diff --git a/client/galaxy/scripts/viz/bbi-data-manager.js b/client/galaxy/scripts/viz/bbi-data-manager.js
index ae7c912d75e..a4efca6f14c 100644
--- a/client/galaxy/scripts/viz/bbi-data-manager.js
+++ b/client/galaxy/scripts/viz/bbi-data-manager.js
@@ -15,7 +15,7 @@ define( ["viz/visualization", "libs/bbi/bigwig"],
             var deferred = $.Deferred();
             this.set_data(region, deferred);
 
-            var url = galaxy_config.root + 'datasets/' + this.get('dataset').id + '/display',
+            var url = Galaxy.root + 'datasets/' + this.get('dataset').id + '/display',
                 self = this;
                 var promise = new $.Deferred();
                 $.when(bigwig.makeBwg(url)).then(function(bb, err) {
diff --git a/client/galaxy/scripts/viz/trackster/painters.js b/client/galaxy/scripts/viz/trackster/painters.js
index 4a1b1c0493f..5108d19737d 100644
--- a/client/galaxy/scripts/viz/trackster/painters.js
+++ b/client/galaxy/scripts/viz/trackster/painters.js
@@ -223,7 +223,7 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
         top_overflow = bot_overflow = false;
         delta_x_px = delta_x_pxs[i];
 
-        x_scaled = Math.ceil((data[i][0] - view_start - 0.5) * w_scale);
+        x_scaled = Math.floor((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 bd0ca20237a..7807c2c9349 100644
--- a/client/galaxy/scripts/viz/trackster/tracks.js
+++ b/client/galaxy/scripts/viz/trackster/tracks.js
@@ -200,7 +200,6 @@ function supportsByteRanges(url) {
             xhr.setRequestHeader("Range", "bytes=0-10");
         },
         success: function(result, status, xhr) {
-            console.log("BYTE RANGE SUPPORT", xhr.status === 206)
             promise.resolve(xhr.status === 206);
         }
     });
@@ -3628,10 +3627,9 @@ var LineTrack = function (view, container, obj_dict) {
     // If server has byte-range support, use BBI data manager to read directly from the BBI file.
     // FIXME: there should be a flag to wait for this check to complete before loading the track.
     var self = this;
-    $.when(supportsByteRanges(galaxy_config.root + 'datasets/' + this.dataset.id + '/display'))
+    $.when(supportsByteRanges(Galaxy.root + 'datasets/' + this.dataset.id + '/display'))
      .then(function(supportsByteRanges) {
          if (supportsByteRanges) {
-             console.log("BBI DATA MANAGER");
              self.data_manager = new bbi.BBIDataManager({
                  dataset: self.dataset
              });
diff --git a/static/maps/viz/bbi-data-manager.js.map b/static/maps/viz/bbi-data-manager.js.map
index 389f691c165..5e85c9fadcf 100644
--- a/static/maps/viz/bbi-data-manager.js.map
+++ b/static/maps/viz/bbi-data-manager.js.map
@@ -1 +1 @@
-{"version":3,"file":"bbi-data-manager.js","sources":["../../src/viz/bbi-data-manager.js"],"names":["define","visualization","bigwig","BBIDataManager","GenomeDataManager","extend","load_data","region","deferred","$","Deferred","this","set_data","url","galaxy_config","root","get","id","self","when","makeBwg","then","bb","readWigData","data","result","prev","max","Number","MIN_VALUE","forEach","d","min","push","score","entry","dataset_type","resolve"],"mappings":"AAAAA,QAAS,oBAAqB,mBACtB,SAASC,EAAeC,GAK5B,GAAIC,GAAiBF,EAAcG,kBAAkBC,QAOjDC,UAAW,SAASC,GAChB,GAAIC,GAAWC,EAAEC,UACjBC,MAAKC,SAASL,EAAQC,EAEtB,EAAA,GAAIK,GAAMC,cAAcC,KAAO,YAAcJ,KAAKK,IAAI,WAAWC,GAAK,WAClEC,EAAOP,IACO,IAAIF,GAAEC,SAuCxB,MAtCID,GAAEU,KAAKjB,EAAOkB,QAAQP,IAAMQ,KAAK,SAASC,GACtCb,EAAEU,KAAKG,EAAGC,YAAYhB,EAAOS,IAAI,SAAUT,EAAOS,IAAI,SAAUT,EAAOS,IAAI,SAASK,KAAK,SAASG,GAGlG,GAAIC,MACAC,GAASC,IAAKC,OAAOC,UACzBL,GAAKM,QAAQ,SAASC,GAGdL,EAAKC,MAAQI,EAAEC,IAAM,IAErBP,EAAOQ,MAAMP,EAAKC,IAAM,EAAG,IAG3BF,EAAOQ,MAAMF,EAAEC,IAAM,EAAG,KAK5BP,EAAOQ,MAAMF,EAAEC,IAAM,EAAGD,EAAEG,QAG1BT,EAAOQ,MAAMF,EAAEJ,IAAKI,EAAEG,QAEtBR,EAAOK,GAGX,IAAII,IACIX,KAAMC,EACNlB,OAAQA,EACR6B,aAAc,SAGtBlB,GAAKN,SAASL,EAAQ4B,GACtB3B,EAAS6B,QAAQF,OAIlB3B,IAIf,QACIL,eAAgBA"}
\ No newline at end of file
+{"version":3,"file":"bbi-data-manager.js","sources":["../../src/viz/bbi-data-manager.js"],"names":["define","visualization","bigwig","BBIDataManager","GenomeDataManager","extend","load_data","region","deferred","$","Deferred","this","set_data","url","Galaxy","root","get","id","self","when","makeBwg","then","bb","readWigData","data","result","prev","max","Number","MIN_VALUE","forEach","d","min","push","score","entry","dataset_type","resolve"],"mappings":"AAAAA,QAAS,oBAAqB,mBACtB,SAASC,EAAeC,GAK5B,GAAIC,GAAiBF,EAAcG,kBAAkBC,QAOjDC,UAAW,SAASC,GAChB,GAAIC,GAAWC,EAAEC,UACjBC,MAAKC,SAASL,EAAQC,EAEtB,EAAA,GAAIK,GAAMC,OAAOC,KAAO,YAAcJ,KAAKK,IAAI,WAAWC,GAAK,WAC3DC,EAAOP,IACO,IAAIF,GAAEC,SAuCxB,MAtCID,GAAEU,KAAKjB,EAAOkB,QAAQP,IAAMQ,KAAK,SAASC,GACtCb,EAAEU,KAAKG,EAAGC,YAAYhB,EAAOS,IAAI,SAAUT,EAAOS,IAAI,SAAUT,EAAOS,IAAI,SAASK,KAAK,SAASG,GAGlG,GAAIC,MACAC,GAASC,IAAKC,OAAOC,UACzBL,GAAKM,QAAQ,SAASC,GAGdL,EAAKC,MAAQI,EAAEC,IAAM,IAErBP,EAAOQ,MAAMP,EAAKC,IAAM,EAAG,IAG3BF,EAAOQ,MAAMF,EAAEC,IAAM,EAAG,KAK5BP,EAAOQ,MAAMF,EAAEC,IAAM,EAAGD,EAAEG,QAG1BT,EAAOQ,MAAMF,EAAEJ,IAAKI,EAAEG,QAEtBR,EAAOK,GAGX,IAAII,IACIX,KAAMC,EACNlB,OAAQA,EACR6B,aAAc,SAGtBlB,GAAKN,SAASL,EAAQ4B,GACtB3B,EAAS6B,QAAQF,OAIlB3B,IAIf,QACIL,eAAgBA"}
\ No newline at end of file
diff --git a/static/maps/viz/trackster/painters.js.map b/static/maps/viz/trackster/painters.js.map
index fba530500bd..4e7175ec2bf 100644
--- a/static/maps/viz/trackster/painters.js.map
+++ b/static/maps/viz/trackster/painters.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/static/maps/viz/trackster/tracks.js.map b/static/maps/viz/trackster/tracks.js.map
index 0170efbfd0a..b06ee84bed0 100644
--- a/static/maps/viz/trackster/tracks.js.map
+++ b/static/maps/viz/trackster/tracks.js.map
@@ -1 +1 @@
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\ 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 fb101b8faf9..a73670b6247 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=[],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}});
+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.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 b152c4521ff..6b3316eb94c 100644
--- a/static/scripts/viz/trackster/painters.js
+++ b/static/scripts/viz/trackster/painters.js
@@ -1,2 +1,2 @@
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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<this.feature_positions[d].length;e++)if(c=this.feature_positions[d][e],a>=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;O<L.length;O++){var P=L[O];i([n+P[0],n+P[1]],z)&&(u=t(n+P[0]),v=t(n+P[1]),u===v&&(v+=1),a.fillStyle=F,a.fillRect(u,J,v-u,H))}for(var Q=0,R=o.length;R>Q;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;Y<W.length;Y++)if(W&&!this.prefs.show_differences||"X"===T){var Z=Math.floor(Math.max(0,(X+Y-l)*g));a.fillStyle=this.base_color_fn(W[Y]),G&&g>E?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<M.length;O++)ca=M[O],da=ca.type,ea=ca.data,"text"===da?(a.save(),a.font="bold "+a.font,a.fillText(ea[0],ea[1],ea[2]),a.restore()):"triangle"===da&&k(a,ea[0],ea[1],ea[2])},draw_element:function(a,b,c,d,e,f,g,h,i){{var k=(c[0],c[1]),l=c[2],m=c[3],n=Math.floor(Math.max(-.5*g,(k-e-.5)*g)),o=Math.ceil(Math.min(i,Math.max(0,(l-e-.5)*g))),p=("Dense"===b?0:0+d)*h,q="Pack"===b?y:x;this.prefs.label_color}if(c[5]instanceof Array){var r=!0;c[4][1]>=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=e<b.canvas.manager.char_width_px?this.prefs.summary_height:v,A.row_height=v,z=!1),this.prefs.show_sample_data&&z&&(b.fillStyle="#F3F3F3",b.globalAlpha=1,b.fillRect(0,this.prefs.summary_height-this.divider_height,c,this.divider_height)),b.textAlign="center";for(var B=0;B<this.data.length;B++)if(f=this.data[B],g=f[1],h=f[3],i=[f[4].split(",")],j=f[7].split(","),k=f.slice(8),i=a.map(a.flatten(i),function(b){var c={type:"snp",value:b,start:0},d=q(h,b);return a.extend(c,d)}),!(g<this.view_start||g>this.view_end)){if(z)for(b.fillStyle="#999999",b.globalAlpha=1,p=0;p<i.length;p++)for(m=this.get_start_draw_pos(g+i[p].start,e),b.fillRect(m,0,r,this.prefs.summary_height),n=this.prefs.summary_height,p=0;p<i.length;p++)b.fillStyle="deletion"===i[p].type?"black":this.base_color_fn(i[p].value),allele_frac=k/j.length,draw_height=Math.ceil(this.prefs.summary_height*allele_frac),b.fillRect(m,n-draw_height,r,draw_height),n-=draw_height;if(this.prefs.show_sample_data)for(n=z?this.prefs.summary_height+this.divider_height:0,p=0;p<j.length;p++,n+=v)if(o=j[p]?j[p].split(/\/|\|/):["0","0"],l=null,o[0]===o[1]?"."===o[0]||"0"!==o[0]&&(l=i[parseInt(o[0],10)-1],b.globalAlpha=1):(l="0"!==o[0]?o[0]:o[1],l=i[parseInt(l,10)-1],b.globalAlpha=.5),l)if(m=this.get_start_draw_pos(g+l.start,e),"snp"===l.type){var C=l.value;b.fillStyle=this.base_color_fn(C),A.draw_details?b.fillText(C,this.get_draw_pos(g,e),n+v):b.fillRect(m,n+1,r,w)}else"deletion"===l.type&&A.draw_deletion(m,n+1,l.len)}b.restore()}}),{Scaler:l,LinePainter:o,LinkedFeaturePainter:B,ReadPainter:C,ArcLinkedFeaturePainter:D,DiagonalHeatmapPainter:H,VariantPainter:J}});
