From 41d0ee4f4392d188ec9ededa35391ef592213608 Mon Sep 17 00:00:00 2001 From: jgoecks Date: Tue, 23 Aug 2016 16:55:20 -0400 Subject: [PATCH] Bring data provided by data manager in line with Trackster's bigwig datatype. Also allow LinePainter to draw regions of variable length. --- client/galaxy/scripts/libs/bbi/bigwig.js | 2 - client/galaxy/scripts/viz/bbi-data-manager.js | 37 +++++++++++-------- .../galaxy/scripts/viz/trackster/painters.js | 12 ++++-- client/galaxy/scripts/viz/trackster/tracks.js | 2 + static/maps/libs/bbi/bigwig.js.map | 2 +- static/maps/viz/bbi-data-manager.js.map | 2 +- static/maps/viz/trackster/painters.js.map | 2 +- static/maps/viz/trackster/tracks.js.map | 2 +- static/scripts/libs/bbi/bigwig.js | 2 +- static/scripts/viz/bbi-data-manager.js | 2 +- static/scripts/viz/trackster/painters.js | 2 +- static/scripts/viz/trackster/tracks.js | 2 +- 12 files changed, 40 insertions(+), 29 deletions(-) diff --git a/client/galaxy/scripts/libs/bbi/bigwig.js b/client/galaxy/scripts/libs/bbi/bigwig.js index e3b94e05deb..81946cb6563 100644 --- a/client/galaxy/scripts/libs/bbi/bigwig.js +++ b/client/galaxy/scripts/libs/bbi/bigwig.js @@ -807,7 +807,6 @@ define(["libs/bbi/spans", "libs/bbi/jszlib", "libs/bbi/jquery-ajax-native"], fun // 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 @@ -815,7 +814,6 @@ define(["libs/bbi/spans", "libs/bbi/jszlib", "libs/bbi/jquery-ajax-native"], fun 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; } } diff --git a/client/galaxy/scripts/viz/bbi-data-manager.js b/client/galaxy/scripts/viz/bbi-data-manager.js index 23d0da9e6d2..ae7c912d75e 100644 --- a/client/galaxy/scripts/viz/bbi-data-manager.js +++ b/client/galaxy/scripts/viz/bbi-data-manager.js @@ -7,7 +7,7 @@ define( ["viz/visualization", "libs/bbi/bigwig"], var BBIDataManager = visualization.GenomeDataManager.extend({ /** - * Load data from server and manages data entries. Adds a Deferred to manager + * Load data from server and manage 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. */ @@ -20,22 +20,29 @@ define( ["viz/visualization", "libs/bbi/bigwig"], 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 = []; + // Transform data into "bigwig" format for LinePainter. "bigwig" format is an array of 2-element arrays + // where each element is [position, score]; unlike real bigwig format, no gaps are allowed. + var result = [], + prev = { max: Number.MIN_VALUE }; 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]); + // If there is a gap between prev and d, fill it with an interval with score 0. + // This is necessary for LinePainter to draw correctly. + if (prev.max !== d.min - 1) { + // +1 to start after previous region. + result.push([prev.max + 1, 0]); + // -2 = -1 for converting from 1-based to 0-based coordinates, + // -1 for ending before current region. + result.push([d.min - 2, 0]); } + + // Add data point for entry start. -1 to convert from wiggle + // 1-based coordinates to 0-based browser coordinates. + result.push([d.min - 1, d.score]); + + // Add data point for entry end: + result.push([d.max, d.score]); + + prev = d; }); var entry = { diff --git a/client/galaxy/scripts/viz/trackster/painters.js b/client/galaxy/scripts/viz/trackster/painters.js index 3bb9afbad8a..4a1b1c0493f 100644 --- a/client/galaxy/scripts/viz/trackster/painters.js +++ b/client/galaxy/scripts/viz/trackster/painters.js @@ -194,12 +194,14 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) { } ctx.beginPath(); - var x_scaled, y, delta_x_px; + var x_scaled, y, delta_x_pxs; if (data.length > 1) { - delta_x_px = Math.ceil((data[1][0] - data[0][0]) * w_scale); + delta_x_pxs = _.map(data.slice(0,-1), function(d, i) { + return Math.ceil((data[i+1][0] - data[i][0]) * w_scale); + }); } else { - delta_x_px = 10; + delta_x_pxs = [10]; } // Painter color can be in either block_color (FeatureTrack) or color pref (LineTrack). @@ -214,12 +216,14 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) { // Paint track. + var delta_x_px; for (var i = 0, len = data.length; i < len; i++) { // Reset attributes for next point. ctx.fillStyle = ctx.strokeStyle = painter_color; top_overflow = bot_overflow = false; + delta_x_px = delta_x_pxs[i]; - x_scaled = Math.ceil((data[i][0] - view_start) * w_scale); + x_scaled = Math.ceil((data[i][0] - view_start - 0.5) * w_scale); y = data[i][1]; // Process Y (scaler) value. diff --git a/client/galaxy/scripts/viz/trackster/tracks.js b/client/galaxy/scripts/viz/trackster/tracks.js index f3a3fd26d37..b74d9c0a994 100644 --- a/client/galaxy/scripts/viz/trackster/tracks.js +++ b/client/galaxy/scripts/viz/trackster/tracks.js @@ -3614,6 +3614,8 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, { var LineTrack = function (view, container, obj_dict) { this.mode = "Histogram"; TiledTrack.call(this, view, container, obj_dict); + // Need left offset for drawing overlap near tile boundaries. + this.left_offset = 30; // var self = this; // $.when(supportsByteRanges(galaxy_config.root + 'datasets/' + this.dataset.id + '/display')) diff --git 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p=e/4,q=l[p],r=l[p+1],s=l[p+2],t=l[p+3],u=g(i,e+16);(0>a||a>q||q==a&&c>=r)&&(0>a||s>a||s==a&&t>=b)&&w.push(u),e+=24}w.length>0&&k(w,f+1)}};return k([d.cirTreeOffset+48],1),e},i.prototype.fetchFeatures=function(a,b){var d=this,e=$.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 Float32Array(a),i=a.byteLength/32,j=0;i>j;++j){{var k=g[8*j],o=g[8*j+1],p=g[8*j+2],q=g[8*j+3],r=(h[8*j+4],h[8*j+5]),s=h[8*j+6];h[8*j+7]}if(c(k,o+1,p)){var t={type:"bigwig",score:s/q,maxScore:r};"bigbed"==this.bwg.type&&(t.type="density"),b(k,o+1,p,t)}}else if("bigwig"==this.bwg.type){var f=new Int16Array(a),g=new Int32Array(a),h=new Float32Array(a),k=g[0],x=g[1],y=(g[2],g[3]),z=g[4],A=e[20],i=f[11];if(A==w)for(var j=0;i>j;++j){var C=h[j+6],D=x+j*y+1,E=x+j*y+z;c(k,D,E)&&b(k,D,E,{score:C})}else if(A==v)for(var j=0;i>j;++j){var o=g[2*j+6]+1,p=o+z-1,C=h[2*j+7];c(k,o,p)&&b(k,o,p,{score:C})}else if(A==u)for(var j=0;i>j;++j){var o=g[3*j+6]+1,p=g[3*j+7],C=h[3*j+8];o>p&&(o=p),c(k,o,p)&&b(k,o,p,{score:C})}else console.log("Currently not handling bwgType="+A)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var F=0,G=this.bwg.definedFieldCount,H=this.bwg.schema;F0?I.split(" "):[],K.length>0&&G>3&&(L.label=K[0]),K.length>1&&G>4){var 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 Int32Array(d),p=m[j],q=n[j/2+1];if(j+=4,0!