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biojs-vis-pdbviewer

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A BioJS 2.0 component to view protein structures

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// modified by Bob Hanson 3/21/2014 6:44:21 AM to reduce this.b$[....] phrases to simply this.b$H Clazz.load(["java.util.Dictionary","$.Enumeration","$.Iterator","$.Map","$.MapEntry","$.NoSuchElementException"],"java.util.Hashtable",["java.lang.IllegalArgumentException","$.IllegalStateException","$.NullPointerException","$.StringBuilder","java.util.AbstractCollection","$.AbstractSet","$.Arrays","$.Collections","$.ConcurrentModificationException","java.util.MapEntry.Type"],function(){ c$=Clazz.decorateAsClass(function(){ this.elementCount=0; this.elementData=null; this.loadFactor=0; this.threshold=0; this.firstSlot=0; this.lastSlot=-1; this.modCount=0; if(!Clazz.isClassDefined("java.util.Hashtable.HashIterator")){ java.util.Hashtable.$Hashtable$HashIterator$(); } if(!Clazz.isClassDefined("java.util.Hashtable.HashEnumerator")){ java.util.Hashtable.$Hashtable$HashEnumerator$(); } Clazz.instantialize(this,arguments); },java.util,"Hashtable",java.util.Dictionary,[java.util.Map,Cloneable,java.io.Serializable]); c$.newEntry=Clazz.defineMethod(c$,"newEntry", ($fz=function(key,value,hash){ return new java.util.Hashtable.Entry(key,value); },$fz.isPrivate=true,$fz),"~O,~O,~N"); Clazz.overrideConstructor(c$, function(){ this.elementCount=0; this.elementData=this.newElementArray(11); this.firstSlot=this.elementData.length; this.loadFactor=0.75; this.computeMaxSize(); }); Clazz.defineMethod(c$,"newElementArray", ($fz=function(size){ return new Array(size); },$fz.isPrivate=true,$fz),"~N"); Clazz.overrideMethod(c$,"clear", function(){ this.elementCount=0; for (var i = this.elementData.length; --i >= 0;) this.elementData[i] = null; this.modCount++; }); Clazz.defineMethod(c$,"clone", function(){ try{ var hashtable=Clazz.superCall(this,java.util.Hashtable,"clone",[]); hashtable.elementData=this.elementData.clone(); var entry; for(var i=this.elementData.length;--i>=0;){ if((entry=this.elementData[i])!=null){ hashtable.elementData[i]=entry.clone(); }} return hashtable; }catch(e){ if(Clazz.instanceOf(e,CloneNotSupportedException)){ return null; }else{ throw e; } } }); Clazz.defineMethod(c$,"computeMaxSize", ($fz=function(){ this.threshold=Math.round((this.elementData.length*this.loadFactor)); },$fz.isPrivate=true,$fz)); Clazz.defineMethod(c$,"contains", function(value){ if(value==null){ throw new NullPointerException(); }for(var i=this.elementData.length;--i>=0;){ var entry=this.elementData[i]; while(entry!=null){ if(value.equals(entry.value)){ return true; }entry=entry.next; } } return false; },"~O"); Clazz.overrideMethod(c$,"containsKey", function(key){ return this.getEntry(key)!=null; },"~O"); Clazz.overrideMethod(c$,"containsValue", function(value){ return this.contains(value); },"~O"); Clazz.overrideMethod(c$,"elements", function(){ if(this.elementCount==0){ return java.util.Hashtable.EMPTY_ENUMERATION; }return Clazz.innerTypeInstance(java.util.Hashtable.HashEnumerator,this,null,false); }); Clazz.overrideMethod(c$,"entrySet", function(){ var b var a = new java.util.Collections.SynchronizedSet(((Clazz.isClassDefined("java.util.Hashtable$2")?0:java.util.Hashtable.