+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(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.floor((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<this.feature_positions[d].length;e++)if(c=this.feature_positions[d][e],a>=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;O<L.length;O++){var P=L[O];i([n+P[0],n+P[1]],z)&&(u=t(n+P[0]),v=t(n+P[1]),u===v&&(v+=1),a.fillStyle=F,a.fillRect(u,J,v-u,H))}for(var Q=0,R=o.length;R>Q;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;Y<W.length;Y++)if(W&&!this.prefs.show_differences||"X"===T){var Z=Math.floor(Math.max(0,(X+Y-l)*g));a.fillStyle=this.base_color_fn(W[Y]),G&&g>E?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<M.length;O++)ca=M[O],da=ca.type,ea=ca.data,"text"===da?(a.save(),a.font="bold "+a.font,a.fillText(ea[0],ea[1],ea[2]),a.restore()):"triangle"===da&&k(a,ea[0],ea[1],ea[2])},draw_element:function(a,b,c,d,e,f,g,h,i){{var k=(c[0],c[1]),l=c[2],m=c[3],n=Math.floor(Math.max(-.5*g,(k-e-.5)*g)),o=Math.ceil(Math.min(i,Math.max(0,(l-e-.5)*g))),p=("Dense"===b?0:0+d)*h,q="Pack"===b?y:x;this.prefs.label_color}if(c[5]instanceof Array){var r=!0;c[4][1]>=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=e<b.canvas.manager.char_width_px?this.prefs.summary_height:v,A.row_height=v,z=!1),this.prefs.show_sample_data&&z&&(b.fillStyle="#F3F3F3",b.globalAlpha=1,b.fillRect(0,this.prefs.summary_height-this.divider_height,c,this.divider_height)),b.textAlign="center";for(var B=0;B<this.data.length;B++)if(f=this.data[B],g=f[1],h=f[3],i=[f[4].split(",")],j=f[7].split(","),k=f.slice(8),i=a.map(a.flatten(i),function(b){var c={type:"snp",value:b,start:0},d=q(h,b);return a.extend(c,d)}),!(g<this.view_start||g>this.view_end)){if(z)for(b.fillStyle="#999999",b.globalAlpha=1,p=0;p<i.length;p++)for(m=this.get_start_draw_pos(g+i[p].start,e),b.fillRect(m,0,r,this.prefs.summary_height),n=this.prefs.summary_height,p=0;p<i.length;p++)b.fillStyle="deletion"===i[p].type?"black":this.base_color_fn(i[p].value),allele_frac=k/j.length,draw_height=Math.ceil(this.prefs.summary_height*allele_frac),b.fillRect(m,n-draw_height,r,draw_height),n-=draw_height;if(this.prefs.show_sample_data)for(n=z?this.prefs.summary_height+this.divider_height:0,p=0;p<j.length;p++,n+=v)if(o=j[p]?j[p].split(/\/|\|/):["0","0"],l=null,o[0]===o[1]?"."===o[0]||"0"!==o[0]&&(l=i[parseInt(o[0],10)-1],b.globalAlpha=1):(l="0"!==o[0]?o[0]:o[1],l=i[parseInt(l,10)-1],b.globalAlpha=.5),l)if(m=this.get_start_draw_pos(g+l.start,e),"snp"===l.type){var C=l.value;b.fillStyle=this.base_color_fn(C),A.draw_details?b.fillText(C,this.get_draw_pos(g,e),n+v):b.fillRect(m,n+1,r,w)}else"deletion"===l.type&&A.draw_deletion(m,n+1,l.len)}b.restore()}}),{Scaler:l,LinePainter:o,LinkedFeaturePainter:B,ReadPainter:C,ArcLinkedFeaturePainter:D,DiagonalHeatmapPainter:H,VariantPainter:J}});
 //# sourceMappingURL=../../../maps/viz/trackster/painters.js.map
\ No newline at end of file
diff --git a/static/scripts/viz/trackster/tracks.js b/static/scripts/viz/trackster/tracks.js
index 727edfdfac0..fbf86103833 100644
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -1,4 +1,4 @@
-define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/dataset/data","mvc/tool/tools","utils/config","viz/bbi-data-manager","ui/editable-text"],function(a,b,c,d,e,f,g,h,i,j,k){function l(a,b){b||(b=0);var c=Math.pow(10,b);return Math.round(a*c)/c}function m(a){var b=$.Deferred();return $.ajax({type:"HEAD",url:a,beforeSend:function(a){a.setRequestHeader("Range","bytes=0-10")},success:function(a,c,d){console.log("BYTE RANGE SUPPORT",206===d.status),b.resolve(206===d.status)}}),b}var n=a.extend,o={},p=function(a,b){o[a.attr("id")]=b},q=function(a,b,c,d){c=".group",o[a.attr("id")]=d,a.bind("drag",{handle:"."+b,relative:!0},function(a,b){var d,e,f,g,h,i=($(this),$(this).parent()),j=i.children(".track,.group"),k=o[$(this).attr("id")];if(e=$(this).parents(c),0!==e.length){f=e.position().top,g=f+e.outerHeight();var l=o[e.attr("id")];if(b.offsetY<f)return $(this).insertBefore(e),l.remove_drawable(k),void l.container.add_drawable_before(k,l);if(b.offsetY>g)return $(this).insertAfter(e),l.remove_drawable(k),void l.container.add_drawable(k)}for(e=null,h=0;h<j.length;h++)if(d=$(j.get(h)),f=d.position().top,g=f+d.outerHeight(),d.is(c)&&this!==d.get(0)&&b.offsetY>=f&&b.offsetY<=g)return b.offsetY-f<g-b.offsetY?d.find(".content-div").prepend(this):d.find(".content-div").append(this),k.container&&k.container.remove_drawable(k),void o[d.attr("id")].add_drawable(k);for(h=0;h<j.length&&(d=$(j.get(h)),!(b.offsetY<d.position().top)||d.hasClass("reference-track")||d.hasClass("intro"));h++);h===j.length?this!==j.get(h-1)&&(i.append(this),o[i.attr("id")].move_drawable(k,h)):this!==j.get(h)&&($(this).insertBefore(j.get(h)),o[i.attr("id")].move_drawable(k,b.deltaY>0?h-1:h))}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})},r=20,s=100,t=12e3,u=400,v=5e3,w=100,x="Cannot display dataset due to an error. ",y="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",z="No data for this chrom/contig.",A="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",B="Tool cannot be rerun: ",C="Ready for display",D=10,E=["Histogram","Line","Filled","Intensity"],F=function(a,b,d){if(F.id_counter||(F.id_counter=0),this.id=F.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.$el,this.container_div.append(this.header_div);var f=e.icons_div;this.action_icons=e.action_icons,this.container_div.hover(function(){f.show()},function(){f.hide()})}};F.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(a){a.config.get_value("content_visible")?(a.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),a.hide_contents(),a.config.set_value("content_visible",!1)):(a.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),a.config.set_value("content_visible",!0),a.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(a){var b=new j.ConfigSettingCollectionView({collection:a.config});b.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(a){$(".tooltip").remove(),a.remove()}}],n(F.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(){$(this).remove(),a.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var G=function(a,b,c){F.call(this,a,b,c),this.obj_type=c.obj_type,this.drawables=[]};n(G.prototype,F.prototype,{unpack_drawables:function(a){this.drawables=[];for(var b,c=0;c<a.length;c++)b=aa(a[c],this.view,this),this.add_drawable(b)},init:function(){for(var a=0;a<this.drawables.length;a++)this.drawables[a].init()},_draw:function(a){for(var b=0;b<this.drawables.length;b++)this.drawables[b]._draw(a)},to_dict:function(){for(var a=[],b=0;b<this.drawables.length;b++)a.push(this.drawables[b].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:a}},add_drawable:function(a){this.drawables.push(a),a.container=this,this.changed()},add_drawable_before:function(a,b){this.changed();var c=this.drawables.indexOf(b);return-1!==c?(this.drawables.splice(c,0,a),!0):!1},replace_drawable:function(a,b,c){var d=this.drawables.indexOf(a);return-1!==d&&(this.drawables[d]=b,c&&a.container_div.replaceWith(b.container_div),this.changed()),d},remove_drawable:function(a){var b=this.drawables.indexOf(a);return-1!==b?(this.drawables.splice(b,1),a.container=null,this.changed(),!0):!1},move_drawable:function(a,b){var c=this.drawables.indexOf(a);return-1!==c?(this.drawables.splice(c,1),this.drawables.splice(b,0,a),this.changed(),!0):!1},get_drawables:function(){return this.drawables},get_tracks:function(a){for(var b,c=this.drawables.slice(0),d=[];0!==c.length;)b=c.shift(),b instanceof a?d.push(b):b.drawables&&(c=c.concat(b.drawables));return d}});var H=function(a,b,c){if(n(c,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),G.call(this,a,b,c),this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),p(this.container_div,this),p(this.content_div,this),q(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($("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in c&&this.unpack_drawables(c.drawables),"filters"in c){var d=this.filters_manager;this.filters_manager=new g.FiltersManager(this,c.filters),d.parent_div.replaceWith(this.filters_manager.parent_div),c.filters.visible&&this.setup_multitrack_filtering()}};n(H.prototype,F.prototype,G.prototype,{action_icons_def:[F.prototype.action_icons_def[0],F.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(a){$(".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()}},F.prototype.action_icons_def[2]],build_container_div:function(){var a=$("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(a),a},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var a=this.drawables.length;if(0===a)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===a)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof T),this.action_icons.filters_icon.hide();else{var b,c,d,e=!0,f=this.drawables[0].get_type(),h=0;for(b=0;a>b;b++){if(d=this.drawables[b],d.get_type()!