From e3c44cd51f1e860f0a34ec1a0bcb866eff492f70 Mon Sep 17 00:00:00 2001 From: James Taylor Date: Thu, 19 Mar 2009 21:36:48 -0400 Subject: [PATCH] Removing some files that are no longer used. --- static/dojo.js | 4698 ----------------------------- static/galaxyIndex.html | 25 - static/galaxyIndex.rst | 23 - static/index_frame_three_col.html | 11 - static/index_jt.css | 335 -- static/toolbox.js | 3 - static/universe.css | 180 -- static/universe.js | 163 - static/wipe.js | 95 - templates/history/list.mako | 196 -- templates/root/masthead.mako | 83 - 11 files changed, 5812 deletions(-) delete mode 100644 static/dojo.js delete mode 100644 static/galaxyIndex.html delete mode 100644 static/galaxyIndex.rst delete mode 100644 static/index_frame_three_col.html delete mode 100644 static/index_jt.css delete mode 100644 static/toolbox.js delete mode 100644 static/universe.css delete mode 100644 static/universe.js delete mode 100644 static/wipe.js delete mode 100644 templates/history/list.mako delete mode 100644 templates/root/masthead.mako diff --git a/static/dojo.js b/static/dojo.js deleted file mode 100644 index 26dfae205b7..00000000000 --- a/static/dojo.js +++ /dev/null @@ -1,4698 +0,0 @@ -/* Copyright (c) 2004-2005 The Dojo Foundation, Licensed under the Academic Free License version 2.1 or above *//* This is a compiled version of Dojo, designed for deployment and not for development. If would like to modify or work with Dojo, please visit http://dojotoolkit.org for more information and to get the 'source' version of this file. */var dj_global=this; -function dj_undef(_1,_2){ -if(!_2){ -_2=dj_global; -} -return (typeof _2[_1]=="undefined"); -} -if(dj_undef("djConfig")){ -var djConfig={}; -} -var dojo; -if(dj_undef("dojo")){ -dojo={}; -} -dojo.version={major:0,minor:1,patch:0,flag:"+",revision:Number("$Rev: 1885 $".match(/[0-9]+/)[0]),toString:function(){ -with(dojo.version){ -return major+"."+minor+"."+patch+flag+" ("+revision+")"; -} -}}; -dojo.evalObjPath=function(_3,_4){ -if(typeof _3!="string"){ -return dj_global; -} -if(_3.indexOf(".")==-1){ -if(dj_undef(_3,dj_global)){ -dj_global[_3]={}; -} -return dj_global[_3]; -} -var _5=_3.split(/\./); -var _6=dj_global; -for(var i=0;i<_5.length;++i){ -if(!_4){ -_6=_6[_5[i]]; -if((typeof _6=="undefined")||(!_6)){ -return _6; -} -}else{ -if(dj_undef(_5[i],_6)){ -_6[_5[i]]={}; -} -_6=_6[_5[i]]; -} -} -return _6; -}; -dojo.errorToString=function(_8){ -return ((!dj_undef("message",_8))?_8.message:(dj_undef("description",_8)?_8:_8.description)); 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-for(var i=0;i=_199.length)){ -_197.appendChild(node); -return; -} -for(var i=0;i<_199.length;i++){ -if((_199.item(i)["getAttribute"])&&(parseInt(_199.item(i).getAttribute("dojoinsertionindex"))>_198)){ -dojo.dom.insertBefore(node,_199.item(i)); -_200=true; -break; -} -} -if(!_200){ -dojo.dom.insertBefore(node,_197); -} -}; -dojo.dom.textContent=function(node,text){ -if(text){ -dojo.dom.replaceChildren(node,document.createTextNode(text)); -return text; -}else{ -var _202=""; -if(node==null){ -return _202; -} -for(var i=0;i"); -} -} -catch(e){ -} -dojo.io.checkChildrenForFile=function(node){ -var _205=false; -var _206=node.getElementsByTagName("input"); -dojo.lang.forEach(_206,function(_207){ -if(_205){ -return; -} -if(_207.getAttribute("type")=="file"){ -_205=true; -} -}); -return _205; -}; -dojo.io.formHasFile=function(_208){ -return dojo.io.checkChildrenForFile(_208); -}; -dojo.io.encodeForm=function(_209,_210){ -if((!_209)||(!_209.tagName)||(!_209.tagName.toLowerCase()=="form")){ -dojo.raise("Attempted to encode a non-form element."); -} -var enc=/utf/i.test(_210||"")?encodeURIComponent:dojo.string.encodeAscii; -var _211=[]; -for(var i=0;i<_209.elements.length;i++){ -var elm=_209.elements[i]; -if(elm.disabled||elm.tagName.toLowerCase()=="fieldset"){ -continue; -} -var name=enc(elm.name); -var type=elm.type.toLowerCase(); -if(type=="select-multiple"){ -for(var j=0;j=0){ -while(!this.historyStack[hsl]["urlHash"]){ -hsl--; -} -lh=this.historyStack[hsl]["urlHash"]; -} -if(lh){ -_238=function(){ -if(window.location.hash!=""){ -setTimeout("window.location.href = '"+lh+"';",1); -} -_240(); -}; -} -this.forwardStack=[]; -var _243=args["forward"]||args["forwardButton"]; -var tfw=function(){ -if(window.location.hash!