biojs-vis-seqlogo/build/hmm.min.js

A sequence logo visualizer

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var t=this.called_on.find(".logo_yaxis"),e=(Math.abs(this.data.max_height),isNaN(this.data.min_height_obs)?0:parseInt(this.data.min_height_obs,10),null),n="Information Content (bits)";e=t[0].getContext("2d"),e.beginPath(),e.moveTo(55,1),e.lineTo(40,1),e.moveTo(55,this.info_content_height),e.lineTo(40,this.info_content_height),e.moveTo(55,this.info_content_height/2),e.lineTo(40,this.info_content_height/2),e.lineWidth=1,e.strokeStyle="#666666",e.stroke(),e.fillStyle="#666666",e.textAlign="right",e.font="bold 10px Arial",e.textBaseline="top",e.fillText(parseFloat(this.data.max_height).toFixed(1),38,0),e.textBaseline="middle",e.fillText(parseFloat(this.data.max_height/2).toFixed(1),38,this.info_content_height/2),e.fillText("0",38,this.info_content_height),"score"===this.data.height_calc&&(n="Score (bits)"),e.save(),e.translate(5,this.height/2-20),e.rotate(-Math.PI/2),e.textAlign="center",e.font="normal 12px Arial",e.fillText(n,1,0),e.restore(),e.fillText("occupancy",55,this.info_content_height+7),this.show_inserts&&(e.fillText("ins. prob.",50,280),e.fillText("ins. len.",46,296))}}},{}],16:[function(t,e){var n=null;e.exports=function(){if(!n){var t=document.createElement("canvas");n=!(!t.getContext||!t.getContext("2d"))}return n}},{}],17:[function(t,e){e.exports={A:"#FF9966",C:"#009999",D:"#FF0000",E:"#CC0033",F:"#00FF00",G:"#f2f20c",H:"#660033",I:"#CC9933",K:"#663300",L:"#FF9933",M:"#CC99CC",N:"#336666",P:"#0099FF",Q:"#6666CC",R:"#990000",S:"#0000FF",T:"#00FFFF",V:"#FFCC33",W:"#66CC66",Y:"#006600"}},{}],18:[function(t,e){e.exports={A:"#cbf751",C:"#5ec0cc",G:"#ffdf59",T:"#b51f16",U:"#b51f16"}},{}],19:[function(t,e){var n=t("jbone");e.exports=function(t,e,i){t.find(".logo_settings_switch, .logo_settings .close").on("click",function(t){t.preventDefault(),n(".logo_settings").toggle()}),t.find(".logo_reset").on("click",function(t){t.preventDefault(),e.changeZoom({target:e.default_zoom})}),t.find(".logo_change").on("click",function(t){t.preventDefault()}),t.find(".logo_zoomin").on("click",function(t){t.preventDefault(),e.changeZoom({distance:.1,direction:"+"})}),t.find(".logo_zoomout").on("click",function(t){t.preventDefault(),e.changeZoom({distance:.1,direction:"-"})}),t.find(".logo_scale").on("change",function(){e.toggleScale(this.value)}),t.find(".logo_color").on("change",function(){e.toggleColorscheme(this.value)}),t.find(".logo_ali_map").on("change",function(){e.toggleAliMap(this.value)}),t.find(".logo_position").on("change",function(){this.value.match(/^\d+$/m)&&e.scrollToColumn(this.value,1)}),i.on("dblclick",function(n){console.log("dblclick",e),offset=e.logo_graphic.offset(),x=parseInt(n.pageX-offset.left,10),window_position=n.pageX-t.parent().offset().left,col=e.columnFromCoordinates(x),console.log("col",col),current=e.zoom,e.changeZoom(1>current?{target:1,offset:window_position,column:col}:{target:.3,offset:window_position,column:col})}),n(document).on(t.attr("id")+".scrolledTo",function(t,n){e.render({target:n})}),n(document).on("keydown",function(t){t.ctrlKey||((61===t.which||107===t.which)&&(zoom+=.1,e.changeZoom({distance:.1,direction:"+"})),(109===t.which||0===t.which)&&(zoom-=.1,e.changeZoom({distance:.1,direction:"-"})))})}},{jbone:7}],20:[function(t,e){_=t("underscore");var n=t("./canvasSupport.js"),i=t("./render/render.js"),o=t("./model/letter.js"),r=t("backbone-viewj"),s=t("./axis"),a=t("./eventListener.js"),l=t("./info/settings.js"),c=t("jbone");e.exports=r.extend({options:{xaxis:!0,yaxis:!0,height:300,column_width:34,debug:!0,scale_height_enabled:!0,scaled_max:!0,zoom_buttons:!0,colorscheme:"default",data:void 