==f){can_composite=!1;break}d instanceof X&&h++}if(e&&this.drawables[0]instanceof V?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),$(".tooltip").remove()),h>1&&h===this.drawables.length){var i,j={};for(d=this.drawables[0],c=0;c<d.filters_manager.filters.length;c++)i=d.filters_manager.filters[c],j[i.name]=[i];for(b=1;b<this.drawables.length;b++)for(d=this.drawables[b],c=0;c<d.filters_manager.filters.length;c++)i=d.filters_manager.filters[c],i.name in j&&j[i.name].push(i);this.filters_manager.remove_all();var k,l;for(var m in j)k=j[m],k.length===h&&(l=new g.NumberFilter({name:k[0].name,index:k[0].index}),this.filters_manager.add_filter(l));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var a=0;a<this.drawables.length;a++)this.drawables[a].filters_manager=this.saved_filters_managers[a];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var a=0;a<this.drawables.length;a++)drawable=this.drawables[a],this.saved_filters_managers.push(drawable.filters_manager),drawable.filters_manager=this.filters_manager}this.filters_manager.init_filters()},show_composite_track:function(){{var a=new T(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,a,!0)}a.request_draw()},add_drawable:function(a){G.prototype.add_drawable.call(this,a),this.update_icons()},remove_drawable:function(a){G.prototype.remove_drawable.call(this,a),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var a=n(G.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),a},request_draw:function(b){a.each(this.drawables,function(a){a.request_draw(b)})}});var I=Backbone.View.extend({initialize:function(a){n(a,{obj_type:"View"}),G.call(this,"View",a.container,a),this.chrom=null,this.vis_id=a.vis_id,this.dbkey=a.dbkey,this.stand_alone=void 0!==a.stand_alone?a.stand_alone:!0,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new b.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=j.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:a.name})},render:function(){this.requested_redraw=!1;var c=this.container,d=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c),this.browser_content_div=$("<div/>").addClass("content").appendTo(c),this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c),this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,p(this.viewport_container,d),this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container);$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){b.select_datasets(Galaxy.root+"visualization/list_current_history_datasets",Galaxy.root+"api/datasets",{"f-dbkey":d.dbkey},function(b){a.each(b,function(a){d.add_drawable(aa(a,d,d))})})});this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var e=function(a){("focusout"===a.type||13===(a.keyCode||a.which)||27===(a.keyCode||a.which))&&(27!==(a.keyCode||a.which)&&d.go_to($(this).val()),$(this).hide(),$(this).val(""),d.location_span.show(),d.chrom_select.show()),a.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",e).appendTo(this.nav_controls),this.location_span=$("<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=$.map(d.get_tracks(X),function(b){return b.data_manager.search_features(a.term).success(function(a){c=c.concat(a)})});$.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=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){d.zoom_out()}).appendTo(this.nav_controls),this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){d.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){d.change_chrom(d.chrom_select.val())}),this.browser_content_div.click(function(){$(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 $("<div/>").addClass("zoom-area").css("height",d.browser_content_div.height()+d.top_labeltrack.height()+1).appendTo($(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 S(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(),$(window).trigger("resize")},get_base_color:function(a){return this.config.get_value(a.toLowerCase()+"_color")||this.config.get_value("n_color")}});n(I.prototype,G.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(a,b,c,d){if(this.timer&&clearTimeout(this.timer),d){var e=this;this.timer=setTimeout(function(){e.trigger("navigate",a+":"+b+"-"+c)},500)}else view.trigger("navigate",a+":"+b+"-"+c)},update_location:function(a,b){this.location_span.text(d.commatize(a)+" - "+d.commatize(b)),this.nav_input.val(this.chrom+":"+d.commatize(a)+"-"+d.commatize(b));var c=this.chrom_select.val();""!==c&&this.trigger_navigate(c,this.low,this.high,!0)},load_chroms:function(a){a.num=w;var b=this,c=$.Deferred();return $.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:a,dataType:"json",success:function(a){if(0!==a.chrom_info.length){if(a.reference){var d=new U(b);b.add_label_track(d),b.reference_track=d}b.chrom_data=a.chrom_info;for(var e='<option value="">Select Chrom/Contig</option>',f=0,g=b.chrom_data.length;g>f;f++){var h=b.chrom_data[f].chrom;e+='<option value="'+h+'">'+h+"</option>"}a.prev_chroms&&(e+='<option value="previous">Previous '+w+"</option>"),a.next_chroms&&(e+='<option value="next">Next '+w+"</option>"),b.chrom_select.html(e),b.chrom_start_index=a.start_index,c.resolve(a.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+b.dbkey)}}),c},change_chrom:function(a,b,c){var d=this;if(!d.chrom_data)return void d.load_chroms_deferred.then(function(){d.change_chrom(a,b,c)});if(a&&"None"!==a){if("previous"===a)return void d.load_chroms({low:this.chrom_start_index-w});if("next"===a)return void d.load_chroms({low:this.chrom_start_index+w});var e=$.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-a<b.max_low?(b.low=b.max_low,b.high=b.max_low+c):b.high-a>b.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){G.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(G.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;b<this.max_low&&(b=this.max_low),c>this.max_high&&(c=this.max_high);var d=this.high-this.low;0!==this.high&&d<this.min_separation&&(c=b+this.min_separation),this.low=Math.floor(b),this.high=Math.ceil(c),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var e=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,f=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0,g=13;this.overview_box.css({left:e,width:Math.max(g,f)}).show(),g>f&&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 J=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()})}}),K=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var a=this.$el.addClass("param-row"),b=this.model,c=($("<div>").addClass("param-label").text(b.get("label")).appendTo(a),$("<div/>").addClass("param-input").html(b.get("html")).appendTo(a));c.find(":input").val(b.get("value")),$("<div style='clear: both;'/>").appendTo(a)},update_value:function(a){this.model.set_value($(a.target).val())}}),L=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.set_visible,this)},render:function(){var a=this;tool=this.model,parent_div=this.$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()});$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(a){var b=new K({model:a});b.render(),parent_div.append(b.$el)}),parent_div.find("input").click(function(){$(this).select()});var b=$("<div>").addClass("param-row").appendTo(parent_div),c=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(b),d=$("<input type='submit'>").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<this.params.length;a++)this.params[a].update_value()},run_on_dataset:function(){var a=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:a.id},null,function(){Galaxy.modal.show({title:a.get("name")+" is Running",body:a.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var a,c=this.model.get("track"),d=this.model,e=new b.GenomeRegion({chrom:c.view.chrom,start:c.view.low,end:c.view.high}),f={target_dataset_id:c.dataset.id,action:"rerun",tool_id:d.id,regions:[e.toJSON()]},g=c,i=d.get("name")+g.tool_region_and_parameters_str(e);if(g.container===view){var j=new H(view,view,{name:c.config.get_value("name")}),k=g.container.replace_drawable(g,j,!1);j.container_div.insertBefore(g.view.content_div.children()[k]),j.add_drawable(g),g.container_div.appendTo(j.content_div),a=j}else a=g.container;var l=new g.constructor(view,a,{name:i,hda_ldda:"hda"});l.init_for_tool_data(),l.change_mode(g.mode),l.set_filters_manager(g.filters_manager.copy(l)),l.update_icons(),a.add_drawable(l),l.tiles_div.text("Starting job."),this.run(f,l,function(a){l.set_dataset(new h.Dataset(a)),l.tiles_div.text("Running job."),l.init()})},run:function(a,b,c){a.inputs=this.model.get_inputs_dict();var e=new d.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(a),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(a){return"pending"!==a}});$.when(e.go()).then(function(a){"no converter"===a?(b.container_div.addClass("error"),b.content_div.text(y)):a.error?