=p)for(var r=0;q>r;++r){var s=j/4,t=o[s],u=o[s+1],v=o[s+2],w=o[s+3],x=g(m,j+16),y=g(m,j+24);(0>c&&(a>t||t==a&&b>=u)||c>0&&(v>a||v==a&&w>=b))&&(/_random/.exec(e.bwg.idsToChroms[t])||(null==f||0>c&&(v>h||v==h&&w>i)||c>0&&(h>t||t==h&&i>u))&&(f={offset:x,size:y},i=0>c?w:u,h=0>c?v:t)),j+=32}else{for(var z=-1,A=-1,B=-1,r=0;q>r;++r){var s=j/4,t=o[s],u=o[s+1],v=o[s+2],w=o[s+3],x=o[s+4]<<32|o[s+5];(0>c&&(a>t||t==a&&b>=u)&&v>=a||c>0&&(v>a||v==a&&w>=b)&&a>=t)&&(0>z||w>A)&&(z=x,A=0>c?w:u,B=0>c?v:t),j+=24}z>=0&&k([z],l+1)}};k([e.cirTreeOffset+48],1)},h.prototype.readWigData=function(a,b,c){var d,e=25e3,f=c-b;if(e>=f||0===this.zoomLevels.length)d=this.getUnzoomedView(),console.log("zoomLevel unzoomed");else for(var g=0;g=this.zoomLevels.length-1)){var g;return g=0>a?this.getUnzoomedView():this.getZoomedView(a),g.readWigDataById(b,c,d,e)}if(this.topLevelReductionCache){for(var h=[],i=this.topLevelReductionCache,j=0;j0?0:3e8;a.fromRef&&(h=b);for(var j=0;j0){if(k>d)if(a.zoom<0){if(l.min>h)return e(l)}else l.max>h&&i.push({chr:a.chr,chrOrd:a.chrOrd,zoom:a.zoom-2,min:l.min,max:l.max,fromRef:a.fromRef})}else if(k>d)if(a.zoom<0){if(l.maxc?-1:1;for(var g=this,h=this.chromsToIDs[a],i=[{chrOrd:0,chr:h,zoom:g.zoomLevels.length-4,min:0,max:3e8,fromRef:!0}],j=1;j<=this.maxID+1;++j){var k=(h+c*j)%(this.maxID+1);0>k&&(k+=this.maxID+1),i.push({chrOrd:j,chr:k,zoom:g.zoomLevels.length-1,min:0,max:3e8})}f()},h.prototype.getAutoSQL=function(a){return this.asOffset?void $.when(f(this.url,this.asOffset,2048)).then(function(b){for(var c=new Uint8Array(b),d="",e=0;ei;++i){var j=e[10*i],l=e[10*i+1],m=g(d,20*i+4),n=e[10*i+8],o=new k(b,j,l,m,n);h.push(o)}a(h)})})},k.prototype.lookup=function(a,b){var c=this;this.bbi.data.slice(this.offset,32).fetch(function(d){function f(d){c.bbi.data.slice(d,4+j*(k+l)).fetch(function(d){var h=new Uint8Array(d),i=new Uint16Array(d),j=(new Uint32Array(d),h[0]),m=i[1],n=4;if(0!=j){for(var o=0;m>o;++o){for(var p="",q=0;k>q;++q){var r=h[n++];0!=r&&(p+=String.fromCharCode(r))}if(p==a){var s=g(h,n),t=e(h,n+8);return c.bbi.getUnzoomedView().fetchFeatures(function(b,d,e,f){return f&&f.length>c.field-3?f[c.field-3]==a:void 0},[{offset:s,size:t}],b)}n+=l}return b([])}for(var u=null,o=0;m>o;++o){for(var p="",q=0;k>q;++q){var r=h[n++];0!=r&&(p+=String.fromCharCode(r))}var v=g(h,n);if(n+=8,a.localeCompare(p)<0&&u)return void f(u);u=v}f(u)})}var h=new Uint8Array(d),i=(new Int16Array(d),new Int32Array(d)),j=(i[0],i[1]),k=i[2],l=i[3],m=(g(h,16),32);f(c.offset+m)})},{makeBwg:j}}); +define(["libs/bbi/spans","libs/bbi/jszlib","libs/bbi/jquery-ajax-native"],function(a,b){"use strict";function c(){}function d(a){a&&(this.id=a)}function e(a,b){return a[b+3]<<24|a[b+2]<<16|a[b+1]<<8|a[b]}function f(a,b,c){Math.pow(10,6);return $.ajax({type:"GET",dataType:"native",url:a,timeout:5e3,beforeSend:function(a){a.setRequestHeader("Range","bytes="+b+"-"+(b+(c-1)))},xhrFields:{responseType:"arraybuffer"}})}function g(a,b){var c=a[b]+a[b+1]*x+a[b+2]*y+a[b+3]*z+a[b+4]*A;return c}function h(){}function i(a,b,c,d){this.bwg=a,this.cirTreeOffset=b,this.cirTreeLength=c,this.isSummary=d}function j(a){var b=$.Deferred(),c=new h;return c.url=a,$.when(f(c.url,0,512)).then(function(a){if(!a)return b.resolve(null,"Couldn't fetch file");var d=a,e=new Uint8Array(d),f=new Int16Array(d),h=new Int32Array(d),i=e[0]+x*e[1]+y*e[2]+z*e[3];if(i==q)c.type="bigwig";else{if(i!=s)return i==r||i==t?b.resolve(null,"Currently don't support big-endian BBI files"):b.resolve(null,"Not a supported format, magic=0x"+i.toString(16));c.type="bigbed"}c.version=f[2],c.numZoomLevels=f[3],c.chromTreeOffset=g(e,8),c.unzoomedDataOffset=g(e,16),c.unzoomedIndexOffset=g(e,24),c.fieldCount=f[16],c.definedFieldCount=f[17],c.asOffset=g(e,36),c.totalSummaryOffset=g(e,44),c.uncompressBufSize=h[13],c.extHeaderOffset=g(e,56),c.zoomLevels=[];for(var j=0;jj;++j)if(0===e){b+=f;var k=g(c,b);b+=8,k-=a.chromTreeOffset,i(k)}else{for(var l="",m=0;f>m;++m){var n=c[b++];0!==n&&(l+=String.fromCharCode(n))}{var o=c[b+3]<<24|c[b+2]<<16|c[b+1]<<8|c[b+0];c[b+7]<<24|c[b+6]<<16|c[b+5]<<8|c[b+4]}b+=8,a.chromsToIDs[l]=o,0===l.indexOf("chr")&&(a.chromsToIDs[l.substr(3)]=o),a.idsToChroms[o]=l,a.maxID=Math.max(a.maxID,o)}};i(h)})},i.prototype.readWigData=function(a,b,c){var d,e=this.bwg.chromsToIDs[a];return d=void 0===e?[]:this.readWigDataById(e,b,c)},i.prototype.readWigDataById=function(a,b,c){var d=this,e=$.Deferred();if(!this.cirHeader)return $.when(f(d.bwg.url,this.cirTreeOffset,48)).then(function(f){d.cirHeader=f;var g=new Int32Array(d.cirHeader);d.cirBlockSize=g[1],$.when(d.readWigDataById(a,b,c)).then(function(a){e.resolve(a)})}),e;var h=[],i=0,j=(Date.now(),function(d,e,f){return(0>a||d==a)&&c>=e&&f>=b}),k=function(a,b){if(d.bwg.instrument&&console.log("level="+b+"; offset="+a+"; time="+(0|Date.now())),i+=a.length,1==a.length&&a[0]-d.cirTreeOffset==48&&d.cachedCirRoot)return o(d.cachedCirRoot,0,b),--i,void(0===i&&$.when(d.fetchFeatures(j,h)).then(function(a){e.resolve(a)}));for(var c,f=4+32*d.cirBlockSize,g=0;go;++o){var p=e/4,q=l[p],r=l[p+1],s=l[p+2],t=l[p+3],u=g(i,e+16),v=g(i,e+24);(0>a||a>q||q==a&&c>=r)&&(0>a||s>a||s==a&&t>=b)&&h.push({offset:u,size:v}),e+=32}else{for(var w=[],o=0;n>o;++o){var p=e/4,q=l[p],r=l[p+1],s=l[p+2],t=l[p+3],u=g(i,e+16);(0>a||a>q||q==a&&c>=r)&&(0>a||s>a||s==a&&t>=b)&&w.push(u),e+=24}w.length>0&&k(w,f+1)}};return k([d.cirTreeOffset+48],1),e},i.prototype.fetchFeatures=function(a,b){var d=this,e=$.