0,start:1,end:void 0,zoom:.4,colors:void 0,divider:!1,show_probs:!1,divider_step:5,show_divider:!1,border:!1,settings:!1,scroller:!0,positionMarker:!0},loadDefault:function(e){this.data=e.data,this.display_ali_map=0,this.alphabet=e.data.alphabet||"dna",this.start=e.start,this.zoom=parseFloat(e.zoom)||.4,this.default_zoom=this.zoom,this.column_width=e.column_width,this.height=e.height,this.canvas_width=5e3,this.scale_height_enabled=e.scale_height_enabled,this.scrollme=null,this.previous_target=0,this.rendered=[],this.previous_zoom=0,void 0==this.data.max_height&&(this.data.max_height=this.calcMaxHeight(this.data.heightArr)),this.data.insert_probs&&this.data.delete_probs||(this.options.show_probs=!1),this.data.max_height=e.scaled_max?e.data.max_height_obs||this.data.max_height||2:e.data.max_height_theory||this.data.max_height||2,e.colors?this.changeColors(e.colors):"aa"===this.alphabet?(this.aa_colors=t("./colors/aa.js"),this.changeColors(this.aa_colors)):(this.dna_colors=t("./colors/dna.js"),this.changeColors(this.dna_colors))},initialize:function(t){if(!n())return void(this.el.textContent="Your browser doesn't support canvas.");void 0==t.data&&(this.el.textContent="No data added."),_.extend(this.options,t);var e=this.options;if(this.loadDefault(e),this.options.show_probs?this.data.processing&&/^observed|weighted/.test(this.data.processing)?(this.show_inserts=0,this.info_content_height=this.height-14):(this.show_inserts=1,this.info_content_height=this.height-44):this.info_content_height=this.height,this.$el=c(this.el),this.initDivs(),this.options.settings){var i=l(this,e);this.$el.append(i)}a(this.$el,this,this.logo_graphic)},initDivs:function(){var t=h("div");t.className="logo_graphic",this.logo_graphic=c(t);var e=h("div");if(e.className="logo_container",e.style.height=this.height,this.container=c(e),this.container.append(t),this.$el.append(e),this.options.divider){var n=h("div");n.className="logo_divider",this.$el.append(n)}this.dom_element=c(t),this.called_on=this.$el,this.options.xaxis&&s.render_x_axis_label.call(this),this.options.yaxis?s.render_y_axis_label.call(this):this.container[0].style.marginLeft="0px"},render:function(){return i.call(this),this},changeColors:function(t){this.colors=t;var e=void 0!=t&&void 0!=t.type;e&&(this.colorscheme="dynamic"),this.buildAlphabet()},buildAlphabet:function(){this.letters={};var t=this.colors;if("dynamic"==this.colorscheme){var e="ABCDEFGHIJKLMNOPQRSTUVWXYZ".split("");t={},e.forEach(function(e){t[e]=""})}for(var n in t)if(t.hasOwnProperty(n)){var i={color:t[n]};this.letters[n]=new o(n,i)}},toggleColorscheme:function(t){var e=this.currentColumn();this.colorscheme=t?"default"===t?"default":"consensus":"default"===this.colorscheme?"consensus":"default",this.rendered=[],this.scrollme.reflow(),this.scrollToColumn(e+1),this.scrollToColumn(e)},toggleScale:function(t){var e=this.currentColumn();this.data.max_height=t?"obs"===t?this.data.max_height_obs:this.data.max_height_theory:this.data.max_height===this.data.max_height_obs?this.data.max_height_theory:this.data.max_height_obs,this.rendered=[],this.logoYAxis&&this.logoYAxis.remove(),s.render_y_axis_label.call(this),this.scrollme.reflow(),this.scrollToColumn(e+1),this.scrollToColumn(e)},toggleAliMap:function(t){var e=this.currentColumn();this.display_ali_map=t?"model"===t?0:1:1===this.display_ali_map?0:1,s.render_x_axis_label(this),this.rendered=[],this.scrollme.reflow(),this.scrollToColumn(e+1),this.scrollToColumn(e)},currentColumn:function(){var