$Hashtable$2$()),b=Clazz.innerTypeInstance(java.util.Hashtable$2,this,null)),this); b && (b.b$H = b.b$["java.util.Hashtable"]); return a; }); Clazz.overrideMethod(c$,"equals", function(object){ if(this===object){ return true; }if(Clazz.instanceOf(object,java.util.Map)){ var map=object; if(this.size()!=map.size()){ return false; }var entries=this.entrySet(); for(var e,$e=map.entrySet().iterator();$e.hasNext()&&((e=$e.next())||true);){ if(!entries.contains(e)){ return false; }} return true; }return false; },"~O"); Clazz.overrideMethod(c$,"get", function(key){ var hash=key.hashCode(); var index=(hash&0x7FFFFFFF)%this.elementData.length; var entry=this.elementData[index]; while(entry!=null){ if(entry.equalsKey(key,hash)){ return entry.value; }entry=entry.next; } return null; },"~O"); Clazz.defineMethod(c$,"getEntry", function(key){ var hash=key.hashCode(); var index=(hash&0x7FFFFFFF)%this.elementData.length; var entry=this.elementData[index]; while(entry!=null){ if(entry.equalsKey(key,hash)){ return entry; }entry=entry.next; } return null; },"~O"); Clazz.overrideMethod(c$,"hashCode", function(){ var result=0; var it=this.entrySet().iterator(); while(it.hasNext()){ var entry=it.next(); var key=entry.getKey(); var value=entry.getValue(); var hash=(key!==this?key.hashCode():0)^(value!==this?(value!=null?value.hashCode():0):0); result+=hash; } return result; }); Clazz.overrideMethod(c$,"isEmpty", function(){ return this.elementCount==0; }); Clazz.overrideMethod(c$,"keys", function(){ if(this.elementCount==0){ return java.util.Hashtable.EMPTY_ENUMERATION; }return Clazz.innerTypeInstance(java.util.Hashtable.HashEnumerator,this,null,true); }); Clazz.overrideMethod(c$,"keySet", function(){ var b var a = new java.util.Collections.SynchronizedSet(((Clazz.isClassDefined("java.util.Hashtable$3")?0:java.util.Hashtable.$Hashtable$3$()),(b=Clazz.innerTypeInstance(java.util.Hashtable$3,this,null))),this); b && (b.b$H = b.b$["java.util.Hashtable"]); return a; }); Clazz.overrideMethod(c$,"put", function(key,value){ if(key!=null&&value!=null){ // BH added ability to use a non-Java key for HTML elements, for example. if(!key.hashCode) { var hc = Math.floor(Math.random()*10000000); key.hashCode = function(){return hc}; key.equals = function(a){return this.hashCode() == a.hashCode()}; } var hash=key.hashCode(); var index=(hash&0x7FFFFFFF)%this.elementData.length; var entry=this.elementData[index]; while(entry!=null&&!entry.equalsKey(key,hash)){ entry=entry.next; } if(entry==null){ this.modCount++; if(++this.elementCount>this.threshold){ this.rehash(); index=(hash&0x7FFFFFFF)%this.elementData.length; }if(index<this.firstSlot){ this.firstSlot=index; }if(index>this.lastSlot){ this.lastSlot=index; } entry=java.util.Hashtable.newEntry(key,value,hash); entry.next=this.elementData[index]; this.elementData[index]=entry; return null; }var result=entry.value; entry.value=value; return result; }throw new NullPointerException(); },"~O,~O"); Clazz.overrideMethod(c$,"putAll", function(map){ for(var entry,$entry=map.entrySet().iterator();$entry.hasNext()&&((entry=$entry.next())||true);){ this.put(entry.getKey(),entry.getValue()); } },"java.util.Map"); Clazz.defineMethod(c$,"rehash", function(){ var length=(this.elementData.length<<1)+1; if(length==0){ length=1; }var newFirst=length; var newLast=-1; var newData=this.newElementArray(length); for(var i=this.lastSlot+1;--i>=this.firstSlot;){ var entry=this.elementData[i]; while(entry!