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 Float32Array(a),i=a.byteLength/32,j=0;i>j;++j){{var k=g[8*j],o=g[8*j+1],p=g[8*j+2],q=g[8*j+3],r=(h[8*j+4],h[8*j+5]),s=h[8*j+6];h[8*j+7]}if(c(k,o+1,p)){var t={type:"bigwig",score:s/q,maxScore:r};"bigbed"==this.bwg.type&&(t.type="density"),b(k,o+1,p,t)}}else if("bigwig"==this.bwg.type){var f=new Int16Array(a),g=new Int32Array(a),h=new Float32Array(a),k=g[0],x=g[1],y=(g[2],g[3]),z=g[4],A=e[20],i=f[11];if(A==w)for(var j=0;i>j;++j){var C=h[j+6],D=x+j*y+1,E=x+j*y+z;c(k,D,E)&&b(k,D,E,{score:C})}else if(A==v)for(var j=0;i>j;++j){var o=g[2*j+6]+1,p=o+z-1,C=h[2*j+7];c(k,o,p)&&b(k,o,p,{score:C})}else if(A==u)for(var j=0;i>j;++j){var o=g[3*j+6]+1,p=g[3*j+7],C=h[3*j+8];o>p&&(o=p),c(k,o,p)&&b(k,o,p,{score:C})}else console.log("Currently not handling bwgType="+A)}else{if("bigbed"!=this.bwg.type)throw Error("Don't know what to do with "+this.bwg.type);for(var F=0,G=this.bwg.definedFieldCount,H=this.bwg.schema;F0?I.split(" "):[],K.length>0&&G>3&&(L.label=K[0]),K.length>1&&G>4){var 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 Int32Array(d),p=m[j],q=n[j/2+1];if(j+=4,0!=p)for(var r=0;q>r;++r){var s=j/4,t=o[s],u=o[s+1],v=o[s+2],w=o[s+3],x=g(m,j+16),y=g(m,j+24);(0>c&&(a>t||t==a&&b>=u)||c>0&&(v>a||v==a&&w>=b))&&(/_random/.exec(e.bwg.idsToChroms[t])||(null==f||0>c&&(v>h||v==h&&w>i)||c>0&&(h>t||t==h&&i>u))&&(f={offset:x,size:y},i=0>c?w:u,h=0>c?v:t)),j+=32}else{for(var z=-1,A=-1,B=-1,r=0;q>r;++r){var s=j/4,t=o[s],u=o[s+1],v=o[s+2],w=o[s+3],x=o[s+4]<<32|o[s+5];(0>c&&(a>t||t==a&&b>=u)&&v>=a||c>0&&(v>a||v==a&&w>=b)&&a>=t)&&(0>z||w>A)&&(z=x,A=0>c?w:u,B=0>c?v:t),j+=24}z>=0&&k([z],l+1)}};k([e.cirTreeOffset+48],1)},h.prototype.readWigData=function(a,b,c){var d,e=25e3,f=c-b;if(e>=f||0===this.zoomLevels.length)d=this.getUnzoomedView();else for(var g=0;g=this.zoomLevels.length-1)){var g;return g=0>a?this.getUnzoomedView():this.getZoomedView(a),g.readWigDataById(b,c,d,e)}if(this.topLevelReductionCache){for(var h=[],i=this.topLevelReductionCache,j=0;j0?0:3e8;a.fromRef&&(h=b);for(var j=0;j0){if(k>d)if(a.zoom<0){if(l.min>h)return e(l)}else l.max>h&&i.push({chr:a.chr,chrOrd:a.chrOrd,zoom:a.zoom-2,min:l.min,max:l.max,fromRef:a.fromRef})}else if(k>d)if(a.zoom<0){if(l.maxc?-1:1;for(var g=this,h=this.chromsToIDs[a],i=[{chrOrd:0,chr:h,zoom:g.zoomLevels.length-4,min:0,max:3e8,fromRef:!0}],j=1;j<=this.maxID+1;++j){var k=(h+c*j)%(this.maxID+1);0>k&&(k+=this.maxID+1),i.push({chrOrd:j,chr:k,zoom:g.zoomLevels.length-1,min:0,max:3e8})}f()},h.prototype.getAutoSQL=function(a){return this.asOffset?void $.when(f(this.url,this.asOffset,2048)).then(function(b){for(var c=new Uint8Array(b),d="",e=0;ei;++i){var j=e[10*i],l=e[10*i+1],m=g(d,20*i+4),n=e[10*i+8],o=new k(b,j,l,m,n);h.push(o)}a(h)})})},k.prototype.lookup=function(a,b){var c=this;this.bbi.data.slice(this.offset,32).fetch(function(d){function f(d){c.bbi.data.slice(d,4+j*(k+l)).fetch(function(d){var h=new Uint8Array(d),i=new Uint16Array(d),j=(new Uint32Array(d),h[0]),m=i[1],n=4;if(0!=j){for(var o=0;m>o;++o){for(var p="",q=0;k>q;++q){var r=h[n++];0!=r&&(p+=String.fromCharCode(r))}if(p==a){var s=g(h,n),t=e(h,n+8);return c.bbi.getUnzoomedView().fetchFeatures(function(b,d,e,f){return f&&f.length>c.field-3?f[c.field-3]==a:void 0},[{offset:s,size:t}],b)}n+=l}return b([])}for(var u=null,o=0;m>o;++o){for(var p="",q=0;k>q;++q){var r=h[n++];0!=r&&(p+=String.fromCharCode(r))}var v=g(h,n);if(n+=8,a.localeCompare(p)<0&&u)return void f(u);u=v}f(u)})}var h=new Uint8Array(d),i=(new Int16Array(d),new Int32Array(d)),j=(i[0],i[1]),k=i[2],l=i[3],m=(g(h,16),32);f(c.offset+m)})},{makeBwg:j}}); //# sourceMappingURL=../../../maps/libs/bbi/bigwig.js.map \ No newline at end of file diff --git a/static/scripts/viz/bbi-data-manager.js b/static/scripts/viz/bbi-data-manager.js index f3e9ee28f4e..fb101b8faf9 100644 --- a/static/scripts/viz/bbi-data-manager.js +++ b/static/scripts/viz/bbi-data-manager.js @@ -1,2 +1,2 @@ -define(["viz/visualization","libs/bbi/bigwig"],function(a,b){var c=a.GenomeDataManager.extend({load_data:function(a){var c=$.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}}); +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=[],f={max:Number.MIN_VALUE};b.forEach(function(a){f.max!==a.min-1&&(d.push([f.max+1,0]),d.push([a.min-2,0])),d.push([a.min-1,a.score]),d.push([a.max,a.score]),f=a});var g={data:d,region:a,dataset_type:"bigwig"};e.set_data(a,g),c.resolve(g)})}),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/painters.js b/static/scripts/viz/trackster/painters.js index bbe8c7e87f0..b152c4521ff 100644 --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -1,2 +1,2 @@ -define(["libs/underscore"],function(a){var b=1001,c=1002,d=1003,e=1004,f=1005,g=1006,h=function(a,h){var i,j=a[0],k=a[1],l=h[0],m=h[1];return i=l>j?l>=k?b:m>=k?d:c:j>m?g:m>=k?f:e},i=function(a,c){var d=h(a,c);return d!==b&&d!==g},j=function(a,b,c,d,e,f){void 0===f&&(f=4);var g,h=d-b,i=e-c,j=Math.floor(Math.sqrt(h*h+i*i)/f),k=h/j,l=i/j;for(g=0;j>g;g++,b+=k,c+=l)g%2===0&&a.fillRect(b,c,f,1)},k=function(a,b,c,d){var e=b-d/2,f=b+d/2,g=c-Math.sqrt(3*d/2);a.beginPath(),a.moveTo(e,g),a.lineTo(f,g),a.lineTo(b,c),a.lineTo(e,g),a.strokeStyle=this.fillStyle,a.fill(),a.stroke(),a.closePath()},l=function(a){this.default_val=a?a:1};l.prototype.gen_val=function(){return this.default_val};var m=function(a){this.incomplete_features=a.incomplete_features,this.feature_mapper=a.feature_mapper},n=function(b,c,d,e,f){this.data=b,this.view_start=c,this.view_end=d,this.prefs=a.extend({},this.default_prefs,e),this.mode=f};n.prototype.default_prefs={},n.prototype.draw=function(){},n.prototype.get_start_draw_pos=function(a,b){return this._chrom_pos_to_draw_pos(a,b,-.5)},n.prototype.get_end_draw_pos=function(a,b){return this._chrom_pos_to_draw_pos(a,b,.5)},n.prototype.get_draw_pos=function(a,b){return this._chrom_pos_to_draw_pos(a,b,0)},n.prototype._chrom_pos_to_draw_pos=function(a,b,c){return Math.floor(b*(Math.max(0,a-this.view_start)+c))};var o=function(a,b,c,d,e){n.call(this,a,b,c,d,e)};o.