13, 13]; + +// +// ZStream.java +// + +function ZStream() { +} + + +ZStream.prototype.inflateInit = function(w, nowrap) { + if (!w) { + w = DEF_WBITS; + } + if (nowrap) { + nowrap = false; + } + this.istate = new Inflate(); + return this.istate.inflateInit(this, nowrap?-w:w); +} + +ZStream.prototype.inflate = function(f) { + if(this.istate==null) return Z_STREAM_ERROR; + return this.istate.inflate(this, f); +} + +ZStream.prototype.inflateEnd = function(){ + if(this.istate==null) return Z_STREAM_ERROR; + var ret=istate.inflateEnd(this); + this.istate = null; + return ret; +} +ZStream.prototype.inflateSync = function(){ + // if(istate == null) return Z_STREAM_ERROR; + return istate.inflateSync(this); +} +ZStream.prototype.inflateSetDictionary = function(dictionary, dictLength){ + // if(istate == null) return Z_STREAM_ERROR; + return istate.inflateSetDictionary(this, dictionary, dictLength); +} + +/* + + public int deflateInit(int level){ + return deflateInit(level, MAX_WBITS); + } + public int deflateInit(int level, boolean nowrap){ + return deflateInit(level, MAX_WBITS, nowrap); + } + public int deflateInit(int level, int bits){ + return deflateInit(level, bits, false); + } + public int deflateInit(int level, int bits, boolean nowrap){ + dstate=new Deflate(); + return dstate.deflateInit(this, level, nowrap?-bits:bits); + } + public int deflate(int flush){ + if(dstate==null){ + return Z_STREAM_ERROR; + } + return dstate.deflate(this, flush); + } + public int deflateEnd(){ + if(dstate==null) return Z_STREAM_ERROR; + int ret=dstate.deflateEnd(); + dstate=null; + return ret; + } + public int deflateParams(int level, int strategy){ + if(dstate==null) return Z_STREAM_ERROR; + return dstate.deflateParams(this, level, strategy); + } + public int deflateSetDictionary (byte[] dictionary, int dictLength){ + if(dstate == null) + return Z_STREAM_ERROR; + return dstate.deflateSetDictionary(this, dictionary, dictLength); + } + +*/ + +/* + // Flush as much pending output as possible. All deflate() output goes + // through this function so some applications may wish to modify it + // to avoid allocating a large strm->next_out buffer and copying into it. + // (See also read_buf()). + void flush_pending(){ + int len=dstate.pending; + + if(len>avail_out) len=avail_out; + if(len==0) return; + + if(dstate.pending_buf.length<=dstate.pending_out || + next_out.length<=next_out_index || + dstate.pending_buf.length<(dstate.pending_out+len) || + next_out.length<(next_out_index+len)){ + System.out.println(dstate.pending_buf.length+", "+dstate.pending_out+ + ", "+next_out.length+", "+next_out_index+", "+len); + System.out.println("avail_out="+avail_out); + } + + System.arraycopy(dstate.pending_buf, dstate.pending_out, + next_out, next_out_index, len); + + next_out_index+=len; + dstate.pending_out+=len; + total_out+=len; + avail_out-=len; + dstate.pending-=len; + if(dstate.pending==0){ + dstate.pending_out=0; + } + } + + // Read a new buffer from the current input stream, update the adler32 + // and total number of bytes read. All deflate() input goes through + // this function so some applications may wish to modify it to avoid + // allocating a large strm->next_in buffer and copying from it. + // (See also flush_pending()). + int read_buf(byte[] buf, int start, int size) { + int len=avail_in; + + if(len>size) len=size; + if(len==0) return 0; + + avail_in-=len; + + if(dstate.noheader==0) { + adler=_adler.adler32(adler, next_in, next_in_index, len); + } + System.arraycopy(next_in, next_in_index, buf, start, len); + next_in_index += len; + total_in += len; + return len; + } + + public void free(){ + next_in=null; + next_out=null; + msg=null; + _adler=null; + } +} +*/ + + +// +// Inflate.java +// + +function Inflate() { + this.was = [0]; +} + +Inflate.prototype.inflateReset = function(z) { + if(z == null || z.istate == null) return Z_STREAM_ERROR; + + z.total_in = z.total_out = 0; + z.msg = null; + z.istate.mode = z.istate.nowrap!=0 ? BLOCKS : METHOD; + z.istate.blocks.reset(z, null); + return Z_OK; +} + +Inflate.prototype.inflateEnd = function(z){ + if(this.blocks != null) + this.blocks.free(z); + this.blocks=null; + return Z_OK; +} + +Inflate.prototype.inflateInit = function(z, w){ + z.msg = null; + this.blocks = null; + + // handle undocumented nowrap option (no zlib header or check) + nowrap = 0; + if(w < 0){ + w = - w; + nowrap = 1; + } + + // set window size + if(w<8 ||w>15){ + this.inflateEnd(z); + return Z_STREAM_ERROR; + } + this.wbits=w; + + z.istate.blocks=new InfBlocks(z, + z.istate.nowrap!=0 ? null : this, + 1<>4)+8>z.istate.wbits){ + z.istate.mode = BAD; + z.msg="invalid window size"; + z.istate.marker = 5; // can't try inflateSync + break; + } + z.istate.mode=FLAG; + case FLAG: + + if(z.avail_in==0)return r;r=f; + + z.avail_in--; z.total_in++; + b = (z.next_in[z.next_in_index++])&0xff; + + if((((z.istate.method << 8)+b) % 31)!=0){ + z.istate.mode = BAD; + z.msg = "incorrect header check"; + z.istate.marker = 5; // can't try inflateSync + break; + } + + if((b&PRESET_DICT)==0){ + z.istate.mode = BLOCKS; + break; + } + z.istate.mode = DICT4; + case DICT4: + + if(z.avail_in==0)return r;r=f; + + z.avail_in--; z.total_in++; + z.istate.need=((z.next_in[z.next_in_index++]&0xff)<<24)&0xff000000; + z.istate.mode=DICT3; + case DICT3: + + if(z.avail_in==0)return r;r=f; + + z.avail_in--; z.total_in++; + z.istate.need+=((z.next_in[z.next_in_index++]&0xff)<<16)&0xff0000; + z.istate.mode=DICT2; + case DICT2: + + if(z.avail_in==0)return r;r=f; + + z.avail_in--; z.total_in++; + z.istate.need+=((z.next_in[z.next_in_index++]&0xff)<<8)&0xff00; + z.istate.mode=DICT1; + case DICT1: + + if(z.avail_in==0)return r;r=f; + + z.avail_in--; z.total_in++; + z.istate.need += (z.next_in[z.next_in_index++]&0xff); + z.adler = z.istate.need; + z.istate.mode = DICT0; + return Z_NEED_DICT; + case DICT0: + z.istate.mode = BAD; + z.msg = "need dictionary"; + z.istate.marker = 0; // can try inflateSync + return Z_STREAM_ERROR; + case BLOCKS: + + r = z.istate.blocks.proc(z, r); + if(r == Z_DATA_ERROR){ + z.istate.mode = BAD; + z.istate.marker = 0; // can try inflateSync + break; + } + if(r == Z_OK){ + r = f; + } + if(r != Z_STREAM_END){ + return r; + } + r = f; + z.istate.blocks.reset(z, z.istate.was); + if(z.istate.nowrap!=0){ + z.istate.mode=DONE; + break; + } + z.istate.mode=CHECK4; + case CHECK4: + + if(z.avail_in==0)return r;r=f; + + z.avail_in--; z.total_in++; + z.istate.need=((z.next_in[z.next_in_index++]&0xff)<<24)&0xff000000; + z.istate.mode=CHECK3; + case CHECK3: + + if(z.avail_in==0)return r;r=f; + + z.avail_in--; z.total_in++; + z.istate.need+=((z.next_in[z.next_in_index++]&0xff)<<16)&0xff0000; + z.istate.mode = CHECK2; + case CHECK2: + + if(z.avail_in==0)return r;r=f; + + z.avail_in--; z.total_in++; + z.istate.need+=((z.next_in[z.next_in_index++]&0xff)<<8)&0xff00; + z.istate.mode = CHECK1; + case CHECK1: + + if(z.avail_in==0)return r;r=f; + + z.avail_in--; z.total_in++; + z.istate.need+=(z.next_in[z.next_in_index++]&0xff); + + if(((z.istate.was[0])) != ((z.istate.need))){ + z.istate.mode = BAD; + z.msg = "incorrect data check"; + z.istate.marker = 5; // can't try inflateSync + break; + } + + z.istate.mode = DONE; + case DONE: + return Z_STREAM_END; + case BAD: + return Z_DATA_ERROR; + default: + return Z_STREAM_ERROR; + } + } + } + + +Inflate.prototype.inflateSetDictionary = function(z, dictionary, dictLength) { + var index=0; + var length = dictLength; + if(z==null || z.istate == null|| z.istate.mode != DICT0) + return Z_STREAM_ERROR; + + if(z._adler.adler32(1, dictionary, 0, dictLength)!=z.adler){ + return Z_DATA_ERROR; + } + + z.adler = z._adler.adler32(0, null, 0, 0); + + if(length >= (1<>> 1){ + case 0: // stored + {b>>>=(3);k-=(3);} + t = k & 7; // go to byte boundary + + {b>>>=(t);k-=(t);} + this.mode = IB_LENS; // get length of stored block + break; + case 1: // fixed + { + var bl=new Int32Array(1); + var bd=new Int32Array(1); + var tl=[]; + var td=[]; + + inflate_trees_fixed(bl, bd, tl, td, z); + this.codes.init(bl[0], bd[0], tl[0], 0, td[0], 0, z); + } + + {b>>>=(3);k-=(3);} + + this.mode = IB_CODES; + break; + case 2: // dynamic + + {b>>>=(3);k-=(3);} + + this.mode = IB_TABLE; + break; + case 3: // illegal + + {b>>>=(3);k-=(3);} + this.mode = BAD; + z.msg = "invalid block type"; + r = Z_DATA_ERROR; + + this.bitb=b; this.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + this.write=q; + return this.inflate_flush(z,r); + } + break; + case IB_LENS: + while(k<(32)){ + if(n!=0){ + r=Z_OK; + } + else{ + this.bitb=b; this.bitk=k; + z.avail_in=n; + z.total_in+=p-z.next_in_index;z.next_in_index=p; + this.write=q; + return this.inflate_flush(z,r); + }; + n--; + b|=(z.next_in[p++]&0xff)<>> 16) & 0xffff) != (b & 0xffff)){ + this.mode = BAD; + z.msg = "invalid stored block lengths"; + r = Z_DATA_ERROR; + + this.bitb=b; this.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + this.write=q; + return this.inflate_flush(z,r); + } + this.left = (b & 0xffff); + b = k = 0; // dump bits + this.mode = this.left!=0 ? IB_STORED : (this.last!=0 ? IB_DRY : IB_TYPE); + break; + case IB_STORED: + if (n == 0){ + this.bitb=b; this.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + write=q; + return this.inflate_flush(z,r); + } + + if(m==0){ + if(q==end&&read!=0){ + q=0; m=(qn) t = n; + if(t>m) t = m; + arrayCopy(z.next_in, p, this.window, q, t); + p += t; n -= t; + q += t; m -= t; + if ((this.left -= t) != 0) + break; + this.mode = (this.last != 0 ? IB_DRY : IB_TYPE); + break; + case IB_TABLE: + + while(k<(14)){ + if(n!=0){ + r=Z_OK; + } + else{ + this.bitb=b; this.bitk=k; + z.avail_in=n; + z.total_in+=p-z.next_in_index;z.next_in_index=p; + this.write=q; + return this.inflate_flush(z,r); + }; + n--; + b|=(z.next_in[p++]&0xff)< 29 || ((t >> 5) & 0x1f) > 29) + { + this.mode = IB_BAD; + z.msg = "too many length or distance symbols"; + r = Z_DATA_ERROR; + + this.bitb=b; this.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + this.write=q; + return this.inflate_flush(z,r); + } + t = 258 + (t & 0x1f) + ((t >> 5) & 0x1f); + if(this.blens==null || this.blens.length>>=(14);k-=(14);} + + this.index = 0; + mode = IB_BTREE; + case IB_BTREE: + while (this.index < 4 + (this.table >>> 10)){ + while(k<(3)){ + if(n!=0){ + r=Z_OK; + } + else{ + this.bitb=b; this.bitk=k; + z.avail_in=n; + z.total_in+=p-z.next_in_index;z.next_in_index=p; + this.write=q; + return this.inflate_flush(z,r); + }; + n--; + b|=(z.next_in[p++]&0xff)<>>=(3);k-=(3);} + } + + while(this.index < 19){ + this.blens[INFBLOCKS_BORDER[this.index++]] = 0; + } + + this.bb[0] = 7; + t = this.inftree.inflate_trees_bits(this.blens, this.bb, this.tb, this.hufts, z); + if (t != Z_OK){ + r = t; + if (r == Z_DATA_ERROR){ + this.blens=null; + this.mode = IB_BAD; + } + + this.bitb=b; this.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + write=q; + return this.inflate_flush(z,r); + } + + this.index = 0; + this.mode = IB_DTREE; + case IB_DTREE: + while (true){ + t = this.table; + if(!(this.index < 258 + (t & 0x1f) + ((t >> 5) & 0x1f))){ + break; + } + + var h; //int[] + var i, j, c; + + t = this.bb[0]; + + while(k<(t)){ + if(n!=0){ + r=Z_OK; + } + else{ + this.bitb=b; this.bitk=k; + z.avail_in=n; + z.total_in+=p-z.next_in_index;z.next_in_index=p; + this.write=q; + return this.inflate_flush(z,r); + }; + n--; + b|=(z.next_in[p++]&0xff)<>>=(t);k-=(t); + this.blens[this.index++] = c; + } + else { // c == 16..18 + i = c == 18 ? 7 : c - 14; + j = c == 18 ? 11 : 3; + + while(k<(t+i)){ + if(n!=0){ + r=Z_OK; + } + else{ + this.bitb=b; this.bitk=k; + z.avail_in=n; + z.total_in+=p-z.next_in_index;z.next_in_index=p; + this.write=q; + return this.inflate_flush(z,r); + }; + n--; + b|=(z.next_in[p++]&0xff)<>>=(t);k-=(t); + + j += (b & inflate_mask[i]); + + b>>>=(i);k-=(i); + + i = this.index; + t = this.table; + if (i + j > 258 + (t & 0x1f) + ((t >> 5) & 0x1f) || + (c == 16 && i < 1)){ + this.blens=null; + this.mode = IB_BAD; + z.msg = "invalid bit length repeat"; + r = Z_DATA_ERROR; + + this.bitb=b; this.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + this.write=q; + return this.inflate_flush(z,r); + } + + c = c == 16 ? this.blens[i-1] : 0; + do{ + this.blens[i++] = c; + } + while (--j!=0); + this.index = i; + } + } + + this.tb[0]=-1; + { + var bl=new Int32Array(1); + var bd=new Int32Array(1); + var tl=new Int32Array(1); + var td=new Int32Array(1); + bl[0] = 9; // must be <= 9 for lookahead assumptions + bd[0] = 6; // must be <= 9 for lookahead assumptions + + t = this.table; + t = this.inftree.inflate_trees_dynamic(257 + (t & 0x1f), + 1 + ((t >> 5) & 0x1f), + this.blens, bl, bd, tl, td, this.hufts, z); + + if (t != Z_OK){ + if (t == Z_DATA_ERROR){ + this.blens=null; + this.mode = BAD; + } + r = t; + + this.bitb=b; this.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + this.write=q; + return this.inflate_flush(z,r); + } + this.codes.init(bl[0], bd[0], this.hufts, tl[0], this.hufts, td[0], z); + } + this.mode = IB_CODES; + case IB_CODES: + this.bitb=b; this.bitk=k; + z.avail_in=n; z.total_in+=p-z.next_in_index;z.next_in_index=p; + this.write=q; + + if ((r = this.codes.proc(this, z, r)) != Z_STREAM_END){ + return this.inflate_flush(z, r); + } + r = Z_OK; + this.codes.free(z); + + p=z.next_in_index; n=z.avail_in;b=this.bitb;k=this.bitk; + q=this.write;m = (q < this.read ? this.read-q-1 : this.end-q); + + if (this.last==0){ + this.mode = IB_TYPE; + break; + } + this.mode = IB_DRY; + case IB_DRY: + this.write=q; + r = this.inflate_flush(z, r); + q=this.write; m = (q < this.read ? this.read-q-1 : this.end-q); + if (this.read != this.write){ + this.bitb=b; this.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + this.write=q; + return this.inflate_flush(z, r); + } + mode = DONE; + case IB_DONE: + r = Z_STREAM_END; + + this.bitb=b; this.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + this.write=q; + return this.inflate_flush(z, r); + case IB_BAD: + r = Z_DATA_ERROR; + + this.bitb=b; this.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + this.write=q; + return this.inflate_flush(z, r); + + default: + r = Z_STREAM_ERROR; + + this.bitb=b; this.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + this.write=q; + return this.inflate_flush(z, r); + } + } + } + +InfBlocks.prototype.free = function(z){ + this.reset(z, null); + this.window=null; + this.hufts=null; +} + +InfBlocks.prototype.set_dictionary = function(d, start, n){ + arrayCopy(d, start, window, 0, n); + this.read = this.write = n; +} + + // Returns true if inflate is currently at the end of a block generated + // by Z_SYNC_FLUSH or Z_FULL_FLUSH. +InfBlocks.prototype.sync_point = function(){ + return this.mode == IB_LENS; +} + + // copy as much as possible from the sliding window to the output area +InfBlocks.prototype.inflate_flush = function(z, r){ + var n; + var p; + var q; + + // local copies of source and destination pointers + p = z.next_out_index; + q = this.read; + + // compute number of bytes to copy as far as end of window + n = ((q <= this.write ? this.write : this.end) - q); + if (n > z.avail_out) n = z.avail_out; + if (n!=0 && r == Z_BUF_ERROR) r = Z_OK; + + // update counters + z.avail_out -= n; + z.total_out += n; + + // update check information + if(this.checkfn != null) + z.adler=this.check=z._adler.adler32(this.check, this.window, q, n); + + // copy as far as end of window + arrayCopy(this.window, q, z.next_out, p, n); + p += n; + q += n; + + // see if more to copy at beginning of window + if (q == this.end){ + // wrap pointers + q = 0; + if (this.write == this.end) + this.write = 0; + + // compute bytes to copy + n = this.write - q; + if (n > z.avail_out) n = z.avail_out; + if (n!=0 && r == Z_BUF_ERROR) r = Z_OK; + + // update counters + z.avail_out -= n; + z.total_out += n; + + // update check information + if(this.checkfn != null) + z.adler=this.check=z._adler.adler32(this.check, this.window, q, n); + + // copy + arrayCopy(this.window, q, z.next_out, p, n); + p += n; + q += n; + } + + // update pointers + z.next_out_index = p; + this.read = q; + + // done + return r; + } + +// +// InfCodes.java +// + +var IC_START=0; // x: set up for LEN +var IC_LEN=1; // i: get length/literal/eob next +var IC_LENEXT=2; // i: getting length extra (have base) +var IC_DIST=3; // i: get distance next +var IC_DISTEXT=4;// i: getting distance extra +var IC_COPY=5; // o: copying bytes in window, waiting for space +var IC_LIT=6; // o: got literal, waiting for output space +var IC_WASH=7; // o: got eob, possibly still output waiting +var IC_END=8; // x: got eob and all data flushed +var IC_BADCODE=9;// x: got error + +function InfCodes() { +} + +InfCodes.prototype.init = function(bl, bd, tl, tl_index, td, td_index, z) { + this.mode=IC_START; + this.lbits=bl; + this.dbits=bd; + this.ltree=tl; + this.ltree_index=tl_index; + this.dtree = td; + this.dtree_index=td_index; + this.tree=null; +} + +InfCodes.prototype.proc = function(s, z, r){ + var j; // temporary storage + var t; // temporary pointer (int[]) + var tindex; // temporary pointer + var e; // extra bits or operation + var b=0; // bit buffer + var k=0; // bits in bit buffer + var p=0; // input data pointer + var n; // bytes available there + var q; // output window write pointer + var m; // bytes to end of window or read pointer + var f; // pointer to copy strings from + + // copy input/output information to locals (UPDATE macro restores) + p=z.next_in_index;n=z.avail_in;b=s.bitb;k=s.bitk; + q=s.write;m=q= 258 && n >= 10){ + + s.bitb=b;s.