=""){ -window.location.href=hash; -} -if(_243){ -_243(); -} -}; -if(args["forward"]){ -args.forward=tfw; -}else{ -if(args["forwardButton"]){ -args.forwardButton=tfw; -} -} -}else{ -if(dojo.render.html.moz){ -if(!this.locationTimer){ -this.locationTimer=setInterval("dojo.io.XMLHTTPTransport.checkLocation();",200); -} -} -} -} -this.historyStack.push({"url":url,"callback":_238,"kwArgs":args,"urlHash":hash}); -}; -this.checkLocation=function(){ -var hsl=this.historyStack.length; -if((window.location.hash==this.initialHash)||(window.location.href==this.initialHref)&&(hsl==1)){ -this.handleBackButton(); -return; -} -if(this.forwardStack.length>0){ -if(this.forwardStack[this.forwardStack.length-1].urlHash==window.location.hash){ -this.handleForwardButton(); -return; -} -} -if((hsl>=2)&&(this.historyStack[hsl-2])){ -if(this.historyStack[hsl-2].urlHash==window.location.hash){ -this.handleBackButton(); -return; -} -} -}; -this.iframeLoaded=function(evt,_245){ -var isp=_245.href.split("?"); -if(isp.length<2){ -if(this.historyStack.length==1){ -this.handleBackButton(); -} -return; -} -var _247=isp[1]; -if(this.moveForward){ -this.moveForward=false; -return; -} -var last=this.historyStack.pop(); -if(!last){ -if(this.forwardStack.length>0){ -var next=this.forwardStack[this.forwardStack.length-1]; -if(_247==next.url.split("?")[1]){ -this.handleForwardButton(); -} -} -return; -} -this.historyStack.push(last); -if(this.historyStack.length>=2){ -if(isp[1]==this.historyStack[this.historyStack.length-2].url.split("?")[1]){ -this.handleBackButton(); -} -}else{ -this.handleBackButton(); -} -}; -this.handleBackButton=function(){ -var last=this.historyStack.pop(); -if(!last){ -return; -} -if(last["callback"]){ -last.callback(); -}else{ -if(last.kwArgs["backButton"]){ -last.kwArgs["backButton"](); -}else{ -if(last.kwArgs["back"]){ -last.kwArgs["back"](); -}else{ -if(last.kwArgs["handle"]){ -last.kwArgs.handle("back"); -} -} -} -} -this.forwardStack.push(last); -}; -this.handleForwardButton=function(){ -var last=this.forwardStack.pop(); -if(!last){ -return; -} -if(last.kwArgs["forward"]){ -last.kwArgs.forward(); -}else{ -if(last.kwArgs["forwardButton"]){ -last.kwArgs.forwardButton(); -}else{ -if(last.kwArgs["handle"]){ -last.kwArgs.handle("forward"); -} -} -} -this.historyStack.push(last); -}; -this.inFlight=[]; -this.inFlightTimer=null; -this.startWatchingInFlight=function(){ -if(!this.inFlightTimer){ -this.inFlightTimer=setInterval("dojo.io.XMLHTTPTransport.watchInFlight();",10); -} -}; -this.watchInFlight=function(){ -for(var x=this.inFlight.length-1;x>=0;x--){ -var tif=this.inFlight[x]; -if(!tif){ -this.inFlight.splice(x,1); -continue; -} -if(4==tif.http.readyState){ -this.inFlight.splice(x,1); -doLoad(tif.req,tif.http,tif.url,tif.query,tif.useCache); -if(this.inFlight.length==0){ -clearInterval(this.inFlightTimer); -this.inFlightTimer=null; -} -} -} -}; -var _251=dojo.hostenv.getXmlhttpObject()?true:false; -this.canHandle=function(_252){ -return _251&&dojo.lang.inArray(_252["mimetype"],["text/plain","text/html","application/xml","text/xml","text/javascript"])&&dojo.lang.inArray(_252["method"].toLowerCase(),["post","get","head"])&&!(_252["formNode"]&&dojo.io.formHasFile(_252["formNode"])); -}; -this.bind=function(_253){ -if(!_253["url"]){ -if(!_253["formNode"]&&(_253["backButton"]||_253["back"]||_253["changeUrl"]||_253["watchForURL"])&&(!djConfig.preventBackButtonFix)){ -this.addToHistory(_253); -return true; -} -} -var url=_253.url; -var _254=""; -if(_253["formNode"]){ -var ta=_253.formNode.getAttribute("action"); -if((ta)&&(!_253["url"])){ -url=ta; -} -var tp=_253.formNode.getAttribute("method"); -if((tp)&&(!_253["method"])){ -_253.method=tp; -} -_254+=dojo.io.encodeForm(_253.formNode,_253.encoding); -} -if(!_253["method"]){ -_253.method="get"; -} -if(_253["content"]){ -_254+=dojo.io.argsFromMap(_253.content,_253.encoding); -} -if(_253["postContent"]&&_253.method.toLowerCase()=="post"){ -_254=_253.postContent; -} -if(_253["backButton"]||_253["back"]||_253["changeUrl"]){ -this.addToHistory(_253); -} -var _257=_253["sync"]?false:true; -var _258=_253["useCache"]==true||(this.useCache==true&&_253["useCache"]!