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},o.prototype.draw=function(a,b,c,d){var e=!1,f=this.prefs.min_value,g=this.prefs.max_value,h=g-f,i=c,j=this.view_start,k=this.mode,l=this.data;a.save();var m=Math.round(c+f/h*c);"Intensity"!==k&&(a.fillStyle="#aaa",a.fillRect(0,m,b,1)),a.beginPath();var n,o,p;p=l.length>1?Math.ceil((l[1][0]-l[0][0])*d):10;for(var q=this.prefs.block_color||this.prefs.color,r=parseInt(q.slice(1),16),s=(16711680&r)>>16,t=(65280&r)>>8,u=255&r,v=!1,w=!1,x=0,y=l.length;y>x;x++)if(a.fillStyle=a.strokeStyle=q,v=w=!1,n=Math.ceil((l[x][0]-j)*d),o=l[x][1],null!==o){if(f>o?(w=!0,o=f):o>g&&(v=!0,o=g),"Histogram"===k)o=Math.round(o/h*i),a.fillRect(n,m,p,-o);else if("Intensity"===k){var z=(o-f)/h,A=Math.round(s+(255-s)*(1-z)),B=Math.round(t+(255-t)*(1-z)),C=Math.round(u+(255-u)*(1-z));a.fillStyle="rgb("+A+","+B+","+C+")",a.fillRect(n,0,p,i)}else o=Math.round(i-(o-f)/h*i),e?a.lineTo(n,o):(e=!0,"Filled"===k?(a.moveTo(n,i),a.lineTo(n,o)):a.moveTo(n,o));if(a.fillStyle=this.prefs.overflow_color,v||w){var D;"Histogram"===k||"Intensity"===k?D=p:(n-=2,D=4),v&&a.fillRect(n,0,D,3),w&&a.fillRect(n,i-3,D,3)}a.fillStyle=q}else e&&"Filled"===k&&a.lineTo(n,i),e=!1;"Filled"===k?(e&&(a.lineTo(n,m),a.lineTo(0,m)),a.fill()):a.stroke(),a.restore()};var p=function(a){this.feature_positions={},this.slot_height=a,this.translation=0,this.y_translation=0};p.prototype.map_feature_data=function(a,b,c,d){this.feature_positions[b]||(this.feature_positions[b]=[]),this.feature_positions[b].push({data:a,x_start:c,x_end:d})},p.prototype.get_feature_data=function(a,b){var c,d=Math.floor((b-this.y_translation)/this.slot_height);if(!this.feature_positions[d])return null;a+=this.translation;for(var e=0;e=c.x_start&&a<=c.x_end)return c.data};var q=function(a,b,c,d,e,f,g){n.call(this,a,b,c,d,e),this.alpha_scaler=f?f:new l,this.height_scaler=g?g:new l,this.max_label_length=200};q.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},a.extend(q.prototype,{get_required_height:function(a,b){var c=this.get_row_height(),d=c,e=this.mode;return("no_detail"===e||"Squish"===e||"Pack"===e)&&(c=a*d),c+this.get_top_padding(b)},get_top_padding:function(){return 0},draw:function(a,b,c,d,e){var f=this.data,g=this.view_start,h=this.view_end;a.save(),a.fillStyle=this.prefs.block_color,a.textAlign="right";for(var i,j=this.get_row_height(),k=new p(j),l=[],n=0,o=f.length;o>n;n++){var q=f[n],r=q[0],s=q[1],t=q[2],u=e&&void 0!==e[r]?e[r].slot:null;("Dense"===this.mode||null!==u)&&h>s&&t>g&&(i=this.draw_element(a,this.mode,q,u,g,h,d,j,b),k.map_feature_data(q,u,i[0],i[1]),(g>s||t>h)&&l.push(q))}return a.restore(),k.y_translation=this.get_top_padding(b),new m({incomplete_features:l,feature_mapper:k})},draw_element:function(){return[0,0]}});var r=10,s=3,t=5,u=10,v=1,w=9,x=3,y=9,z=2,A="#ccc",B=function(a,b,c,d,e,f,g){q.call(this,a,b,c,d,e,f,g),this.draw_background_connector=!0,this.draw_individual_connectors=!1};a.extend(B.prototype,q.prototype,{get_row_height:function(){var a,b=this.mode;return a="Dense"===b?r:"no_detail"===b?s:"Squish"===b?t:u},draw_element:function(a,b,c,d,e,f,g,h,i){var j,k=(c[0],c[1]),l=c[2],m=c[3],n=c[4],o=Math.floor(Math.max(0,(k-e-.5)*g)),p=Math.ceil(Math.min(i,Math.max(0,(l-e-.5)*g))),q=o,r=p,j=("Dense"===b?0:0+d)*h+this.get_top_padding(i),s=null,t=null,u=n&&"+"!==n&&"."!==n?this.prefs.reverse_strand_color:this.prefs.block_color;if(label_color=this.prefs.label_color,a.globalAlpha=this.alpha_scaler.gen_val(c),"Dense"===b&&(d=1),"no_detail"===b)a.fillStyle=u,a.fillRect(o,j+5,p-o,v);else{var B=c[5],C=c[6],D=c[7],E=!0;B&&C&&(s=Math.floor(Math.max(0,(B-e)*g)),t=Math.ceil(Math.min(i,Math.max(0,(C-e)*g))));var F,G;if("Squish"===b?(F=1,G=x,E=!1):"Dense"===b?(F=5,G=w):(F=5,G=y),D){var H,I;"Squish"===b||"Dense"===b?(H=j+Math.floor(x/2)+1,I=1):n?(H=j,I=G):(H+=x/2+1,I=1),this.draw_background_connector&&("Squish"===b||"Dense"===b?a.fillStyle=A:n?"+"===n?a.fillStyle=a.canvas.manager.get_pattern("right_strand"):"-"===n&&(a.fillStyle=a.canvas.manager.get_pattern("left_strand")):a.fillStyle=A,a.fillRect(o,H,p-o,I));for(var J=0,K=D.length;K>J;J++){var L,M,N=D[J],O=Math.floor(Math.max(0,(N[0]-e-.5)*g)),P=Math.ceil(Math.min(i,Math.max((N[1]-e-.5)*g)));if(!(O>P)){if(a.fillStyle=u,a.fillRect(O,j+(G-F)/2+1,P-O,F),void 0!==s&&C>B&&!(O>t||s>P)){var Q=Math.max(O,s),R=Math.min(P,t);a.fillRect(Q,j+1,R-Q,G),1===D.length&&"Pack"===b&&("+"===n?a.fillStyle=a.canvas.manager.get_pattern("right_strand_inv"):"-"===n&&(a.fillStyle=a.canvas.manager.get_pattern("left_strand_inv")),R>Q+14&&(Q+=2,R-=2),a.fillRect(Q,j+1,R-Q,G))}this.draw_individual_connectors&&L&&this.draw_connector(a,L,M,O,P,j),L=O,M=P}}if("Pack"===b){a.globalAlpha=1,a.fillStyle="white";var S=this.height_scaler.gen_val(c),T=Math.ceil(G*S),U=Math.round((G-T)/2);1!==S&&(a.fillRect(o,H+1,p-o,U),a.fillRect(o,H+G-U+1,p-o,U))}}else a.fillStyle=u,a.fillRect(o,j+1,p-o,G),n&&E&&("+"===n?a.fillStyle=a.canvas.manager.get_pattern("right_strand_inv"):"-"===n&&(a.fillStyle=a.canvas.manager.get_pattern("left_strand_inv")),a.fillRect(o,j+1,p-o,G));a.globalAlpha=1,m&&"Pack"===b&&k>e&&(a.fillStyle=label_color,0===e&&o-a.measureText(m).width<0?(a.textAlign="left",a.fillText(m,p+z,j+8,this.max_label_length),r+=a.measureText(m).width+z):(a.textAlign="right",a.fillText(m,o-z,j+8,this.max_label_length),q-=a.measureText(m).width+z))}return a.globalAlpha=1,[q,r]}});var C=function(a,b,c,d,e,f,g,h,i){q.call(this,a,b,c,d,e,f,g),this.ref_seq=h?h.data:null,this.base_color_fn=i};a.extend(C.prototype,q.prototype,{get_row_height:function(){var a,b=this.mode;return"Dense"===b?a=r:"Squish"===b?a=t:(a=u,this.prefs.show_insertions&&(a*=2)),a},_parse_cigar:function(b){var c="MIDNSHP=X",d=[[0,0]],e=d[0],f=0,g=a.map(b.match(/[0-9]+[MIDNSHP=X]/g),function(a){var b=parseInt(a.slice(0,-1),10),g=a.slice(-1);return"N"===g?0!