(b.container_div.addClass("error"),b.content_div.text(B+a.message)):c(a)})}}),M=function(a,b){f.Scaler.call(this,b),this.filter=a};M.prototype.gen_val=function(a){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(a[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var N=function(a,b,c,d,e){this.track=a,this.region=b,this.low=b.get("start"),this.high=b.get("end"),this.w_scale=c,this.canvas=d,this.html_elt=$("<div class='track-tile'/>").append(d),this.data=e,this.stale=!1};N.prototype.predisplay_actions=function(){};var O=function(a,b,c,d,e){N.call(this,a,b,c,d,e)};O.prototype.predisplay_actions=function(){};var P=function(a,b,c,d,e,f,g,h,i,j,k){N.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};n(P.prototype,N.prototype),P.prototype.predisplay_actions=function(){};var Q=function(a,c,d){n(d,{drag_handle_class:"draghandle"}),F.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:v,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=$("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in d&&!d.resize||this.add_resize_handle())};n(Q.prototype,F.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},F.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(a){a.view.set_overview(a)}},F.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(a){a.filters_manager.visible()?a.filters_manager.clear_filters():a.filters_manager.init_filters(),a.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(a){a.tool.toggle(),a.tool.is_visible()?a.set_name(a.config.get_value("name")+a.tool_region_and_parameters_str()):a.revert_name(),$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(c){var d="<strong>Tool</strong>:"+c.tool.get("name")+"<br/><strong>Dataset</strong>:"+c.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',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}})}},F.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&F.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(a){this.dataset=a,this.data_manager.set("dataset",a)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var a=this,b=!1,c=!1,d=$("<div class='track-resize'>");$(a.container_div).hover(function(){a.config.get_value("content_visible")&&(b=!0,d.show())},function(){b=!1,c||d.hide()}),d.hide().bind("dragstart",function(b,d){c=!0,d.original_height=$(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);$(a.tiles_div).css("height",d),a.visible_height_px=a.max_height_px===d?0:d,a.on_resize()}).bind("dragend",function(){a.tile_cache.clear(),c=!1,b||d.hide(),a.config.set_value("height",a.visible_height_px),a.changed()}).appendTo(a.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof S?"LabelTrack":this instanceof U?"ReferenceTrack":this instanceof V?"LineTrack":this instanceof Z?"ReadTrack":this instanceof Y?"VariantTrack":this instanceof T?"CompositeTrack":this instanceof X?"FeatureTrack":"";
+define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/dataset/data","mvc/tool/tools","utils/config","viz/bbi-data-manager","ui/editable-text"],function(a,b,c,d,e,f,g,h,i,j,k){function l(a,b){b||(b=0);var c=Math.pow(10,b);return Math.round(a*c)/c}function m(a){var b=$.Deferred();return $.ajax({type:"HEAD",url:a,beforeSend:function(a){a.setRequestHeader("Range","bytes=0-10")},success:function(a,c,d){b.resolve(206===d.status)}}),b}var n=a.extend,o={},p=function(a,b){o[a.attr("id")]=b},q=function(a,b,c,d){c=".group",o[a.attr("id")]=d,a.bind("drag",{handle:"."+b,relative:!0},function(a,b){var d,e,f,g,h,i=($(this),$(this).parent()),j=i.children(".track,.group"),k=o[$(this).attr("id")];if(e=$(this).parents(c),0!==e.length){f=e.position().top,g=f+e.outerHeight();var l=o[e.attr("id")];if(b.offsetY<f)return $(this).insertBefore(e),l.remove_drawable(k),void l.container.add_drawable_before(k,l);if(b.offsetY>g)return $(this).insertAfter(e),l.remove_drawable(k),void l.container.add_drawable(k)}for(e=null,h=0;h<j.length;h++)if(d=$(j.get(h)),f=d.position().top,g=f+d.outerHeight(),d.is(c)&&this!==d.get(0)&&b.offsetY>=f&&b.offsetY<=g)return b.offsetY-f<g-b.offsetY?d.find(".content-div").prepend(this):d.find(".content-div").append(this),k.container&&k.container.remove_drawable(k),void o[d.attr("id")].add_drawable(k);for(h=0;h<j.length&&(d=$(j.get(h)),!(b.offsetY<d.position().top)||d.hasClass("reference-track")||d.hasClass("intro"));h++);h===j.length?this!==j.get(h-1)&&(i.append(this),o[i.attr("id")].move_drawable(k,h)):this!==j.get(h)&&($(this).insertBefore(j.get(h)),o[i.attr("id")].move_drawable(k,b.deltaY>0?h-1:h))}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})},r=20,s=100,t=12e3,u=400,v=5e3,w=100,x="Cannot display dataset due to an error. ",y="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",z="No data for this chrom/contig.",A="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",B="Tool cannot be rerun: ",C="Ready for display",D=10,E=["Histogram","Line","Filled","Intensity"],F=function(a,b,d){if(F.id_counter||(F.id_counter=0),this.id=F.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.$el,this.container_div.append(this.header_div);var f=e.icons_div;this.action_icons=e.action_icons,this.container_div.hover(function(){f.show()},function(){f.hide()})}};F.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(a){a.config.get_value("content_visible")?(a.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),a.hide_contents(),a.config.set_value("content_visible",!1)):(a.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),a.config.set_value("content_visible",!0),a.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(a){var b=new j.ConfigSettingCollectionView({collection:a.config});b.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(a){$(".tooltip").remove(),a.remove()}}],n(F.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(){$(this).remove(),a.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var G=function(a,b,c){F.call(this,a,b,c),this.obj_type=c.obj_type,this.drawables=[]};n(G.prototype,F.prototype,{unpack_drawables:function(a){this.drawables=[];for(var b,c=0;c<a.length;c++)b=aa(a[c],this.view,this),this.add_drawable(b)},init:function(){for(var a=0;a<this.drawables.length;a++)this.drawables[a].init()},_draw:function(a){for(var b=0;b<this.drawables.length;b++)this.drawables[b]._draw(a)},to_dict:function(){for(var a=[],b=0;b<this.drawables.length;b++)a.push(this.drawables[b].to_dict());return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:a}},add_drawable:function(a){this.drawables.push(a),a.container=this,this.changed()},add_drawable_before:function(a,b){this.changed();var c=this.drawables.indexOf(b);return-1!==c?(this.drawables.splice(c,0,a),!0):!1},replace_drawable:function(a,b,c){var d=this.drawables.indexOf(a);return-1!==d&&(this.drawables[d]=b,c&&a.container_div.replaceWith(b.container_div),this.changed()),d},remove_drawable:function(a){var b=this.drawables.indexOf(a);return-1!==b?(this.drawables.splice(b,1),a.container=null,this.changed(),!0):!1},move_drawable:function(a,b){var c=this.drawables.indexOf(a);return-1!==c?(this.drawables.splice(c,1),this.drawables.splice(b,0,a),this.changed(),!0):!1},get_drawables:function(){return this.drawables},get_tracks:function(a){for(var b,c=this.drawables.slice(0),d=[];0!==c.length;)b=c.shift(),b instanceof a?d.push(b):b.drawables&&(c=c.concat(b.drawables));return d}});var H=function(a,b,c){if(n(c,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"}),G.call(this,a,b,c),this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),p(this.container_div,this),p(this.content_div,this),q(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($("<div style='clear: both'/>")),this.saved_filters_managers=[],"drawables"in c&&this.unpack_drawables(c.drawables),"filters"in c){var d=this.filters_manager;this.filters_manager=new g.FiltersManager(this,c.filters),d.parent_div.replaceWith(this.filters_manager.parent_div),c.filters.visible&&this.setup_multitrack_filtering()}};n(H.prototype,F.prototype,G.prototype,{action_icons_def:[F.prototype.action_icons_def[0],F.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(a){$(".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()}},F.prototype.action_icons_def[2]],build_container_div:function(){var a=$("<div/>").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(a),a},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var a=this.drawables.length;if(0===a)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===a)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof T),this.action_icons.filters_icon.hide();else{var b,c,d,e=!0,f=this.drawables[0].get_type(),h=0;for(b=0;a>b;b++){if(d=this.drawables[b],d.get_type()!==f){can_composite=!1;break}d instanceof X&&h++}if(e&&this.drawables[0]instanceof V?