=false); -if(_258){ -var _259=getFromCache(url,_254,_253.method); -if(_259){ -doLoad(_253,_259,url,_254,false); -return; -} -} -var http=dojo.hostenv.getXmlhttpObject(); -var _260=false; -if(_257){ -this.inFlight.push({"req":_253,"http":http,"url":url,"query":_254,"useCache":_258}); -this.startWatchingInFlight(); -} -if(_253.method.toLowerCase()=="post"){ -http.open("POST",url,_257); -setHeaders(http,_253); -http.setRequestHeader("Content-Type",_253["contentType"]||"application/x-www-form-urlencoded"); -http.send(_254); -}else{ -var _261=url; -if(_254!=""){ -_261+=(url.indexOf("?")>-1?"&":"?")+_254; -} -http.open(_253.method.toUpperCase(),_261,_257); -setHeaders(http,_253); -http.send(null); -} -if(!_257){ -doLoad(_253,http,url,_254,_258); -} -return; -}; -dojo.io.transports.addTransport("XMLHTTPTransport"); -}; -dojo.require("dojo.lang"); -dojo.provide("dojo.event"); -dojo.event=new function(){ -var _262=0; -this.anon={}; -this.canTimeout=dojo.lang.isFunction(dj_global["setTimeout"])||dojo.lang.isAlien(dj_global["setTimeout"]); -this.nameAnonFunc=function(_263,_264){ -var nso=(_264||this.anon); -if((dj_global["djConfig"])&&(djConfig["slowAnonFuncLookups"]==true)){ -for(var x in nso){ -if(nso[x]===_263){ -dojo.debug(x); -return x; -} -} -} -var ret="__"+_262++; -while(typeof nso[ret]!="undefined"){ -ret="__"+_262++; -} -nso[ret]=_263; -return ret; -}; -this.createFunctionPair=function(obj,cb){ -var ret=[]; -if(typeof obj=="function"){ -ret[1]=dojo.event.nameAnonFunc(obj,dj_global); -ret[0]=dj_global; -return ret; -}else{ -if((typeof obj=="object")&&(typeof cb=="string")){ -return [obj,cb]; -}else{ -if((typeof obj=="object")&&(typeof cb=="function")){ -ret[1]=dojo.event.nameAnonFunc(cb,obj); -ret[0]=obj; -return ret; -} -} -} -return null; -}; -this.matchSignature=function(args,_266){ -var end=Math.min(args.length,_266.length); -for(var x=0;x2)?args[0]:"after",precedence:"last",once:false,delay:null,rate:0}; -switch(args.length){ -case 0: -return; -case 1: -return; -case 2: -ao.srcFunc=args[0]; -ao.adviceFunc=args[1]; -break; -case 3: -if((typeof args[0]=="object")&&(typeof args[1]=="string")&&(typeof args[2]=="string")){ -ao.adviceType="after"; -ao.srcObj=args[0]; -ao.srcFunc=args[1]; -ao.adviceFunc=args[2]; -}else{ -if((typeof args[1]=="string")&&(typeof args[2]=="string")){ -ao.srcFunc=args[1]; -ao.adviceFunc=args[2]; -}else{ -if((typeof args[0]=="object")&&(typeof args[1]=="string")&&(typeof args[2]=="function")){ -ao.adviceType="after"; -ao.srcObj=args[0]; -ao.srcFunc=args[1]; -var _269=dojo.event.nameAnonFunc(args[2],ao.adviceObj); -ao.adviceObj[_269]=args[2]; -ao.adviceFunc=_269; -}else{ -if((typeof args[0]=="function")&&(typeof args[1]=="object")&&(typeof args[2]=="string")){ -ao.adviceType="after"; -ao.srcObj=dj_global; -var _269=dojo.event.nameAnonFunc(args[0],ao.srcObj); -ao.srcObj[_269]=args[0]; -ao.srcFunc=_269; -ao.adviceObj=args[1]; -ao.adviceFunc=args[2]; -} -} -} -} -break; -case 4: -if((typeof args[0]=="object")&&(typeof args[2]=="object")){ -ao.adviceType="after"; -ao.srcObj=args[0]; -ao.srcFunc=args[1]; -ao.adviceObj=args[2]; -ao.adviceFunc=args[3]; -}else{ -if((typeof args[1]).toLowerCase()=="object"){ -ao.srcObj=args[1]; -ao.srcFunc=args[2]; -ao.adviceObj=dj_global; -ao.adviceFunc=args[3]; -}else{ -if((typeof args[2]).toLowerCase()=="object"){ -ao.srcObj=dj_global; -ao.srcFunc=args[1]; -ao.adviceObj=args[2]; -ao.adviceFunc=args[3]; -}else{ -ao.srcObj=ao.adviceObj=ao.aroundObj=dj_global; -ao.srcFunc=args[1]; -ao.adviceFunc=args[2]; -ao.aroundFunc=args[3]; -} -} -} -break; -case 6: -ao.srcObj=args[1]; -ao.srcFunc=args[2]; -ao.adviceObj=args[3]; -ao.adviceFunc=args[4]; -ao.aroundFunc=args[5]; -ao.aroundObj=dj_global; -break; -default: -ao.srcObj=args[1]; -ao.srcFunc=args[2]; -ao.adviceObj=args[3]; -ao.adviceFunc=args[4]; -ao.aroundObj=args[5]; -ao.aroundFunc=args[6]; -ao.once=args[7]; -ao.delay=args[8]; -ao.rate=args[9]; -break; -} -if((typeof ao.srcFunc).toLowerCase()!="string"){ -ao.srcFunc=dojo.lang.getNameInObj(ao.srcObj,ao.srcFunc); -} -if((typeof ao.adviceFunc).toLowerCase()!="string"){ -ao.adviceFunc=dojo.lang.getNameInObj(ao.adviceObj,ao.adviceFunc); -} -if((ao.aroundObj)&&((typeof ao.aroundFunc).toLowerCase()!