==e[1]&&(e=[f+b,f+b],d.push(e)):-1==="ISHP".indexOf(g)&&(e[1]+=b,f+=b),[c.indexOf(g),b]});return{blocks:d,cigar:g}},draw_read:function(a,b,g,j,l,m,n,o,p,q){var r=function(a,b,c){return-1!=="M=NXD".indexOf(b)&&(a+=c),a},s=function(a,b,c){return-1!=="IX".indexOf(b)&&(a+=c),a},t=function(a){return Math.floor(Math.max(0,(a-l-.5)*g))};a.textAlign="center";var u,v,z=[l,m],B=0,C=0,D=Math.round(g/2),E=a.canvas.manager.char_width_px,F="+"===p?this.prefs.detail_block_color:this.prefs.reverse_strand_color,G="Pack"===b,H=G?y:x,J=j+1,K=new I(a,H,g,b),L=[],M=[],N=this._parse_cigar(o);o=N.cigar,L=N.blocks;for(var O=0;OQ;Q++){var S=o[Q],T="MIDNSHP=X"[S[0]],U=S[1],V=n+B;if(u=t(V),v=t(V+U),i([V,V+U],z))switch(u===v&&(v+=1),T){case"H":case"S":case"P":break;case"M":B+=U;break;case"=":case"X":var W="";"X"===T?W=q.slice(C,C+U):this.ref_seq&&(W=this.ref_seq.slice(Math.max(0,V-l),Math.min(V-l+U,m-l)));for(var X=Math.max(V,l),Y=0;YE?a.fillText(W[Y],Z,j+9):g>.05&&a.fillRect(Z-D,J,Math.max(1,Math.round(g)),H)}"X"===T&&(C+=U),B+=U;break;case"N":a.fillStyle=A,a.fillRect(u,J+(H-1)/2,v-u,1),B+=U;break;case"D":K.draw_deletion(u,J,U),B+=U;break;case"I":var $=u-D;if(i([V,V+U],z)){var _=q.slice(C,C+U);if(this.prefs.show_insertions){var aa=u-(v-u)/2;if(("Pack"===b||"Auto"===this.mode)&&void 0!==q&&g>E){switch(a.fillStyle="yellow",a.fillRect(aa-D,j-9,v-u,9),M[M.length]={type:"triangle",data:[$,j+4,5]},a.fillStyle=A,h([V,V+U],z)){case d:_=_.slice(l-V);break;case e:_=_.slice(0,V-m);break;case f:break;case c:_=_.slice(l-V,V-m)}for(var Y=0,ba=_.length;ba>Y;Y++){var Z=Math.floor(Math.max(0,(V+Y-l)*g));a.fillText(_[Y],Z-(v-u)/2,j)}}else a.fillStyle="yellow",a.fillRect(aa,j+("Dense"!==this.mode?2:5),v-u,"Dense"!==b?x:w)}else("Pack"===b||"Auto"===this.mode)&&void 0!==q&&g>E&&M.push({type:"text",data:[_.length,$,j+9]})}C+=U}else B=r(B,T,U),C=s(C,T,U)}a.fillStyle="yellow";for(var ca,da,ea,O=0;O=e&&c[4][0]<=f&&c[4][2]?this.draw_read(a,b,g,p,e,f,c[4][0],c[4][2],c[4][3],c[4][4]):r=!1,c[5][1]>=e&&c[5][0]<=f&&c[5][2]?this.draw_read(a,b,g,p,e,f,c[5][0],c[5][2],c[5][3],c[5][4]):r=!1;var s=Math.ceil(Math.min(i,Math.max(-.5*g,(c[4][1]-e-.5)*g))),t=Math.floor(Math.max(-.5*g,(c[5][0]-e-.5)*g));if(r&&t>s){a.fillStyle=A;var u=p+1+(q-1)/2;j(a,s,u,t,u)}}else this.draw_read(a,b,g,p,e,f,k,c[4],c[5],c[6]);return"Pack"===b&&k>=e&&"."!==m&&(a.fillStyle=this.prefs.label_color,0===e&&n-a.measureText(m).width<0?(a.textAlign="left",a.fillText(m,o+z,p+9,this.max_label_length)):(a.textAlign="right",a.fillText(m,n-z,p+9,this.max_label_length))),[0,0]}});var D=function(a,b,c,d,e,f,g){B.call(this,a,b,c,d,e,f,g),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};a.extend(D.prototype,q.prototype,B.prototype,{calculate_longest_feature_length:function(){for(var a=0,b=0,c=this.data.length;c>b;b++){var d=this.data[b],e=d[1],f=d[2];a=Math.max(a,f-e)}return a},get_top_padding:function(a){var b=this.view_end-this.view_start,c=a/b;return Math.min(128,Math.ceil(this.longest_feature_length/2*c))},draw_connector:function(a,b,c,d,e,f){{var g=(c+d)/2,h=d-g;Math.PI}h>0&&(a.beginPath(),a.arc(g,f,d-g,Math.PI,0),a.stroke())}});var E=function(a,b){this.rgb=Array.isArray(a)?a:6==a.length?a.match(/.{2}/g).map(function(a){return parseInt(a,16)}):7==a.length?a.substring(1,7).match(/.{2}/g).map(function(a){return parseInt(a,16)}):a.split("").map(function(a){return parseInt(a+a,16)}),this.alpha="number"==typeof b?b:1};E.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(a){return Math.round(a)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(a){return a=Math.round(a),a=(a>255?255:0>a?0:a).toString(16),1===a.length?"0"+a:a}).join("")},toHSL:function(){var a,b,c=this.rgb[0]/255,d=this.rgb[1]/255,e=this.rgb[2]/255,f=this.alpha,g=Math.max(c,d,e),h=Math.min(c,d,e),i=(g+h)/2,j=g-h;if(g===h)a=b=0;else{switch(b=i>.5?j/(2-g-h):j/(g+h),g){case c:a=(d-e)/j+(e>d?6:0);break;case d:a=(e-c)/j+2;break;case e:a=(c-d)/j+4}a/=6}return{h:360*a,s:b,l:i,a:f}},toARGB:function(){var a=[Math.round(255*this.alpha)].concat(this.rgb);return"#"+a.map(function(a){return a=Math.round(a),a=(a>255?255:0>a?0:a).toString(16),1===a.length?"0"+a:a}).join("")},mix:function(a,b){color1=this;var c=b,d=2*c-1,e=color1.toHSL().a-a.toHSL().a,f=((d*e==-1?d:(d+e)/(1+d*e))+1)/2,g=1-f,h=[color1.rgb[0]*f+a.rgb[0]*g,color1.rgb[1]*f+a.rgb[1]*g,color1.rgb[2]*f+a.rgb[2]*g],i=color1.alpha*c+a.alpha*(1-c);return new E(h,i)}};var F=function(a,b,c,d){this.start_color=new E(a),this.end_color=new E(b),this.start_value=c,this.end_value=d,this.value_range=d-c};F.prototype.map_value=function(a){return a=Math.max(a,this.start_value),a=Math.min(a,this.end_value),a=(a-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-a).toCSS()};var G=function(a,b,c,d,e){this.positive_ramp=new F(b,c,0,e),this.negative_ramp=new F(b,a,0,-d),this.start_value=d,this.end_value=e};G.prototype.map_value=function(a){return a=Math.max(a,this.start_value),a=Math.min(a,this.end_value),a>=0?this.positive_ramp.map_value(a):this.negative_ramp.map_value(-a)};var H=function(a,b,c,d,e){n.call(this,a,b,c,d,e);var f,g;if(void 0===this.prefs.min_value){var h=1/0;for(f=0,g=this.data.length;g>f;f++)h=Math.min(h,this.data[f][6]);this.prefs.min_value=h}if(void 0===this.prefs.max_value){var i=-(1/0);for(f=0,g=this.data.length;g>f;f++)i=Math.max(i,this.data[f][6]);this.prefs.max_value=i}};H.