t=this.scrollme.scroller.getValues().left,e=this.column_width*this.zoom,n=t/e,i=this.container.width()/e/2,o=Math.ceil(n+i);return o},changeZoom:function(t){var e=.3,n=null;if(t.target?e=t.target:t.distance&&(e=(parseFloat(this.zoom)-parseFloat(t.distance)).toFixed(1),"+"===t.direction&&(e=(parseFloat(this.zoom)+parseFloat(t.distance)).toFixed(1))),e>1?e=1:.1>e&&(e=.1),n=this.logo_graphic.width()*e/this.zoom,n>this.container.width())if(t.column){this.zoom=e,this.render({zoom:this.zoom}),this.scrollme.reflow();var i=this.coordinatesFromColumn(t.column);this.scrollme.scroller.scrollTo(i-t.offset)}else{var o=this.currentColumn();this.zoom=e,this.render({zoom:this.zoom}),this.scrollme.reflow(),this.scrollToColumn(o)}return this.zoom},columnFromCoordinates:function(t){var e=Math.ceil(t/(this.column_width*this.zoom));return e},coordinatesFromColumn:function(t){var e=t-1,n=e*this.column_width*this.zoom+this.column_width*this.zoom/2;return n},scrollToColumn:function(t,e){var n=this.logo_container.width()/2,i=this.coordinatesFromColumn(t);this.scrollme.scroller.scrollTo(i-n,0,e)},calcMaxHeight:function(t){return t.reduce(function(t,e){var n=0;for(var i in e)n+=e[i];return n>t?n:t},0)}});var h=function(t){return document.createElement(t)}},{"./axis":15,"./canvasSupport.js":16,"./colors/aa.js":17,"./colors/dna.js":18,"./eventListener.js":19,"./info/settings.js":21,"./model/letter.js":22,"./render/render.js":26,"backbone-viewj":1,jbone:7,underscore:8}],21:[function(t,e){var n=t("jbone");e.exports=function(t,e){var i=n('<form class="logo_form"><fieldset><label for="position">Column number</label><input type="text" name="position" class="logo_position"></input><button class="button logo_change">Go</button></fieldset></form>'),o=n('<div class="logo_settings"></div>');if(o.append('<span class="close">x</span>'),t.scale_height_enabled&&t.data.max_height_obs<t.data.max_height_theory){var r="",s="",a="",l="";t.data.max_height_obs===t.data.max_height?r="checked":s="checked"}var c='<fieldset><legend>Scale</legend><label><input type="radio" name="scale" class="logo_scale" value="obs" '+r+"/>Maximum Observed "+l+'</label></br><label><input type="radio" name="scale" class="logo_scale" value="theory" '+s+"/>Maximum Theoretical "+a+"</label></fieldset>";if(o.append(c),"score"!==t.data.height_calc&&"aa"===t.data.alphabet&&t.data.probs_arr){var h=null,u=null,f="",_="";"default"===t.colorscheme?h="checked":u="checked",e.help&&(f='<a class="help" href="/help#colors_default" title="Each letter receives its own color."><span aria-hidden="true" data-icon="?"></span><span class="reader-text">help</span></a>',_='<a class="help" href="/help#colors_consensus" title="Letters are colored as in Clustalx and Jalview, with colors depending on composition of the column."><span aria-hidden="true" data-icon="?"></span><span class="reader-text">help</span></a>');var d='<fieldset><legend>Color Scheme</legend><label><input type="radio" name="color" class="logo_color" value="default" '+h+"/>Default "+f+'</label></br><label><input type="radio" name="color" class="logo_color" value="consensus" '+u+"/>Consensus Colors "+_+"</label></fieldset>";o.append(d)}if(t.data.ali_map){var p=null,m=null,g="",v="";0===t.display_ali_map?p="checked":m="checked",e.help&&(g='<a class="help" href="/help#coords_model" title="The coordinates along the top of the plot show the model position."><span aria-hidden="true" data-icon="?"></span><span class="reader-text">help</span></a>',v='<a class="help" href="/help#coords_ali" title="The coordinates along the top of the plot show the column in the alignment associated with the model"><span aria-hidden="true" data-icon="?"