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + s.write=q; + r = this.inflate_fast(this.lbits, this.dbits, + this.ltree, this.ltree_index, + this.dtree, this.dtree_index, + s, z); + + p=z.next_in_index;n=z.avail_in;b=s.bitb;k=s.bitk; + q=s.write;m=q>>=(this.tree[tindex+1]); + k-=(this.tree[tindex+1]); + + e=this.tree[tindex]; + + if(e == 0){ // literal + this.lit = this.tree[tindex+2]; + this.mode = IC_LIT; + break; + } + if((e & 16)!=0 ){ // length + this.get = e & 15; + this.len = this.tree[tindex+2]; + this.mode = IC_LENEXT; + break; + } + if ((e & 64) == 0){ // next table + this.need = e; + this.tree_index = tindex/3 + this.tree[tindex+2]; + break; + } + if ((e & 32)!=0){ // end of block + this.mode = IC_WASH; + break; + } + this.mode = IC_BADCODE; // invalid code + z.msg = "invalid literal/length code"; + r = Z_DATA_ERROR; + + s.bitb=b;s.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + s.write=q; + return s.inflate_flush(z,r); + + case IC_LENEXT: // i: getting length extra (have base) + j = this.get; + + while(k<(j)){ + if(n!=0)r=Z_OK; + else{ + + s.bitb=b;s.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + s.write=q; + return s.inflate_flush(z,r); + } + n--; b|=(z.next_in[p++]&0xff)<>=j; + k-=j; + + this.need = this.dbits; + this.tree = this.dtree; + this.tree_index = this.dtree_index; + this.mode = IC_DIST; + case IC_DIST: // i: get distance next + j = this.need; + + while(k<(j)){ + if(n!=0)r=Z_OK; + else{ + + s.bitb=b;s.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + s.write=q; + return s.inflate_flush(z,r); + } + n--; b|=(z.next_in[p++]&0xff)<>=this.tree[tindex+1]; + k-=this.tree[tindex+1]; + + e = (this.tree[tindex]); + if((e & 16)!=0){ // distance + this.get = e & 15; + this.dist = this.tree[tindex+2]; + this.mode = IC_DISTEXT; + break; + } + if ((e & 64) == 0){ // next table + this.need = e; + this.tree_index = tindex/3 + this.tree[tindex+2]; + break; + } + this.mode = IC_BADCODE; // invalid code + z.msg = "invalid distance code"; + r = Z_DATA_ERROR; + + s.bitb=b;s.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + s.write=q; + return s.inflate_flush(z,r); + + case IC_DISTEXT: // i: getting distance extra + j = this.get; + + while(k<(j)){ + if(n!=0)r=Z_OK; + else{ + + s.bitb=b;s.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + s.write=q; + return s.inflate_flush(z,r); + } + n--; b|=(z.next_in[p++]&0xff)<>=j; + k-=j; + + this.mode = IC_COPY; + case IC_COPY: // o: copying bytes in window, waiting for space + f = q - this.dist; + while(f < 0){ // modulo window size-"while" instead + f += s.end; // of "if" handles invalid distances + } + while (this.len!=0){ + + if(m==0){ + if(q==s.end&&s.read!=0){q=0;m=q 7){ // return unused byte, if any + k -= 8; + n++; + p--; // can always return one + } + + s.write=q; r=s.inflate_flush(z,r); + q=s.write;m=q= 258 && n >= 10 + // get literal/length code + while(k<(20)){ // max bits for literal/length code + n--; + b|=(z.next_in[p++]&0xff)<>=(tp[tp_index_t_3+1]); k-=(tp[tp_index_t_3+1]); + + s.window[q++] = tp[tp_index_t_3+2]; + m--; + continue; + } + do { + + b>>=(tp[tp_index_t_3+1]); k-=(tp[tp_index_t_3+1]); + + if((e&16)!=0){ + e &= 15; + c = tp[tp_index_t_3+2] + (b & inflate_mask[e]); + + b>>=e; k-=e; + + // decode distance base of block to copy + while(k<(15)){ // max bits for distance code + n--; + b|=(z.next_in[p++]&0xff)<>=(tp[tp_index_t_3+1]); k-=(tp[tp_index_t_3+1]); + + if((e&16)!=0){ + // get extra bits to add to distance base + e &= 15; + while(k<(e)){ // get extra bits (up to 13) + n--; + b|=(z.next_in[p++]&0xff)<>=(e); k-=(e); + + // do the copy + m -= c; + if (q >= d){ // offset before dest + // just copy + r=q-d; + if(q-r>0 && 2>(q-r)){ + s.window[q++]=s.window[r++]; // minimum count is three, + s.window[q++]=s.window[r++]; // so unroll loop a little + c-=2; + } + else{ + s.window[q++]=s.window[r++]; // minimum count is three, + s.window[q++]=s.window[r++]; // so unroll loop a little + c-=2; + } + } + else{ // else offset after destination + r=q-d; + do{ + r+=s.end; // force pointer in window + }while(r<0); // covers invalid distances + e=s.end-r; + if(c>e){ // if source crosses, + c-=e; // wrapped copy + if(q-r>0 && e>(q-r)){ + do{s.window[q++] = s.window[r++];} + while(--e!=0); + } + else{ + arrayCopy(s.window, r, s.window, q, e); + q+=e; r+=e; e=0; + } + r = 0; // copy rest from start of window + } + + } + + // copy all or what's left + do{s.window[q++] = s.window[r++];} + while(--c!=0); + break; + } + else if((e&64)==0){ + t+=tp[tp_index_t_3+2]; + t+=(b&inflate_mask[e]); + tp_index_t_3=(tp_index+t)*3; + e=tp[tp_index_t_3]; + } + else{ + z.msg = "invalid distance code"; + + c=z.avail_in-n;c=(k>>3)>3:c;n+=c;p-=c;k-=c<<3; + + s.bitb=b;s.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + s.write=q; + + return Z_DATA_ERROR; + } + } + while(true); + break; + } + + if((e&64)==0){ + t+=tp[tp_index_t_3+2]; + t+=(b&inflate_mask[e]); + tp_index_t_3=(tp_index+t)*3; + if((e=tp[tp_index_t_3])==0){ + + b>>=(tp[tp_index_t_3+1]); k-=(tp[tp_index_t_3+1]); + + s.window[q++]=tp[tp_index_t_3+2]; + m--; + break; + } + } + else if((e&32)!=0){ + + c=z.avail_in-n;c=(k>>3)>3:c;n+=c;p-=c;k-=c<<3; + + s.bitb=b;s.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + s.write=q; + + return Z_STREAM_END; + } + else{ + z.msg="invalid literal/length code"; + + c=z.avail_in-n;c=(k>>3)>3:c;n+=c;p-=c;k-=c<<3; + + s.bitb=b;s.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + s.write=q; + + return Z_DATA_ERROR; + } + } + while(true); + } + while(m>=258 && n>= 10); + + // not enough input or output--restore pointers and return + c=z.avail_in-n;c=(k>>3)>3:c;n+=c;p-=c;k-=c<<3; + + s.bitb=b;s.bitk=k; + z.avail_in=n;z.total_in+=p-z.next_in_index;z.next_in_index=p; + s.write=q; + + return Z_OK; +} + +// +// InfTree.java +// + +function InfTree() { +} + +InfTree.prototype.huft_build = function(b, bindex, n, s, d, e, t, m, hp, hn, v) { + + // Given a list of code lengths and a maximum table size, make a set of + // tables to decode that set of codes. Return Z_OK on success, Z_BUF_ERROR + // if the given code set is incomplete (the tables are still built in this + // case), Z_DATA_ERROR if the input is invalid (an over-subscribed set of + // lengths), or Z_MEM_ERROR if not enough memory. + + var a; // counter for codes of length k + var f; // i repeats in table every f entries + var g; // maximum code length + var h; // table level + var i; // counter, current code + var j; // counter + var k; // number of bits in current code + var l; // bits per table (returned in m) + var mask; // (1 << w) - 1, to avoid cc -O bug on HP + var p; // pointer into c[], b[], or v[] + var q; // points to current table + var w; // bits before this table == (l * h) + var xp; // pointer into x + var y; // number of dummy codes added + var z; // number of entries in current table + + // Generate counts for each bit length + + p = 0; i = n; + do { + this.c[b[bindex+p]]++; p++; i--; // assume all entries <= BMAX + }while(i!=0); + + if(this.c[0] == n){ // null input--all zero length codes + t[0] = -1; + m[0] = 0; + return Z_OK; + } + + // Find minimum and maximum length, bound *m by those + l = m[0]; + for (j = 1; j <= BMAX; j++) + if(this.c[j]!=0) break; + k = j; // minimum code length + if(l < j){ + l = j; + } + for (i = BMAX; i!=0; i--){ + if(this.c[i]!=0) break; + } + g = i; // maximum code length + if(l > i){ + l = i; + } + m[0] = l; + + // Adjust last length count to fill out codes, if needed + for (y = 1 << j; j < i; j++, y <<= 1){ + if ((y -= this.c[j]) < 0){ + return Z_DATA_ERROR; + } + } + if ((y -= this.c[i]) < 0){ + return Z_DATA_ERROR; + } + this.c[i] += y; + + // Generate starting offsets into the value table for each length + this.x[1] = j = 0; + p = 1; xp = 2; + while (--i!=0) { // note that i == g from above + this.x[xp] = (j += this.c[p]); + xp++; + p++; + } + + // Make a table of values in order of bit lengths + i = 0; p = 0; + do { + if ((j = b[bindex+p]) != 0){ + this.v[this.x[j]++] = i; + } + p++; + } + while (++i < n); + n = this.x[g]; // set n to length of v + + // Generate the Huffman codes and for each, make the table entries + this.x[0] = i = 0; // first Huffman code is zero + p = 0; // grab values in bit order + h = -1; // no tables yet--level -1 + w = -l; // bits decoded == (l * h) + this.u[0] = 0; // just to keep compilers happy + q = 0; // ditto + z = 0; // ditto + + // go through the bit lengths (k already is bits in shortest code) + for (; k <= g; k++){ + a = this.c[k]; + while (a--!=0){ + // here i is the Huffman code of length k bits for value *p + // make tables up to required level + while (k > w + l){ + h++; + w += l; // previous table always l bits + // compute minimum size table less than or equal to l bits + z = g - w; + z = (z > l) ? l : z; // table size upper limit + if((f=1<<(j=k-w))>a+1){ // try a k-w bit table + // too few codes for k-w bit table + f -= a + 1; // deduct codes from patterns left + xp = k; + if(j < z){ + while (++j < z){ // try smaller tables up to z bits + if((f <<= 1) <= this.c[++xp]) + break; // enough codes to use up j bits + f -= this.c[xp]; // else deduct codes from patterns + } + } + } + z = 1 << j; // table entries for j-bit table + + // allocate new table + if (this.hn[0] + z > MANY){ // (note: doesn't matter for fixed) + return Z_DATA_ERROR; // overflow of MANY + } + this.u[h] = q = /*hp+*/ this.hn[0]; // DEBUG + this.hn[0] += z; + + // connect to last table, if there is one + if(h!=0){ + this.x[h]=i; // save pattern for backing up + this.r[0]=j; // bits in this table + this.r[1]=l; // bits to dump before this table + j=i>>>(w - l); + this.r[2] = (q - this.u[h-1] - j); // offset to this table + arrayCopy(this.r, 0, hp, (this.u[h-1]+j)*3, 3); // connect to last table + } + else{ + t[0] = q; // first table is returned result + } + } + + // set up table entry in r + this.r[1] = (k - w); + if (p >= n){ + this.r[0] = 128 + 64; // out of values--invalid code + } + else if (v[p] < s){ + this.r[0] = (this.v[p] < 256 ? 0 : 32 + 64); // 256 is end-of-block + this.r[2] = this.v[p++]; // simple code is just the value + } + else{ + this.r[0]=(e[this.v[p]-s]+16+64); // non-simple--look up in lists + this.r[2]=d[this.v[p++] - s]; + } + + // fill code-like entries with r + f=1<<(k-w); + for (j=i>>>w;j>>= 1){ + i ^= j; + } + i ^= j; + + // backup over finished tables + mask = (1 << w) - 1; // needed on HP, cc -O bug + while ((i & mask) != this.x[h]){ + h--; // don't need to update q + w -= l; + mask = (1 << w) - 1; + } + } + } + // Return Z_BUF_ERROR if we were given an incomplete table + return y != 0 && g != 1 ? Z_BUF_ERROR : Z_OK; +} + +InfTree.prototype.inflate_trees_bits = function(c, bb, tb, hp, z) { + var result; + this.initWorkArea(19); + this.hn[0]=0; + result = this.huft_build(c, 0, 19, 19, null, null, tb, bb, hp, this.hn, this.v); + + if(result == Z_DATA_ERROR){ + z.msg = "oversubscribed dynamic bit lengths tree"; + } + else if(result == Z_BUF_ERROR || bb[0] == 0){ + z.msg = "incomplete dynamic bit lengths tree"; + result = Z_DATA_ERROR; + } + return result; +} + +InfTree.prototype.inflate_trees_dynamic = function(nl, nd, c, bl, bd, tl, td, hp, z) { + var result; + + // build literal/length tree + this.initWorkArea(288); + this.hn[0]=0; + result = this.huft_build(c, 0, nl, 257, cplens, cplext, tl, bl, hp, this.hn, this.v); + if (result != Z_OK || bl[0] == 0){ + if(result == Z_DATA_ERROR){ + z.msg = "oversubscribed literal/length tree"; + } + else if (result != Z_MEM_ERROR){ + z.msg = "incomplete literal/length tree"; + result = Z_DATA_ERROR; + } + return result; + } + + // build distance tree + this.initWorkArea(288); + result = this.huft_build(c, nl, nd, 0, cpdist, cpdext, td, bd, hp, this.hn, this.v); + + if (result != Z_OK || (bd[0] == 0 && nl > 257)){ + if (result == Z_DATA_ERROR){ + z.msg = "oversubscribed distance tree"; + } + else if (result == Z_BUF_ERROR) { + z.msg = "incomplete distance tree"; + result = Z_DATA_ERROR; + } + else if (result != Z_MEM_ERROR){ + z.msg = "empty distance tree with lengths"; + result = Z_DATA_ERROR; + } + return result; + } + + return Z_OK; +} +/* + static int inflate_trees_fixed(int[] bl, //literal desired/actual bit depth + int[] bd, //distance desired/actual bit depth + int[][] tl,//literal/length tree result + int[][] td,//distance tree result + ZStream z //for memory allocation + ){ + +*/ + +function inflate_trees_fixed(bl, bd, tl, td, z) { + bl[0]=fixed_bl; + bd[0]=fixed_bd; + tl[0]=fixed_tl; + td[0]=fixed_td; + return Z_OK; +} + +InfTree.prototype.initWorkArea = function(vsize){ + if(this.hn==null){ + this.hn=new Int32Array(1); + this.v=new Int32Array(vsize); + this.c=new Int32Array(BMAX+1); + this.r=new Int32Array(3); + this.u=new Int32Array(BMAX); + this.x=new Int32Array(BMAX+1); + } + if(this.v.length 100) { + arrayCopy_fast(new Uint8Array(src.buffer, src.byteOffset + srcOffset, count), dest, destOffset); + } else { + arrayCopy_slow(src, srcOffset, dest, destOffset, count); + } + +} + +function arrayCopy_slow(src, srcOffset, dest, destOffset, count) { + + // dlog('_slow call: srcOffset=' + srcOffset + '; destOffset=' + destOffset + '; count=' + count); + + for (var i = 0; i < count; ++i) { + dest[destOffset + i] = src[srcOffset + i]; + } +} + +function arrayCopy_fast(src, dest, destOffset) { + dest.set(src, destOffset); +} + + + // largest prime smaller than 65536 +var ADLER_BASE=65521; + // NMAX is the largest n such that 255n(n+1)/2 + (n+1)(BASE-1) <= 2^32-1 +var ADLER_NMAX=5552; + +function adler32(adler, /* byte[] */ buf, index, len){ + if(buf == null){ return 1; } + + var s1=adler&0xffff; + var s2=(adler>>16)&0xffff; + var k; + + while(len > 0) { + k=len=16){ + s1+=buf[index++]&0xff; s2+=s1; + s1+=buf[index++]&0xff; s2+=s1; + s1+=buf[index++]&0xff; s2+=s1; + s1+=buf[index++]&0xff; s2+=s1; + s1+=buf[index++]&0xff; s2+=s1; + s1+=buf[index++]&0xff; s2+=s1; + s1+=buf[index++]&0xff; s2+=s1; + s1+=buf[index++]&0xff; s2+=s1; + s1+=buf[index++]&0xff; s2+=s1; + s1+=buf[index++]&0xff; s2+=s1; + s1+=buf[index++]&0xff; s2+=s1; + s1+=buf[index++]&0xff; s2+=s1; + s1+=buf[index++]&0xff; s2+=s1; + s1+=buf[index++]&0xff; s2+=s1; + s1+=buf[index++]&0xff; s2+=s1; + s1+=buf[index++]&0xff; s2+=s1; + k-=16; + } + if(k!=0){ + do{ + s1+=buf[index++]&0xff; s2+=s1; + } + while(--k!