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},H.prototype.draw=function(a,b,c,d){var e,f,g,h,i,j,k=this.prefs.min_value,l=this.prefs.max_value,m=this.view_start,n=(this.mode,this.data),o=1/Math.sqrt(2),p=new G(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,k,l),q=function(a){return(a-m)*d};a.save(),a.rotate(-45*Math.PI/180),a.scale(o,o);for(var r=0,s=n.length;s>r;r++)e=n[r],f=q(e[1]),g=q(e[2]),h=q(e[4]),i=q(e[5]),j=e[6],a.fillStyle=p.map_value(j),a.fillRect(f,h,g-f,i-h);a.restore()};var I=function(a,b,c,d){this.ctx=a,this.row_height=b,this.px_per_base=c,this.draw_details=("Pack"===d||"Auto"===d)&&c>=a.canvas.manager.char_width_px,this.delete_details_thickness=.2};a.extend(I.prototype,{draw_deletion:function(a,b,c){this.ctx.fillStyle="black";var d=(this.draw_details?this.delete_details_thickness:1)*this.row_height;b+=.5*(this.row_height-d),this.ctx.fillRect(a,b,c*this.px_per_base,d)}});var J=function(a,b,c,d,e,f){n.call(this,a,b,c,d,e),this.base_color_fn=f,this.divider_height=1};return a.extend(J.prototype,n.prototype,{get_row_height:function(){var a,b=this.mode;return a="Dense"===b?r:"Squish"===b?t:u},get_required_height:function(a){var b=this.prefs.summary_height;return a>1&&this.prefs.show_sample_data&&(b+=this.divider_height+a*this.get_row_height()),b},draw:function(b,c,d,e){b.save();var f,g,h,i,j,k,l,m,n,o,p,q=function(a,b){var c=a.length,d=b.length,e=0,f=1,g=null;return"-"===b?(g="deletion",f=a.length):0===a.indexOf(b)&&c>d?(g="deletion",f=c-d,e=d):0===b.indexOf(a)&&d>c&&(g="insertion",f=d-c,e=d),null!==g?{type:g,start:e,len:f}:{}},r=Math.max(1,Math.floor(e)),s=this.data.length?this.data[0][7].split(",").length:0,v="Squish"===this.mode?t:u,w=.1>e?v:"Squish"===this.mode?x:y,z=!0,A=new I(b,v,e,this.mode);1===s&&(v=w=ethis.view_end)){if(z)for(b.fillStyle="#999999",b.globalAlpha=1,p=0;pj?l>=k?b:m>=k?d:c:j>m?g:m>=k?f:e},i=function(a,c){var d=h(a,c);return d!==b&&d!==g},j=function(a,b,c,d,e,f){void 0===f&&(f=4);var g,h=d-b,i=e-c,j=Math.floor(Math.sqrt(h*h+i*i)/f),k=h/j,l=i/j;for(g=0;j>g;g++,b+=k,c+=l)g%2===0&&a.fillRect(b,c,f,1)},k=function(a,b,c,d){var e=b-d/2,f=b+d/2,g=c-Math.sqrt(3*d/2);a.beginPath(),a.moveTo(e,g),a.lineTo(f,g),a.lineTo(b,c),a.lineTo(e,g),a.strokeStyle=this.fillStyle,a.fill(),a.stroke(),a.closePath()},l=function(a){this.default_val=a?a:1};l.prototype.gen_val=function(){return this.default_val};var m=function(a){this.incomplete_features=a.incomplete_features,this.feature_mapper=a.feature_mapper},n=function(b,c,d,e,f){this.data=b,this.view_start=c,this.view_end=d,this.prefs=a.extend({},this.default_prefs,e),this.mode=f};n.prototype.default_prefs={},n.prototype.draw=function(){},n.prototype.get_start_draw_pos=function(a,b){return this._chrom_pos_to_draw_pos(a,b,-.5)},n.prototype.get_end_draw_pos=function(a,b){return this._chrom_pos_to_draw_pos(a,b,.5)},n.prototype.get_draw_pos=function(a,b){return this._chrom_pos_to_draw_pos(a,b,0)},n.prototype._chrom_pos_to_draw_pos=function(a,b,c){return Math.floor(b*(Math.max(0,a-this.view_start)+c))};var o=function(a,b,c,d,e){n.call(this,a,b,c,d,e)};o.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Histogram",color:"#000",overflow_color:"#F66"},o.prototype.draw=function(b,c,d,e){var f=!1,g=this.prefs.min_value,h=this.prefs.max_value,i=h-g,j=d,k=this.view_start,l=this.mode,m=this.data;b.save();var n=Math.round(d+g/i*d);"Intensity"!==l&&(b.fillStyle="#aaa",b.fillRect(0,n,c,1)),b.beginPath();var o,p,q;q=m.length>1?a.map(m.slice(0,-1),function(a,b){return Math.ceil((m[b+1][0]-m[b][0])*e)}):[10];for(var r,s=this.prefs.block_color||this.prefs.color,t=parseInt(s.slice(1),16),u=(16711680&t)>>16,v=(65280&t)>>8,w=255&t,x=!1,y=!1,z=0,A=m.length;A>z;z++)if(b.fillStyle=b.strokeStyle=s,x=y=!1,r=q[z],o=Math.ceil((m[z][0]-k-.5)*e),p=m[z][1],null!==p){if(g>p?(y=!0,p=g):p>h&&(x=!0,p=h),"Histogram"===l)p=Math.round(p/i*j),b.fillRect(o,n,r,-p);else if("Intensity"===l){var B=(p-g)/i,C=Math.round(u+(255-u)*(1-B)),D=Math.round(v+(255-v)*(1-B)),E=Math.round(w+(255-w)*(1-B));b.fillStyle="rgb("+C+","+D+","+E+")",b.fillRect(o,0,r,j)}else p=Math.round(j-(p-g)/i*j),f?b.lineTo(o,p):(f=!0,"Filled"===l?(b.moveTo(o,j),b.lineTo(o,p)):b.moveTo(o,p));if(b.fillStyle=this.prefs.overflow_color,x||y){var F;"Histogram"===l||"Intensity"===l?F=r:(o-=2,F=4),x&&b.fillRect(o,0,F,3),y&&b.fillRect(o,j-3,F,3)}b.fillStyle=s}else f&&"Filled"===l&&b.lineTo(o,j),f=!1;"Filled"===l?(f&&(b.lineTo(o,n),b.lineTo(0,n)),b.fill()):b.stroke(),b.restore()};var p=function(a){this.feature_positions={},this.slot_height=a,this.translation=0,this.y_translation=0};p.prototype.map_feature_data=function(a,b,c,d){this.feature_positions[b]||(this.feature_positions[b]=[]),this.feature_positions[b].push({data:a,x_start:c,x_end:d})},p.prototype.get_feature_data=function(a,b){var c,d=Math.floor((b-this.y_translation)/this.slot_height);if(!this.feature_positions[d])return null;a+=this.translation;for(var e=0;e=c.x_start&&a<=c.x_end)return c.data};var q=function(a,b,c,d,e,f,g){n.call(this,a,b,c,d,e),this.alpha_scaler=f?f:new l,this.height_scaler=g?g:new l,this.max_label_length=200};q.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"},a.extend(q.prototype,{get_required_height:function(a,b){var c=this.get_row_height(),d=c,e=this.mode;return("no_detail"===e||"Squish"===e||"Pack"===e)&&(c=a*d),c+this.get_top_padding(b)},get_top_padding:function(){return 0},draw:function(a,b,c,d,e){var f=this.data,g=this.view_start,h=this.view_end;a.save(),a.fillStyle=this.prefs.block_color,a.textAlign="right";for(var i,j=this.get_row_height(),k=new p(j),l=[],n=0,o=f.length;o>n;n++){var q=f[n],r=q[0],s=q[1],t=q[2],u=e&&void 0!==e[r]?e[r].slot:null;("Dense"===this.mode||null!==u)&&h>s&&t>g&&(i=this.draw_element(a,this.mode,q,u,g,h,d,j,b),k.map_feature_data(q,u,i[0],i[1]),(g>s||t>h)&&l.push(q))}return a.restore(),k.y_translation=this.get_top_padding(b),new m({incomplete_features:l,feature_mapper:k})},draw_element:function(){return[0,0]}});var r=10,s=3,t=5,u=10,v=1,w=9,x=3,y=9,z=2,A="#ccc",B=function(a,b,c,d,e,f,g){q.call(this,a,b,c,d,e,f,g),this.draw_background_connector=!0,this.draw_individual_connectors=!1};a.extend(B.prototype,q.prototype,{get_row_height:function(){var a,b=this.mode;return a="Dense"===b?r:"no_detail"===b?s:"Squish"===b?t:u},draw_element:function(a,b,c,d,e,f,g,h,i){var j,k=(c[0],c[1]),l=c[2],m=c[3],n=c[4],o=Math.floor(Math.max(0,(k-e-.5)*g)),p=Math.ceil(Math.min(i,Math.max(0,(l-e-.5)*g))),q=o,r=p,j=("Dense"===b?0:0+d)*h+this.get_top_padding(i),s=null,t=null,u=n&&"+"!