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),$(".tooltip").remove()),h>1&&h===this.drawables.length){var i,j={};for(d=this.drawables[0],c=0;c<d.filters_manager.filters.length;c++)i=d.filters_manager.filters[c],j[i.name]=[i];for(b=1;b<this.drawables.length;b++)for(d=this.drawables[b],c=0;c<d.filters_manager.filters.length;c++)i=d.filters_manager.filters[c],i.name in j&&j[i.name].push(i);this.filters_manager.remove_all();var k,l;for(var m in j)k=j[m],k.length===h&&(l=new g.NumberFilter({name:k[0].name,index:k[0].index}),this.filters_manager.add_filter(l));this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var a=0;a<this.drawables.length;a++)this.drawables[a].filters_manager=this.saved_filters_managers[a];this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var a=0;a<this.drawables.length;a++)drawable=this.drawables[a],this.saved_filters_managers.push(drawable.filters_manager),drawable.filters_manager=this.filters_manager}this.filters_manager.init_filters()},show_composite_track:function(){{var a=new T(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});this.container.replace_drawable(this,a,!0)}a.request_draw()},add_drawable:function(a){G.prototype.add_drawable.call(this,a),this.update_icons()},remove_drawable:function(a){G.prototype.remove_drawable.call(this,a),this.update_icons()},to_dict:function(){this.filters_manager.visible()&&this._restore_filter_managers();var a=n(G.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});return this.filters_manager.visible()&&this.setup_multitrack_filtering(),a},request_draw:function(b){a.each(this.drawables,function(a){a.request_draw(b)})}});var I=Backbone.View.extend({initialize:function(a){n(a,{obj_type:"View"}),G.call(this,"View",a.container,a),this.chrom=null,this.vis_id=a.vis_id,this.dbkey=a.dbkey,this.stand_alone=void 0!==a.stand_alone?a.stand_alone:!0,this.label_tracks=[],this.tracks_to_be_redrawn=[],this.max_low=0,this.max_high=0,this.zoom_factor=3,this.min_separation=30,this.has_changes=!1,this.load_chroms_deferred=null,this.render(),this.canvas_manager=new b.CanvasManager(this.container.get(0).ownerDocument),this.reset(),this.config=j.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:a.name})},render:function(){this.requested_redraw=!1;var c=this.container,d=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c),this.browser_content_div=$("<div/>").addClass("content").appendTo(c),this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c),this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,p(this.viewport_container,d),this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container);$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){b.select_datasets(Galaxy.root+"visualization/list_current_history_datasets",Galaxy.root+"api/datasets",{"f-dbkey":d.dbkey},function(b){a.each(b,function(a){d.add_drawable(aa(a,d,d))})})});this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview),this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav),this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var e=function(a){("focusout"===a.type||13===(a.keyCode||a.which)||27===(a.keyCode||a.which))&&(27!==(a.keyCode||a.which)&&d.go_to($(this).val()),$(this).hide(),$(this).val(""),d.location_span.show(),d.chrom_select.show()),a.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",e).appendTo(this.nav_controls),this.location_span=$("<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=$.map(d.get_tracks(X),function(b){return b.data_manager.search_features(a.term).success(function(a){c=c.concat(a)})});$.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=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){d.zoom_out()}).appendTo(this.nav_controls),this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){d.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){d.change_chrom(d.chrom_select.val())}),this.browser_content_div.click(function(){$(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 $("<div/>").addClass("zoom-area").css("height",d.browser_content_div.height()+d.top_labeltrack.height()+1).appendTo($(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 S(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(),$(window).trigger("resize")},get_base_color:function(a){return this.config.get_value(a.toLowerCase()+"_color")||this.config.get_value("n_color")}});n(I.prototype,G.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(a,b,c,d){if(this.timer&&clearTimeout(this.timer),d){var e=this;this.timer=setTimeout(function(){e.trigger("navigate",a+":"+b+"-"+c)},500)}else view.trigger("navigate",a+":"+b+"-"+c)},update_location:function(a,b){this.location_span.text(d.commatize(a)+" - "+d.commatize(b)),this.nav_input.val(this.chrom+":"+d.commatize(a)+"-"+d.commatize(b));var c=this.chrom_select.val();""!==c&&this.trigger_navigate(c,this.low,this.high,!0)},load_chroms:function(a){a.num=w;var b=this,c=$.Deferred();return $.ajax({url:Galaxy.root+"api/genomes/"+this.dbkey,data:a,dataType:"json",success:function(a){if(0!==a.chrom_info.length){if(a.reference){var d=new U(b);b.add_label_track(d),b.reference_track=d}b.chrom_data=a.chrom_info;for(var e='<option value="">Select Chrom/Contig</option>',f=0,g=b.chrom_data.length;g>f;f++){var h=b.chrom_data[f].chrom;e+='<option value="'+h+'">'+h+"</option>"}a.prev_chroms&&(e+='<option value="previous">Previous '+w+"</option>"),a.next_chroms&&(e+='<option value="next">Next '+w+"</option>"),b.chrom_select.html(e),b.chrom_start_index=a.start_index,c.resolve(a.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+b.dbkey)}}),c},change_chrom:function(a,b,c){var d=this;if(!d.chrom_data)return void d.load_chroms_deferred.then(function(){d.change_chrom(a,b,c)});if(a&&"None"!==a){if("previous"===a)return void d.load_chroms({low:this.chrom_start_index-w});if("next"===a)return void d.load_chroms({low:this.chrom_start_index+w});var e=$.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-a<b.max_low?(b.low=b.max_low,b.high=b.max_low+c):b.high-a>b.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){G.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(G.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;b<this.max_low&&(b=this.max_low),c>this.max_high&&(c=this.max_high);var d=this.high-this.low;0!==this.high&&d<this.min_separation&&(c=b+this.min_separation),this.low=Math.floor(b),this.high=Math.ceil(c),this.update_location(this.low,this.high),this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var e=this.low/(this.max_high-this.max_low)*this.overview_viewport.width()||0,f=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width()||0,g=13;this.overview_box.css({left:e,width:Math.max(g,f)}).show(),g>f&&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 J=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()})}}),K=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var a=this.$el.addClass("param-row"),b=this.model,c=($("<div>").addClass("param-label").text(b.get("label")).appendTo(a),$("<div/>").addClass("param-input").html(b.get("html")).appendTo(a));c.find(":input").val(b.get("value")),$("<div style='clear: both;'/>").appendTo(a)},update_value:function(a){this.model.set_value($(a.target).val())}}),L=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.set_visible,this)},render:function(){var a=this;tool=this.model,parent_div=this.$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()});$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(a){var b=new K({model:a});b.render(),parent_div.append(b.$el)}),parent_div.find("input").click(function(){$(this).select()});var b=$("<div>").addClass("param-row").appendTo(parent_div),c=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(b),d=$("<input type='submit'>").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<this.params.length;a++)this.params[a].update_value()},run_on_dataset:function(){var a=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:a.id},null,function(){Galaxy.modal.show({title:a.get("name")+" is Running",body:a.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var a,c=this.model.get("track"),d=this.model,e=new b.GenomeRegion({chrom:c.view.chrom,start:c.view.low,end:c.view.high}),f={target_dataset_id:c.dataset.id,action:"rerun",tool_id:d.id,regions:[e.toJSON()]},g=c,i=d.get("name")+g.tool_region_and_parameters_str(e);if(g.container===view){var j=new H(view,view,{name:c.config.get_value("name")}),k=g.container.replace_drawable(g,j,!1);j.container_div.insertBefore(g.view.content_div.children()[k]),j.add_drawable(g),g.container_div.appendTo(j.content_div),a=j}else a=g.container;var l=new g.constructor(view,a,{name:i,hda_ldda:"hda"});l.init_for_tool_data(),l.change_mode(g.mode),l.set_filters_manager(g.filters_manager.copy(l)),l.update_icons(),a.add_drawable(l),l.tiles_div.text("Starting job."),this.run(f,l,function(a){l.set_dataset(new h.Dataset(a)),l.tiles_div.text("Running job."),l.init()})},run:function(a,b,c){a.inputs=this.model.get_inputs_dict();var e=new d.ServerStateDeferred({ajax_settings:{url:Galaxy.root+"api/tools",data:JSON.stringify(a),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(a){return"pending"!==a}});$.when(e.go()).then(function(a){"no converter"===a?(b.container_div.addClass("error"),b.content_div.text(y)):a.error?