=null){ var index=(entry.getKeyHash()&0x7FFFFFFF)%length; if(index<newFirst){ newFirst=index; }if(index>newLast){ newLast=index; }var next=entry.next; entry.next=newData[index]; newData[index]=entry; entry=next; } } this.firstSlot=newFirst; this.lastSlot=newLast; this.elementData=newData; this.computeMaxSize(); }); Clazz.overrideMethod(c$,"remove", function(key){ var hash=key.hashCode(); var index=(hash&0x7FFFFFFF)%this.elementData.length; var last=null; var entry=this.elementData[index]; while(entry!=null&&!entry.equalsKey(key,hash)){ last=entry; entry=entry.next; } if(entry!=null){ this.modCount++; if(last==null){ this.elementData[index]=entry.next; }else{ last.next=entry.next; }this.elementCount--; var result=entry.value; entry.value=null; return result; }return null; },"~O"); Clazz.overrideMethod(c$,"size", function(){ return this.elementCount; }); Clazz.overrideMethod(c$,"toString", function(){ if(this.isEmpty()){ return"{}"; }var buffer=new StringBuilder(this.size()*28); buffer.append('{'); for(var i=this.lastSlot;i>=this.firstSlot;i--){ var entry=this.elementData[i]; while(entry!=null){ if(entry.key!==this){ buffer.append(entry.key); }else{ buffer.append("(this Map)"); }buffer.append('='); if(entry.value!==this){ buffer.append(entry.value); }else{ buffer.append("(this Map)"); }buffer.append(", "); entry=entry.next; } } if(this.elementCount>0){ buffer.setLength(buffer.length()-2); }buffer.append('}'); return buffer.toString(); }); Clazz.overrideMethod(c$,"values", function(){ var b var a = new java.util.Collections.SynchronizedCollection(((Clazz.isClassDefined("java.util.Hashtable$4")?0:java.util.Hashtable.$Hashtable$4$()),(b=Clazz.innerTypeInstance(java.util.Hashtable$4,this,null))),this); b && (b.b$H = b.b$["java.util.Hashtable"]); return a; }); c$.$Hashtable$HashIterator$=function(){ Clazz.pu$h(self.c$); c$=Clazz.decorateAsClass(function(){ Clazz.prepareCallback(this,arguments); this.position=0; this.expectedModCount=0; this.type=null; this.lastEntry=null; this.lastPosition=0; this.canRemove=false; Clazz.instantialize(this,arguments); },java.util.Hashtable,"HashIterator",null,java.util.Iterator); Clazz.makeConstructor(c$, function(a){ this.type=a; this.b$H = this.b$["java.util.Hashtable"]; this.position=this.b$H.lastSlot; this.expectedModCount=this.b$H.modCount; },"java.util.MapEntry.Type"); Clazz.overrideMethod(c$,"hasNext", function(){ if(this.lastEntry!=null&&this.lastEntry.next!=null){ return true; }while(this.position>=this.b$H.firstSlot){ if(this.b$H.elementData[this.position]==null){ this.position--; }else{ return true; }} return false; }); Clazz.overrideMethod(c$,"next", function(){ if(this.expectedModCount==this.b$H.modCount){ if(this.lastEntry!=null){ this.lastEntry=this.lastEntry.next; }if(this.lastEntry==null){ while(this.position>=this.b$H.firstSlot&&(this.lastEntry=this.b$H.elementData[this.position])==null){ this.position--; } if(this.lastEntry!=null){ this.lastPosition=this.position; this.position--; }}if(this.lastEntry!