==n&&"."!==n?this.prefs.reverse_strand_color:this.prefs.block_color;if(label_color=this.prefs.label_color,a.globalAlpha=this.alpha_scaler.gen_val(c),"Dense"===b&&(d=1),"no_detail"===b)a.fillStyle=u,a.fillRect(o,j+5,p-o,v);else{var B=c[5],C=c[6],D=c[7],E=!0;B&&C&&(s=Math.floor(Math.max(0,(B-e)*g)),t=Math.ceil(Math.min(i,Math.max(0,(C-e)*g))));var F,G;if("Squish"===b?(F=1,G=x,E=!1):"Dense"===b?(F=5,G=w):(F=5,G=y),D){var H,I;"Squish"===b||"Dense"===b?(H=j+Math.floor(x/2)+1,I=1):n?(H=j,I=G):(H+=x/2+1,I=1),this.draw_background_connector&&("Squish"===b||"Dense"===b?a.fillStyle=A:n?"+"===n?a.fillStyle=a.canvas.manager.get_pattern("right_strand"):"-"===n&&(a.fillStyle=a.canvas.manager.get_pattern("left_strand")):a.fillStyle=A,a.fillRect(o,H,p-o,I));for(var J=0,K=D.length;K>J;J++){var L,M,N=D[J],O=Math.floor(Math.max(0,(N[0]-e-.5)*g)),P=Math.ceil(Math.min(i,Math.max((N[1]-e-.5)*g)));if(!(O>P)){if(a.fillStyle=u,a.fillRect(O,j+(G-F)/2+1,P-O,F),void 0!==s&&C>B&&!(O>t||s>P)){var Q=Math.max(O,s),R=Math.min(P,t);a.fillRect(Q,j+1,R-Q,G),1===D.length&&"Pack"===b&&("+"===n?a.fillStyle=a.canvas.manager.get_pattern("right_strand_inv"):"-"===n&&(a.fillStyle=a.canvas.manager.get_pattern("left_strand_inv")),R>Q+14&&(Q+=2,R-=2),a.fillRect(Q,j+1,R-Q,G))}this.draw_individual_connectors&&L&&this.draw_connector(a,L,M,O,P,j),L=O,M=P}}if("Pack"===b){a.globalAlpha=1,a.fillStyle="white";var S=this.height_scaler.gen_val(c),T=Math.ceil(G*S),U=Math.round((G-T)/2);1!==S&&(a.fillRect(o,H+1,p-o,U),a.fillRect(o,H+G-U+1,p-o,U))}}else a.fillStyle=u,a.fillRect(o,j+1,p-o,G),n&&E&&("+"===n?a.fillStyle=a.canvas.manager.get_pattern("right_strand_inv"):"-"===n&&(a.fillStyle=a.canvas.manager.get_pattern("left_strand_inv")),a.fillRect(o,j+1,p-o,G));a.globalAlpha=1,m&&"Pack"===b&&k>e&&(a.fillStyle=label_color,0===e&&o-a.measureText(m).width<0?(a.textAlign="left",a.fillText(m,p+z,j+8,this.max_label_length),r+=a.measureText(m).width+z):(a.textAlign="right",a.fillText(m,o-z,j+8,this.max_label_length),q-=a.measureText(m).width+z))}return a.globalAlpha=1,[q,r]}});var C=function(a,b,c,d,e,f,g,h,i){q.call(this,a,b,c,d,e,f,g),this.ref_seq=h?h.data:null,this.base_color_fn=i};a.extend(C.prototype,q.prototype,{get_row_height:function(){var a,b=this.mode;return"Dense"===b?a=r:"Squish"===b?a=t:(a=u,this.prefs.show_insertions&&(a*=2)),a},_parse_cigar:function(b){var c="MIDNSHP=X",d=[[0,0]],e=d[0],f=0,g=a.map(b.match(/[0-9]+[MIDNSHP=X]/g),function(a){var b=parseInt(a.slice(0,-1),10),g=a.slice(-1);return"N"===g?0!==e[1]&&(e=[f+b,f+b],d.push(e)):-1==="ISHP".indexOf(g)&&(e[1]+=b,f+=b),[c.indexOf(g),b]});return{blocks:d,cigar:g}},draw_read:function(a,b,g,j,l,m,n,o,p,q){var r=function(a,b,c){return-1!=="M=NXD".indexOf(b)&&(a+=c),a},s=function(a,b,c){return-1!=="IX".indexOf(b)&&(a+=c),a},t=function(a){return Math.floor(Math.max(0,(a-l-.5)*g))};a.textAlign="center";var u,v,z=[l,m],B=0,C=0,D=Math.round(g/2),E=a.canvas.manager.char_width_px,F="+"===p?this.prefs.detail_block_color:this.prefs.reverse_strand_color,G="Pack"===b,H=G?y:x,J=j+1,K=new I(a,H,g,b),L=[],M=[],N=this._parse_cigar(o);o=N.cigar,L=N.blocks;for(var O=0;OQ;Q++){var S=o[Q],T="MIDNSHP=X"[S[0]],U=S[1],V=n+B;if(u=t(V),v=t(V+U),i([V,V+U],z))switch(u===v&&(v+=1),T){case"H":case"S":case"P":break;case"M":B+=U;break;case"=":case"X":var W="";"X"===T?W=q.slice(C,C+U):this.ref_seq&&(W=this.ref_seq.slice(Math.max(0,V-l),Math.min(V-l+U,m-l)));for(var X=Math.max(V,l),Y=0;YE?a.fillText(W[Y],Z,j+9):g>.05&&a.fillRect(Z-D,J,Math.max(1,Math.round(g)),H)}"X"===T&&(C+=U),B+=U;break;case"N":a.fillStyle=A,a.fillRect(u,J+(H-1)/2,v-u,1),B+=U;break;case"D":K.draw_deletion(u,J,U),B+=U;break;case"I":var $=u-D;if(i([V,V+U],z)){var _=q.slice(C,C+U);if(this.prefs.show_insertions){var aa=u-(v-u)/2;if(("Pack"===b||"Auto"===this.mode)&&void 0!==q&&g>E){switch(a.fillStyle="yellow",a.fillRect(aa-D,j-9,v-u,9),M[M.length]={type:"triangle",data:[$,j+4,5]},a.fillStyle=A,h([V,V+U],z)){case d:_=_.slice(l-V);break;case e:_=_.slice(0,V-m);break;case f:break;case c:_=_.slice(l-V,V-m)}for(var Y=0,ba=_.length;ba>Y;Y++){var Z=Math.floor(Math.max(0,(V+Y-l)*g));a.fillText(_[Y],Z-(v-u)/2,j)}}else a.fillStyle="yellow",a.fillRect(aa,j+("Dense"!==this.mode?2:5),v-u,"Dense"!==b?x:w)}else("Pack"===b||"Auto"===this.mode)&&void 0!==q&&g>E&&M.push({type:"text",data:[_.length,$,j+9]})}C+=U}else B=r(B,T,U),C=s(C,T,U)}a.fillStyle="yellow";for(var ca,da,ea,O=0;O=e&&c[4][0]<=f&&c[4][2]?this.draw_read(a,b,g,p,e,f,c[4][0],c[4][2],c[4][3],c[4][4]):r=!1,c[5][1]>=e&&c[5][0]<=f&&c[5][2]?this.draw_read(a,b,g,p,e,f,c[5][0],c[5][2],c[5][3],c[5][4]):r=!1;var s=Math.ceil(Math.min(i,Math.max(-.5*g,(c[4][1]-e-.5)*g))),t=Math.floor(Math.max(-.5*g,(c[5][0]-e-.5)*g));if(r&&t>s){a.fillStyle=A;var u=p+1+(q-1)/2;j(a,s,u,t,u)}}else this.draw_read(a,b,g,p,e,f,k,c[4],c[5],c[6]);return"Pack"===b&&k>=e&&"."!==m&&(a.fillStyle=this.prefs.label_color,0===e&&n-a.measureText(m).width<0?(a.textAlign="left",a.fillText(m,o+z,p+9,this.max_label_length)):(a.textAlign="right",a.fillText(m,n-z,p+9,this.max_label_length))),[0,0]}});var D=function(a,b,c,d,e,f,g){B.call(this,a,b,c,d,e,f,g),this.longest_feature_length=this.calculate_longest_feature_length(),this.draw_background_connector=!1,this.draw_individual_connectors=!0};a.extend(D.prototype,q.prototype,B.prototype,{calculate_longest_feature_length:function(){for(var a=0,b=0,c=this.data.length;c>b;b++){var d=this.data[b],e=d[1],f=d[2];a=Math.max(a,f-e)}return a},get_top_padding:function(a){var b=this.view_end-this.view_start,c=a/b;return Math.min(128,Math.ceil(this.longest_feature_length/2*c))},draw_connector:function(a,b,c,d,e,f){{var g=(c+d)/2,h=d-g;Math.PI}h>0&&(a.beginPath(),a.arc(g,f,d-g,Math.PI,0),a.stroke())}});var E=function(a,b){this.rgb=Array.isArray(a)?a:6==a.length?a.match(/.