="string")){ -ao.aroundFunc=dojo.lang.getNameInObj(ao.aroundObj,ao.aroundFunc); -} -if(!ao.srcObj){ -dojo.raise("bad srcObj for srcFunc: "+ao.srcFunc); -} -if(!ao.adviceObj){ -dojo.raise("bad adviceObj for adviceFunc: "+ao.adviceFunc); -} -return ao; -} -this.connect=function(){ -var ao=interpolateArgs(arguments); -var mjp=dojo.event.MethodJoinPoint.getForMethod(ao.srcObj,ao.srcFunc); -if(ao.adviceFunc){ -var mjp2=dojo.event.MethodJoinPoint.getForMethod(ao.adviceObj,ao.adviceFunc); -} -mjp.kwAddAdvice(ao); -return mjp; -}; -this.connectBefore=function(){ -var args=["before"]; -for(var i=0;i=this.jp_.around.length){ -return this.jp_.object[this.jp_.methodname].apply(this.jp_.object,this.args); -}else{ -var ti=this.jp_.around[this.around_index]; -var mobj=ti[0]||dj_global; -var meth=ti[1]; -return mobj[meth].call(mobj,this); -} -}; -dojo.event.MethodJoinPoint=function(obj,_280){ -this.object=obj||dj_global; -this.methodname=_280; -this.methodfunc=this.object[_280]; -this.before=[]; -this.after=[]; -this.around=[]; -}; -dojo.event.MethodJoinPoint.getForMethod=function(obj,_281){ -if(!obj){ -obj=dj_global; -} -if(!obj[_281]){ -obj[_281]=function(){ -}; -}else{ -if((!dojo.lang.isFunction(obj[_281]))&&(!dojo.lang.isAlien(obj[_281]))){ -return null; -} -} -var _282=_281+"$joinpoint"; -var _283=_281+"$joinpoint$method"; -var _284=obj[_282]; -if(!_284){ -var _285=false; -if(dojo.event["browser"]){ -if((obj["attachEvent"])||(obj["nodeType"])||(obj["addEventListener"])){ -_285=true; -dojo.event.browser.addClobberNodeAttrs(obj,[_282,_283,_281]); -} -} -obj[_283]=obj[_281]; -_284=obj[_282]=new dojo.event.MethodJoinPoint(obj,_283); -obj[_281]=function(){ -var args=[]; -if((_285)&&(!arguments.length)&&(window.event)){ -args.push(dojo.event.browser.fixEvent(window.event)); -}else{ -for(var x=0;x0){ -dojo.lang.forEach(this.before,_287,true); -} -var _302; -if(this.around.length>0){ -var mi=new dojo.event.MethodInvocation(this,obj,args); -_302=mi.proceed(); -}else{ -if(this.methodfunc){ -_302=this.object[this.methodname].apply(this.object,args); -} -} -if(this.after.length>0){ -dojo.lang.forEach(this.after,_287,true); -} -return (this.methodfunc)?_302:null; -}; -dojo.event.MethodJoinPoint.prototype.getArr=function(kind){ -var arr=this.after; -if((typeof kind=="string")&&(kind.indexOf("before")!=-1)){ -arr=this.before; -}else{ -if(kind=="around"){ -arr=this.around; -} -} -return arr; -}; -dojo.event.MethodJoinPoint.prototype.kwAddAdvice=function(args){ -this.addAdvice(args["adviceObj"],args["adviceFunc"],args["aroundObj"],args["aroundFunc"],args["adviceType"],args["precedence"],args["once"],args["delay"],args["rate"]); -}; -dojo.event.MethodJoinPoint.prototype.addAdvice=function(_305,_306,_307,_308,_309,_310,once,_312,rate){ -var arr=this.getArr(_309); -if(!arr){ -dojo.raise("bad this: "+this); -} -var ao=[_305,_306,_307,_308,_312,rate]; -if(once){ -if(this.hasAdvice(_305,_306,_309,arr)>=0){ -return; -} -} -if(_310=="first"){ -arr.unshift(ao); -}else{ -arr.push(ao); -} -}; -dojo.event.MethodJoinPoint.prototype.hasAdvice=function(_313,_314,_315,arr){ -if(!arr){ -arr=this.getArr(_315); -} -var ind=-1; -for(var x=0;x=0;i=i-1){ -var el=na[i]; -if(djConfig.ieClobberMinimal){ -if(el["__clobberAttrs__"]){ -for(var j=0;j=0;p=p-1){ -var ta=this.clobberArr[p]; -nukeProp(el,ta); -} -} -} -na=null; -}; -}; -if((dojo.render.html.ie)&&((!dojo.hostenv.ie_prevent_clobber_)||(djConfig.ieClobberMinimal))){ -window.onunload=function(){ -dojo_ie_clobber.clobber(); -try{ -if((dojo["widget"])&&(dojo.widget["manager"])){ -dojo.widget.manager.destroyAll(); -} -} -catch(e){ -} -try{ -window.onload=null; -} -catch(e){ -} -try{ -window.onunload=null; -} -catch(e){ -} -dojo_ie_clobber.clobberNodes=[]; -}; -} -dojo.event.browser=new function(){ -var _346=0; -this.clean=function(node){ -if(dojo.render.html.ie){ -dojo_ie_clobber.clobber(node); -} -}; -this.addClobberAttr=function(type){ -dojo_ie_clobber.addClobberAttr(type); -}; -this.addClobberAttrs=function(){ -for(var x=0;x0&&!(j==1&&segs[0]=="")&&segs[j]==".."&&segs[j-1]!=".."){ -if(j==segs.length-1){ -segs.splice(j,1); -segs[j-1]=""; -}else{ -segs.splice(j-1,2); -j-=2; -} -} -} -} -_365.path=segs.join("/"); -} -} -} -} -uri=""; -if(_365.scheme!=null){ -uri+=_365.scheme+":"; -} -if(_365.authority!=null){ -uri+="//"+_365.authority; -} -uri+=_365.path; -if(_365.query!=null){ -uri+="?"+_365.query; -} -if(_365.fragment!=null){ -uri+="#"+_365.fragment; -} -} -this.uri=uri.toString(); -var _369="^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\\?([^#]*))?(#(.*))?$"; -var r=this.uri.match(new RegExp(_369)); -this.scheme=r[2]||(r[1]?"":null); -this.authority=r[4]||(r[3]?"":null); -this.path=r[5]; -this.query=r[7]||(r[6]?"":null); -this.fragment=r[9]||(r[8]?"":null); -if(this.authority!