></span><span class="reader-text">help</span></a>');var b='<fieldset><legend>Coordinates</legend><label><input type="radio" name="coords" class="logo_ali_map" value="model" '+p+"/>Model "+g+'</label></br><label><input type="radio" name="coords" class="logo_ali_map" value="alignment" '+m+"/>Alignment "+v+"</label></fieldset>";o.append(b)}var x=n('<div class="logo_controls"></div>');return t.zoom_enabled&&x.append('<button class="logo_zoomout button">-</button><button class="logo_zoomin button">+</button>'),o.children().length>0&&(x.append('<button class="logo_settings_switch button">Settings</button>'),x.append(o)),i.append(x),i}},{jbone:7}],22:[function(t,e){e.exports=function(t,e){e=e||{},this.value=t,this.width=parseInt(e.width,10)||100,"W"===this.value&&(this.width+=30*this.width/100),this.height=parseInt(e.height,10)||100,this.color=e.color||"#000000",this.fontSize=e.fontSize||138,this.scaled=function(){},this.draw=function(t,e,n,i,o,r){var s=e/this.height,a=n/this.width,l=t.font;t.transform(a,0,0,s,i,o),t.fillStyle=r||this.color,t.textAlign="center",t.font="bold "+this.fontSize+"px Arial",t.fillText(this.value,0,0),t.setTransform(1,0,0,1,0,0),t.fillStyle="#000000",t.font=l}}},{}],23:[function(t,e){e.exports=function(t,e,n){t.beginPath(),t.moveTo(0,e),t.lineTo(n,e),t.lineWidth=1,t.strokeStyle="#999999",t.stroke()}},{}],24:[function(t,e){e.exports=function(t,e,n,i,o,r,s){t.font=r+"px Arial",t.textAlign=s?"right":"center",t.fillStyle="#666666",t.fillText(o,e+i/2,n)}},{}],25:[function(t,e){e.exports=function(t,e,n,i,o){o=o||"#999999",t.beginPath(),t.moveTo(e,n),t.lineTo(e,n+i),t.lineWidth=1,t.strokeStyle=o,t.stroke()}},{}],26:[function(t,e){function n(t,e,n,i,o){var s=r(t).find("#canv_"+i);return s.length||(r(t).append('<canvas class="canvas_logo" id="canv_'+i+'"  height="'+e+'" width="'+n+'" style="left:'+o*i+'px"></canvas>'),s=r(t).find("#canv_"+i)),r(s).attr("width",n).attr("height",e),s[0]}var i=t("./render_with_text.js"),o=t("./render_with_rects.js"),r=t("jbone");e.exports=function(t){if(this.data){t=t||{};var e=t.zoom||this.zoom,r=t.target||1,s=(t.scaled||null,this.dom_element.parent().attr("width")),a=1,l=null,c=null,h=0;if(this.previous_target=r,t.start&&(this.start=t.start),t.end&&(this.end=t.end),.1>=e?e=.1:e>=1&&(e=1),this.zoom=e,l=this.end||this.data.heightArr.length,c=this.start||1,l=l>this.data.heightArr.length?this.data.heightArr.length:l,l=c>l?c:l,c=c>l?l:c,c=c>1?c:1,this.y=this.height-20,this.max_width=this.column_width*(l-c+1),s>this.max_width&&(e=1,this.zoom_enabled=!1),this.zoom=e,this.zoomed_column=this.column_width*e,this.total_width=this.zoomed_column*(l-c+1),1>e)for(;this.total_width<s&&(this.zoom+=.1,this.zoomed_column=this.column_width*this.zoom,this.total_width=this.zoomed_column*(l-c+1),this.zoom_enabled=!1,!(e>=1)););r>this.total_width&&(r=this.total_width),this.dom_element.attr({width:this.total_width+"px"}).css({width:this.total_width+"px"}),this.canvas_width=this.total_width;var u=Math.ceil(this.total_width/this.canvas_width);for(this.columns_per_canvas=Math.ceil(this.canvas_width/this.zoomed_column),this.previous_zoom!