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Merged in mgehring/galaxy-central (pull request #79)
This commit is contained in:
James Taylor
@@ -1484,14 +1484,15 @@ class ChromatinInteractionsDataProvider( GenomeDataProvider ):
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return { 'data': rval, 'message': message }
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def get_default_max_vals( self ):
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return 50000;
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return 100000;
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class ChromatinInteractionsTabixDataProvider( TabixDataProvider, ChromatinInteractionsDataProvider ):
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def get_iterator( self, chrom, start=0, end=sys.maxint ):
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"""
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"""
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# Modify start as needed to get earlier interactions with start region.
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start = max( 0, int( start ) - 1000000 )
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span = int( end ) - int( start )
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filter_start = max( 0, int( start ) - span - span/2 )
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def filter( iter ):
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for line in iter:
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feature = line.split()
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@@ -1500,9 +1501,10 @@ class ChromatinInteractionsTabixDataProvider( TabixDataProvider, ChromatinIntera
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c = feature[3]
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s2 = int( feature[4] )
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e2 = int( feature[5] )
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if ( s1 <= end and e1 >= start ) and ( s2 <= end and e2 >= start ):
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#if ( s1 <= filter_end and e1 >= filter_start ) and ( s2 <= filter_end and e2 >= filter_start ) and ( max( s1, s2 ) - min( e1, e2 ) <= span * 2 ):
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if ( ( s1 + s2 ) / 2 <= end ) and ( ( e1 + e2 ) / 2 >= start ) and ( c == chrom ):
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yield line
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return filter( TabixDataProvider.get_iterator( self, chrom, start, end ) )
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return filter( TabixDataProvider.get_iterator( self, chrom, filter_start, end ) )
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#
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# -- Helper methods. --
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@@ -1 +1 @@
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define(["libs/underscore","viz/trackster/util"],function(b,e){var c=Backbone.Model.extend({initialize:function(f){var g=this.get("key");this.set("id",g);var h=b.find(c.known_settings_defaults,function(i){return i.key===g});if(h){this.set(b.extend({},h,f))}if(this.get("type")==="color"&&!this.get("value")){this.set("value",e.get_random_color())}this.on("change:value",this.cast_value,this)},cast_value:function(){var f=this.get("type"),g=this.get("value");if(f==="float"){g=parseFloat(g)}else{if(f==="int"){g=parseInt(g,10)}}this.set("value")}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var d=Backbone.Collection.extend({model:c,to_key_value_dict:function(){var f={};this.each(function(g){f[g.get("key")]=g.get("value")});return f},get_value:function(f){var g=this.get(f);if(g){return g.get("value")}return undefined}},{from_config_dict:function(g){var f=b.map(b.keys(g),function(h){return{key:h,value:g[h]}});return new d(f)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var i=this.model;var f=this.$el;var h;function g(n,j){for(var r=0;r<n.length;r++){h=n[r];if(h.hidden){continue}var l="param_"+r;var v=i.values[h.key];var x=$("<div class='form-row' />").appendTo(j);x.append($("<label />").attr("for",l).text(h.label+":"));if(type==="bool"){x.append($('<input type="checkbox" />').attr("id",l).attr("name",l).attr("checked",v))}else{if(type==="text"){x.append($('<input type="text"/>').attr("id",l).val(v).click(function(){$(this).select()}))}else{if(type==="select"){var t=$("<select />").attr("id",l);for(var p=0;p<h.options.length;p++){$("<option/>").text(h.options[p].label).attr("value",h.options[p].value).appendTo(t)}t.val(v);x.append(t)}else{if(type==="color"){var w=$("<div/>").appendTo(x),s=$("<input />").attr("id",l).attr("name",l).val(v).css("float","left").appendTo(w).click(function(z){$(".bs-tooltip").removeClass("in");var y=$(this).siblings(".bs-tooltip").addClass("in");y.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(y).height()/2)+($(this).height()/2)}).show();y.click(function(A){A.stopPropagation()});$(document).bind("click.color-picker",function(){y.hide();$(document).unbind("click.color-picker")});z.stopPropagation()}),q=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(w).attr("title","Set new random color").tooltip(),u=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(w).hide(),m=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(u),k=$("<div class='tooltip-arrow'></div>").appendTo(u),o=$.farbtastic(m,{width:100,height:100,callback:s,color:v});w.append($("<div/>").css("clear","both"));(function(y){q.click(function(){y.setColor(e.get_random_color())})})(o)}else{x.append($("<input />").attr("id",l).attr("name",l).val(v))}}}}if(h.help){x.append($("<div class='help'/>").text(h.help))}}}g(this.params,f);return this},render_in_modal:function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){this.update_from_form();hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(i){if((i.keyCode||i.which)===27){h()}else{if((i.keyCode||i.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);if(this.$el.children().length===0){this.render()}show_modal("Configure",drawable.config.build_form(),{Cancel:h,OK:f})},update_from_form:function(){var f=this;this.collection.each(function(h,g){if(!h.get("hidden")){var j="param_"+g;var i=f.$el.find("#"+j).val();if(type==="bool"){i=container.find("#"+j).is(":checked")}h.set("value",i)}})}});return{ConfigSettingCollection:d,ConfigSettingCollectionView:a}});