=0); + } + s1%=ADLER_BASE; + s2%=ADLER_BASE; + } + return (s2<<16)|s1; +} + + + +function jszlib_inflate_buffer(buffer, start, length, afterUncOffset) { + if (!start) { + buffer = new Uint8Array(buffer); + } else if (!length) { + buffer = new Uint8Array(buffer, start, buffer.byteLength - start); + } else { + buffer = new Uint8Array(buffer, start, length); + } + + var z = new ZStream(); + z.inflateInit(DEF_WBITS, true); + z.next_in = buffer; + z.next_in_index = 0; + z.avail_in = buffer.length; + + var oBlockList = []; + var totalSize = 0; + while (true) { + var obuf = new Uint8Array(32000); + z.next_out = obuf; + z.next_out_index = 0; + z.avail_out = obuf.length; + var status = z.inflate(Z_NO_FLUSH); + if (status != Z_OK && status != Z_STREAM_END && status != Z_BUF_ERROR) { + throw z.msg; + } + if (z.avail_out != 0) { + var newob = new Uint8Array(obuf.length - z.avail_out); + arrayCopy(obuf, 0, newob, 0, (obuf.length - z.avail_out)); + obuf = newob; + } + oBlockList.push(obuf); + totalSize += obuf.length; + if (status == Z_STREAM_END || status == Z_BUF_ERROR) { + break; + } + } + + if (afterUncOffset) { + afterUncOffset[0] = (start || 0) + z.next_in_index; + } + + if (oBlockList.length == 1) { + return oBlockList[0].buffer; + } else { + var out = new Uint8Array(totalSize); + var cursor = 0; + for (var i = 0; i < oBlockList.length; ++i) { + var b = oBlockList[i]; + arrayCopy(b, 0, out, cursor, b.length); + cursor += b.length; + } + return out.buffer; + } +} + +return { + inflateBuffer: jszlib_inflate_buffer, + arrayCopy: arrayCopy + }; +}); diff --git a/client/galaxy/scripts/libs/bbi/spans.js b/client/galaxy/scripts/libs/bbi/spans.js new file mode 100644 index 00000000000..7c61b8594c4 --- /dev/null +++ b/client/galaxy/scripts/libs/bbi/spans.js @@ -0,0 +1,257 @@ +/* -*- mode: javascript; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +// +// Dalliance Genome Explorer +// (c) Thomas Down 2006-2010 +// +// spans.js: JavaScript Intset/Location port. +// + +define([], function() { + +"use strict"; + + +function Range(min, max) +{ + if (typeof(min) != 'number' || typeof(max) != 'number') + throw 'Bad range ' + min + ',' + max; + this._min = min; + this._max = max; +} + +Range.prototype.min = function() { + return this._min; +} + +Range.prototype.max = function() { + return this._max; +} + +Range.prototype.contains = function(pos) { + return pos >= this._min && pos <= this._max; +} + +Range.prototype.isContiguous = function() { + return true; +} + +Range.prototype.ranges = function() { + return [this]; +} + +Range.prototype._pushRanges = function(ranges) { + ranges.push(this); +} + +Range.prototype.toString = function() { + return '[' + this._min + '-' + this._max + ']'; +} + +function _Compound(ranges) { + // given: a set of unsorted possibly overlapping ranges + // sort the input ranges + var sorted = ranges.sort(_rangeOrder); + // merge overlaps between adjacent ranges + var merged = []; + var current = sorted.shift(); + sorted.forEach(function(range) { + if (range._min <= current._max) { + if (range._max > current._max) { + current._max = range._max; + } + } + else { + merged.push(current); + current = range; + } + }); + merged.push(current); + this._ranges = merged; +} + +_Compound.prototype.min = function() { + return this._ranges[0].min(); +} + +_Compound.prototype.max = function() { + return this._ranges[this._ranges.length - 1].max(); +} + +// returns the index of the first range that is not less than pos +_Compound.prototype.lower_bound = function(pos) { + // first check if pos is out of range + var r = this.ranges(); + if (pos > this.max()) return r.length; + if (pos < this.min()) return 0; + // do a binary search + var a=0, b=r.length - 1; + while (a <= b) { + var m = Math.floor((a+b)/2); + if (pos > r[m]._max) { + a = m+1; + } + else if (pos < r[m]._min) { + b = m-1; + } + else { + return m; + } + } + return a; +} + +_Compound.prototype.contains = function(pos) { + var lb = this.lower_bound(pos); + if (lb < this._ranges.length && this._ranges[lb].contains(pos)) { + return true; + } + return false; +} + +_Compound.prototype.insertRange = function(range) { + var lb = this.lower_bound(range._min); + if (lb === this._ranges.length) { // range follows this + this._ranges.push(range); + return; + } + + var r = this.ranges(); + if (range._max < r[lb]._min) { // range preceeds lb + this._ranges.splice(lb,0,range); + return; + } + + // range overlaps lb (at least) + if (r[lb]._min < range._min) range._min = r[lb]._min; + var ub = lb+1; + while (ub < r.length && r[ub]._min <= range._max) { + ub++; + } + ub--; + // ub is the upper bound of the new range + if (r[ub]._max > range._max) range._max = r[ub]._max; + + // splice range into this._ranges + this._ranges.splice(lb,ub-lb+1,range); + return; +} + +_Compound.prototype.isContiguous = function() { + return this._ranges.length > 1; +} + +_Compound.prototype.ranges = function() { + return this._ranges; +} + +_Compound.prototype._pushRanges = function(ranges) { + for (var ri = 0; ri < this._ranges.length; ++ri) + ranges.push(this._ranges[ri]); +} + +_Compound.prototype.toString = function() { + var s = ''; + for (var r = 0; r < this._ranges.length; ++r) { + if (r>0) { + s = s + ','; + } + s = s + this._ranges[r].toString(); + } + return s; +} + +function union(s0, s1) { + if (! (s0 instanceof _Compound)) { + if (! (s0 instanceof Array)) + s0 = [s0]; + s0 = new _Compound(s0); + } + + if (s1) + s0.insertRange(s1); + + return s0; +} + +function intersection(s0, s1) { + var r0 = s0.ranges(); + var r1 = s1.ranges(); + var l0 = r0.length, l1 = r1.length; + var i0 = 0, i1 = 0; + var or = []; + + while (i0 < l0 && i1 < l1) { + var s0 = r0[i0], s1 = r1[i1]; + var lapMin = Math.max(s0.min(), s1.min()); + var lapMax = Math.min(s0.max(), s1.max()); + if (lapMax >= lapMin) { + or.push(new Range(lapMin, lapMax)); + } + if (s0.max() > s1.max()) { + ++i1; + } else { + ++i0; + } + } + + if (or.length == 0) { + return null; // FIXME + } else if (or.length == 1) { + return or[0]; + } else { + return new _Compound(or); + } +} + +function coverage(s) { + var tot = 0; + var rl = s.ranges(); + for (var ri = 0; ri < rl.length; ++ri) { + var r = rl[ri]; + tot += (r.max() - r.min() + 1); + } + return tot; +} + + + +function rangeOrder(a, b) +{ + if (a.min() < b.min()) { + return -1; + } else if (a.min() > b.min()) { + return 1; + } else if (a.max() < b.max()) { + return -1; + } else if (b.max() > a.max()) { + return 1; + } else { + return 0; + } +} + +function _rangeOrder(a, b) +{ + if (a._min < b._min) { + return -1; + } else if (a._min > b._min) { + return 1; + } else if (a._max < b._max) { + return -1; + } else if (b._max > a._max) { + return 1; + } else { + return 0; + } +} + +return { + Range: Range, + union: union, + intersection: intersection, + coverage: coverage, + rangeOver: rangeOrder, + _rangeOrder: _rangeOrder +}; +}); diff --git a/client/galaxy/scripts/viz/bbi-data-manager.js b/client/galaxy/scripts/viz/bbi-data-manager.js new file mode 100644 index 00000000000..23d0da9e6d2 --- /dev/null +++ b/client/galaxy/scripts/viz/bbi-data-manager.js @@ -0,0 +1,60 @@ +define( ["viz/visualization", "libs/bbi/bigwig"], + function(visualization, bigwig) { + + /** + * Data manager for BBI datasets/files, including BigWig and BigBed. + */ + var BBIDataManager = visualization.GenomeDataManager.extend({ + + /** + * Load data from server and manages data entries. Adds a Deferred to manager + * for region; when data becomes available, replaces Deferred with data. + * Returns the Deferred that resolves when data is available. + */ + load_data: function(region, mode, resolution, extra_params) { + var deferred = $.Deferred(); + this.set_data(region, deferred); + + var url = galaxy_config.root + 'datasets/' + this.get('dataset').id + '/display', + self = this; + var promise = new $.Deferred(); + $.when(bigwig.makeBwg(url)).then(function(bb, err) { + $.when(bb.readWigData(region.get("chrom"), region.get("start"), region.get("end"))).then(function(data) { + // Transform data into "bigwig" format. "bigwig" format is an array of 2-element arrays + // where each array is [position, score]. + var result = []; + data.forEach(function(d) { + // Each data element includes a min and max. If min and max are the same, + // then entry is single base-pair resolution and only a single data point + // is added. Otherwise entry is multiple base pairs and two data points are + // added, one for the start and one for the end. + + // Add data point for entry start. + result.push([d.min, d.score]); + + if (d.min !== d.max) { + // Multi base-pair entry, so two data points are generated. + result.push([d.max, d.score]); + } + }); + + var entry = { + data: result, + region: region, + dataset_type: 'bigwig' + }; + + self.set_data(region, entry); + deferred.resolve(entry); + }); + }); + + return deferred; + }, + }); + + return { + BBIDataManager: BBIDataManager + }; + +}); diff --git a/client/galaxy/scripts/viz/trackster/tracks.js b/client/galaxy/scripts/viz/trackster/tracks.js index a84f2e660fc..f3a3fd26d37 100644 --- a/client/galaxy/scripts/viz/trackster/tracks.js +++ b/client/galaxy/scripts/viz/trackster/tracks.js @@ -9,8 +9,9 @@ define([ "mvc/dataset/data", "mvc/tool/tools", "utils/config", + "viz/bbi-data-manager", "ui/editable-text", -], function(_, visualization, viz_views, util, slotting, painters, filters_mod, data, tools_mod, config_mod) { +], function(_, visualization, viz_views, util, slotting, painters, filters_mod, data, tools_mod, config_mod, bbi) { var extend = _.extend; @@ -187,6 +188,18 @@ function round(num, places) { return Math.round(num * val) / val; } +/** + * Check if a server can do byte range requests. + */ +function supportsByteRanges(url) { + var promise = $.Deferred(); + $.get(url).success(function (result, status, xhr) { + promise.resolve(xhr.getResponseHeader("Accept-Ranges") === "bytes"); + }); + + return promise; +} + /** * Drawables hierarchy: * @@ -3078,7 +3091,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { if ( [undefined, null, 0].indexOf(this.config.get_value("max_value")) !== -1 ) { this.config.set_value("max_value", _.max( _.map(result.data, function(d) { return d[1]; }) ) || 0); } - + var canvas = ctx.canvas, painter = new painters.LinePainter(result.data, region.get('start'), region.get('end'), this.config.to_key_value_dict(), mode); painter.draw(ctx, canvas.width, canvas.height, w_scale); @@ -3601,7 +3614,22 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, { var LineTrack = function (view, container, obj_dict) { this.mode = "Histogram"; TiledTrack.call(this, view, container, obj_dict); + + // var self = this; + // $.when(supportsByteRanges(galaxy_config.root + 'datasets/' + this.dataset.id + '/display')) + // .then(function(supportsByteRanges) { + // if (supportsByteRanges) { + // self.data_manager = new bbi.BBIDataManager({ + // dataset: this.dataset + // }); + // } + // + // }); + this.data_manager = new bbi.BBIDataManager({ + dataset: this.dataset + }); }; + extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, { display_modes: CONTINUOUS_DATA_MODES, diff --git a/static/maps/libs/bbi/bigwig.js.map b/static/maps/libs/bbi/bigwig.js.map new file mode 100644 index 00000000000..d42e36b83f9 --- /dev/null +++ b/static/maps/libs/bbi/bigwig.js.map @@ -0,0 +1 @@ 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p=e/4,q=l[p],r=l[p+1],s=l[p+2],t=l[p+3],u=g(i,e+16);(0>a||a>q||q==a&&c>=r)&&(0>a||s>a||s==a&&t>=b)&&w.push(u),e+=24}w.length>0&&k(w,f+1)}};return k([d.cirTreeOffset+48],1),e},i.prototype.fetchFeatures=function(a,b){var d=this,e=$.Deferred();if(b.sort(function(a,b){return(0|a.offset)-(0|b.offset)}),0===b.length)return[];var g=[],h=function(a,b,e,f){f||(f={});var h=new c;h._chromId=a,h.segment=d.bwg.idsToChroms[a],h.min=b,h.max=e,h.type=d.bwg.type;for(var i in f)h[i]=f[i];g.push(h)},i=function(){if(0===b.length){{Date.now()}return e.resolve(g)}var c=b[0];if(c.data)d.parseFeatures(c.data,h,a),b.splice(0,1),i();else{for(var j=c.offset,k=c.size,l=1;lc;){var f,g=b[e];if(d.bwg.uncompressBufSize>0)f=o(a,c+2,g.size-2);else{var h=new Uint8Array(g.size);p(new Uint8Array(a,c,g.size),0,h,0,g.size),f=h.buffer}g.data=f,c+=g.size,++e}i()})}};return i(),e},i.prototype.parseFeatures=function(a,b,c){var e=new Uint8Array(a);if(this.isSummary)for(var f=new Int16Array(a),g=new Int32Array(a),h=new 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C=parseInt(K[1]);isNaN(C)||(L.score=C)}if(K.length>2&&G>5&&(L.orientation=K[2]),K.length>5&&G>8){var M=K[5];B.test(M)&&(L.itemRgb="rgb("+M+")")}if(K.length>G-3&&H)for(var N=G-3;NG)b(k,o+1,p,L);else{var O=0|K[3],P=0|K[4],Q=0|K[6],R=K[7].split(","),S=K[8].split(",");if(L.exonFrames){var T=L.exonFrames.split(",");L.exonFrames=void 0}L.type="transcript";var U=new d;for(var V in L)U[V]=L[V];if(U.id=K[0],U.segment=this.bwg.idsToChroms[k],U.min=o+1,U.max=p,U.notes=[],L.groups=[U],K.length>9){var W=L.geneName||K[9],X=W;K.length>10&&(X=K[10]),L.geneName2&&(X=L.geneName2);var Y=$.extend({},U);Y.id=W,Y.label=X,Y.type="gene",L.groups.push(Y)}for(var Z=[],_=0;Q>_;++_){var aa=(0|S[_])+o,ba=aa+(0|R[_]),ca=new l(aa,ba);Z.push(ca)}for(var da=m(Z),ea=da.ranges(),fa=0;faO){var ha="+"==L.orientation?new l(O,P+3):new l(O-3,P),ia=n(da,ha);if(ia){L.type="translation";for(var ja=ia.ranges(),ka=0,la=0;ja[0].min()>ea[la].max();)la++;for(var fa=0;fa=0&&2>=na&&(L.readframe=na,L.readframeExplicit=!0)}var oa=ga.max()-ga.min();ka=(ka+oa)%3,b(k,ga.min()+1,ga.max(),L)}}}}}}},i.prototype.getFirstAdjacent=function(a,b,c,d){var e=this.bwg.chromsToIDs[a];return void 0===e?d([]):void this.getFirstAdjacentById(e,b,c,d)},i.prototype.getFirstAdjacentById=function(a,b,c,d){var e=this;if(!this.cirHeader)return void this.bwg.data.slice(this.cirTreeOffset,48).fetch(function(f){e.cirHeader=f;var g=new Int32Array(e.cirHeader);e.cirBlockSize=g[1],e.getFirstAdjacentById(a,b,c,d)});var f=null,h=-1,i=-1,j=0,k=(Date.now(),function(a,b){j+=a.length;for(var c,d=4+32*e.cirBlockSize,f=0;f0&&(0!=a||b>0)?e.getFirstAdjacentById(0,0,c,d):0>c&&(a!=e.bwg.maxID||1e9>b)?e.getFirstAdjacentById(e.bwg.maxID,1e9,c,d):d([]);e.fetchFeatures(function(d,e,f){return 0>c&&(a>d||b>f)||c>0&&(d>a||e>b)},[f],function(a){for(var b=null,e=-1,f=-1,g=0;gc&&(i>e||k>f)||c>0&&(e>i||f>j))&&(b=h,f=0>c?k:j,e=i)}return d(null!=b?[b]:[])})}})},o=function(d,j,l){var m=new Uint8Array(d),n=new Int16Array(d),o=new 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exports?module.exports=b(require("jquery")):b(a.jQuery)}(this,function(a){var b=a.ajaxSettings;b.responseFields.native="responseNative",b.converters["* native"]=!0;var c={},d=0,e={0:200,1223:204},f={},g=jQuery.ajaxSettings.xhr();window.ActiveXObject&&a(window).on("unload",function(){for(var a in f)f[a]()}),c.cors=!!g&&"withCredentials"in g,c.ajax=g=!!g,a.ajaxTransport("native",function(a){var b;return c.cors||g&&!a.crossDomain?{send:function(c,g){var h,i=a.xhr(),j=++d,k={};if(i.open(a.type,a.url,a.async,a.username,a.password),a.xhrFields)for(h in a.xhrFields)i[h]=a.xhrFields[h];a.mimeType&&i.overrideMimeType&&i.overrideMimeType(a.mimeType),a.crossDomain||c["X-Requested-With"]||(c["X-Requested-With"]="XMLHttpRequest");for(h in c)i.setRequestHeader(h,c[h]);b=function(a){return function(){b&&(delete 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Uint8Array(c),this.end=c,this.checkfn=b,this.mode=O,this.reset(a,null),this.left=0,this.table=0,this.index=0,this.blens=null,this.bb=new Int32Array(1),this.tb=new Int32Array(1),this.codes=new d,this.last=0,this.bitk=0,this.bitb=0,this.read=0,this.write=0,this.check=0,this.inftree=new e}function d(){}function e(){}function f(a,b,c,d){return a[0]=Y,b[0]=Z,c[0]=$,d[0]=_,s}function g(a,b,c,d,e){if(0!=e){if(!a)throw"Undef src";if(!c)throw"Undef dest";0==b&&e==a.length?i(a,c,d):ra?i(a.subarray(b,b+e),c,d):1==a.BYTES_PER_ELEMENT&&e>100?i(new Uint8Array(a.buffer,a.byteOffset+b,e),c,d):h(a,b,c,d,e)}}function h(a,b,c,d,e){for(var f=0;e>f;++f)c[d+f]=a[b+f]}function i(a,b,c){b.set(a,c)}function j(b,c,d,e){b=c?d?new Uint8Array(b,c,d):new Uint8Array(b,c,b.byteLength-c):new Uint8Array(b);var f=new a;f.inflateInit(l,!0),f.next_in=b,f.next_in_index=0,f.avail_in=b.length;for(var h=[],i=0;;){var j=new Uint8Array(32e3);f.next_out=j,f.next_out_index=0,f.avail_out=j.length;var k=f.inflate(p);if(k!=s&&k!=t&&k!=y)throw f.msg;if(0!=f.avail_out){var m=new Uint8Array(j.length-f.avail_out);g(j,0,m,0,j.length-f.avail_out),j=m}if(h.push(j),i+=j.length,k==t||k==y)break}if(e&&(e[0]=(c||0)+f.next_in_index),1==h.length)return h[0].buffer;for(var n=new Uint8Array(i),o=0,q=0;qb&&(b=-b,nowrap=1),8>b||b>15?(this.inflateEnd(a),v):(this.wbits=b,a.istate.blocks=new c(a,0!=a.istate.nowrap?null:this,1<>4)+8>a.istate.wbits){a.istate.mode=M,a.msg="invalid window size",a.istate.marker=5;break}a.istate.mode=A;case A:if(0==a.avail_in)return c;if(c=b,a.avail_in--,a.total_in++,d=255&a.next_in[a.next_in_index++],((a.istate.method<<8)+d)%31!=0){a.istate.mode=M,a.msg="incorrect header check",a.istate.marker=5;break}if(0==(d&o)){a.istate.mode=G;break}a.istate.mode=B;case B:if(0==a.avail_in)return c;c=b,a.avail_in--,a.total_in++,a.istate.need=(255&a.next_in[a.next_in_index++])<<24&4278190080,a.istate.mode=C;case C:if(0==a.avail_in)return c;c=b,a.avail_in--,a.total_in++,a.istate.need+=(255&a.next_in[a.next_in_index++])<<16&16711680,a.istate.mode=D;case D:if(0==a.avail_in)return c;c=b,a.avail_in--,a.total_in++,a.istate.need+=(255&a.next_in[a.next_in_index++])<<8&65280,a.istate.mode=E;case E:return 0==a.avail_in?c:(c=b,a.avail_in--,a.total_in++,a.istate.need+=255&a.next_in[a.next_in_index++],a.adler=a.istate.need,a.istate.mode=F,u);case F:return a.istate.mode=M,a.msg="need dictionary",a.istate.marker=0,v;case G:if(c=a.istate.blocks.proc(a,c),c==w){a.istate.mode=M,a.istate.marker=0;break}if(c==s&&(c=b),c!=t)return c;if(c=b,a.istate.blocks.reset(a,a.istate.was),0!=a.istate.nowrap){a.istate.mode=L;break}a.istate.mode=H;case H:if(0==a.avail_in)return c;c=b,a.avail_in--,a.total_in++,a.istate.need=(255&a.next_in[a.next_in_index++])<<24&4278190080,a.istate.mode=I;case I:if(0==a.avail_in)return c;c=b,a.avail_in--,a.total_in++,a.istate.need+=(255&a.next_in[a.next_in_index++])<<16&16711680,a.istate.mode=J;case J:if(0==a.avail_in)return c;c=b,a.avail_in--,a.total_in++,a.istate.need+=(255&a.next_in[a.next_in_index++])<<8&65280,a.istate.mode=K;case K:if(0==a.avail_in)return c;if(c=b,a.avail_in--,a.total_in++,a.istate.need+=255&a.next_in[a.next_in_index++],a.istate.was[0]!=a.istate.need){a.istate.mode=M,a.msg="incorrect data check",a.istate.marker=5;break}a.istate.mode=L;case L:return t;case M:return w;default:return v}},b.prototype.inflateSetDictionary=function(a,b,c){var d=0,e=c;return null==a||null==a.istate||a.istate.mode!=F?v:a._adler.adler32(1,b,0,c)!=a.adler?w:(a.adler=a._adler.adler32(0,null,0,0),e>=1<d;)a.next_in[c]==ea[d]?d++:d=0!=a.next_in[c]?0:4-d,c++,b--;return a.total_in+=c-a.next_in_index,a.next_in_index=c,a.avail_in=b,a.istate.marker=d,4!