=null){ -_369="^((([^:]+:)?([^@]+))@)?([^:]*)(:([0-9]+))?$"; -r=this.authority.match(new RegExp(_369)); -this.user=r[3]||null; -this.password=r[4]||null; -this.host=r[5]; -this.port=r[7]||null; -} -this.toString=function(){ -return this.uri; -}; -}; -}; -dojo.provide("dojo.math"); -dojo.math.degToRad=function(x){ -return (x*Math.PI)/180; -}; -dojo.math.radToDeg=function(x){ -return (x*180)/Math.PI; -}; -dojo.math.factorial=function(n){ -if(n<1){ -return 0; -} -var _371=1; -for(var i=1;i<=n;i++){ -_371*=i; -} -return _371; -}; -dojo.math.permutations=function(n,k){ -if(n==0||k==0){ -return 1; -} -return (dojo.math.factorial(n)/dojo.math.factorial(n-k)); -}; -dojo.math.combinations=function(n,r){ -if(n==0||r==0){ -return 1; -} -return (dojo.math.factorial(n)/(dojo.math.factorial(n-r)*dojo.math.factorial(r))); -}; -dojo.math.bernstein=function(t,n,i){ -return (dojo.math.combinations(n,i)*Math.pow(t,i)*Math.pow(1-t,n-i)); -}; -dojo.math.gaussianRandom=function(){ -var k=2; -do{ -var i=2*Math.random()-1; -var j=2*Math.random()-1; -k=i*i+j*j; -}while(k>=1); -k=Math.sqrt((-2*Math.log(k))/k); -return i*k; -}; -dojo.math.mean=function(){ -var _373=dojo.lang.isArray(arguments[0])?arguments[0]:arguments; -var mean=0; -for(var i=0;i<_373.length;i++){ -mean+=_373[i]; -} -return mean/_373.length; -}; -dojo.math.round=function(_375,_376){ -if(!_376){ -var _377=1; -}else{ -var _377=Math.pow(10,_376); -} -return Math.round(_375*_377)/_377; -}; -dojo.math.sd=function(){ -var _378=dojo.lang.isArray(arguments[0])?arguments[0]:arguments; -return Math.sqrt(dojo.math.variance(_378)); -}; -dojo.math.variance=function(){ -var _379=dojo.lang.isArray(arguments[0])?arguments[0]:arguments; -var mean=0,squares=0; -for(var i=0;i<_379.length;i++){ -mean+=_379[i]; -squares+=Math.pow(_379[i],2); -} -return (squares/_379.length)-Math.pow(mean/_379.length,2); -}; -dojo.provide("dojo.graphics.color"); -dojo.require("dojo.lang"); -dojo.require("dojo.math"); -dojo.graphics.color.Color=function(r,g,b,a){ -if(dojo.lang.isArray(r)){ -this.r=r[0]; -this.g=r[1]; -this.b=r[2]; -this.a=r[3]||1; -}else{ -if(dojo.lang.isString(r)){ -var rgb=dojo.graphics.color.extractRGB(r); -this.r=rgb[0]; -this.g=rgb[1]; -this.b=rgb[2]; -this.a=g||1; -}else{ -if(r instanceof dojo.graphics.color.Color){ -this.r=r.r; -this.b=r.b; -this.g=r.g; -this.a=r.a; -}else{ -this.r=r; -this.g=g; -this.b=b; -this.a=a; -} -} -} -}; -dojo.graphics.color.Color.prototype.toRgb=function(_383){ -if(_383){ -return this.toRgba(); -}else{ -return [this.r,this.g,this.b]; -} -}; -dojo.graphics.color.Color.prototype.toRgba=function(){ -return [this.r,this.g,this.b,this.a]; -}; -dojo.graphics.color.Color.prototype.toHex=function(){ -return dojo.graphics.color.rgb2hex(this.toRgb()); -}; -dojo.graphics.color.Color.prototype.toCss=function(){ -return "rgb("+this.toRgb().join()+")"; -}; -dojo.graphics.color.Color.prototype.toString=function(){ -return this.toHex(); -}; -dojo.graphics.color.Color.prototype.toHsv=function(){ -return dojo.graphics.color.rgb2hsv(this.toRgb()); -}; -dojo.graphics.color.Color.prototype.toHsl=function(){ -return dojo.graphics.color.rgb2hsl(this.toRgb()); -}; -dojo.graphics.color.Color.prototype.blend=function(_384,_385){ -return dojo.graphics.color.blend(this.toRgb(),new Color(_384).toRgb(),_385); -}; -dojo.graphics.color.named={white:[255,255,255],black:[0,0,0],red:[255,0,0],green:[0,255,0],blue:[0,0,255],navy:[0,0,128],gray:[128,128,128],silver:[192,192,192]}; -dojo.graphics.color.blend=function(a,b,_386){ -if(typeof a=="string"){ -return dojo.graphics.color.blendHex(a,b,_386); -} -if(!_386){ -_386=0; -}else{ -if(_386>1){ -_386=1; -}else{ -if(_386<-1){ -_386=-1; -} -} -} -var c=new Array(3); -for(var i=0;i<3;i++){ -var half=Math.abs(a[i]-b[i])/2; -c[i]=Math.floor(Math.min(a[i],b[i])+half+(half*_386)); -} -return c; -}; -dojo.graphics.color.blendHex=function(a,b,_389){ -return dojo.graphics.color.rgb2hex(dojo.graphics.color.blend(dojo.graphics.color.hex2rgb(a),dojo.graphics.color.hex2rgb(b),_389)); -}; -dojo.graphics.color.extractRGB=function(_390){ -var hex="0123456789abcdef"; -_390=_390.toLowerCase(); -if(_390.indexOf("rgb")==0){ -dojo.debug("e1"); -var _392=_390.match(/rgba*\((\d+), *(\d+), *(\d+)/i); -var ret=_392.splice(1,3); -return ret; -}else{ -var _393=dojo.graphics.color.hex2rgb(_390); -if(_393){ -return _393; -}else{ -return dojo.graphics.color.named[_390]||[255,255,255]; -} -} -}; -dojo.graphics.color.hex2rgb=function(hex){ -var _394="0123456789ABCDEF"; -var rgb=new Array(3); -if(hex.indexOf("#")==0){ -hex=hex.substring(1); -} -hex=hex.toUpperCase(); -if(hex.replace(new RegExp("["+_394+"]","g"),"")!