==this.zoom&&(this.dom_element.find("canvas").remove(),this.previous_zoom=this.zoom,this.rendered=[]),this.canvases=[],this.contexts=[],h=0;u>h;h++){var f=this.columns_per_canvas*h+c,_=f+this.columns_per_canvas-1;_>l&&(_=l);var d=(_-f+1)*this.zoomed_column;d>a&&(a=d);var p=a*h,m=p+d;if(m+m/2>r&&r>p-p/2)if(this.canvases[h]=n(this.dom_element,this.height,d,h,a),this.contexts[h]=this.canvases[h].getContext("2d"),this.contexts[h].setTransform(1,0,0,1,0,0),this.contexts[h].clearRect(0,0,d,this.height),this.contexts[h].fillStyle="#ffffff",this.contexts[h].fillRect(0,0,m,this.height),this.zoomed_column>12){var g=parseInt(10*e,10);g=g>10?10:g,this.debug&&o.call(this,f,_,h,1),i.call(this,f,_,h,g)}else o.call(this,f,_,h)}!this.scrollme&&this.options.scroller&&(this.scrollme=new EasyScroller(this.dom_element[0],{scrollingX:1,scrollingY:0,eventTarget:this.called_on})),1!==r&&this.scrollme.reflow()}}},{"./render_with_rects.js":27,"./render_with_text.js":28,jbone:7}],27:[function(t,e){function n(t,e,n,i,o,r,s,a){var l="#ffffff";a?(o>.1?l="#d7301f":o>.05?l="#fc8d59":o>.03&&(l="#fdcc8a"),t.fillStyle=l,t.fillRect(e,n+15,i,10),l="#ffffff",r>9?l="#d7301f":r>7?l="#fc8d59":r>4&&(l="#fdcc8a"),t.fillStyle=l,t.fillRect(e,n+30,i,10)):n+=30,l="#ffffff",.75>s?l="#2171b5":.85>s?l="#6baed6":.95>s&&(l="#bdd7e7"),t.fillStyle=l,t.fillRect(e,n,i,10)}var i=t("./draw/border.js"),o=t("./draw/ticks.js"),r=t("./draw/column_number.js");e.exports=function(t,e,s,a){var l=0,c=t,h=null,u=0,f=Math.abs(this.data.max_height),_=Math.abs(this.data.min_height_obs),d=f+_,p=Math.round(100*Math.abs(this.data.max_height)/d),m=Math.round(this.info_content_height*p/100),g=(this.info_content_height-m,10);for(u=t;e>=u;u++){if(this.data.mmline&&1===this.data.mmline[u-1])this.contexts[s].fillStyle="#cccccc",this.contexts[s].fillRect(l,10,this.zoomed_column,this.height-40);else{var v=this.data.heightArr[u-1],b=0,x=(v.length,0);for(var x in v)if(values=[x,v[x]],values[1]>.01){var y=parseFloat(values[1])/this.data.max_height,w=l,T=(this.info_content_height-2)*y,j=this.info_content_height-2-b-T,S=null;S="dynamic"===this.colorscheme?this.colors.getColor(values[0],{pos:u-1}):"consensus"===this.colorscheme?this.cmap[u-1][values[0]]||"#7a7a7a":this.colors[values[0]],a?(this.contexts[s].strokeStyle=S,this.contexts[s].strokeRect(w,j,this.zoomed_column,T)):(this.contexts[s].fillStyle=S,this.contexts[s].fillRect(w,j,this.zoomed_column,T)),b+=T}}this.zoom<.2?g=20:this.zoom<.3&&(g=10),this.options.positionMarker&&u%g===0&&(this.options.show_probs&&o(this.contexts[s],l+this.zoomed_column,this.height-30,parseFloat(this.height),"#dddddd"),o(this.contexts[s],l+this.zoomed_column,0,5),h=this.display_ali_map?this.data.ali_map[u-1]:c,r(this.contexts[s],l-2,10,this.zoomed_column,h,10,!0)),this.options.show_probs&&n(this.contexts[s],l,this.height-42,this.zoomed_column,this.data.insert_probs[u-1],this.data.insert_lengths[u-1],this.data.delete_probs[u-1],this.show_inserts),this.options.show_probs&&(this.show_inserts?i(this.contexts[s],this.height-45,this.total_width):i(this.contexts[s],this.height-15,this.total_width)),this.options.border&&i(this.contexts[s],0,this.total_width),l+=this.zoomed_column,c++}}},{"./draw/border.js":23,"./draw/column_number.js":24,"./draw/ticks.js":25}],28:[function(t,e){function n(t,e,n,o,r,s,a){var l=n-4,c="#ffffff",h="#555555";a&&(l=n-35),.75>r?(c="#2171b5",h="#ffffff"):.85>r?c="#6baed6":.95>r&&(c="#bdd7e7"),i(t,e,l,r,s,o,c,h)}function i(t,e,n,i,o,r,s,a){t.font=o+"px Arial",t.fillStyle=s,t.fillRect(e,n-10,r,14),t.textAlign="center",t.fillStyle=a,t.fillText(i,e+r/2,n)}function o(t,e){var n=e.ralign?e.x+t.zoomed_column:e.x,i=e.ralign?e.x+2:e.x;l(t.contexts[e.context_num],n,t.height-30,-30-t.height,"#dddddd"),l(t.contexts[e.context_num],n,0,5),c(t.contexts[e.context_num],i,10,t.zoomed_column,e.column_num,e.fontsize,e.ralign)}function r(t,e,n,o,r,s){var a=n-20,c="#ffffff",h="#555555";r>.1?(c="#d7301f",h="#ffffff"):r>.05?c="#fc8d59":r>.03&&(c="#fdcc8a"),i(t,e,a,r,s,o,c,h),r>.03&&l(t,e+o,n-30,