=d?w:(e=a.total_in,f=a.total_out,this.inflateReset(a),a.total_in=e,a.total_out=f,a.istate.mode=G,s)},b.prototype.inflateSyncPoint=function(a){return null==a||null==a.istate||null==a.istate.blocks?v:a.istate.blocks.sync_point()};var fa=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];c.prototype.reset=function(a,b){b&&(b[0]=this.check),this.mode==U&&this.codes.free(a),this.mode=O,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(a.adler=this.check=a._adler.adler32(0,null,0,0))},c.prototype.proc=function(a,b){var c,d,e,h,i,j,k;for(h=a.next_in_index,i=a.avail_in,d=this.bitb,e=this.bitk,j=this.write,k=je;){if(0==i)return this.bitb=d,this.bitk=e,a.avail_in=i,a.total_in+=h-a.next_in_index,a.next_in_index=h,this.write=j,this.inflate_flush(a,b);b=s,i--,d|=(255&a.next_in[h++])<>>1){case 0:d>>>=3,e-=3,c=7&e,d>>>=c,e-=c,this.mode=P;break;case 1:var l=new Int32Array(1),m=new Int32Array(1),n=[],o=[];f(l,m,n,o,a),this.codes.init(l[0],m[0],n[0],0,o[0],0,a),d>>>=3,e-=3,this.mode=U;break;case 2:d>>>=3,e-=3,this.mode=R;break;case 3:return d>>>=3,e-=3,this.mode=M,a.msg="invalid block type",b=w,this.bitb=d,this.bitk=e,a.avail_in=i,a.total_in+=h-a.next_in_index,a.next_in_index=h,this.write=j,this.inflate_flush(a,b)}break;case P:for(;32>e;){if(0==i)return this.bitb=d,this.bitk=e,a.avail_in=i,a.total_in+=h-a.next_in_index,a.next_in_index=h,this.write=j,this.inflate_flush(a,b);b=s,i--,d|=(255&a.next_in[h++])<>>16&65535)!=(65535&d))return this.mode=M,a.msg="invalid stored block lengths",b=w,this.bitb=d,this.bitk=e,a.avail_in=i,a.total_in+=h-a.next_in_index,a.next_in_index=h,this.write=j,this.inflate_flush(a,b);this.left=65535&d,d=e=0,this.mode=0!=this.left?Q:0!=this.last?V:O;break;case Q:if(0==i)return this.bitb=d,this.bitk=e,a.avail_in=i,a.total_in+=h-a.next_in_index,a.next_in_index=h,write=j,this.inflate_flush(a,b);if(0==k&&(j==end&&0!=read&&(j=0,k=ji&&(c=i),c>k&&(c=k),g(a.next_in,h,this.window,j,c),h+=c,i-=c,j+=c,k-=c,0!=(this.left-=c))break;this.mode=0!=this.last?V:O;break;case R:for(;14>e;){if(0==i)return this.bitb=d,this.bitk=e,a.avail_in=i,a.total_in+=h-a.next_in_index,a.next_in_index=h,this.write=j,this.inflate_flush(a,b);b=s,i--,d|=(255&a.next_in[h++])<29||(c>>5&31)>29)return this.mode=X,a.msg="too many length or distance symbols",b=w,this.bitb=d,this.bitk=e,a.avail_in=i,a.total_in+=h-a.next_in_index,a.next_in_index=h,this.write=j,this.inflate_flush(a,b);if(c=258+(31&c)+(c>>5&31),null==this.blens||this.blens.lengthp;p++)this.blens[p]=0;d>>>=14,e-=14,this.index=0,mode=S;case S:for(;this.index<4+(this.table>>>10);){for(;3>e;){if(0==i)return this.bitb=d,this.bitk=e,a.avail_in=i,a.total_in+=h-a.next_in_index,a.next_in_index=h,this.write=j,this.inflate_flush(a,b);b=s,i--,d|=(255&a.next_in[h++])<>>=3,e-=3}for(;this.index<19;)this.blens[fa[this.index++]]=0;if(this.bb[0]=7,c=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,a),c!=s)return b=c,b==w&&(this.blens=null,this.mode=X),this.bitb=d,this.bitk=e,a.avail_in=i,a.total_in+=h-a.next_in_index,a.next_in_index=h,write=j,this.inflate_flush(a,b);this.index=0,this.mode=T;case T:for(;;){if(c=this.table,!(this.index<258+(31&c)+(c>>5&31)))break;var p,q,r;for(c=this.bb[0];c>e;){if(0==i)return this.bitb=d,this.bitk=e,a.avail_in=i,a.total_in+=h-a.next_in_index,a.next_in_index=h,this.write=j,this.inflate_flush(a,b);b=s,i--,d|=(255&a.next_in[h++])<r)d>>>=c,e-=c,this.blens[this.index++]=r;else{for(p=18==r?7:r-14,q=18==r?11:3;c+p>e;){if(0==i)return this.bitb=d,this.bitk=e,a.avail_in=i,a.total_in+=h-a.next_in_index,a.next_in_index=h,this.write=j,this.inflate_flush(a,b);b=s,i--,d|=(255&a.next_in[h++])<>>=c,e-=c,q+=d&N[p],d>>>=p,e-=p,p=this.index,c=this.table,p+q>258+(31&c)+(c>>5&31)||16==r&&1>p)return this.blens=null,this.mode=X,a.msg="invalid bit length repeat",b=w,this.bitb=d,this.bitk=e,a.avail_in=i,a.total_in+=h-a.next_in_index,a.next_in_index=h,this.write=j,this.inflate_flush(a,b);r=16==r?this.blens[p-1]:0;do this.blens[p++]=r;while(0!=--q);this.index=p}}this.tb[0]=-1;var l=new Int32Array(1),m=new Int32Array(1),n=new Int32Array(1),o=new Int32Array(1);if(l[0]=9,m[0]=6,c=this.table,c=this.inftree.inflate_trees_dynamic(257+(31&c),1+(c>>5&31),this.blens,l,m,n,o,this.hufts,a),c!=s)return c==w&&(this.blens=null,this.mode=M),b=c,this.bitb=d,this.bitk=e,a.avail_in=i,a.total_in+=h-a.next_in_index,a.next_in_index=h,this.write=j,this.inflate_flush(a,b);this.codes.init(l[0],m[0],this.hufts,n[0],this.hufts,o[0],a),this.mode=U;case U:if(this.bitb=d,this.bitk=e,a.avail_in=i,a.total_in+=h-a.next_in_index,a.next_in_index=h,this.write=j,(b=this.codes.proc(this,a,b))!=t)return this.inflate_flush(a,b);if(b=s,this.codes.free(a),h=a.next_in_index,i=a.avail_in,d=this.bitb,e=this.bitk,j=this.write,k=ja.avail_out&&(c=a.avail_out),0!=c&&b==y&&(b=s),a.avail_out-=c,a.total_out+=c,null!=this.checkfn&&(a.adler=this.check=a._adler.adler32(this.check,this.window,e,c)),g(this.window,e,a.next_out,d,c),d+=c,e+=c,e==this.end&&(e=0,this.write==this.end&&(this.write=0),c=this.write-e,c>a.avail_out&&(c=a.avail_out),0!=c&&b==y&&(b=s),a.avail_out-=c,a.total_out+=c,null!=this.checkfn&&(a.adler=this.check=a._adler.adler32(this.check,this.window,e,c)),g(this.window,e,a.next_out,d,c),d+=c,e+=c),a.next_out_index=d,this.read=e,b};var ga=0,ha=1,ia=2,ja=3,ka=4,la=5,ma=6,na=7,oa=8,pa=9;d.prototype.init=function(a,b,c,d,e,f){this.mode=ga,this.lbits=a,this.dbits=b,this.ltree=c,this.ltree_index=d,this.dtree=e,this.dtree_index=f,this.tree=null},d.prototype.proc=function(a,b,c){var d,e,f,g,h,i,j,k=0,l=0,m=0;for(m=b.next_in_index,g=b.avail_in,k=a.bitb,l=a.bitk,h=a.write,i=h=258&&g>=10&&(a.bitb=k,a.bitk=l,b.avail_in=g,b.total_in+=m-b.next_in_index,b.next_in_index=m,a.write=h,c=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,a,b),m=b.next_in_index,g=b.avail_in,k=a.bitb,l=a.bitk,h=a.write,i=hl;){if(0==g)return a.bitb=k,a.bitk=l,b.avail_in=g,b.total_in+=m-b.next_in_index,b.next_in_index=m,a.write=h,a.inflate_flush(b,c);c=s,g--,k|=(255&b.next_in[m++])<>>=this.tree[e+1],l-=this.tree[e+1],f=this.tree[e],0==f){this.lit=this.tree[e+2],this.mode=ma;break}if(0!=(16&f)){this.get=15&f,this.len=this.tree[e+2],this.mode=ia;break}if(0==(64&f)){this.need=f,this.tree_index=e/3+this.tree[e+2];break}if(0!=(32&f)){this.mode=na;break}return this.mode=pa,b.msg="invalid literal/length code",c=w,a.bitb=k,a.bitk=l,b.avail_in=g,b.total_in+=m-b.next_in_index,b.next_in_index=m,a.write=h,a.inflate_flush(b,c);case ia:for(d=this.get;d>l;){if(0==g)return a.bitb=k,a.bitk=l,b.avail_in=g,b.total_in+=m-b.next_in_index,b.next_in_index=m,a.write=h,a.inflate_flush(b,c);c=s,g--,k|=(255&b.next_in[m++])<>=d,l-=d,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=ja;case ja:for(d=this.need;d>l;){if(0==g)return a.bitb=k,a.bitk=l,b.avail_in=g,b.total_in+=m-b.next_in_index,b.next_in_index=m,a.write=h,a.inflate_flush(b,c);c=s,g--,k|=(255&b.next_in[m++])<>=this.tree[e+1],l-=this.tree[e+1],f=this.tree[e],0!=(16&f)){this.get=15&f,this.dist=this.tree[e+2],this.mode=ka;break}if(0==(64&f)){this.need=f,this.tree_index=e/3+this.tree[e+2];break}return this.mode=pa,b.msg="invalid distance code",c=w,a.bitb=k,a.bitk=l,b.avail_in=g,b.total_in+=m-b.next_in_index,b.next_in_index=m,a.write=h,a.inflate_flush(b,c);case ka:for(d=this.get;d>l;){if(0==g)return a.bitb=k,a.bitk=l,b.avail_in=g,b.total_in+=m-b.next_in_index,b.next_in_index=m,a.write=h,a.inflate_flush(b,c);c=s,g--,k|=(255&b.next_in[m++])<>=d,l-=d,this.mode=la;case la:for(j=h-this.dist;0>j;)j+=a.end;for(;0!=this.len;){if(0==i&&(h==a.end&&0!=a.read&&(h=0,i=h7&&(l-=8,g++,m--),a.write=h,c=a.inflate_flush(b,c),h=a.write,i=ho;)q--,n|=(255&i.next_in[p++])<>=k[B+1],o-=k[B+1],0!=(16&m)){for(m&=15,y=k[B+2]+(n&N[m]),n>>=m,o-=m;15>o;)q--,n|=(255&i.next_in[p++])<>=k[B+1],o-=k[B+1],0!=(16&m)){for(m&=15;m>o;)q--,n|=(255&i.next_in[p++])<>=m,o-=m,u-=y,r>=z)A=r-z,r-A>0&&2>r-A?(h.window[r++]=h.window[A++],h.window[r++]=h.window[A++],y-=2):(h.window[r++]=h.window[A++],h.window[r++]=h.window[A++],y-=2);else{A=r-z;do A+=h.end;while(0>A);if(m=h.end-A,y>m){if(y-=m,r-A>0&&m>r-A){do h.window[r++]=h.window[A++];while(0!=--m)}else g(h.window,A,h.window,r,m),r+=m,A+=m,m=0;A=0}}do h.window[r++]=h.window[A++];while(0!=--y);break}if(0!=(64&m))return i.msg="invalid distance code",y=i.avail_in-q,y=y>o>>3?o>>3:y,q+=y,p-=y,o-=y<<3,h.bitb=n,h.bitk=o,i.avail_in=q,i.total_in+=p-i.next_in_index,i.next_in_index=p,h.write=r,w;j+=k[B+2],j+=n&N[m],B=3*(l+j),m=k[B]}break}if(0!=(64&m))return 0!=(32&m)?(y=i.avail_in-q,y=y>o>>3?o>>3:y,q+=y,p-=y,o-=y<<3,h.bitb=n,h.bitk=o,i.avail_in=q,i.total_in+=p-i.next_in_index,i.next_in_index=p,h.write=r,t):(i.msg="invalid literal/length code",y=i.avail_in-q,y=y>o>>3?o>>3:y,q+=y,p-=y,o-=y<<3,h.bitb=n,h.bitk=o,i.avail_in=q,i.total_in+=p-i.next_in_index,i.next_in_index=p,h.write=r,w);if(j+=k[B+2],j+=n&N[m],B=3*(l+j),0==(m=k[B])){n>>=k[B+1],o-=k[B+1],h.window[r++]=k[B+2],u--;break}}else n>>=k[B+1],o-=k[B+1],h.window[r++]=k[B+2],u--}while(u>=258&&q>=10);return y=i.avail_in-q,y=y>o>>3?o>>3:y,q+=y,p-=y,o-=y<<3,h.bitb=n,h.bitk=o,i.avail_in=q,i.total_in+=p-i.next_in_index,i.next_in_index=p,h.write=r,s},e.prototype.huft_build=function(a,b,c,d,e,f,h,i,j,k,l){var o,p,q,r,t,u,v,x,z,A,B,C,D,E,F;A=0,t=c;do this.c[a[b+A]]++,A++,t--;while(0!=t);if(this.c[0]==c)return h[0]=-1,i[0]=0,s;for(x=i[0],u=1;n>=u&&0==this.c[u];u++);for(v=u,u>x&&(x=u),t=n;0!=t&&0==this.c[t];t--);for(q=t,x>t&&(x=t),i[0]=x,E=1<u;u++,E<<=1)if((E-=this.c[u])<0)return w;if((E-=this.c[t])<0)return w;for(this.c[t]+=E,this.x[1]=u=0,A=1,D=2;0!=--t;)this.x[D]=u+=this.c[A],D++,A++;t=0,A=0;do 0!=(u=a[b+A])&&(this.v[this.x[u]++]=t),A++;while(++t=v;v++)for(o=this.c[v];0!=o--;){for(;v>C+x;){if(r++,C+=x,F=q-C,F=F>x?x:F,(p=1<<(u=v-C))>o+1&&(p-=o+1,D=v,F>u))for(;++um)return w;this.u[r]=B=this.hn[0],this.hn[0]+=F,0!=r?(this.x[r]=t,this.r[0]=u,this.r[1]=x,u=t>>>C-x,this.r[2]=B-this.u[r-1]-u,g(this.r,0,j,3*(this.u[r-1]+u),3)):h[0]=B}for(this.r[1]=v-C,A>=c?this.r[0]=192:l[A]>>C;F>u;u+=p)g(this.r,0,j,3*(B+u),3);for(u=1<>>=1)t^=u;for(t^=u,z=(1<257?(j==w?i.msg="oversubscribed distance tree":j==y?(i.msg="incomplete distance tree",j=w):j!=x&&(i.msg="empty distance tree with lengths",j=w),j):s)},e.prototype.initWorkArea=function(a){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(a),this.c=new Int32Array(n+1),this.r=new Int32Array(3),this.u=new Int32Array(n),this.x=new Int32Array(n+1)),this.v.lengthb;b++)this.v[b]=0;for(var b=0;n+1>b;b++)this.c[b]=0;for(var b=0;3>b;b++)this.r[b]=0;g(this.c,0,this.u,0,n),g(this.c,0,this.x,0,n+1)};var qa=new Uint8Array(1),ra="function"==typeof qa.subarray;return{inflateBuffer:j,arrayCopy:g}}); +//# sourceMappingURL=../../../maps/libs/bbi/jszlib.js.map \ No newline at end of file diff --git a/static/scripts/libs/bbi/spans.js b/static/scripts/libs/bbi/spans.js new file mode 100644 index 00000000000..0fcb9024e26 --- /dev/null +++ b/static/scripts/libs/bbi/spans.js @@ -0,0 +1,2 @@ +define([],function(){"use strict";function a(a,b){if("number"!=typeof a||"number"!=typeof b)throw"Bad range "+a+","+b;this._min=a,this._max=b}function b(a){var b=a.sort(g),c=[],d=b.shift();b.forEach(function(a){a._min<=d._max?a._max>d._max&&(d._max=a._max):(c.push(d),d=a)}),c.push(d),this._ranges=c}function c(a,c){return a instanceof b||(a instanceof Array||(a=[a]),a=new b(a)),c&&a.insertRange(c),a}function d(c,d){for(var e=c.ranges(),f=d.ranges(),g=e.length,h=f.length,i=0,j=0,k=[];g>i&&h>j;){var c=e[i],d=f[j],l=Math.max(c.min(),d.min()),m=Math.min(c.max(),d.max());m>=l&&k.push(new a(l,m)),c.max()>d.max()?++j:++i}return 0==k.length?null:1==k.length?k[0]:new b(k)}function e(a){for(var b=0,c=a.ranges(),d=0;db.min()?1:a.max()a.max()?1:0}function g(a,b){return a._minb._min?1:a._maxa._max?1:0}return a.prototype.min=function(){return this._min},a.prototype.max=function(){return this._max},a.prototype.contains=function(a){return a>=this._min&&a<=this._max},a.prototype.isContiguous=function(){return!0},a.prototype.ranges=function(){return[this]},a.prototype._pushRanges=function(a){a.push(this)},a.prototype.toString=function(){return"["+this._min+"-"+this._max+"]"},b.prototype.min=function(){return this._ranges[0].min()},b.prototype.max=function(){return this._ranges[this._ranges.length-1].max()},b.prototype.lower_bound=function(a){var b=this.ranges();if(a>this.max())return b.length;if(a=c;){var e=Math.floor((c+d)/2);if(a>b[e]._max)c=e+1;else{if(!(aa._max&&(a._max=c[d]._max),this._ranges.splice(b,d-b+1,a)},b.prototype.isContiguous=function(){return this._ranges.length>1},b.prototype.ranges=function(){return this._ranges},b.prototype._pushRanges=function(a){for(var b=0;b0&&(a+=","),a+=this._ranges[b].toString();return a},{Range:a,union:c,intersection:d,coverage:e,rangeOver:f,_rangeOrder:g}}); +//# sourceMappingURL=../../../maps/libs/bbi/spans.js.map \ No newline at end of file diff --git a/static/scripts/viz/bbi-data-manager.js b/static/scripts/viz/bbi-data-manager.js new file mode 100644 index 00000000000..f3e9ee28f4e --- /dev/null +++ b/static/scripts/viz/bbi-data-manager.js @@ -0,0 +1,2 @@ +define(["viz/visualization","libs/bbi/bigwig"],function(a,b){var c=a.GenomeDataManager.extend({load_data:function(a){var c=$.Deferred();this.set_data(a,c);{var d=galaxy_config.root+"datasets/"+this.get("dataset").id+"/display",e=this;new $.Deferred}return $.when(b.makeBwg(d)).then(function(b){$.when(b.readWigData(a.get("chrom"),a.get("start"),a.get("end"))).then(function(b){var d=[];b.forEach(function(a){d.push([a.min,a.score]),a.min!==a.max&&d.push([a.max,a.score])});var f={data:d,region:a,dataset_type:"bigwig"};e.set_data(a,f),c.resolve(f)})}),c}});return{BBIDataManager:c}}); +//# sourceMappingURL=../../maps/viz/bbi-data-manager.js.map \ No newline at end of file diff --git a/static/scripts/viz/trackster/tracks.js b/static/scripts/viz/trackster/tracks.js index 3c47203d3ed..600ab98d317 100644 --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1,4 +1,4 @@ -define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/dataset/data","mvc/tool/tools","utils/config","ui/editable-text"],function(a,b,c,d,e,f,g,h,i,j){function k(a,b){b||(b=0);var c=Math.pow(10,b);return Math.round(a*c)/c}var l=a.extend,m={},n=function(a,b){m[a.attr("id")]=b},o=function(a,b,c,d){c=".group",m[a.attr("id")]=d,a.bind("drag",{handle:"."+b,relative:!0},function(a,b){var d,e,f,g,h,i=($(this),$(this).parent()),j=i.children(".track,.group"),k=m[$(this).attr("id")];if(e=$(this).parents(c),0!==e.length){f=e.position().top,g=f+e.outerHeight();var l=m[e.attr("id")];if(b.offsetYg)return $(this).insertAfter(e),l.remove_drawable(k),void l.container.add_drawable(k)}for(e=null,h=0;h=f&&b.offsetY<=g)return b.offsetY-f0?h-1:h))}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})},p=20,q=100,r=12e3,s=400,t=5e3,u=100,v="Cannot display dataset due to an error. ",w="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",x="No data for this chrom/contig.",y="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",A="Ready for display",B=10,C=["Histogram","Line","Filled","Intensity"],D=function(a,b,d){if(D.id_counter||(D.id_counter=0),this.id=D.id_counter++,this.view=a,this.container=b,this.drag_handle_class=d.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=j.ConfigSettingCollection.from_models_and_saved_values(this.config_params,d.prefs),this.config.get_value("name")||this.config.set_value("name",d.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,d.header!==!1){var e=new c.TrackHeaderView({model:this,id:this.id});this.header_div=e.$el,this.container_div.append(this.header_div);var f=e.icons_div;this.action_icons=e.action_icons,this.container_div.hover(function(){f.show()},function(){f.hide()})}};D.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(a){a.config.get_value("content_visible")?(a.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),a.hide_contents(),a.config.set_value("content_visible",!1)):(a.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),a.config.set_value("content_visible",!0),a.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(a){var b=new j.ConfigSettingCollectionView({collection:a.config});b.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(a){$(".tooltip").remove(),a.remove()}}],l(D.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return this.enabled&&this.config.get_value("content_visible")?!0:!1},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(a){this.old_name=this.config.get_value("name"),this.config.set_value("name",a)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var a=this.view;this.container_div.hide(0,function(){$(this).remove(),a.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var E=function(a,b,c){D.call(this,a,b,c),this.obj_type=c.obj_type,this.drawables=[]};l(E.prototype,D.prototype,{unpack_drawables:function(a){this.drawables=[];for(var b,c=0;c").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),n(this.container_div,this),n(this.content_div,this),o(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new g.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after($("