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define(["libs/underscore","viz/trackster/util"],function(b,e){var c=Backbone.Model.extend({initialize:function(f){var g=this.get("key");this.set("id",g);var h=b.find(c.known_settings_defaults,function(i){return i.key===g});if(h){this.set(b.extend({},h,f))}if(this.get("type")==="color"&&!this.get("value")){this.set("value",e.get_random_color())}this.on("change:value",this.cast_value,this)},cast_value:function(){var f=this.get("type"),g=this.get("value");if(f==="float"){g=parseFloat(g)}else{if(f==="int"){g=parseInt(g,10)}}this.set("value")}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var d=Backbone.Collection.extend({model:c,to_key_value_dict:function(){var f={};this.each(function(g){f[g.get("key")]=g.get("value")});return f},get_value:function(f){var g=this.get(f);if(g){return g.get("value")}return undefined}},{from_config_dict:function(g){var f=b.map(b.keys(g),function(h){return{key:h,value:g[h]}});return new d(f)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var i=this.model;var f=this.$el;var h;function g(n,j){for(var r=0;r<n.length;r++){h=n[r];if(h.hidden){continue}var l="param_"+r;var v=i.values[h.key];var x=$("<div class='form-row' />").appendTo(j);x.append($("<label />").attr("for",l).text(h.label+":"));if(type==="bool"){x.append($('<input type="checkbox" />').attr("id",l).attr("name",l).attr("checked",v))}else{if(type==="text"){x.append($('<input type="text"/>').attr("id",l).val(v).click(function(){$(this).select()}))}else{if(type==="select"){var t=$("<select />").attr("id",l);for(var p=0;p<h.options.length;p++){$("<option/>").text(h.options[p].label).attr("value",h.options[p].value).appendTo(t)}t.val(v);x.append(t)}else{if(type==="color"){var w=$("<div/>").appendTo(x),s=$("<input />").attr("id",l).attr("name",l).val(v).css("float","left").appendTo(w).click(function(z){$(".bs-tooltip").removeClass("in");var y=$(this).siblings(".bs-tooltip").addClass("in");y.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(y).height()/2)+($(this).height()/2)}).show();y.click(function(A){A.stopPropagation()});$(document).bind("click.color-picker",function(){y.hide();$(document).unbind("click.color-picker")});z.stopPropagation()}),q=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(w).attr("title","Set new random color").tooltip(),u=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(w).hide(),m=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(u),k=$("<div class='tooltip-arrow'></div>").appendTo(u),o=$.farbtastic(m,{width:100,height:100,callback:s,color:v});w.append($("<div/>").css("clear","both"));(function(y){q.click(function(){y.setColor(e.get_random_color())})})(o)}else{x.append($("<input />").attr("id",l).attr("name",l).val(v))}}}}if(h.help){x.append($("<div class='help'/>").text(h.help))}}}g(this.params,f);return this},render_in_modal:function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){this.update_from_form();hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(i){if((i.keyCode||i.which)===27){h()}else{if((i.keyCode||i.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);if(this.$el.children().length===0){this.render()}show_modal("Configure",drawable.config.build_form(),{Cancel:h,OK:f})},update_from_form:function(){var f=this;this.collection.each(function(h,g){if(!h.get("hidden")){var j="param_"+g;var i=f.$el.find("#"+j).val();if(type==="bool"){i=container.find("#"+j).is(":checked")}h.set("value",i)}})}});return{ConfigSettingCollection:d,ConfigSettingCollectionView:a}});
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File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
@@ -49,8 +49,8 @@ var ConfigSetting = Backbone.Model.extend({
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{ key: 'max_value', label: 'Max Value', type: 'float', default_value: null },
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{ key: 'mode', type: 'string', default_value: this.mode, hidden: true },
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{ key: 'height', type: 'int', default_value: 32, hidden: true },
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{ key: 'pos_color', label: 'Positive Color', type: 'color', default_value: "4169E1" },
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{ key: 'negative_color', label: 'Negative Color', type: 'color', default_value: "FF8C00" },
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{ key: 'pos_color', label: 'Positive Color', type: 'color', default_value: "#FF8C00" },
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{ key: 'neg_color', label: 'Negative Color', type: 'color', default_value: "#4169E1" },
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{ key: 'block_color', label: 'Block color', type: 'color', default_value: null },
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{ key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