=null){ this.canRemove=true; return this.type.get(this.lastEntry); }throw new java.util.NoSuchElementException(); }throw new java.util.ConcurrentModificationException(); }); Clazz.overrideMethod(c$,"remove", function(){ if(this.expectedModCount==this.b$H.modCount){ if(this.canRemove){ this.canRemove=false; { var a=false; var b=this.b$H.elementData[this.lastPosition]; if(b===this.lastEntry){ this.b$H.elementData[this.lastPosition]=b.next; a=true; }else{ while(b!=null&&b.next!==this.lastEntry){ b=b.next; } if(b!=null){ b.next=this.lastEntry.next; a=true; }}if(a){ this.b$H.modCount++; this.b$H.elementCount--; this.expectedModCount++; return; }}}else{ throw new IllegalStateException(); }}throw new java.util.ConcurrentModificationException(); }); c$=Clazz.p0p(); }; c$.$Hashtable$HashEnumerator$=function(){ Clazz.pu$h(self.c$); c$=Clazz.decorateAsClass(function(){ Clazz.prepareCallback(this,arguments); this.key=false; this.start=0; this.entry=null; Clazz.instantialize(this,arguments); },java.util.Hashtable,"HashEnumerator",null,java.util.Enumeration); Clazz.makeConstructor(c$, function(a){ this.key=a; this.b$H = this.b$["java.util.Hashtable"]; this.start=this.b$H.lastSlot+1; },"~B"); Clazz.overrideMethod(c$,"hasMoreElements", function(){ if(this.entry!=null){ return true; } while(--this.start>=this.b$H.firstSlot){ if(this.b$H.elementData[this.start]!=null){ this.entry=this.b$H.elementData[this.start]; return true; }} return false; }); Clazz.overrideMethod(c$,"nextElement", function(){ if(this.hasMoreElements()){ var a=this.key?this.entry.key:this.entry.value; this.entry=this.entry.next; return a; }throw new java.util.NoSuchElementException(); }); c$=Clazz.p0p(); }; c$.$Hashtable$2$=function(){ // private class EntrySet extends AbstractSet<Map.Entry<K,V>> Clazz.pu$h(self.c$); c$=Clazz.declareAnonymous(java.util,"Hashtable$2",java.util.AbstractSet); Clazz.overrideMethod(c$,"size", function(){ return this.b$H.elementCount; }); Clazz.overrideMethod(c$,"clear", function(){ this.b$H.clear(); }); Clazz.overrideMethod(c$,"remove", function(object){ if(this.contains(object)){ this.b$H.remove((object).getKey()); return true; }return false; },"~O"); Clazz.defineMethod(c$,"contains", function(object){ var entry=this.b$H.getEntry((object).getKey()); return object.equals(entry); },"~O"); Clazz.defineMethod(c$,"iterator", function(){ return Clazz.innerTypeInstance(java.util.Hashtable.HashIterator,this,null,((Clazz.isClassDefined("java.util.Hashtable$2$1")?0:java.util.Hashtable.$Hashtable$2$1$()),Clazz.innerTypeInstance(java.util.Hashtable$2$1,this,null))); }); c$=Clazz.p0p(); }; c$.$Hashtable$2$1$=function(){ // EntrySet.HashIterator Clazz.pu$h(self.c$); c$=Clazz.declareAnonymous(java.util,"Hashtable$2$1",null,java.util.MapEntry.Type); Clazz.overrideMethod(c$,"get", function(entry){ return entry; },"java.util.MapEntry"); c$=Clazz.p0p(); }; c$.$Hashtable$3$=function(){ // private class KeySet extends AbstractSet<K> Clazz.pu$h(self.c$); c$=Clazz.declareAnonymous(java.util,"Hashtable$3",java.util.AbstractSet); Clazz.overrideMethod(c$,"contains", function(object){ return this.b$H.containsKey(object); },"~O"); Clazz.overrideMethod(c$,"size", function(){ return this.b$H.elementCount; }); Clazz.overrideMethod(c$,"clear", function(){ this.b$H.clear(); }); Clazz.overrideMethod(c$,"remove", function(key){ if(this.b$H.containsKey(key)){ this.b$H.remove(key); return true; }return false; },"~O"); Clazz.overrideMethod(c$,"iterator", function(){ return Clazz.innerTypeInstance(java.util.Hashtable.HashIterator,this,null,((Clazz.isClassDefined("java.util.Hashtable$3$1")?0:java.util.Hashtable.