(b.container_div.addClass("error"),b.content_div.text(B+a.message)):c(a)})}}),M=function(a,b){f.Scaler.call(this,b),this.filter=a};M.prototype.gen_val=function(a){return this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high?this.default_val:(parseFloat(a[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low)};var N=function(a,b,c,d,e){this.track=a,this.region=b,this.low=b.get("start"),this.high=b.get("end"),this.w_scale=c,this.canvas=d,this.html_elt=$("<div class='track-tile'/>").append(d),this.data=e,this.stale=!1};N.prototype.predisplay_actions=function(){};var O=function(a,b,c,d,e){N.call(this,a,b,c,d,e)};O.prototype.predisplay_actions=function(){};var P=function(a,b,c,d,e,f,g,h,i,j,k){N.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};n(P.prototype,N.prototype),P.prototype.predisplay_actions=function(){};var Q=function(a,c,d){n(d,{drag_handle_class:"draghandle"}),F.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:v,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=$("<div class='track-content'>").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in d&&!d.resize||this.add_resize_handle())};n(Q.prototype,F.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},F.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(a){a.view.set_overview(a)}},F.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(a){a.filters_manager.visible()?a.filters_manager.clear_filters():a.filters_manager.init_filters(),a.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(a){a.tool.toggle(),a.tool.is_visible()?a.set_name(a.config.get_value("name")+a.tool_region_and_parameters_str()):a.revert_name(),$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(c){var d="<strong>Tool</strong>:"+c.tool.get("name")+"<br/><strong>Dataset</strong>:"+c.config.get_value("name")+'<br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',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}})}},F.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&F.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(a){this.dataset=a,this.data_manager.set("dataset",a)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var a=this,b=!1,c=!1,d=$("<div class='track-resize'>");$(a.container_div).hover(function(){a.config.get_value("content_visible")&&(b=!0,d.show())},function(){b=!1,c||d.hide()}),d.hide().bind("dragstart",function(b,d){c=!0,d.original_height=$(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 S?"LabelTrack":this instanceof U?"ReferenceTrack":this instanceof V?"LineTrack":this instanceof Z?"ReadTrack":this instanceof Y?"VariantTrack":this instanceof T?"CompositeTrack":this instanceof X?"FeatureTrack":"";
 
-},show_message:function(a){return this.tiles_div.remove(),$("<span/>").addClass("message").html(a).appendTo(this.content_div)},init:function(a){var b=this;if(b.enabled=!1,b.tile_cache.clear(),b.data_manager.clear(),b.content_div.children().remove(),b.container_div.removeClass("nodata error pending"),b.tiles_div=$("<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 $.getJSON(this.dataset.url(),d,function(a){if(a&&"error"!==a&&"error"!==a.kind)"no converter"===a?(b.container_div.addClass("error"),b.show_message(y)):"no data"===a||void 0!==a.data&&(null===a.data||0===a.data.length)?(b.container_div.addClass("nodata"),b.show_message(z)):"pending"===a?(b.container_div.addClass("pending"),b.show_message(A),setTimeout(function(){b.init()},b.data_query_wait)):("data"===a||"data"===a.status)&&(a.valid_chroms&&(b.valid_chroms=a.valid_chroms,b.update_icons()),b.tiles_div.text(C),b.view.chrom?(b.tiles_div.text(""),b.tiles_div.css("height",b.visible_height_px+"px"),b.enabled=!0,$.when.apply($,b.predraw_init()).done(function(){c.resolve(),b.container_div.removeClass("nodata error pending"),b.request_draw()})):c.resolve());else{b.container_div.addClass("error");var d=b.show_message(x);a.message&&(d.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+a.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),d.append($("<span/>").text(" ")),d.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){b.init(!0)})))}}),this.update_icons(),c}},predraw_init:function(){var a=this;return $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(b){var c=b.data;if(c&&void 0!==c.min&&void 0!==c.max){var d=c.min,e=c.max;d=Math.floor(Math.min(0,Math.max(d,c.mean-2*c.sd))),e=Math.ceil(Math.max(0,Math.min(e,c.mean+2*c.sd))),a.config.set_default_value("min_value",d),a.config.set_default_value("max_value",e),a.config.set_value("min_value",d),a.config.set_value("max_value",e)}})},get_drawables:function(){return this}});var R=function(c,d,e){Q.call(this,c,d,e);var f=this;if(q(f.container_div,f.drag_handle_class,".group",f),this.filters_manager=new g.FiltersManager(this,"filters"in e?e.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=e.tool?new J(a.extend(e.tool,{track:this,tool_state:e.tool_state})):null,this.tile_cache=new b.Cache(D),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var h=new L({model:this.tool});h.render(),this.dynamic_tool_div=h.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div),e.mode&&this.change_mode(e.mode)};n(R.prototype,F.prototype,Q.prototype,{action_icons_def:Q.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();n(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 $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(b){var c=b.data;if(isNaN(parseFloat(a.config.get_value("min_value")))||isNaN(parseFloat(a.config.get_value("max_value")))){var d=c.min,e=c.max;d=Math.floor(Math.min(0,Math.max(d,c.mean-2*c.sd))),e=Math.ceil(Math.max(0,Math.min(e,c.mean+2*c.sd))),a.config.set_value("min_value",d),a.config.set_value("max_value",e)}})},change_mode:function(a){var b=this;return b.mode=a,b.config.set_value("mode",a),"Auto"===a&&this.data_manager.clear(),b.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+b.mode+")"),b},update_icons:function(){var a=this;a.action_icons.filters_icon.toggle(a.filters_available),a.action_icons.tools_icon.toggle(null!==a.tool),a.action_icons.param_space_viz_icon.toggle(null!==a.tool)},_gen_tile_cache_key:function(a,b){return a+"_"+b},request_draw:function(a){a&&a.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(a,this)},before_draw:function(){this.max_height_px=0},_draw:function(c){if(this.can_draw()){var d=c&&c.clear_after,e=this.view.low,f=this.view.high,g=this.view.container.width(),h=this.view.resolution_px_b,i=1/h;this.is_overview&&(e=this.view.max_low,f=this.view.max_high,h=g/(view.max_high-view.max_low),i=1/h),this.before_draw(),this.tiles_div.children().addClass("remove");for(var j,k,l=Math.floor(u*i),m=Math.floor(e/l),n=[],o=[];f>m*l;)j=new b.GenomeRegion({chrom:this.view.chrom,start:m*l,end:Math.min((m+1)*l,this.view.max_high)}),k=this.draw_helper(j,h,c),n.push(k),$.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=$("<div/>").text(h).make_text_editable({num_cols:12,on_finish:function(a){$(".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 O});if(e.length>0){this.max_height_px=0;var f=this;a.each(b,function(a){a instanceof O||(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",r)})}},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(E,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 O(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 S=function(a,b){Q.call(this,a,b,{resize:!1,header:!1}),this.container_div.addClass("label-track")};n(S.prototype,Q.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=$("<div/>").addClass("label-container");e<a.high;){var h=Math.floor((e-a.low)/b*f);g.append($("<div/>").addClass("pos-label").text(d.commatize(e)).css({left:h})),e+=c}this.content_div.children(":first").remove(),this.content_div.append(g)}});var T=function(b,c,d){if(R.call(this,b,c,d),this.drawables=[],"drawables"in d){for(var e,f=0;f<d.drawables.length;f++)e=d.drawables[f],this.drawables[f]=aa(e,b,null),e.left_offset>this.left_offset&&(this.left_offset=e.left_offset);this.enabled=!0}a.each(this.drawables,function(a){(a instanceof X||a instanceof Z)&&a.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};n(T.prototype,R.prototype,{display_modes:E,config_params:a.union(F.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(a){$(".tooltip").remove(),a.show_group()}}].concat(R.prototype.action_icons_def),to_dict:G.prototype.to_dict,add_drawable:G.prototype.add_drawable,unpack_drawables:G.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}),Q.prototype.on_resize.call(this)},change_mode:function(a){R.prototype.change_mode.call(this,a);for(var b=0;b<this.drawables.length;b++)this.drawables[b].change_mode(a)},init:function(){for(var a=[],b=0;b<this.drawables.length;b++)a.push(this.drawables[b].init());var c=this;$.when.apply($,a).then(function(){c.enabled=!0,c.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:F.