{2}/g).map(function(a){return parseInt(a,16)}):7==a.length?a.substring(1,7).match(/.{2}/g).map(function(a){return parseInt(a,16)}):a.split("").map(function(a){return parseInt(a+a,16)}),this.alpha="number"==typeof b?b:1};E.prototype={eval:function(){return this},toCSS:function(){return this.alpha<1?"rgba("+this.rgb.map(function(a){return Math.round(a)}).concat(this.alpha).join(", ")+")":"#"+this.rgb.map(function(a){return a=Math.round(a),a=(a>255?255:0>a?0:a).toString(16),1===a.length?"0"+a:a}).join("")},toHSL:function(){var a,b,c=this.rgb[0]/255,d=this.rgb[1]/255,e=this.rgb[2]/255,f=this.alpha,g=Math.max(c,d,e),h=Math.min(c,d,e),i=(g+h)/2,j=g-h;if(g===h)a=b=0;else{switch(b=i>.5?j/(2-g-h):j/(g+h),g){case c:a=(d-e)/j+(e>d?6:0);break;case d:a=(e-c)/j+2;break;case e:a=(c-d)/j+4}a/=6}return{h:360*a,s:b,l:i,a:f}},toARGB:function(){var a=[Math.round(255*this.alpha)].concat(this.rgb);return"#"+a.map(function(a){return a=Math.round(a),a=(a>255?255:0>a?0:a).toString(16),1===a.length?"0"+a:a}).join("")},mix:function(a,b){color1=this;var c=b,d=2*c-1,e=color1.toHSL().a-a.toHSL().a,f=((d*e==-1?d:(d+e)/(1+d*e))+1)/2,g=1-f,h=[color1.rgb[0]*f+a.rgb[0]*g,color1.rgb[1]*f+a.rgb[1]*g,color1.rgb[2]*f+a.rgb[2]*g],i=color1.alpha*c+a.alpha*(1-c);return new E(h,i)}};var F=function(a,b,c,d){this.start_color=new E(a),this.end_color=new E(b),this.start_value=c,this.end_value=d,this.value_range=d-c};F.prototype.map_value=function(a){return a=Math.max(a,this.start_value),a=Math.min(a,this.end_value),a=(a-this.start_value)/this.value_range,this.start_color.mix(this.end_color,1-a).toCSS()};var G=function(a,b,c,d,e){this.positive_ramp=new F(b,c,0,e),this.negative_ramp=new F(b,a,0,-d),this.start_value=d,this.end_value=e};G.prototype.map_value=function(a){return a=Math.max(a,this.start_value),a=Math.min(a,this.end_value),a>=0?this.positive_ramp.map_value(a):this.negative_ramp.map_value(-a)};var H=function(a,b,c,d,e){n.call(this,a,b,c,d,e);var f,g;if(void 0===this.prefs.min_value){var h=1/0;for(f=0,g=this.data.length;g>f;f++)h=Math.min(h,this.data[f][6]);this.prefs.min_value=h}if(void 0===this.prefs.max_value){var i=-(1/0);for(f=0,g=this.data.length;g>f;f++)i=Math.max(i,this.data[f][6]);this.prefs.max_value=i}};H.prototype.default_prefs={min_value:void 0,max_value:void 0,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"},H.prototype.draw=function(a,b,c,d){var e,f,g,h,i,j,k=this.prefs.min_value,l=this.prefs.max_value,m=this.view_start,n=(this.mode,this.data),o=1/Math.sqrt(2),p=new G(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,k,l),q=function(a){return(a-m)*d};a.save(),a.rotate(-45*Math.PI/180),a.scale(o,o);for(var r=0,s=n.length;s>r;r++)e=n[r],f=q(e[1]),g=q(e[2]),h=q(e[4]),i=q(e[5]),j=e[6],a.fillStyle=p.map_value(j),a.fillRect(f,h,g-f,i-h);a.restore()};var I=function(a,b,c,d){this.ctx=a,this.row_height=b,this.px_per_base=c,this.draw_details=("Pack"===d||"Auto"===d)&&c>=a.canvas.manager.char_width_px,this.delete_details_thickness=.2};a.extend(I.prototype,{draw_deletion:function(a,b,c){this.ctx.fillStyle="black";var d=(this.draw_details?this.delete_details_thickness:1)*this.row_height;b+=.5*(this.row_height-d),this.ctx.fillRect(a,b,c*this.px_per_base,d)}});var J=function(a,b,c,d,e,f){n.call(this,a,b,c,d,e),this.base_color_fn=f,this.divider_height=1};return a.extend(J.prototype,n.prototype,{get_row_height:function(){var a,b=this.mode;return a="Dense"===b?r:"Squish"===b?t:u},get_required_height:function(a){var b=this.prefs.summary_height;return a>1&&this.prefs.show_sample_data&&(b+=this.divider_height+a*this.get_row_height()),b},draw:function(b,c,d,e){b.save();var f,g,h,i,j,k,l,m,n,o,p,q=function(a,b){var c=a.length,d=b.length,e=0,f=1,g=null;return"-"===b?(g="deletion",f=a.length):0===a.indexOf(b)&&c>d?(g="deletion",f=c-d,e=d):0===b.indexOf(a)&&d>c&&(g="insertion",f=d-c,e=d),null!==g?{type:g,start:e,len:f}:{}},r=Math.max(1,Math.floor(e)),s=this.data.length?this.data[0][7].split(",").length:0,v="Squish"===this.mode?t:u,w=.1>e?v:"Squish"===this.mode?x:y,z=!0,A=new I(b,v,e,this.mode);1===s&&(v=w=ethis.view_end)){if(z)for(b.fillStyle="#999999",b.globalAlpha=1,p=0;pg)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 $.getJSON(this.dataset.url(),d,function(a){if(a&&"error"!==a&&"error"!==a.kind)"no converter"===a?(b.container_div.addClass("error"),b.show_message(x)):"no data"===a||void 0!==a.data&&(null===a.data||0===a.data.length)?(b.container_div.addClass("nodata"),b.show_message(y)):"pending"===a?(b.container_div.addClass("pending"),b.show_message(z),setTimeout(function(){b.init()},b.data_query_wait)):("data"===a||"data"===a.status)&&(a.valid_chroms&&(b.valid_chroms=a.valid_chroms,b.update_icons()),b.tiles_div.text(B),b.view.chrom?(b.tiles_div.text(""),b.tiles_div.css("height",b.visible_height_px+"px"),b.enabled=!0,$.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}),$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var Y=function(a,b,c){W.call(this,a,b,c),this.painter=f.ReadPainter,this.update_icons()};m(Y.prototype,E.prototype,Q.prototype,W.prototype,{config_params:a.union(E.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var Z={CompositeTrack:S,DrawableGroup:G,DiagonalHeatmapTrack:V,FeatureTrack:W,LineTrack:U,ReadTrack:Y,VariantTrack:X,VcfTrack:X},_=function(a,b,c){if("copy"in a)return a.copy(c);var d=a.obj_type;return d||(d=a.track_type),new Z[d](b,c,a)};return{TracksterView:H,DrawableGroup:G,LineTrack:U,FeatureTrack:W,DiagonalHeatmapTrack:V,ReadTrack:Y,VariantTrack:X,CompositeTrack:S,object_from_template:_}}); +},init:function(a){var b=this;if(b.enabled=!1,b.tile_cache.clear(),b.data_manager.clear(),b.content_div.children().remove(),b.container_div.removeClass("nodata error pending"),b.tiles_div=$("
").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.left_offset=30,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