=""){ -return null; -} -if(hex.length==3){ -rgb[0]=hex.charAt(0)+hex.charAt(0); -rgb[1]=hex.charAt(1)+hex.charAt(1); -rgb[2]=hex.charAt(2)+hex.charAt(2); -}else{ -rgb[0]=hex.substring(0,2); -rgb[1]=hex.substring(2,4); -rgb[2]=hex.substring(4); -} -for(var i=0;i0)&&(l<1)){ -s=_403/((l<0.5)?(2*l):(2-2*l)); -} -h=0; -if(_403>0){ -if((max==r)&&(max!=g)){ -h+=(g-b)/_403; -} -if((max==g)&&(max!=b)){ -h+=(2+(b-r)/_403); -} -if((max==b)&&(max!=r)){ -h+=(4+(r-g)/_403); -} -h*=60; -} -h=(h==0)?360:Math.ceil((h/360)*255); -s=Math.ceil(s*255); -l=Math.ceil(l*255); -return [h,s,l]; -}; -dojo.graphics.color.hsl2rgb=function(h,s,l){ -if(dojo.lang.isArray(h)){ -l=h[2]||0; -s=h[1]||0; -h=h[0]||0; -} -h=(h/255)*360; -if(h==360){ -h=0; -} -s=s/255; -l=l/255; -while(h<0){ -h+=360; -} -while(h>360){ -h-=360; -} -if(h<120){ -r=(120-h)/60; -g=h/60; -b=0; -}else{ -if(h<240){ -r=0; -g=(240-h)/60; -b=(h-120)/60; -}else{ -r=(h-240)/60; -g=0; -b=(360-h)/60; -} -} -r=Math.min(r,1); -g=Math.min(g,1); -b=Math.min(b,1); -r=2*s*r+(1-s); -g=2*s*g+(1-s); -b=2*s*b+(1-s); -if(l<0.5){ -r=l*r; -g=l*g; -b=l*b; -}else{ -r=(1-l)*r+2*l-1; -g=(1-l)*g+2*l-1; -b=(1-l)*b+2*l-1; -} -r=Math.ceil(r*255); -g=Math.ceil(g*255); -b=Math.ceil(b*255); -return [r,g,b]; -}; -dojo.provide("dojo.style"); -dojo.require("dojo.dom"); -dojo.require("dojo.uri.Uri"); -dojo.require("dojo.graphics.color"); -dojo.style.boxSizing={marginBox:"margin-box",borderBox:"border-box",paddingBox:"padding-box",contentBox:"content-box"}; -dojo.style.getBoxSizing=function(node){ -if(dojo.render.html.ie||dojo.render.html.opera){ -var cm=document["compatMode"]; -if(cm=="BackCompat"||cm=="QuirksMode"){ -return dojo.style.boxSizing.borderBox; -}else{ -return dojo.style.boxSizing.contentBox; -} -}else{ -if(arguments.length==0){ -node=document.documentElement; -} -var _405=dojo.style.getStyle(node,"-moz-box-sizing"); -if(!_405){ -_405=dojo.style.getStyle(node,"box-sizing"); -} -return (_405?_405:dojo.style.boxSizing.contentBox); -} -}; -dojo.style.isBorderBox=function(node){ -return (dojo.style.getBoxSizing(node)==dojo.style.boxSizing.borderBox); -}; -dojo.style.getUnitValue=function(_406,_407,_408){ -var _409={value:0,units:"px"}; -var s=dojo.style.getComputedStyle(_406,_407); -if(s==""||(s=="auto"&&_408)){ -return _409; -} -if(dojo.lang.isUndefined(s)){ -_409.value=NaN; -}else{ -var _410=s.match(/([\d.]+)([a-z%]*)/i); -if(!_410){ -_409.value=NaN; -}else{ -_409.value=Number(_410[1]); -_409.units=_410[2].toLowerCase(); -} -} -return _409; 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-var _419=dojo.style.getPixelValue(node,"padding-right",true); -return left+_419; -}; -dojo.style.getContentWidth=function(node){ -return node.offsetWidth-dojo.style.getPaddingWidth(node)-dojo.style.getBorderWidth(node); -}; -dojo.style.getInnerWidth=function(node){ -return node.offsetWidth; -}; -dojo.style.getOuterWidth=function(node){ -return dojo.style.getInnerWidth(node)+dojo.style.getMarginWidth(node); -}; -dojo.style.setOuterWidth=function(node,_420){ -if(!dojo.style.isBorderBox(node)){ -_420-=dojo.style.getPaddingWidth(node)+dojo.style.getBorderWidth(node); -} -_420-=dojo.style.getMarginWidth(node); -if(!isNaN(_420)&&_420>0){ -node.style.width=_420+"px"; -return true; -}else{ -return false; -} -}; -dojo.style.getContentBoxWidth=dojo.style.getContentWidth; -dojo.style.getBorderBoxWidth=dojo.style.getInnerWidth; -dojo.style.getMarginBoxWidth=dojo.style.getOuterWidth; -dojo.style.setMarginBoxWidth=dojo.style.setOuterWidth; -dojo.style.getMarginHeight=function(node){ -var _421=dojo.style.isPositionAbsolute(node); 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-}else{ -if(dojo.render.html.ie){ -_460.unselectable="on"; -} -} -} -}; -dojo.html.enableSelection=function(_461){ -if(arguments.length==0){ -_461=dojo.html.body(); -} -if(dojo.render.html.mozilla){ -_461.style.MozUserSelect=""; -}else{ -if(dojo.render.html.safari){ -_461.style.KhtmlUserSelect=""; -}else{ -if(dojo.render.html.ie){ -_461.unselectable="off"; -} -} -} -}; -dojo.html.selectElement=function(_462){ -if(document.selection&&dojo.html.body().createTextRange){ -var _463=dojo.html.body().createTextRange(); -_463.moveToElementText(_462); -_463.select(); -}else{ -if(window.getSelection){ -var _464=window.getSelection(); -if(_464.selectAllChildren){ -_464.selectAllChildren(_462); -} -} -} -}; -dojo.html.isSelectionCollapsed=function(){ -if(document.selection){ -return document.selection.createRange().text==""; -}else{ -if(window.getSelection){ -var _465=window.getSelection(); -if(dojo.lang.isString(_465)){ -return _465==""; -}else{ -return _465.isCollapsed; -} -} -} -}; -dojo.html.getEventTarget=function(evt){ -if((window["event"])&&(window.event["srcElement"])){ -return window.event.srcElement; 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-dojo.hostenv.conditionalLoadModule({browser:["dojo.fx.html"]}); -dojo.hostenv.moduleLoaded("dojo.fx.*"); -dojo.provide("dojo.graphics.htmlEffects"); -dojo.require("dojo.fx.*"); -dj_deprecated("dojo.graphics.htmlEffects is deprecated, use dojo.fx.html instead"); -dojo.graphics.htmlEffects=dojo.fx.html; -dojo.hostenv.conditionalLoadModule({browser:["dojo.graphics.htmlEffects"]}); -dojo.hostenv.moduleLoaded("dojo.graphics.*"); - diff --git a/static/galaxyIndex.html b/static/galaxyIndex.html deleted file mode 100644 index 40378df0361..00000000000 --- a/static/galaxyIndex.html +++ /dev/null @@ -1,25 +0,0 @@ - - - - - - -Welcome to Galaxy - - - - -
-

Welcome to Galaxy

-

Galaxy is a web-based data analysis framework for comparative genomics. It exists in two flavors:

-
    -
  • Galaxy2 - features genomic datasets and allows various operations on genomic coordinates
    • -
  • Galaxy1 - the old version that is still maintained but not actively developed
    • -
-
-

Galaxy aims to be a zero configuration entirely self contained system, that provides a lightweight webserver, an embedded database and a multi-threaded job manager. Tools (and their parameters) can be specified via simple XML based configuration files. Galaxy allows you to deploy a wide variety of bioinformatics tools through the web. It renders all HTML widgets the tools need, verifies inputs, and stores and manages the outputs that these tools create.

-
-

The Center for Comparative Genomics and Bioinformatics at Penn State | 2005

-
- - diff --git a/static/galaxyIndex.rst b/static/galaxyIndex.rst deleted file mode 100644 index f48eac8eed1..00000000000 --- a/static/galaxyIndex.rst +++ /dev/null @@ -1,23 +0,0 @@ -Welcome to Galaxy -================= - -Galaxy is a web-based data analysis framework for comparative genomics. It exists in two flavors: - -* `Galaxy2`__ - features genomic datasets and allows various operations on genomic coordinates -* `Galaxy1`__ - the old version that is still maintained but not actively developed - -.. __: http://g2.bx.psu.edu:9000 - -.. __: http://galaxy.cse.psu.edu - - ------ - -Galaxy aims to be a zero configuration entirely self contained system, that provides a lightweight webserver, an embedded database and a multi-threaded job manager. Tools (and their parameters) can be specified via simple XML based configuration files. Galaxy allows you to deploy a wide variety of bioinformatics tools through the web. It renders all HTML widgets the tools need, verifies inputs, and stores and manages the outputs that these tools create. - ------ - -`The Center for Comparative Genomics and Bioinformatics`__ at `Penn State`__ | 2005 - -.. __: http://www.bx.psu.edu -.. __: http://www.psu.edu \ No newline at end of file diff --git a/static/index_frame_three_col.html b/static/index_frame_three_col.html deleted file mode 100644 index 3e2764bcebe..00000000000 --- a/static/index_frame_three_col.html +++ /dev/null @@ -1,11 +0,0 @@ - - - -Galaxy - - - - - - - \ No newline at end of file diff --git a/static/index_jt.css b/static/index_jt.css deleted file mode 100644 index 7ddc415e16d..00000000000 --- a/static/index_jt.css +++ /dev/null @@ -1,335 +0,0 @@ -body -{ - margin: 0; - padding: 0; - border: 0; - font: smaller verdana, "Bitstream Vera Sans", geneva, arial, helvetica, helve, sans-serif; - background: #3690c0; -} - -body.toolMenuPage -{ - background: #045a8d; - color: #d0d1e6; - /*background-image: url(/static/images/toolsExpandingMenu.gif);*/ - background-repeat: no-repeat; 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- margin-left: 30px; -} - -.tool_name a { - font-weight: bold; -} - -.tool_form { - background-color: #FFFFCC; - border: 1px solid #EEEEEE; - margin: 5px; -} - -.info { - color: #990000; - font-style: italic; -} - -.border { - border: 1px solid #8cacbb; - background: #FFFFFF; -} - -.rline { - border-bottom: 1px solid #EEEEEE; -} - -.bline { - border-bottom: 1px solid #999999; -} - -.tline { - padding-top: 5pt; - border-top: 1px solid #999999; -} - -.grey { - border: 1px #FFFFFF solid; -} - -.greyborder { - background: #EFEFEF; - border: 1px #CCCCCC solid; -} - -.big { font-size: large; font-weight: bold; color: #000066} -.mark {color: #CC3300} - -.smaller {font-size: smaller} -.larger {font-size: larger} - -.larger {font-size: larger; color: #000066} -.head { - font-size: large; - font-weight: bold; - color: #CC0000; -} - -.ok_bgr { - background: #AEFF5E; - border: 1px #76EC00 solid; - border-color: #66CC00 #66CC00 #66CC00 #66CC00; -} - -.err_bgr { - background: #FFCE7B; - border: 1px solid #FFA500; - border-color:#FFA500 #FFA500 #FFA500 #FFA500; -} - -.grey { - background: #EFEFEF; -} - -.greyborder { - background: #EFEFEF; - border: 1px #CCCCCC solid; -} - - -.utextarea { - font: 110% "Courier New", Courier, monospace; - border: 1px solid #8cacbb; - color: Black; - background-color: white; - width: 95%; - padding: 5pt; -} -.uinput { - font-family: "Lucida Grande", Verdana, Lucida, Helvetica, Arial, sans-serif; - visibility: visible; - border: 1px solid #8cacbb; - color: Black; - background-color: white; - vertical-align: middle; -} - -.hg17 { color: #FF6600; } -.hg16 { color: #02AC20; } -.bed { color: #009999; } -.xbed { color: #006666; } -.txt { color: #0066FF; } -.text { color: #0066FF; } -.png { color: #33CC33; } -.gif { color: #009900; } -.html { color: #3399FF; } -.htm { color: #3399FF; } -.jpg { color: #006600; } -.jpeg { color: #006600; } -.fasta { color: #0066CC; } -.pdf { color: #003366; } -.wig { color: #3366CC; } -.gff { color: #0000FF; } -.fa { color: #FF3333; } -.acedb { color: #FF6666; } -.asn1 { color: #CC6666; } -.clustal { color: #993333; } -.codata { color: #FF0000; } -.embl { color: #009999; } -.fitch { color: #FF3300; } -.gcg { color: #66CC00; } -.genbank { color: #999900; } -.hennig86 { color: #666633; } -.ig { color: #CCCC99; } -.jackknifer { color: #FFCC99; } -.jackknifernon { color: #FFCC99; } -.mega { color: #99FF00; } -.meganon { color: #99FF00; } -.msf { color: #66FF33; } -.pir { color: #009933; } -.ncbi { color: #339933; } -.nexus { color: #009900; } -.nexusnon { color: #CCFF99; } -.phylip { color: #99CC66; } -.phylipnon { color: #336600; } -.selex { color: #99FF33; } -.staden { color: #00CC66; } -.strider { color: #33FF99; } -.swiss { color: #006633; } -.dbmotif { color: #339966; } -.diffseq { color: #66CC99; } -.excel { color: #99FFCC; } -.feattable { color: #99CCFF; } -.motif { color: #6699CC; } -.regions { color: #336699; } -.seqtable { color: #663300; } -.simple { color: #996633; } -.srs { color: #CC9966; } -.table { color: #CC6600; } -.tagseq { color: #FF9933; } -.pair { color: #FFCC66; } -.markx0 { color: #CC9933; } -.markx1 { color: #CC9933; } -.markx2 { color: #CC9933; } -.markx3 { color: #CC9933; } -.markx10 { color: #CC9933; } -.srspair { color: #CC9966; } -.score { color: #663333; } -.nametable { color: #00CC33; } diff --git a/static/universe.js b/static/universe.js deleted file mode 100644 index 11498720d19..00000000000 --- a/static/universe.js +++ /dev/null @@ -1,163 +0,0 @@ -var open_ids = [] -var cookie_name = "universe_ui" -var now = new Date(); -now.setTime(now.getTime() + 365 * 24 * 60 * 60 * 1000); - -// -// cookie management off the web -// http://www.webreference.com/js/column8/property.html -// -function setCookie(name, value, expires, path, domain, secure) { - var curCookie = name + "=" + escape(value) + - ((expires) ? "; expires=" + expires.toGMTString() : "") + - ((path) ? "; path=" + path : "") + - ((domain) ? "; domain=" + domain : "") + - ((secure) ? "; secure" : ""); - document.cookie = curCookie; -} - -function getCookie(name) { - var dc = document.cookie; - var prefix = name + "="; - var begin = dc.indexOf("; " + prefix); - if (begin == -1) { - begin = dc.indexOf(prefix); - if (begin != 0) return null; - } else - begin += 2; - var end = document.cookie.indexOf(";", begin); - if (end == -1) - end = dc.length; - return unescape(dc.substring(begin + prefix.length, end)); -} - - -function main(){ - init_ids() - //debugger - for (i=0; i