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var a,b=new H(this.view,this.container,{name:this.config.get_value("name")}),c=0;c<this.drawables.length;c++)a=this.drawables[c],a.update_icons(),b.add_drawable(a),a.container=b,b.content_div.append(a.container_div);this.container.replace_drawable(this,b,!0);b.request_draw({clear_tile_cache:!0})},before_draw:function(){var b=a.min(a.map(this.drawables,function(a){return a.config.get_value("min_value")})),c=a.max(a.map(this.drawables,function(a){return a.config.get_value("max_value")}));this.config.set_value("min_value",b),this.config.set_value("max_value",c),a.each(this.drawables,function(a){a.config.set_value("min_value",b),a.config.set_value("max_value",c)})},update_all_min_max:function(){var b=this.config.get_value("min_value"),c=this.config.get_value("max_value");a.each(this.drawables,function(a){a.config.set_value("min_value",b),a.config.set_value("max_value",c)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(a,b,c){var d,e=-1;for(d=0;d<a.length;d++){var f=a[d].html_elt.find("canvas").height();f>e&&(e=f)}for(d=0;d<a.length;d++){var g=a[d];g.html_elt.find("canvas").height()!==e&&(this.draw_helper(g.region,c,{force:!0,height:e}),g.html_elt.remove())}var h=this,i=function(){h.update_all_min_max()};this._add_yaxis_label("min",i),this._add_yaxis_label("max",i)}});var U=function(a){R.call(this,a,{content_div:a.top_labeltrack},{resize:!1,header:!1}),this.left_offset=a.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new b.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};n(U.prototype,F.prototype,R.prototype,{config_params:a.union(F.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}]),init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:F.prototype.can_draw,draw_helper:function(a,b,c){var d,e=this.tiles_div.is(":visible"),f=null;return b>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),d=!0,f=R.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 N(this,d,e,h,f)}});var V=function(a,b,c){this.mode="Histogram",R.call(this,a,b,c),this.left_offset=30;var d=this;$.when(m(galaxy_config.root+"datasets/"+this.dataset.id+"/display")).then(function(a){a&&(console.log("BBI DATA MANAGER"),d.data_manager=new k.BBIDataManager({dataset:d.dataset}))})};n(V.prototype,F.prototype,R.prototype,{display_modes:E,config_params:a.union(F.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 W=function(a,b,c){this.mode="Heatmap",R.call(this,a,b,c)};n(W.prototype,F.prototype,R.prototype,{display_modes:["Heatmap"],config_params:a.union(F.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 N(this,d,e,g,a.data)}});var X=function(a,b,c){R.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()};n(X.prototype,F.prototype,R.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:a.union(F.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){R.prototype.postdraw_actions.call(this,b,c,d,e);var f,g=this,h=a.filter(b,function(a){return a instanceof O});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;k<l.length;k++)l[k].update_ui_elt();var m,n,o=!1;for(f=0;f<b.length;f++)if(b[f].data.length)for(m=b[f].data[0],k=0;k<l.length;k++)if(n=l[k],n.applies_to(m)&&n.min!==n.max){o=!0;break}g.filters_available!==o&&(g.filters_available=o,g.filters_available||g.filters_manager.hide(),g.update_icons())}if(b[0]instanceof P){var p=!0;for(f=0;f<b.length;f++)if(!b[f].all_slotted){p=!1;break}this.action_icons.show_more_rows_icon.toggle(!p)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(a){"Auto"===this.mode&&("no_detail"===a&&(a="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+a+")"))},incremental_slots:function(a,b,c){var d=this.view.canvas_manager.dummy_context,f=this.slotters[a];return f&&f.mode===c||(f=new e.FeatureSlotter(a,c,s,function(a){return d.measureText(a)}),this.slotters[a]=f),f.slot_features(b)},get_mode:function(a){return mode="no_detail"===a.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>t?"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 M(this.filters_manager.alpha_filter):null,x=this.filters_manager.height_filter?new M(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 P(h,d,e,i,a.data,c,a.message,all_slotted,z,incomplete_features,f)}});var Y=function(a,b,c){R.call(this,a,b,c),this.painter=f.VariantPainter,this.summary_draw_height=30,this.left_offset=30};n(Y.prototype,F.prototype,R.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:a.union(F.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 N(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=[Q.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){R.prototype.postdraw_actions.call(this,b,c,d,e);var f=a.filter(b,function(a){return a instanceof O}),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($("<div/>").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("<br/>");this.tiles_div.prepend($("<div/>").html(i).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}h=("Squish"===this.mode?5:10)+"px",$(this.tiles_div).find(".sample").css({"font-size":h,"line-height":h}),$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var Z=function(a,b,c){X.call(this,a,b,c),this.painter=f.ReadPainter,this.update_icons()};n(Z.prototype,F.prototype,R.prototype,X.prototype,{config_params:a.union(F.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:void 0,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var _={CompositeTrack:T,DrawableGroup:H,DiagonalHeatmapTrack:W,FeatureTrack:X,LineTrack:V,ReadTrack:Z,VariantTrack:Y,VcfTrack:Y},aa=function(a,b,c){if("copy"in a)return a.copy(c);var d=a.obj_type;return d||(d=a.track_type),new _[d](b,c,a)};return{TracksterView:I,DrawableGroup:H,LineTrack:V,FeatureTrack:X,DiagonalHeatmapTrack:W,ReadTrack:Z,VariantTrack:Y,CompositeTrack:T,object_from_template:aa}});
+},show_message:function(a){return this.tiles_div.remove(),$("<span/>").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=$("<div/>").addClass("tiles").appendTo(b.content_div),b.dataset.id){var c=$.Deferred(),d={hda_ldda:b.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:b.view.chrom,retry:a};return $.getJSON(this.dataset.url(),d,function(a){if(a&&"error"!==a&&"error"!==a.kind)"no converter"===a?(b.container_div.addClass("error"),b.show_message(y)):"no data"===a||void 0!==a.data&&(null===a.data||0===a.data.length)?(b.container_div.addClass("nodata"),b.show_message(z)):"pending"===a?(b.container_div.addClass("pending"),b.show_message(A),setTimeout(function(){b.init()},b.data_query_wait)):("data"===a||"data"===a.status)&&(a.valid_chroms&&(b.valid_chroms=a.valid_chroms,b.update_icons()),b.tiles_div.text(C),b.view.chrom?(b.tiles_div.text(""),b.tiles_div.css("height",b.visible_height_px+"px"),b.enabled=!0,$.when.apply($,b.predraw_init()).done(function(){c.resolve(),b.container_div.removeClass("nodata error pending"),b.request_draw()})):c.resolve());else{b.container_div.addClass("error");var d=b.show_message(x);a.message&&(d.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+a.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})})),d.append($("<span/>").text(" ")),d.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){b.init(!0)})))}}),this.update_icons(),c}},predraw_init:function(){var a=this;return $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(b){var c=b.data;if(c&&void 0!==c.min&&void 0!==c.max){var d=c.min,e=c.max;d=Math.floor(Math.min(0,Math.max(d,c.mean-2*c.sd))),e=Math.ceil(Math.max(0,Math.min(e,c.mean+2*c.sd))),a.config.set_default_value("min_value",d),a.config.set_default_value("max_value",e),a.config.set_value("min_value",d),a.config.set_value("max_value",e)}})},get_drawables:function(){return this}});var R=function(c,d,e){Q.call(this,c,d,e);var f=this;if(q(f.container_div,f.drag_handle_class,".group",f),this.filters_manager=new g.FiltersManager(this,"filters"in e?e.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=e.tool?new J(a.extend(e.tool,{track:this,tool_state:e.tool_state})):null,this.tile_cache=new b.Cache(D),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var h=new L({model:this.tool});h.render(),this.dynamic_tool_div=h.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div),e.mode&&this.change_mode(e.mode)};n(R.prototype,F.prototype,Q.prototype,{action_icons_def:Q.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();n(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 $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(b){var c=b.data;if(isNaN(parseFloat(a.config.get_value("min_value")))||isNaN(parseFloat(a.config.get_value("max_value")))){var d=c.min,e=c.max;d=Math.floor(Math.min(0,Math.max(d,c.mean-2*c.sd))),e=Math.ceil(Math.max(0,Math.min(e,c.mean+2*c.sd))),a.config.set_value("min_value",d),a.config.set_value("max_value",e)}})},change_mode:function(a){var b=this;return b.mode=a,b.config.set_value("mode",a),"Auto"===a&&this.data_manager.clear(),b.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+b.mode+")"),b},update_icons:function(){var a=this;a.action_icons.filters_icon.toggle(a.filters_available),a.action_icons.tools_icon.toggle(null!