")),this.saved_filters_managers=[],"drawables"in c&&this.unpack_drawables(c.drawables),"filters"in c){var d=this.filters_manager;this.filters_manager=new g.FiltersManager(this,c.filters),d.parent_div.replaceWith(this.filters_manager.parent_div),c.filters.visible&&this.setup_multitrack_filtering()}};l(F.prototype,D.prototype,E.prototype,{action_icons_def:[D.prototype.action_icons_def[0],D.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(a){$(".tooltip").remove(),a.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(a){a.filters_manager.visible()?(a.filters_manager.clear_filters(),a._restore_filter_managers()):(a.setup_multitrack_filtering(),a.request_draw({clear_tile_cache:!0})),a.filters_manager.toggle()}},D.prototype.action_icons_def[2]],build_container_div:function(){var a=$("
").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(a),a},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var a=this.drawables.length;if(0===a)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===a)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof R),this.action_icons.filters_icon.hide();else{var b,c,d,e=!0,f=this.drawables[0].get_type(),h=0;for(b=0;a>b;b++){if(d=this.drawables[b],d.get_type()!==f){can_composite=!1;break}d instanceof V&&h++}if(e&&this.drawables[0]instanceof T?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),$(".tooltip").remove()),h>1&&h===this.drawables.length){var i,j={};for(d=this.drawables[0],c=0;c0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var a=0;a0){this.saved_filters_managers=[];for(var a=0;a").addClass("top-container").appendTo(c),this.browser_content_div=$("
").addClass("content").appendTo(c),this.bottom_container=$("
").addClass("bottom-container").appendTo(c),this.top_labeltrack=$("
").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=$("
").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,n(this.viewport_container,d),this.intro_div=$("
").addClass("intro").appendTo(this.viewport_container);$("
").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){b.select_datasets(Galaxy.root+"visualization/list_current_history_datasets",Galaxy.root+"api/datasets",{"f-dbkey":d.dbkey},function(b){a.each(b,function(a){d.add_drawable(Z(a,d,d))})})});this.nav_container=$("
").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=$("
").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=$("
").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=$("
").addClass("overview-viewport").appendTo(this.overview),this.overview_close=$("").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=$("
").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=$("
").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=$("
").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=$("
").addClass("nav-controls").appendTo(this.nav),this.chrom_select=$("").addClass("nav-input").hide().bind("keyup focusout",e).appendTo(this.nav_controls),this.location_span=$("").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){d.location_span.hide(),d.chrom_select.hide(),d.nav_input.val(d.chrom+":"+d.low+"-"+d.high),d.nav_input.css("display","inline-block"),d.nav_input.select(),d.nav_input.focus(),d.nav_input.autocomplete({source:function(a,b){var c=[],e=$.map(d.get_tracks(V),function(b){return b.data_manager.search_features(a.term).success(function(a){c=c.concat(a)})});$.when.apply($,e).done(function(){b($.map(c,function(a){return{label:a[0],value:a[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=$("").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=$("").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){d.zoom_out()}).appendTo(this.nav_controls),this.zi_link=$("").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){d.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){d.change_chrom(d.chrom_select.val())}),this.browser_content_div.click(function(){$(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(a){d.zoom_in(a.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(a,b){this.current_x=b.offsetX}).bind("drag",function(a,b){var c=b.offsetX-this.current_x;this.current_x=b.offsetX;var e=Math.round(c/d.viewport_container.width()*(d.max_high-d.max_low));d.move_delta(-e)}),this.overview_close.click(function(){d.reset_overview()}),this.viewport_container.bind("draginit",function(a){return a.clientX>d.viewport_container.width()-16?!1:void 0}).bind("dragstart",function(a,b){b.original_low=d.low,b.current_height=a.clientY,b.current_x=b.offsetX}).bind("drag",function(a,b){var c=$(this),e=b.offsetX-b.current_x,f=c.scrollTop()-(a.clientY-b.current_height);c.scrollTop(f),b.current_height=a.clientY,b.current_x=b.offsetX;var g=Math.round(e/d.viewport_container.width()*(d.high-d.low));d.move_delta(g)}),this.top_labeltrack.bind("dragstart",function(){return $("
").addClass("zoom-area").css("height",d.browser_content_div.height()+d.top_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(a,b){$(b.proxy).css({left:Math.min(a.pageX,b.startX)-d.container.offset().left,width:Math.abs(a.pageX-b.startX)});var c=Math.min(a.pageX,b.startX)-d.container.offset().left,e=Math.max(a.pageX,b.startX)-d.container.offset().left,f=d.high-d.low,g=d.viewport_container.width();d.update_location(Math.round(c/g*f)+d.low,Math.round(e/g*f)+d.low)}).bind("dragend",function(a,b){var c=Math.min(a.pageX,b.startX),e=Math.max(a.pageX,b.startX),f=d.high-d.low,g=d.viewport_container.width(),h=d.low;d.low=Math.round(c/g*f)+h,d.high=Math.round(e/g*f)+h,$(b.proxy).remove(),d.request_redraw()}),this.add_label_track(new Q(this,{content_div:this.top_labeltrack})),$(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){d.resize_window()},500)}),$(document).bind("redraw",function(){d.redraw()}),this.reset(),$(window).trigger("resize")},get_base_color:function(a){return this.config.get_value(a.toLowerCase()+"_color")||this.config.get_value("n_color")}});l(G.prototype,E.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(a,b,c,d){if(this.timer&&clearTimeout(this.timer),d){var e=this;this.timer=setTimeout(function(){e.trigger("navigate",a+":"+b+"-"+c)},500)}else view.trigger("navigate",a+":"+b+"-"+c)},update_location:function(a,b){this.location_span.text(d.commatize(a)+" - "+d.commatize(b)),this.nav_input.val(this.chrom+":"+d.commatize(a)+"-"+d.commatize(b));var c=this.chrom_select.val();""!==c&&this.trigger_navigate(c,this.low,this.high,!0)},load_chroms:function(a){a.num=u;var b=this,c=$.Deferred();return $.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:a,dataType:"json",success:function(a){if(0!==a.chrom_info.length){if(a.reference){var d=new S(b);b.add_label_track(d),b.reference_track=d}b.chrom_data=a.chrom_info;for(var e='',f=0,g=b.chrom_data.length;g>f;f++){var h=b.chrom_data[f].chrom;e+='"}a.prev_chroms&&(e+='"),a.next_chroms&&(e+='"),b.chrom_select.html(e),b.chrom_start_index=a.start_index,c.resolve(a.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+b.dbkey)}}),c},change_chrom:function(a,b,c){var d=this;if(!d.chrom_data)return void d.load_chroms_deferred.then(function(){d.change_chrom(a,b,c)});if(a&&"None"!==a){if("previous"===a)return void d.load_chroms({low:this.chrom_start_index-u});if("next"===a)return void d.load_chroms({low:this.chrom_start_index+u});var e=$.grep(d.chrom_data,function(b){return b.chrom===a})[0];if(void 0===e)return void d.load_chroms({chrom:a},function(){d.change_chrom(a,b,c)});if(a!==d.chrom){d.chrom=a,d.chrom_select.val(d.chrom),d.max_high=e.len-1,d.reset();for(var f=0,g=d.drawables.length;g>f;f++){var h=d.drawables[f];h.init&&h.init()}d.reference_track&&d.reference_track.init()}void 0===b&&void 0===c?(d.low=0,d.high=d.max_high):(d.low=void 0!==b?Math.max(b,0):0,void 0===c?(d.low=Math.max(d.low-15,0),d.high=d.low+30):d.high=Math.min(c,d.max_high)),d.request_redraw()}},go_to:function(a){a=a.replace(/,/g,""),a=a.replace(/:|\-/g," ");var b=a.split(/\s+/),c=b[0],d=b[1]?parseInt(b[1],10):void 0,e=b[2]?parseInt(b[2],10):void 0;this.change_chrom(c,d,e)},move_fraction:function(a){var b=this,c=b.high-b.low;this.move_delta(a*c)},move_delta:function(a){var b=this,c=b.high-b.low;b.low-ab.max_high?(b.high=b.max_high,b.low=b.max_high-c):(b.high-=a,b.low-=a),b.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){b.request_redraw()},200);var d=b.chrom_select.val();this.trigger_navigate(d,b.low,b.high,!0)},add_drawable:function(a){E.prototype.add_drawable.call(this,a),a.init(),this.changed(),this.update_intro_div();var b=this;a.config.on("change",function(){b.changed()})},add_label_track:function(a){a.view=this,a.init(),this.label_tracks.push(a)},remove_drawable:function(a,b){if(E.prototype.remove_drawable.call(this,a),b){var c=this;a.container_div.hide(0,function(){$(this).remove(),c.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(b,c){var d=this,e=c?[c]:d.drawables;a.each(e,function(c){var e=a.find(d.tracks_to_be_redrawn,function(a){return a[0]===c});e?e[1]=b:d.tracks_to_be_redrawn.push([c,b])}),this.requested_redraw||(requestAnimationFrame(function(){d._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var b=this.low,c=this.high;bthis.max_high&&(c=this.max_high);var d=this.high-this.low;0!==this.high&&df&&this.overview_box.css("left",e-(g-f)/2),this.overview_highlight&&this.overview_highlight.css({left:e,width:f}),a.each(this.tracks_to_be_redrawn,function(a){var b=a[0],c=a[1];b&&b._draw(c)}),this.tracks_to_be_redrawn=[],a.each(this.label_tracks,function(a){a._draw()})},zoom_in:function(a){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var b=this.high-this.low,c=b/2+this.low,d=b/this.zoom_factor/2;a&&(c=a/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(c-d),this.high=Math.round(c+d),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var a=this.high-this.low,b=a/2+this.low,c=a*this.zoom_factor/2;this.low=Math.round(b-c),this.high=Math.round(b+c),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(a){if(this.overview_drawable){if(this.overview_drawable.dataset.id===a.dataset.id)return;this.overview_viewport.find(".track").remove()}var b=a.copy({content_div:this.overview_viewport}),c=this;b.header_div.hide(),b.is_overview=!0,c.overview_drawable=b,this.overview_drawable.postdraw_actions=function(){c.overview_highlight.show().height(c.overview_drawable.content_div.height()),c.overview_viewport.height(c.overview_drawable.content_div.height()+c.overview_box.outerHeight()),c.overview_close.show(),c.resize_window()},c.overview_drawable.request_draw(),this.changed()},reset_overview:function(){$(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var H=i.Tool.extend({defaults:{track:null},initialize:function(a){i.Tool.prototype.initialize.call(this,a);var b=!0;void 0!==a.tool_state&&void 0!==a.tool_state.hidden&&(b=a.tool_state.hidden),this.set("hidden",b),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(){return a.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),I=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var a=this.$el.addClass("param-row"),b=this.model,c=($("
").addClass("param-label").text(b.get("label")).appendTo(a),$("
").addClass("param-input").html(b.get("html")).appendTo(a));c.find(":input").val(b.get("value")),$("
").appendTo(a)},update_value:function(a){this.model.set_value($(a.target).val())}}),J=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.set_visible,this)},render:function(){var a=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide(),parent_div.bind("drag",function(a){a.stopPropagation()}).click(function(a){a.stopPropagation()}).bind("dblclick",function(a){a.stopPropagation()}).keydown(function(a){a.stopPropagation()});$("
").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(a){var b=new I({model:a});b.render(),parent_div.append(b.$el)}),parent_div.find("input").click(function(){$(this).select()});var b=$("
").addClass("param-row").appendTo(parent_div),c=$("").attr("value","Run on complete dataset").appendTo(b),d=$("").attr("value","Run on visible region").appendTo(b);d.click(function(){a.run_on_region()}),c.click(function(){a.run_on_dataset()}),tool.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var a=0;a").append(d),this.data=e,this.stale=!1};L.prototype.predisplay_actions=function(){};var M=function(a,b,c,d,e){L.call(this,a,b,c,d,e)};M.prototype.predisplay_actions=function(){};var N=function(a,b,c,d,e,f,g,h,i,j,k){L.call(this,a,b,c,d,e),this.mode=f,this.all_slotted=h,this.feature_mapper=i,this.has_icons=!1,this.incomplete_features=j,this.other_tiles_features_drawn={},this.seq_data=k};l(N.prototype,L.prototype),N.prototype.predisplay_actions=function(){};var O=function(a,c,d){l(d,{drag_handle_class:"draghandle"}),D.call(this,a,c,d),this.dataset=null,d.dataset&&(this.dataset=d.dataset instanceof Backbone.Model?d.dataset:new h.Dataset(d.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in d?d.data_query_wait:t,this.data_manager="data_manager"in d?d.data_manager:new b.GenomeDataManager({dataset:this.dataset,genome:new b.Genome({key:a.dbkey,chroms_info:{chrom_info:a.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=$("
").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in d&&!d.resize||this.add_resize_handle())};l(O.prototype,D.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},D.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(a){a.view.set_overview(a)}},D.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(a){a.filters_manager.visible()?a.filters_manager.clear_filters():a.filters_manager.init_filters(),a.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(a){a.tool.toggle(),a.tool.is_visible()?a.set_name(a.config.get_value("name")+a.tool_region_and_parameters_str()):a.revert_name(),$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(c){var d="Tool:"+c.tool.get("name")+"
Dataset:"+c.config.get_value("name")+'
Region(s): ',e=function(){Galaxy.modal.hide(),$(window).unbind("keypress.check_enter_esc")},f=function(){var d,e=$('select[name="regions"] option:selected').val(),f=new b.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),g=a.map($(".bookmark"),function(a){return new b.GenomeRegion({from_str:$(a).children(".position").text()})});d="cur"===e?[f]:"bookmarks"===e?g:[f].concat(g),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+$.param({dataset_id:c.dataset.id,hda_ldda:c.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(d).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:d,buttons:{No:e,Yes:f}})}},D.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&D.prototype.can_draw.call(this)},build_container_div:function(){return $("
").addClass("track").attr("id","track_"+this.id)},set_dataset:function(a){this.dataset=a,this.data_manager.set("dataset",a)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var a=this,b=!1,c=!1,d=$("
");$(a.container_div).hover(function(){a.config.get_value("content_visible")&&(b=!0,d.show())},function(){b=!1,c||d.hide()}),d.hide().bind("dragstart",function(b,d){c=!0,d.original_height=$(a.content_div).height()}).bind("drag",function(b,c){var d=Math.min(Math.max(c.original_height+c.deltaY,a.min_height_px),a.max_height_px);$(a.tiles_div).css("height",d),a.visible_height_px=a.max_height_px===d?0:d,a.on_resize()}).bind("dragend",function(){a.tile_cache.clear(),c=!1,b||d.hide(),a.config.set_value("height",a.visible_height_px),a.changed()}).appendTo(a.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof Q?"LabelTrack":this instanceof S?"ReferenceTrack":this instanceof T?"LineTrack":this instanceof X?"ReadTrack":this instanceof W?"VariantTrack":this instanceof R?"CompositeTrack":this instanceof V?"FeatureTrack":""},show_message:function(a){return this.tiles_div.remove(),$("").addClass("message").html(a).appendTo(this.content_div); +define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/dataset/data","mvc/tool/tools","utils/config","viz/bbi-data-manager","ui/editable-text"],function(a,b,c,d,e,f,g,h,i,j,k){function l(a,b){b||(b=0);var c=Math.pow(10,b);return Math.round(a*c)/c}var m=a.extend,n={},o=function(a,b){n[a.attr("id")]=b},p=function(a,b,c,d){c=".group",n[a.attr("id")]=d,a.bind("drag",{handle:"."+b,relative:!0},function(a,b){var d,e,f,g,h,i=($(this),$(this).parent()),j=i.children(".track,.group"),k=n[$(this).attr("id")];if(e=$(this).parents(c),0!==e.length){f=e.position().top,g=f+e.outerHeight();var l=n[e.attr("id")];if(b.offsetYg)return $(this).insertAfter(e),l.remove_drawable(k),void l.container.add_drawable(k)}for(e=null,h=0;h=f&&b.offsetY<=g)return b.offsetY-f0?h-1:h))}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})},q=20,r=100,s=12e3,t=400,u=5e3,v=100,w="Cannot display dataset due to an error. ",x="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",y="No data for this chrom/contig.",z="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",A="Tool cannot be rerun: ",B="Ready for display",C=10,D=["Histogram","Line","Filled","Intensity"],E=function(a,b,d){if(E.id_counter||(E.id_counter=0),this.id=E.id_counter++,this.view=a,this.container=b,this.drag_handle_class=d.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=j.ConfigSettingCollection.from_models_and_saved_values(this.config_params,d.prefs),this.config.get_value("name")||this.config.set_value("name",d.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,d.header!==!1){var e=new c.TrackHeaderView({model:this,id:this.id});this.header_div=e.$el,this.container_div.append(this.header_div);var f=e.icons_div;this.action_icons=e.action_icons,this.container_div.hover(function(){f.show()},function(){f.hide()})}};E.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(a){a.config.get_value("content_visible")?(a.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),a.hide_contents(),a.config.set_value("content_visible",!1)):(a.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),a.config.set_value("content_visible",!0),a.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(a){var b=new j.ConfigSettingCollectionView({collection:a.config});b.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(a){$(".tooltip").remove(),a.remove()}}],m(E.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return this.enabled&&this.config.get_value("content_visible")?!0:!1},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(a){this.old_name=this.config.get_value("name"),this.config.set_value("name",a)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var a=this.view;this.container_div.hide(0,function(){$(this).remove(),a.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var F=function(a,b,c){E.call(this,a,b,c),this.obj_type=c.obj_type,this.drawables=[]};m(F.prototype,E.prototype,{unpack_drawables:function(a){this.drawables=[];for(var b,c=0;c").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),o(this.container_div,this),o(this.content_div,this),p(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new g.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after($("