$Hashtable$3$1$()),Clazz.innerTypeInstance(java.util.Hashtable$3$1,this,null))); }); c$=Clazz.p0p(); }; c$.$Hashtable$3$1$=function(){ // KeySet.HashIterator Clazz.pu$h(self.c$); c$=Clazz.declareAnonymous(java.util,"Hashtable$3$1",null,java.util.MapEntry.Type); Clazz.overrideMethod(c$,"get", function(entry){ return entry.key; },"java.util.MapEntry"); c$=Clazz.p0p(); }; c$.$Hashtable$4$=function(){ // private class ValueCollection extends AbstractCollection<V> Clazz.pu$h(self.c$); c$=Clazz.declareAnonymous(java.util,"Hashtable$4",java.util.AbstractCollection); Clazz.overrideMethod(c$,"contains", function(object){ return this.b$H.contains(object); },"~O"); Clazz.overrideMethod(c$,"size", function(){ return this.b$H.elementCount; }); Clazz.overrideMethod(c$,"clear", function(){ this.b$H.clear(); }); Clazz.overrideMethod(c$,"iterator", function(){ return Clazz.innerTypeInstance(java.util.Hashtable.HashIterator,this,null,((Clazz.isClassDefined("java.util.Hashtable$4$1")?0:java.util.Hashtable.$Hashtable$4$1$()),Clazz.innerTypeInstance(java.util.Hashtable$4$1,this,null))); }); c$=Clazz.p0p(); }; c$.$Hashtable$4$1$=function(){ // ValueCollection.HashIterator Clazz.pu$h(self.c$); c$=Clazz.declareAnonymous(java.util,"Hashtable$4$1",null,java.util.MapEntry.Type); Clazz.overrideMethod(c$,"get", function(entry){ return entry.value; },"java.util.MapEntry"); c$=Clazz.p0p(); }; c$.$Hashtable$1$=function(){ // private class Enumerator<T> implements Enumeration<T>, Iterator<T> Clazz.pu$h(self.c$); c$=Clazz.declareAnonymous(java.util,"Hashtable$1",null,java.util.Enumeration); Clazz.overrideMethod(c$,"hasMoreElements", function(){ return false; }); Clazz.overrideMethod(c$,"nextElement", function(){ throw new java.util.NoSuchElementException(); }); c$=Clazz.p0p(); }; Clazz.pu$h(self.c$); c$=Clazz.decorateAsClass(function(){ this.next=null; this.hashcode=0; Clazz.instantialize(this,arguments); },java.util.Hashtable,"Entry",java.util.MapEntry); Clazz.overrideConstructor(c$, function(a,b){ // _k for @j2sOverride this.key = a; this.value = b; //Clazz.superConstructor(this,java.util.Hashtable.Entry,[a,b]); this.hashcode=a.hashCode(); }); Clazz.defineMethod(c$,"clone", function(){ var a=Clazz.superCall(this,java.util.Hashtable.Entry,"clone",[]); if(this.next!=null){ a.next=this.next.clone(); } return a; }); Clazz.overrideMethod(c$,"setValue", function(a){ if(a==null){ throw new NullPointerException(); }var b=this.value; this.value=a; return b; },"~O"); Clazz.defineMethod(c$,"getKeyHash", function(){ return this.key.hashCode(); }); Clazz.defineMethod(c$,"equalsKey", function(a,b){ return this.hashcode==a.hashCode()&&this.key.equals(a); },"~O,~N"); Clazz.overrideMethod(c$,"toString", function(){ return this.key+"="+this.value; }); c$=Clazz.p0p(); c$.EMPTY_ENUMERATION=c$.prototype.EMPTY_ENUMERATION=((Clazz.isClassDefined("java.util.Hashtable$1")?0:java.util.Hashtable.$Hashtable$1$()),Clazz.innerTypeInstance(java.util.Hashtable$1,this,null)); });