==a.tool),a.action_icons.param_space_viz_icon.toggle(null!==a.tool)},_gen_tile_cache_key:function(a,b){return a+"_"+b},request_draw:function(a){a&&a.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(a,this)},before_draw:function(){this.max_height_px=0},_draw:function(c){if(this.can_draw()){var d=c&&c.clear_after,e=this.view.low,f=this.view.high,g=this.view.container.width(),h=this.view.resolution_px_b,i=1/h;this.is_overview&&(e=this.view.max_low,f=this.view.max_high,h=g/(view.max_high-view.max_low),i=1/h),this.before_draw(),this.tiles_div.children().addClass("remove");for(var j,k,l=Math.floor(u*i),m=Math.floor(e/l),n=[],o=[];f>m*l;)j=new b.GenomeRegion({chrom:this.view.chrom,start:m*l,end:Math.min((m+1)*l,this.view.max_high)}),k=this.draw_helper(j,h,c),n.push(k),$.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=$("<div/>").text(h).make_text_editable({num_cols:12,on_finish:function(a){$(".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 O});if(e.length>0){this.max_height_px=0;var f=this;a.each(b,function(a){a instanceof O||(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",r)})}},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(E,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 O(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 S=function(a,b){Q.call(this,a,b,{resize:!1,header:!1}),this.container_div.addClass("label-track")};n(S.prototype,Q.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=$("<div/>").addClass("label-container");e<a.high;){var h=Math.floor((e-a.low)/b*f);g.append($("<div/>").addClass("pos-label").text(d.commatize(e)).css({left:h})),e+=c}this.content_div.children(":first").remove(),this.content_div.append(g)}});var T=function(b,c,d){if(R.call(this,b,c,d),this.drawables=[],"drawables"in d){for(var e,f=0;f<d.drawables.length;f++)e=d.drawables[f],this.drawables[f]=aa(e,b,null),e.left_offset>this.left_offset&&(this.left_offset=e.left_offset);this.enabled=!0}a.each(this.drawables,function(a){(a instanceof X||a instanceof Z)&&a.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};n(T.prototype,R.prototype,{display_modes:E,config_params:a.union(F.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(a){$(".tooltip").remove(),a.show_group()}}].concat(R.prototype.action_icons_def),to_dict:G.prototype.to_dict,add_drawable:G.prototype.add_drawable,unpack_drawables:G.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}),Q.prototype.on_resize.call(this)},change_mode:function(a){R.prototype.change_mode.call(this,a);for(var b=0;b<this.drawables.length;b++)this.drawables[b].change_mode(a)},init:function(){for(var a=[],b=0;b<this.drawables.length;b++)a.push(this.drawables[b].init());var c=this;$.when.apply($,a).then(function(){c.enabled=!0,c.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide(),this.action_icons.tools_icon.hide(),this.action_icons.param_space_viz_icon.hide()},can_draw:F.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){for(var a,b=new H(this.view,this.container,{name:this.config.get_value("name")}),c=0;c<this.drawables.length;c++)a=this.drawables[c],a.update_icons(),b.add_drawable(a),a.container=b,b.content_div.append(a.container_div);this.container.replace_drawable(this,b,!0);b.request_draw({clear_tile_cache:!0})},before_draw:function(){var b=a.min(a.map(this.drawables,function(a){return a.config.get_value("min_value")})),c=a.max(a.map(this.drawables,function(a){return a.config.get_value("max_value")}));this.config.set_value("min_value",b),this.config.set_value("max_value",c),a.each(this.drawables,function(a){a.config.set_value("min_value",b),a.config.set_value("max_value",c)})},update_all_min_max:function(){var b=this.config.get_value("min_value"),c=this.config.get_value("max_value");a.each(this.drawables,function(a){a.config.set_value("min_value",b),a.config.set_value("max_value",c)}),this.request_draw({clear_tile_cache:!0})},postdraw_actions:function(a,b,c){var d,e=-1;for(d=0;d<a.length;d++){var f=a[d].html_elt.find("canvas").height();f>e&&(e=f)}for(d=0;d<a.length;d++){var g=a[d];g.html_elt.find("canvas").height()!==e&&(this.draw_helper(g.region,c,{force:!0,height:e}),g.html_elt.remove())}var h=this,i=function(){h.update_all_min_max()};this._add_yaxis_label("min",i),this._add_yaxis_label("max",i)}});var U=function(a){R.call(this,a,{content_div:a.top_labeltrack},{resize:!1,header:!1}),this.left_offset=a.canvas_manager.char_width_px,this.container_div.addClass("reference-track"),this.data_url=Galaxy.root+"api/genomes/"+this.view.dbkey,this.data_url_extra_params={reference:!0},this.data_manager=new b.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset}),this.hide_contents()};n(U.prototype,F.prototype,R.prototype,{config_params:a.union(F.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:!0}]),init:function(){this.data_manager.clear(),this.enabled=!0},predraw_init:function(){},can_draw:F.prototype.can_draw,draw_helper:function(a,b,c){var d,e=this.tiles_div.is(":visible"),f=null;return b>this.view.canvas_manager.char_width_px?(this.tiles_div.show(),d=!0,f=R.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 N(this,d,e,h,f)}});var V=function(a,b,c){this.mode="Histogram",R.call(this,a,b,c),this.left_offset=30;var d=this;$.when(m(Galaxy.root+"datasets/"+this.dataset.id+"/display")).then(function(a){a&&(d.data_manager=new k.BBIDataManager({dataset:d.dataset}))})};n(V.prototype,F.prototype,R.prototype,{display_modes:E,config_params:a.union(F.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 W=function(a,b,c){this.mode="Heatmap",R.call(this,a,b,c)};n(W.prototype,F.prototype,R.prototype,{display_modes:["Heatmap"],config_params:a.union(F.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 N(this,d,e,g,a.data)}});var X=function(a,b,c){R.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()};n(X.prototype,F.prototype,R.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:a.union(F.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){R.prototype.postdraw_actions.call(this,b,c,d,e);var f,g=this,h=a.filter(b,function(a){return a instanceof O});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;k<l.length;k++)l[k].update_ui_elt();var m,n,o=!1;for(f=0;f<b.length;f++)if(b[f].data.length)for(m=b[f].data[0],k=0;k<l.length;k++)if(n=l[k],n.applies_to(m)&&n.min!==n.max){o=!0;break}g.filters_available!==o&&(g.filters_available=o,g.filters_available||g.filters_manager.hide(),g.update_icons())}if(b[0]instanceof P){var p=!0;for(f=0;f<b.length;f++)if(!b[f].all_slotted){p=!1;break}this.action_icons.show_more_rows_icon.toggle(!p)}else this.action_icons.show_more_rows_icon.hide()},update_auto_mode:function(a){"Auto"===this.mode&&("no_detail"===a&&(a="feature spans"),this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+a+")"))},incremental_slots:function(a,b,c){var d=this.view.canvas_manager.dummy_context,f=this.slotters[a];return f&&f.mode===c||(f=new e.FeatureSlotter(a,c,s,function(a){return d.measureText(a)}),this.slotters[a]=f),f.slot_features(b)},get_mode:function(a){return mode="no_detail"===a.extra_info||this.is_overview?"no_detail":this.view.high-this.view.low>t?"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 M(this.filters_manager.alpha_filter):null,x=this.filters_manager.height_filter?new M(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 P(h,d,e,i,a.data,c,a.message,all_slotted,z,incomplete_features,f)}});var Y=function(a,b,c){R.call(this,a,b,c),this.painter=f.VariantPainter,this.summary_draw_height=30,this.left_offset=30};n(Y.prototype,F.prototype,R.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:a.union(F.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 N(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=[Q.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){R.prototype.postdraw_actions.call(this,b,c,d,e);var f=a.filter(b,function(a){return a instanceof O}),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($("<div/>").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("<br/>");this.tiles_div.prepend($("<div/>").html(i).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}h=("Squish"===this.mode?5:10)+"px",$(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 Z=function(a,b,c){X.call(this,a,b,c),this.painter=f.ReadPainter,this.update_icons()};n(Z.prototype,F.prototype,R.prototype,X.prototype,{config_params:a.union(F.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 _={CompositeTrack:T,DrawableGroup:H,DiagonalHeatmapTrack:W,FeatureTrack:X,LineTrack:V,ReadTrack:Z,VariantTrack:Y,VcfTrack:Y},aa=function(a,b,c){if("copy"in a)return a.copy(c);var d=a.obj_type;return d||(d=a.track_type),new _[d](b,c,a)};return{TracksterView:I,DrawableGroup:H,LineTrack:V,FeatureTrack:X,DiagonalHeatmapTrack:W,ReadTrack:Z,VariantTrack:Y,CompositeTrack:T,object_from_template:aa}});
 //# sourceMappingURL=../../../maps/viz/trackster/tracks.js.map
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