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{ key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false },
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@@ -1058,6 +1058,10 @@ var Color = function (rgb, a) {
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this.rgb = rgb.match(/.{2}/g).map(function (c) {
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return parseInt(c, 16);
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});
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} else if (rgb.length == 7) {
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this.rgb = rgb.substring(1,7).match(/.{2}/g).map(function (c) {
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return parseInt(c, 16);
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});
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} else {
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this.rgb = rgb.split('').map(function (c) {
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return parseInt(c + c, 16);
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@@ -1207,8 +1211,8 @@ DiagonalHeatmapPainter.prototype.default_prefs = {
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min_value: undefined,
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max_value: undefined,
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mode: "Heatmap",
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pos_color: "4169E1",
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neg_color: "FF8C00"
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pos_color: "#FF8C00",
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neg_color: "#4169E1"
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};
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DiagonalHeatmapPainter.prototype.draw = function(ctx, width, height, w_scale) {
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@@ -1222,7 +1226,7 @@ DiagonalHeatmapPainter.prototype.draw = function(ctx, width, height, w_scale) {
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data = this.data,
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invsqrt2 = 1 / Math.sqrt(2);
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var ramp = ( new SplitRamp( this.prefs.neg_color, "FFFFFF", this.prefs.pos_color, min_value, max_value ) );
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var ramp = ( new SplitRamp( this.prefs.neg_color, "#FFFFFF", this.prefs.pos_color, min_value, max_value ) );
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var d, s1, e1, s2, e2, value;
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@@ -1248,6 +1252,8 @@ DiagonalHeatmapPainter.prototype.draw = function(ctx, width, height, w_scale) {
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e2 = scale( d[5] );
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value = d[6];
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//console.log( "!!!", value, ramp.map_value( value ) );
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ctx.fillStyle = ( ramp.map_value( value ) );
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ctx.fillRect( s1, s2, ( e1 - s1 ), ( e2 - s2 ) );
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@@ -3639,9 +3639,9 @@ var DiagonalHeatmapTrack = function (view, container, obj_dict) {
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track: this,
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params: [
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{ key: 'name', label: 'Name', type: 'text', default_value: this.name },
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{ key: 'pos_color', label: 'Positive Color', type: 'color', default_value: "4169E1" },
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{ key: 'negative_color', label: 'Negative Color', type: 'color', default_value: "FF8C00" },
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{ key: 'min_value', label: 'Min Value', type: 'float', default_value: 0 },
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{ key: 'pos_color', label: 'Positive Color', type: 'color', default_value: "#FF8C00" },
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{ key: 'neg_color', label: 'Negative Color', type: 'color', default_value: "#4169E1" },
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{ key: 'min_value', label: 'Min Value', type: 'float', default_value: -1 },
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{ key: 'max_value', label: 'Max Value', type: 'float', default_value: 1 },
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{ key: 'mode', type: 'string', default_value: this.mode, hidden: true },
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{ key: 'height', type: 'int', default_value: 500, hidden: true }
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@@ -3716,7 +3716,7 @@ var FeatureTrack = function(view, container, obj_dict) {
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// Define and restore track configuration.
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var
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block_color = util.get_random_color(),
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reverse_strand_color = util.get_random_color( [ block_color, "#ffffff" ] );
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reverse_strand_color = util.get_random_color( [ block_color, "#FFFFFF" ] );
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this.config = new DrawableConfig( {
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track: this,
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params: [
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