")),this.saved_filters_managers=[],"drawables"in c&&this.unpack_drawables(c.drawables),"filters"in c){var d=this.filters_manager;this.filters_manager=new g.FiltersManager(this,c.filters),d.parent_div.replaceWith(this.filters_manager.parent_div),c.filters.visible&&this.setup_multitrack_filtering()}};m(G.prototype,E.prototype,F.prototype,{action_icons_def:[E.prototype.action_icons_def[0],E.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(a){$(".tooltip").remove(),a.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(a){a.filters_manager.visible()?(a.filters_manager.clear_filters(),a._restore_filter_managers()):(a.setup_multitrack_filtering(),a.request_draw({clear_tile_cache:!0})),a.filters_manager.toggle()}},E.prototype.action_icons_def[2]],build_container_div:function(){var a=$("
").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(a),a},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var a=this.drawables.length;if(0===a)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===a)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof S),this.action_icons.filters_icon.hide();else{var b,c,d,e=!0,f=this.drawables[0].get_type(),h=0;for(b=0;a>b;b++){if(d=this.drawables[b],d.get_type()!==f){can_composite=!1;break}d instanceof W&&h++}if(e&&this.drawables[0]instanceof U?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),$(".tooltip").remove()),h>1&&h===this.drawables.length){var i,j={};for(d=this.drawables[0],c=0;c0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var a=0;a0){this.saved_filters_managers=[];for(var a=0;a").addClass("top-container").appendTo(c),this.browser_content_div=$("
").addClass("content").appendTo(c),this.bottom_container=$("
").addClass("bottom-container").appendTo(c),this.top_labeltrack=$("
").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=$("
").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,o(this.viewport_container,d),this.intro_div=$("
").addClass("intro").appendTo(this.viewport_container);$("
").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){b.select_datasets(Galaxy.root+"visualization/list_current_history_datasets",Galaxy.root+"api/datasets",{"f-dbkey":d.dbkey},function(b){a.each(b,function(a){d.add_drawable(_(a,d,d))})})});this.nav_container=$("
").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=$("
").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=$("
").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=$("
").addClass("overview-viewport").appendTo(this.overview),this.overview_close=$("").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=$("
").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=$("
").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=$("
").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=$("
").addClass("nav-controls").appendTo(this.nav),this.chrom_select=$("").addClass("nav-input").hide().bind("keyup focusout",e).appendTo(this.nav_controls),this.location_span=$("").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){d.location_span.hide(),d.chrom_select.hide(),d.nav_input.val(d.chrom+":"+d.low+"-"+d.high),d.nav_input.css("display","inline-block"),d.nav_input.select(),d.nav_input.focus(),d.nav_input.autocomplete({source:function(a,b){var c=[],e=$.map(d.get_tracks(W),function(b){return b.data_manager.search_features(a.term).success(function(a){c=c.concat(a)})});$.when.apply($,e).done(function(){b($.map(c,function(a){return{label:a[0],value:a[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=$("").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=$("").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){d.zoom_out()}).appendTo(this.nav_controls),this.zi_link=$("").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){d.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){d.change_chrom(d.chrom_select.val())}),this.browser_content_div.click(function(){$(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(a){d.zoom_in(a.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(a,b){this.current_x=b.offsetX}).bind("drag",function(a,b){var c=b.offsetX-this.current_x;this.current_x=b.offsetX;var e=Math.round(c/d.viewport_container.width()*(d.max_high-d.max_low));d.move_delta(-e)}),this.overview_close.click(function(){d.reset_overview()}),this.viewport_container.bind("draginit",function(a){return a.clientX>d.viewport_container.width()-16?!1:void 0}).bind("dragstart",function(a,b){b.original_low=d.low,b.current_height=a.clientY,b.current_x=b.offsetX}).bind("drag",function(a,b){var c=$(this),e=b.offsetX-b.current_x,f=c.scrollTop()-(a.clientY-b.current_height);c.scrollTop(f),b.current_height=a.clientY,b.current_x=b.offsetX;var g=Math.round(e/d.viewport_container.width()*(d.high-d.low));d.move_delta(g)}),this.top_labeltrack.bind("dragstart",function(){return $("
").addClass("zoom-area").css("height",d.browser_content_div.height()+d.top_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(a,b){$(b.proxy).css({left:Math.min(a.pageX,b.startX)-d.container.offset().left,width:Math.abs(a.pageX-b.startX)});var c=Math.min(a.pageX,b.startX)-d.container.offset().left,e=Math.max(a.pageX,b.startX)-d.container.offset().left,f=d.high-d.low,g=d.viewport_container.width();d.update_location(Math.round(c/g*f)+d.low,Math.round(e/g*f)+d.low)}).bind("dragend",function(a,b){var c=Math.min(a.pageX,b.startX),e=Math.max(a.pageX,b.startX),f=d.high-d.low,g=d.viewport_container.width(),h=d.low;d.low=Math.round(c/g*f)+h,d.high=Math.round(e/g*f)+h,$(b.proxy).remove(),d.request_redraw()}),this.add_label_track(new R(this,{content_div:this.top_labeltrack})),$(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){d.resize_window()},500)}),$(document).bind("redraw",function(){d.redraw()}),this.reset(),$(window).trigger("resize")},get_base_color:function(a){return this.config.get_value(a.toLowerCase()+"_color")||this.config.get_value("n_color")}});m(H.prototype,F.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(a,b,c,d){if(this.timer&&clearTimeout(this.timer),d){var e=this;this.timer=setTimeout(function(){e.trigger("navigate",a+":"+b+"-"+c)},500)}else view.trigger("navigate",a+":"+b+"-"+c)},update_location:function(a,b){this.location_span.text(d.commatize(a)+" - "+d.commatize(b)),this.nav_input.val(this.chrom+":"+d.commatize(a)+"-"+d.commatize(b));var c=this.chrom_select.val();""!==c&&this.trigger_navigate(c,this.low,this.high,!0)},load_chroms:function(a){a.num=v;var b=this,c=$.Deferred();return $.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:a,dataType:"json",success:function(a){if(0!==a.chrom_info.length){if(a.reference){var d=new T(b);b.add_label_track(d),b.reference_track=d}b.chrom_data=a.chrom_info;for(var e='',f=0,g=b.chrom_data.length;g>f;f++){var h=b.chrom_data[f].chrom;e+='"}a.prev_chroms&&(e+='"),a.next_chroms&&(e+='"),b.chrom_select.html(e),b.chrom_start_index=a.start_index,c.resolve(a.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+b.dbkey)}}),c},change_chrom:function(a,b,c){var d=this;if(!d.chrom_data)return void d.load_chroms_deferred.then(function(){d.change_chrom(a,b,c)});if(a&&"None"!==a){if("previous"===a)return void d.load_chroms({low:this.chrom_start_index-v});if("next"===a)return void d.load_chroms({low:this.chrom_start_index+v});var e=$.grep(d.chrom_data,function(b){return b.chrom===a})[0];if(void 0===e)return void d.load_chroms({chrom:a},function(){d.change_chrom(a,b,c)});if(a!==d.chrom){d.chrom=a,d.chrom_select.val(d.chrom),d.max_high=e.len-1,d.reset();for(var f=0,g=d.drawables.length;g>f;f++){var h=d.drawables[f];h.init&&h.init()}d.reference_track&&d.reference_track.init()}void 0===b&&void 0===c?(d.low=0,d.high=d.max_high):(d.low=void 0!==b?Math.max(b,0):0,void 0===c?(d.low=Math.max(d.low-15,0),d.high=d.low+30):d.high=Math.min(c,d.max_high)),d.request_redraw()}},go_to:function(a){a=a.replace(/,/g,""),a=a.replace(/:|\-/g," ");var b=a.split(/\s+/),c=b[0],d=b[1]?parseInt(b[1],10):void 0,e=b[2]?parseInt(b[2],10):void 0;this.change_chrom(c,d,e)},move_fraction:function(a){var b=this,c=b.high-b.low;this.move_delta(a*c)},move_delta:function(a){var b=this,c=b.high-b.low;b.low-ab.max_high?(b.high=b.max_high,b.low=b.max_high-c):(b.high-=a,b.low-=a),b.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){b.request_redraw()},200);var d=b.chrom_select.val();this.trigger_navigate(d,b.low,b.high,!0)},add_drawable:function(a){F.prototype.add_drawable.call(this,a),a.init(),this.changed(),this.update_intro_div();var b=this;a.config.on("change",function(){b.changed()})},add_label_track:function(a){a.view=this,a.init(),this.label_tracks.push(a)},remove_drawable:function(a,b){if(F.prototype.remove_drawable.call(this,a),b){var c=this;a.container_div.hide(0,function(){$(this).remove(),c.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(b,c){var d=this,e=c?[c]:d.drawables;a.each(e,function(c){var e=a.find(d.tracks_to_be_redrawn,function(a){return a[0]===c});e?e[1]=b:d.tracks_to_be_redrawn.push([c,b])}),this.requested_redraw||(requestAnimationFrame(function(){d._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var b=this.low,c=this.high;bthis.max_high&&(c=this.max_high);var d=this.high-this.low;0!==this.high&&df&&this.overview_box.css("left",e-(g-f)/2),this.overview_highlight&&this.overview_highlight.css({left:e,width:f}),a.each(this.tracks_to_be_redrawn,function(a){var b=a[0],c=a[1];b&&b._draw(c)}),this.tracks_to_be_redrawn=[],a.each(this.label_tracks,function(a){a._draw()})},zoom_in:function(a){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var b=this.high-this.low,c=b/2+this.low,d=b/this.zoom_factor/2;a&&(c=a/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(c-d),this.high=Math.round(c+d),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var a=this.high-this.low,b=a/2+this.low,c=a*this.zoom_factor/2;this.low=Math.round(b-c),this.high=Math.round(b+c),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(a){if(this.overview_drawable){if(this.overview_drawable.dataset.id===a.dataset.id)return;this.overview_viewport.find(".track").remove()}var b=a.copy({content_div:this.overview_viewport}),c=this;b.header_div.hide(),b.is_overview=!0,c.overview_drawable=b,this.overview_drawable.postdraw_actions=function(){c.overview_highlight.show().height(c.overview_drawable.content_div.height()),c.overview_viewport.height(c.overview_drawable.content_div.height()+c.overview_box.outerHeight()),c.overview_close.show(),c.resize_window()},c.overview_drawable.request_draw(),this.changed()},reset_overview:function(){$(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var I=i.Tool.extend({defaults:{track:null},initialize:function(a){i.Tool.prototype.initialize.call(this,a);var b=!0;void 0!==a.tool_state&&void 0!==a.tool_state.hidden&&(b=a.tool_state.hidden),this.set("hidden",b),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(){return a.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),J=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var a=this.$el.addClass("param-row"),b=this.model,c=($("
").addClass("param-label").text(b.get("label")).appendTo(a),$("
").addClass("param-input").html(b.get("html")).appendTo(a));c.find(":input").val(b.get("value")),$("
").appendTo(a)},update_value:function(a){this.model.set_value($(a.target).val())}}),K=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.set_visible,this)},render:function(){var a=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide(),parent_div.bind("drag",function(a){a.stopPropagation()}).click(function(a){a.stopPropagation()}).bind("dblclick",function(a){a.stopPropagation()}).keydown(function(a){a.stopPropagation()});$("
").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(a){var b=new J({model:a});b.render(),parent_div.append(b.$el)}),parent_div.find("input").click(function(){$(this).select()});var b=$("
").addClass("param-row").appendTo(parent_div),c=$("").attr("value","Run on complete dataset").appendTo(b),d=$("").attr("value","Run on visible region").appendTo(b);d.click(function(){a.run_on_region()}),c.click(function(){a.run_on_dataset()}),tool.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var a=0;a").append(d),this.data=e,this.stale=!1};M.prototype.predisplay_actions=function(){};var N=function(a,b,c,d,e){M.call(this,a,b,c,d,e)};N.prototype.predisplay_actions=function(){};var O=function(a,b,c,d,e,f,g,h,i,j,k){M.call(this,a,b,c,d,e),this.mode=f,this.all_slotted=h,this.feature_mapper=i,this.has_icons=!1,this.incomplete_features=j,this.other_tiles_features_drawn={},this.seq_data=k};m(O.prototype,M.prototype),O.prototype.predisplay_actions=function(){};var P=function(a,c,d){m(d,{drag_handle_class:"draghandle"}),E.call(this,a,c,d),this.dataset=null,d.dataset&&(this.dataset=d.dataset instanceof Backbone.Model?d.dataset:new h.Dataset(d.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in d?d.data_query_wait:u,this.data_manager="data_manager"in d?d.data_manager:new b.GenomeDataManager({dataset:this.dataset,genome:new b.Genome({key:a.dbkey,chroms_info:{chrom_info:a.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=$("
").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in d&&!d.resize||this.add_resize_handle())};m(P.prototype,E.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},E.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(a){a.view.set_overview(a)}},E.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(a){a.filters_manager.visible()?a.filters_manager.clear_filters():a.filters_manager.init_filters(),a.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(a){a.tool.toggle(),a.tool.is_visible()?a.set_name(a.config.get_value("name")+a.tool_region_and_parameters_str()):a.revert_name(),$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(c){var d="Tool:"+c.tool.get("name")+"
Dataset:"+c.config.get_value("name")+'
Region(s): ',e=function(){Galaxy.modal.hide(),$(window).unbind("keypress.check_enter_esc")},f=function(){var d,e=$('select[name="regions"] option:selected').val(),f=new b.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),g=a.map($(".bookmark"),function(a){return new b.GenomeRegion({from_str:$(a).children(".position").text()})});d="cur"===e?[f]:"bookmarks"===e?g:[f].concat(g),Galaxy.modal.hide(),window.location.href=Galaxy.root+"visualization/sweepster?"+$.param({dataset_id:c.dataset.id,hda_ldda:c.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(d).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:d,buttons:{No:e,Yes:f}})}},E.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&E.prototype.can_draw.call(this)},build_container_div:function(){return $("
").addClass("track").attr("id","track_"+this.id)},set_dataset:function(a){this.dataset=a,this.data_manager.set("dataset",a)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var a=this,b=!1,c=!1,d=$("
");$(a.container_div).hover(function(){a.config.get_value("content_visible")&&(b=!0,d.show())},function(){b=!1,c||d.hide()}),d.hide().bind("dragstart",function(b,d){c=!0,d.original_height=$(a.content_div).height()}).bind("drag",function(b,c){var d=Math.min(Math.max(c.original_height+c.deltaY,a.min_height_px),a.max_height_px);$(a.tiles_div).css("height",d),a.visible_height_px=a.max_height_px===d?0:d,a.on_resize()}).bind("dragend",function(){a.tile_cache.clear(),c=!1,b||d.hide(),a.config.set_value("height",a.visible_height_px),a.changed()}).appendTo(a.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof R?"LabelTrack":this instanceof T?"ReferenceTrack":this instanceof U?"LineTrack":this instanceof Y?"ReadTrack":this instanceof X?"VariantTrack":this instanceof S?"CompositeTrack":this instanceof W?"FeatureTrack":""},show_message:function(a){return this.tiles_div.remove(),$("").addClass("message").html(a).appendTo(this.content_div); -},init:function(a){var b=this;if(b.enabled=!1,b.tile_cache.clear(),b.data_manager.clear(),b.content_div.children().remove(),b.container_div.removeClass("nodata error pending"),b.tiles_div=$("
").addClass("tiles").appendTo(b.content_div),b.dataset.id){var c=$.Deferred(),d={hda_ldda:b.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:b.view.chrom,retry:a};return $.getJSON(this.dataset.url(),d,function(a){if(a&&"error"!==a&&"error"!==a.kind)"no converter"===a?(b.container_div.addClass("error"),b.show_message(w)):"no data"===a||void 0!==a.data&&(null===a.data||0===a.data.length)?(b.container_div.addClass("nodata"),b.show_message(x)):"pending"===a?(b.container_div.addClass("pending"),b.show_message(y),setTimeout(function(){b.init()},b.data_query_wait)):("data"===a||"data"===a.status)&&(a.valid_chroms&&(b.valid_chroms=a.valid_chroms,b.update_icons()),b.tiles_div.text(A),b.view.chrom?(b.tiles_div.text(""),b.tiles_div.css("height",b.visible_height_px+"px"),b.enabled=!0,$.when.apply($,b.predraw_init()).done(function(){c.resolve(),b.container_div.removeClass("nodata error pending"),b.request_draw()})):c.resolve());else{b.container_div.addClass("error");var d=b.show_message(v);a.message&&(d.append($("").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"
"+a.message+"
",buttons:{Close:function(){Galaxy.modal.hide()}}})})),d.append($("").text(" ")),d.append($("").text("Try again").click(function(){b.init(!0)})))}}),this.update_icons(),c}},predraw_init:function(){var a=this;return $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(b){var c=b.data;if(c&&void 0!==c.min&&void 0!==c.max){var d=c.min,e=c.max;d=Math.floor(Math.min(0,Math.max(d,c.mean-2*c.sd))),e=Math.ceil(Math.max(0,Math.min(e,c.mean+2*c.sd))),a.config.set_default_value("min_value",d),a.config.set_default_value("max_value",e),a.config.set_value("min_value",d),a.config.set_value("max_value",e)}})},get_drawables:function(){return this}});var P=function(c,d,e){O.call(this,c,d,e);var f=this;if(o(f.container_div,f.drag_handle_class,".group",f),this.filters_manager=new g.FiltersManager(this,"filters"in e?e.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=e.tool?new H(a.extend(e.tool,{track:this,tool_state:e.tool_state})):null,this.tile_cache=new b.Cache(B),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var h=new J({model:this.tool});h.render(),this.dynamic_tool_div=h.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=$("
").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=$("
").addClass("overlay").appendTo(this.content_div),e.mode&&this.change_mode(e.mode)};l(P.prototype,D.prototype,O.prototype,{action_icons_def:O.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(a){$(".tooltip").remove(),a.slotters[a.view.resolution_px_b].max_rows*=2,a.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(a){var b=this.to_dict();l(b,{data_manager:this.data_manager});var c=new this.constructor(this.view,a,b);return c.change_mode(this.mode),c.enabled=this.enabled,c},set_filters_manager:function(a){this.filters_manager=a,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var a=this;return $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(b){var c=b.data;if(isNaN(parseFloat(a.config.get_value("min_value")))||isNaN(parseFloat(a.config.get_value("max_value")))){var d=c.min,e=c.max;d=Math.floor(Math.min(0,Math.max(d,c.mean-2*c.sd))),e=Math.ceil(Math.max(0,Math.min(e,c.mean+2*c.sd))),a.config.set_value("min_value",d),a.config.set_value("max_value",e)}})},change_mode:function(a){var b=this;return b.mode=a,b.config.set_value("mode",a),"Auto"===a&&this.data_manager.clear(),b.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+b.mode+")"),b},update_icons:function(){var a=this;a.action_icons.filters_icon.toggle(a.filters_available),a.action_icons.tools_icon.toggle(null!==a.tool),a.action_icons.param_space_viz_icon.toggle(null!==a.tool)},_gen_tile_cache_key:function(a,b){return a+"_"+b},request_draw:function(a){a&&a.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(a,this)},before_draw:function(){this.max_height_px=0},_draw:function(c){if(this.can_draw()){var d=c&&c.clear_after,e=this.view.low,f=this.view.high,g=this.view.container.width(),h=this.view.resolution_px_b,i=1/h;this.is_overview&&(e=this.view.max_low,f=this.view.max_high,h=g/(view.max_high-view.max_low),i=1/h),this.before_draw(),this.tiles_div.children().addClass("remove");for(var j,k,l=Math.floor(s*i),m=Math.floor(e/l),n=[],o=[];f>m*l;)j=new b.GenomeRegion({chrom:this.view.chrom,start:m*l,end:Math.min((m+1)*l,this.view.max_high)}),k=this.draw_helper(j,h,c),n.push(k),$.when(k).then(function(a){o.push(a)}),m+=1;d||this.tiles_div.children(".remove").removeClass("remove").remove();var p=this;$.when.apply($,n).then(function(){p.tiles_div.children(".remove").remove(),o=a.filter(o,function(a){return null!==a}),0!==o.length&&p.postdraw_actions(o,g,h,d)})}},_add_yaxis_label:function(a,b){var c=this,d="max"===a?"top":"bottom",e="max"===a?"max":"min",f="max"===a?"max_value":"min_value",g=this.container_div.find(".yaxislabel."+d),h=k(c.config.get_value(f),1);b=b||function(){c.request_draw({clear_tile_cache:!0})},0!==g.length?g.text(h):(g=$("
").text(h).make_text_editable({num_cols:12,on_finish:function(a){$(".tooltip").remove(),c.config.set_value(f,k(a,1)),b()},help_text:"Set "+e+" value"}).addClass("yaxislabel "+d).css("color",this.config.get_value("label_color")),this.container_div.prepend(g))},postdraw_actions:function(b,c,d){var e=a.filter(b,function(a){return a instanceof M});if(e.length>0){this.max_height_px=0;var f=this;a.each(b,function(a){a instanceof M||(a.html_elt.remove(),f.draw_helper(a.region,d,{force:!0,mode:"Coverage"}))}),f._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var g=a.find(b,function(a){return a.has_icons});g&&a.each(b,function(a){a.has_icons||a.html_elt.css("padding-top",p)})}},get_mode:function(){return this.mode},update_auto_mode:function(){},_get_drawables:function(){return[this]},draw_helper:function(b,c,e){e||(e={});var f=e.force,g=e.mode||this.mode,h=1/c,i=this,j=this._get_drawables(),k=this._gen_tile_cache_key(c,b),l=function(a){return a&&"track"in a},m=f?void 0:i.tile_cache.get_elt(k);if(m)return l(m)&&i.show_tile(m,c),m;if(e.data_fetch===!1)return null;var n=function(){var c=a.find(C,function(a){return a===g})?"Coverage":g,d=a.map(j,function(a){return a.data_manager.get_data(b,c,h,i.data_url_extra_params)});return view.reference_track&&d.push(view.reference_track.data_manager.get_data(b,g,h,view.reference_track.data_url_extra_params)),d},o=$.Deferred();return i.tile_cache.set_elt(k,o),$.when.apply($,n()).then(function(){var f,g=n(),h=g;if(a.find(g,function(a){return d.is_deferred(a)}))return i.tile_cache.set_elt(k,void 0),void $.when(i.draw_helper(b,c,e)).then(function(a){o.resolve(a)});view.reference_track&&(f=view.reference_track.data_manager.subset_entry(g.pop(),b));var l=[],m=[];a.each(j,function(a,b){var d=a.mode,e=h[b];"Auto"===d&&(d=a.get_mode(e),a.update_auto_mode(d)),l.push(d),m.push(a.get_canvas_height(e,d,c,t))});var p,q=i.view.canvas_manager.new_canvas(),r=b.get("start"),s=b.get("end"),t=Math.ceil((s-r)*c)+i.left_offset,u=a.max(m);q.width=t,q.height=e.height||u;var v=q.getContext("2d");v.translate(i.left_offset,0),j.length>1&&(v.globalAlpha=.5,v.globalCompositeOperation="source-over"),a.each(j,function(a,d){p=a.draw_tile(h[d],v,l[d],b,c,f)}),void 0!==p&&(i.tile_cache.set_elt(k,p),i.show_tile(p,c)),o.resolve(p)}),o},get_canvas_height:function(){return this.visible_height_px},_draw_line_track_tile:function(b,c,d,e,g){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",a.max(a.map(b.data,function(a){return a[1]}))||0);var h=c.canvas,i=new f.LinePainter(b.data,e.get("start"),e.get("end"),this.config.to_key_value_dict(),d);return i.draw(c,h.width,h.height,g),new M(this,e,g,h,b.data)},draw_tile:function(){},show_tile:function(a,b){var c=a.html_elt;a.predisplay_actions();var d=Math.round((a.low-(this.is_overview?this.view.max_low:this.view.low))*b);this.left_offset&&(d-=this.left_offset),c.css("left",d),c.hasClass("remove")?c.removeClass("remove"):this.tiles_div.append(c),c.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,c.height()-2),c.parent().children().css("height",this.max_height_px+"px");var e=this.max_height_px;0!==this.visible_height_px&&(e=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",e+"px")},tool_region_and_parameters_str:function(b){var c=this,d=void 0!==b?b.toString():"all",e=a.values(c.tool.get_inputs_dict()).join(", ");return" - region=["+d+"], parameters=["+e+"]"},data_and_mode_compatible:function(a,b){return"Auto"===b?!0:"Coverage"===b?"bigwig"===a.dataset_type:"bigwig"===a.dataset_type||"no_detail"===a.extra_info?!1:!0},can_subset:function(a){return a.message||"no_detail"===a.extra_info?!1:"bigwig"===a.dataset_type?a.data[1][0]-a.data[0][0]===1:!0},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var Q=function(a,b){O.call(this,a,b,{resize:!1,header:!1}),this.container_div.addClass("label-track")};l(Q.prototype,O.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(){for(var a=this.view,b=a.high-a.low,c=Math.floor(Math.pow(10,Math.floor(Math.log(b)/Math.log(10)))),e=Math.floor(a.low/c)*c,f=this.view.container.width(),g=$("
").addClass("label-container");e").addClass("pos-label").text(d.commatize(e)).css({left:h})),e+=c}this.content_div.children(":first").remove(),this.content_div.append(g)}});var R=function(b,c,d){if(P.call(this,b,c,d),this.drawables=[],"drawables"in d){for(var e,f=0;fthis.left_offset&&(this.left_offset=e.left_offset);this.enabled=!0}a.each(this.drawables,function(a){(a instanceof V||a instanceof X)&&a.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};l(R.prototype,P.prototype,{display_modes:C,config_params:a.union(D.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(a){$(".tooltip").remove(),a.show_group()}}].concat(P.prototype.action_icons_def),to_dict:E.prototype.to_dict,add_drawable:E.prototype.add_drawable,unpack_drawables:E.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var b=this.visible_height_px;a.each(this.drawables,function(a){a.visible_height_px=b}),O.prototype.on_resize.call(this)},change_mode:function(a){P.prototype.change_mode.call(this,a);for(var b=0;be&&(e=f)}for(d=0;dthis.view.canvas_manager.char_width_px?(this.tiles_div.show(),d=!0,f=P.prototype.draw_helper.call(this,a,b,c)):(d=!1,this.tiles_div.hide()),e!==d&&this.view.resize_viewport(),f},can_subset:function(){return!0},draw_tile:function(a,b,c,d,e){var f=this.data_manager.subset_entry(a,d),g=f.data,h=b.canvas;b.font=b.canvas.manager.default_font,b.textAlign="center";for(var i=0,j=g.length;j>i;i++)b.fillStyle=this.view.get_base_color(g[i]),b.fillText(g[i],Math.floor(i*e),10);return new L(this,d,e,h,f)}});var T=function(a,b,c){this.mode="Histogram",P.call(this,a,b,c)};l(T.prototype,D.prototype,P.prototype,{display_modes:C,config_params:a.union(D.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(a,b,c,d,e){return this._draw_line_track_tile(a,b,c,d,e)},can_subset:function(a){return a.data[1][0]-a.data[0][0]===1},postdraw_actions:function(){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var U=function(a,b,c){this.mode="Heatmap",P.call(this,a,b,c)};l(U.prototype,D.prototype,P.prototype,{display_modes:["Heatmap"],config_params:a.union(D.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var a=this;return $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(a){a.data})},draw_tile:function(a,b,c,d,e){var g=b.canvas,h=new f.DiagonalHeatmapPainter(a.data,d.get("start"),d.get("end"),this.config.to_key_value_dict(),c);return h.draw(b,g.width,g.height,e),new L(this,d,e,g,a.data)}});var V=function(a,b,c){P.call(this,a,b,c),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};l(V.prototype,D.prototype,P.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:a.union(D.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){this.painter="arcs"===this.config.get_value("connector_style")?f.ArcLinkedFeaturePainter:f.LinkedFeaturePainter},postdraw_actions:function(b,c,d,e){P.prototype.postdraw_actions.call(this,b,c,d,e);var f,g=this,h=a.filter(b,function(a){return a instanceof M});if(0===h.length){var i={};a.each(a.pluck(b,"incomplete_features"),function(b){a.each(b,function(a){i[a[0]]=a})});var j=this;a.each(b,function(b){var c=a.omit(i,a.map(b.incomplete_features,function(a){return a[0]}));if(c=a.omit(c,a.keys(b.other_tiles_features_drawn)),0!==a.size(c)){var d={data:a.values(c)},e=j.view.canvas_manager.new_canvas(),f=e.getContext("2d");e.height=Math.max(b.canvas.height,j.get_canvas_height(d,b.mode,b.w_scale,100)),e.width=b.canvas.width,f.drawImage(b.canvas,0,0),f.translate(g.left_offset,0);var h=j.draw_tile(d,f,b.mode,b.region,b.w_scale,b.seq_data);$(b.canvas).replaceWith($(h.canvas)),b.canvas=e,a.extend(b.other_tiles_features_drawn,i)}})}if(g.filters_manager){var k,l=g.filters_manager.filters;for(k=0;kr?"Squish":"Pack",mode},get_canvas_height:function(a,b,c,d){if("Coverage"===b||"bigwig"===a.dataset_type)return this.summary_draw_height;var e=this.incremental_slots(c,a.data,b),f=new this.painter(null,null,null,this.config.to_key_value_dict(),b);return Math.max(this.min_height_px,f.get_required_height(e,d))},draw_tile:function(a,b,c,d,e,f,g){var h=this,i=b.canvas,j=d.get("start"),k=d.get("end"),l=this.left_offset;if("bigwig"===a.dataset_type)return this._draw_line_track_tile(a,b,c,d,e);var m=[],n=this.slotters[e].slots;if(all_slotted=!0,a.data)for(var o=this.filters_manager.filters,p=0,q=a.data.length;q>p;p++){for(var r,s=a.data[p],t=!1,u=0,v=o.length;v>u;u++)if(r=o[u],r.update_attrs(s),!r.keep(s)){t=!0;break}t||(m.push(s),s[0]in n||(all_slotted=!1))}var w=this.filters_manager.alpha_filter?new K(this.filters_manager.alpha_filter):null,x=this.filters_manager.height_filter?new K(this.filters_manager.height_filter):null,y=new this.painter(m,j,k,this.config.to_key_value_dict(),c,w,x,f,function(a){return h.view.get_base_color(a)}),z=null;if(b.fillStyle=this.config.get_value("block_color"),b.font=b.canvas.manager.default_font,b.textAlign="right",a.data){var A=y.draw(b,i.width,i.height,e,n);z=A.feature_mapper,incomplete_features=A.incomplete_features,z.translation=-l}return g?void 0:new N(h,d,e,i,a.data,c,a.message,all_slotted,z,incomplete_features,f)}});var W=function(a,b,c){P.call(this,a,b,c),this.painter=f.VariantPainter,this.summary_draw_height=30,this.left_offset=30};l(W.prototype,D.prototype,P.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:a.union(D.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(a,b,c,d,e){if("bigwig"===a.dataset_type)return this._draw_line_track_tile(a,b,"Histogram",d,e);var f=this.view,g=new this.painter(a.data,d.get("start"),d.get("end"),this.config.to_key_value_dict(),c,function(a){return f.get_base_color(a)});return g.draw(b,b.canvas.width,b.canvas.height,e),new L(this,d,e,b.canvas,a.data)},get_canvas_height:function(a,b){if("bigwig"===a.dataset_type)return this.summary_draw_height;var c=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;0===c&&0!==a.data.length&&(c=a.data[0][7].match(/,/g),c=null===c?1:c.length+1);var d=new this.painter(null,null,null,this.config.to_key_value_dict(),b);return d.get_required_height(c)},predraw_init:function(){var a=[O.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||a.push(this.dataset.fetch()),a},postdraw_actions:function(b,c,d,e){P.prototype.postdraw_actions.call(this,b,c,d,e);var f=a.filter(b,function(a){return a instanceof M}),g=this.dataset.get_metadata("sample_names");if(0===f.length&&this.config.get_value("show_labels")&&g&&g.length>1){var h;if(0===this.container_div.find(".yaxislabel.variant").length&&(h=this.config.get_value("summary_height")/2,this.tiles_div.prepend($("
").text("Summary").addClass("yaxislabel variant top").css({"font-size":h+"px",top:(this.config.get_value("summary_height")-h)/2+"px"})),this.config.get_value("show_sample_data"))){var i=g.join("
");this.tiles_div.prepend($("
").html(i).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}h=("Squish"===this.mode?5:10)+"px",$(this.tiles_div).find(".sample").css({"font-size":h,"line-height":h}),$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var X=function(a,b,c){V.call(this,a,b,c),this.painter=f.ReadPainter,this.update_icons()};l(X.prototype,D.prototype,P.prototype,V.prototype,{config_params:a.union(D.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var Y={CompositeTrack:R,DrawableGroup:F,DiagonalHeatmapTrack:U,FeatureTrack:V,LineTrack:T,ReadTrack:X,VariantTrack:W,VcfTrack:W},Z=function(a,b,c){if("copy"in a)return a.copy(c);var d=a.obj_type;return d||(d=a.track_type),new Y[d](b,c,a)};return{TracksterView:G,DrawableGroup:F,LineTrack:T,FeatureTrack:V,DiagonalHeatmapTrack:U,ReadTrack:X,VariantTrack:W,CompositeTrack:R,object_from_template:Z}}); +},init:function(a){var b=this;if(b.enabled=!1,b.tile_cache.clear(),b.data_manager.clear(),b.content_div.children().remove(),b.container_div.removeClass("nodata error pending"),b.tiles_div=$("
").addClass("tiles").appendTo(b.content_div),b.dataset.id){var c=$.Deferred(),d={hda_ldda:b.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:b.view.chrom,retry:a};return $.getJSON(this.dataset.url(),d,function(a){if(a&&"error"!==a&&"error"!==a.kind)"no converter"===a?(b.container_div.addClass("error"),b.show_message(x)):"no data"===a||void 0!==a.data&&(null===a.data||0===a.data.length)?(b.container_div.addClass("nodata"),b.show_message(y)):"pending"===a?(b.container_div.addClass("pending"),b.show_message(z),setTimeout(function(){b.init()},b.data_query_wait)):("data"===a||"data"===a.status)&&(a.valid_chroms&&(b.valid_chroms=a.valid_chroms,b.update_icons()),b.tiles_div.text(B),b.view.chrom?(b.tiles_div.text(""),b.tiles_div.css("height",b.visible_height_px+"px"),b.enabled=!0,$.when.apply($,b.predraw_init()).done(function(){c.resolve(),b.container_div.removeClass("nodata error pending"),b.request_draw()})):c.resolve());else{b.container_div.addClass("error");var d=b.show_message(w);a.message&&(d.append($("").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"
"+a.message+"
",buttons:{Close:function(){Galaxy.modal.hide()}}})})),d.append($("").text(" ")),d.append($("").text("Try again").click(function(){b.init(!0)})))}}),this.update_icons(),c}},predraw_init:function(){var a=this;return $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(b){var c=b.data;if(c&&void 0!==c.min&&void 0!==c.max){var d=c.min,e=c.max;d=Math.floor(Math.min(0,Math.max(d,c.mean-2*c.sd))),e=Math.ceil(Math.max(0,Math.min(e,c.mean+2*c.sd))),a.config.set_default_value("min_value",d),a.config.set_default_value("max_value",e),a.config.set_value("min_value",d),a.config.set_value("max_value",e)}})},get_drawables:function(){return this}});var Q=function(c,d,e){P.call(this,c,d,e);var f=this;if(p(f.container_div,f.drag_handle_class,".group",f),this.filters_manager=new g.FiltersManager(this,"filters"in e?e.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=e.tool?new I(a.extend(e.tool,{track:this,tool_state:e.tool_state})):null,this.tile_cache=new b.Cache(C),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var h=new K({model:this.tool});h.render(),this.dynamic_tool_div=h.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=$("
").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=$("
").addClass("overlay").appendTo(this.content_div),e.mode&&this.change_mode(e.mode)};m(Q.prototype,E.prototype,P.prototype,{action_icons_def:P.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(a){$(".tooltip").remove(),a.slotters[a.view.resolution_px_b].max_rows*=2,a.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(a){var b=this.to_dict();m(b,{data_manager:this.data_manager});var c=new this.constructor(this.view,a,b);return c.change_mode(this.mode),c.enabled=this.enabled,c},set_filters_manager:function(a){this.filters_manager=a,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var a=this;return $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(b){var c=b.data;if(isNaN(parseFloat(a.config.get_value("min_value")))||isNaN(parseFloat(a.config.get_value("max_value")))){var d=c.min,e=c.max;d=Math.floor(Math.min(0,Math.max(d,c.mean-2*c.sd))),e=Math.ceil(Math.max(0,Math.min(e,c.mean+2*c.sd))),a.config.set_value("min_value",d),a.config.set_value("max_value",e)}})},change_mode:function(a){var b=this;return b.mode=a,b.config.set_value("mode",a),"Auto"===a&&this.data_manager.clear(),b.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+b.mode+")"),b},update_icons:function(){var a=this;a.action_icons.filters_icon.toggle(a.filters_available),a.action_icons.tools_icon.toggle(null!==a.tool),a.action_icons.param_space_viz_icon.toggle(null!==a.tool)},_gen_tile_cache_key:function(a,b){return a+"_"+b},request_draw:function(a){a&&a.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(a,this)},before_draw:function(){this.max_height_px=0},_draw:function(c){if(this.can_draw()){var d=c&&c.clear_after,e=this.view.low,f=this.view.high,g=this.view.container.width(),h=this.view.resolution_px_b,i=1/h;this.is_overview&&(e=this.view.max_low,f=this.view.max_high,h=g/(view.max_high-view.max_low),i=1/h),this.before_draw(),this.tiles_div.children().addClass("remove");for(var j,k,l=Math.floor(t*i),m=Math.floor(e/l),n=[],o=[];f>m*l;)j=new b.GenomeRegion({chrom:this.view.chrom,start:m*l,end:Math.min((m+1)*l,this.view.max_high)}),k=this.draw_helper(j,h,c),n.push(k),$.when(k).then(function(a){o.push(a)}),m+=1;d||this.tiles_div.children(".remove").removeClass("remove").remove();var p=this;$.when.apply($,n).then(function(){p.tiles_div.children(".remove").remove(),o=a.filter(o,function(a){return null!==a}),0!==o.length&&p.postdraw_actions(o,g,h,d)})}},_add_yaxis_label:function(a,b){var c=this,d="max"===a?"top":"bottom",e="max"===a?"max":"min",f="max"===a?"max_value":"min_value",g=this.container_div.find(".yaxislabel."+d),h=l(c.config.get_value(f),1);b=b||function(){c.request_draw({clear_tile_cache:!0})},0!==g.length?g.text(h):(g=$("
").text(h).make_text_editable({num_cols:12,on_finish:function(a){$(".tooltip").remove(),c.config.set_value(f,l(a,1)),b()},help_text:"Set "+e+" value"}).addClass("yaxislabel "+d).css("color",this.config.get_value("label_color")),this.container_div.prepend(g))},postdraw_actions:function(b,c,d){var e=a.filter(b,function(a){return a instanceof N});if(e.length>0){this.max_height_px=0;var f=this;a.each(b,function(a){a instanceof N||(a.html_elt.remove(),f.draw_helper(a.region,d,{force:!0,mode:"Coverage"}))}),f._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var g=a.find(b,function(a){return a.has_icons});g&&a.each(b,function(a){a.has_icons||a.html_elt.css("padding-top",q)})}},get_mode:function(){return this.mode},update_auto_mode:function(){},_get_drawables:function(){return[this]},draw_helper:function(b,c,e){e||(e={});var f=e.force,g=e.mode||this.mode,h=1/c,i=this,j=this._get_drawables(),k=this._gen_tile_cache_key(c,b),l=function(a){return a&&"track"in a},m=f?void 0:i.tile_cache.get_elt(k);if(m)return l(m)&&i.show_tile(m,c),m;if(e.data_fetch===!1)return null;var n=function(){var c=a.find(D,function(a){return a===g})?"Coverage":g,d=a.map(j,function(a){return a.data_manager.get_data(b,c,h,i.data_url_extra_params)});return view.reference_track&&d.push(view.reference_track.data_manager.get_data(b,g,h,view.reference_track.data_url_extra_params)),d},o=$.Deferred();return i.tile_cache.set_elt(k,o),$.when.apply($,n()).then(function(){var f,g=n(),h=g;if(a.find(g,function(a){return d.is_deferred(a)}))return i.tile_cache.set_elt(k,void 0),void $.when(i.draw_helper(b,c,e)).then(function(a){o.resolve(a)});view.reference_track&&(f=view.reference_track.data_manager.subset_entry(g.pop(),b));var l=[],m=[];a.each(j,function(a,b){var d=a.mode,e=h[b];"Auto"===d&&(d=a.get_mode(e),a.update_auto_mode(d)),l.push(d),m.push(a.get_canvas_height(e,d,c,t))});var p,q=i.view.canvas_manager.new_canvas(),r=b.get("start"),s=b.get("end"),t=Math.ceil((s-r)*c)+i.left_offset,u=a.max(m);q.width=t,q.height=e.height||u;var v=q.getContext("2d");v.translate(i.left_offset,0),j.length>1&&(v.globalAlpha=.5,v.globalCompositeOperation="source-over"),a.each(j,function(a,d){p=a.draw_tile(h[d],v,l[d],b,c,f)}),void 0!==p&&(i.tile_cache.set_elt(k,p),i.show_tile(p,c)),o.resolve(p)}),o},get_canvas_height:function(){return this.visible_height_px},_draw_line_track_tile:function(b,c,d,e,g){-1!==[void 0,null].indexOf(this.config.get_value("min_value"))&&this.config.set_value("min_value",0),-1!==[void 0,null,0].indexOf(this.config.get_value("max_value"))&&this.config.set_value("max_value",a.max(a.map(b.data,function(a){return a[1]}))||0);var h=c.canvas,i=new f.LinePainter(b.data,e.get("start"),e.get("end"),this.config.to_key_value_dict(),d);return i.draw(c,h.width,h.height,g),new N(this,e,g,h,b.data)},draw_tile:function(){},show_tile:function(a,b){var c=a.html_elt;a.predisplay_actions();var d=Math.round((a.low-(this.is_overview?this.view.max_low:this.view.low))*b);this.left_offset&&(d-=this.left_offset),c.css("left",d),c.hasClass("remove")?c.removeClass("remove"):this.tiles_div.append(c),c.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,c.height()-2),c.parent().children().css("height",this.max_height_px+"px");var e=this.max_height_px;0!==this.visible_height_px&&(e=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",e+"px")},tool_region_and_parameters_str:function(b){var c=this,d=void 0!==b?b.toString():"all",e=a.values(c.tool.get_inputs_dict()).join(", ");return" - region=["+d+"], parameters=["+e+"]"},data_and_mode_compatible:function(a,b){return"Auto"===b?!0:"Coverage"===b?"bigwig"===a.dataset_type:"bigwig"===a.dataset_type||"no_detail"===a.extra_info?!1:!0},can_subset:function(a){return a.message||"no_detail"===a.extra_info?!1:"bigwig"===a.dataset_type?a.data[1][0]-a.data[0][0]===1:!0},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var R=function(a,b){P.call(this,a,b,{resize:!1,header:!1}),this.container_div.addClass("label-track")};m(R.prototype,P.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(){for(var a=this.view,b=a.high-a.low,c=Math.floor(Math.pow(10,Math.floor(Math.log(b)/Math.log(10)))),e=Math.floor(a.low/c)*c,f=this.view.container.width(),g=$("
").addClass("label-container");e").addClass("pos-label").text(d.commatize(e)).css({left:h})),e+=c}this.content_div.children(":first").remove(),this.content_div.append(g)}});var S=function(b,c,d){if(Q.call(this,b,c,d),this.drawables=[],"drawables"in d){for(var e,f=0;fthis.left_offset&&(this.left_offset=e.left_offset);this.enabled=!0}a.each(this.drawables,function(a){(a instanceof W||a instanceof Y)&&a.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};m(S.prototype,Q.prototype,{display_modes:D,config_params:a.union(E.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(a){$(".tooltip").remove(),a.show_group()}}].concat(Q.prototype.action_icons_def),to_dict:F.prototype.to_dict,add_drawable:F.prototype.add_drawable,unpack_drawables:F.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var b=this.visible_height_px;a.each(this.drawables,function(a){a.visible_height_px=b}),P.prototype.on_resize.call(this)},change_mode:function(a){Q.prototype.change_mode.call(this,a);for(var b=0;be&&(e=f)}for(d=0;dthis.view.canvas_manager.char_width_px?(this.tiles_div.show(),d=!0,f=Q.prototype.draw_helper.call(this,a,b,c)):(d=!1,this.tiles_div.hide()),e!==d&&this.view.resize_viewport(),f},can_subset:function(){return!0},draw_tile:function(a,b,c,d,e){var f=this.data_manager.subset_entry(a,d),g=f.data,h=b.canvas;b.font=b.canvas.manager.default_font,b.textAlign="center";for(var i=0,j=g.length;j>i;i++)b.fillStyle=this.view.get_base_color(g[i]),b.fillText(g[i],Math.floor(i*e),10);return new M(this,d,e,h,f)}});var U=function(a,b,c){this.mode="Histogram",Q.call(this,a,b,c),this.data_manager=new k.BBIDataManager({dataset:this.dataset})};m(U.prototype,E.prototype,Q.prototype,{display_modes:D,config_params:a.union(E.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(a,b,c,d,e){return this._draw_line_track_tile(a,b,c,d,e)},can_subset:function(a){return a.data[1][0]-a.data[0][0]===1},postdraw_actions:function(){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var V=function(a,b,c){this.mode="Heatmap",Q.call(this,a,b,c)};m(V.prototype,E.prototype,Q.prototype,{display_modes:["Heatmap"],config_params:a.union(E.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"int",default_value:void 0},{key:"max_value",label:"Max Value",type:"int",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},predraw_init:function(){var a=this;return $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(a){a.data})},draw_tile:function(a,b,c,d,e){var g=b.canvas,h=new f.DiagonalHeatmapPainter(a.data,d.get("start"),d.get("end"),this.config.to_key_value_dict(),c);return h.draw(b,g.width,g.height,e),new M(this,d,e,g,a.data)}});var W=function(a,b,c){Q.call(this,a,b,c),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};m(W.prototype,E.prototype,Q.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:a.union(E.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){this.painter="arcs"===this.config.get_value("connector_style")?f.ArcLinkedFeaturePainter:f.LinkedFeaturePainter},postdraw_actions:function(b,c,d,e){Q.prototype.postdraw_actions.call(this,b,c,d,e);var f,g=this,h=a.filter(b,function(a){return a instanceof N});if(0===h.length){var i={};a.each(a.pluck(b,"incomplete_features"),function(b){a.each(b,function(a){i[a[0]]=a})});var j=this;a.each(b,function(b){var c=a.omit(i,a.map(b.incomplete_features,function(a){return a[0]}));if(c=a.omit(c,a.keys(b.other_tiles_features_drawn)),0!==a.size(c)){var d={data:a.values(c)},e=j.view.canvas_manager.new_canvas(),f=e.getContext("2d");e.height=Math.max(b.canvas.height,j.get_canvas_height(d,b.mode,b.w_scale,100)),e.width=b.canvas.width,f.drawImage(b.canvas,0,0),f.translate(g.left_offset,0);var h=j.draw_tile(d,f,b.mode,b.region,b.w_scale,b.seq_data);$(b.canvas).replaceWith($(h.canvas)),b.canvas=e,a.extend(b.other_tiles_features_drawn,i)}})}if(g.filters_manager){var k,l=g.filters_manager.filters;for(k=0;ks?"Squish":"Pack",mode},get_canvas_height:function(a,b,c,d){if("Coverage"===b||"bigwig"===a.dataset_type)return this.summary_draw_height;var e=this.incremental_slots(c,a.data,b),f=new this.painter(null,null,null,this.config.to_key_value_dict(),b);return Math.max(this.min_height_px,f.get_required_height(e,d))},draw_tile:function(a,b,c,d,e,f,g){var h=this,i=b.canvas,j=d.get("start"),k=d.get("end"),l=this.left_offset;if("bigwig"===a.dataset_type)return this._draw_line_track_tile(a,b,c,d,e);var m=[],n=this.slotters[e].slots;if(all_slotted=!0,a.data)for(var o=this.filters_manager.filters,p=0,q=a.data.length;q>p;p++){for(var r,s=a.data[p],t=!1,u=0,v=o.length;v>u;u++)if(r=o[u],r.update_attrs(s),!r.keep(s)){t=!0;break}t||(m.push(s),s[0]in n||(all_slotted=!1))}var w=this.filters_manager.alpha_filter?new L(this.filters_manager.alpha_filter):null,x=this.filters_manager.height_filter?new L(this.filters_manager.height_filter):null,y=new this.painter(m,j,k,this.config.to_key_value_dict(),c,w,x,f,function(a){return h.view.get_base_color(a)}),z=null;if(b.fillStyle=this.config.get_value("block_color"),b.font=b.canvas.manager.default_font,b.textAlign="right",a.data){var A=y.draw(b,i.width,i.height,e,n);z=A.feature_mapper,incomplete_features=A.incomplete_features,z.translation=-l}return g?void 0:new O(h,d,e,i,a.data,c,a.message,all_slotted,z,incomplete_features,f)}});var X=function(a,b,c){Q.call(this,a,b,c),this.painter=f.VariantPainter,this.summary_draw_height=30,this.left_offset=30};m(X.prototype,E.prototype,Q.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:a.union(E.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(a,b,c,d,e){if("bigwig"===a.dataset_type)return this._draw_line_track_tile(a,b,"Histogram",d,e);var f=this.view,g=new this.painter(a.data,d.get("start"),d.get("end"),this.config.to_key_value_dict(),c,function(a){return f.get_base_color(a)});return g.draw(b,b.canvas.width,b.canvas.height,e),new M(this,d,e,b.canvas,a.data)},get_canvas_height:function(a,b){if("bigwig"===a.dataset_type)return this.summary_draw_height;var c=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;0===c&&0!==a.data.length&&(c=a.data[0][7].match(/,/g),c=null===c?1:c.length+1);var d=new this.painter(null,null,null,this.config.to_key_value_dict(),b);return d.get_required_height(c)},predraw_init:function(){var a=[P.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||a.push(this.dataset.fetch()),a},postdraw_actions:function(b,c,d,e){Q.prototype.postdraw_actions.call(this,b,c,d,e);var f=a.filter(b,function(a){return a instanceof N}),g=this.dataset.get_metadata("sample_names");if(0===f.length&&this.config.get_value("show_labels")&&g&&g.length>1){var h;if(0===this.container_div.find(".yaxislabel.variant").length&&(h=this.config.get_value("summary_height")/2,this.tiles_div.prepend($("
").text("Summary").addClass("yaxislabel variant top").css({"font-size":h+"px",top:(this.config.get_value("summary_height")-h)/2+"px"})),this.config.get_value("show_sample_data"))){var i=g.join("
");this.tiles_div.prepend($("
").html(i).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}h=("Squish"===this.mode?5:10)+"px",$(this.tiles_div).find(".sample").css({"font-size":h,"line-height":h}),$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var Y=function(a,b,c){W.call(this,a,b,c),this.painter=f.ReadPainter,this.update_icons()};m(Y.prototype,E.prototype,Q.prototype,W.prototype,{config_params:a.union(E.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var Z={CompositeTrack:S,DrawableGroup:G,DiagonalHeatmapTrack:V,FeatureTrack:W,LineTrack:U,ReadTrack:Y,VariantTrack:X,VcfTrack:X},_=function(a,b,c){if("copy"in a)return a.copy(c);var d=a.obj_type;return d||(d=a.track_type),new Z[d](b,c,a)};return{TracksterView:H,DrawableGroup:G,LineTrack:U,FeatureTrack:W,DiagonalHeatmapTrack:V,ReadTrack:Y,VariantTrack:X,CompositeTrack:S,object_from_template:_}}); //# sourceMappingURL=../../../maps/viz/trackster/tracks.js.map \ No newline at end of file