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biojs-vis-pdbviewer

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A BioJS 2.0 component to view protein structures

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Clazz.load(["java.util.AbstractMap","$.AbstractSet","$.Iterator","$.Map","$.MapEntry"],"java.util.HashMap",["java.lang.IllegalArgumentException","$.IllegalStateException","java.util.AbstractCollection","$.Arrays","$.ConcurrentModificationException","java.util.MapEntry.Type","java.util.NoSuchElementException"],function(){ c$=Clazz.decorateAsClass(function(){ this.elementCount=0; this.elementData=null; this.loadFactor=0; this.threshold=0; this.modCount=0; Clazz.instantialize(this,arguments); },java.util,"HashMap",java.util.AbstractMap,[java.util.Map,Cloneable,java.io.Serializable]); Clazz.defineMethod(c$,"newElementArray", function(s){ return new Array(s); },"~N"); Clazz.makeConstructor(c$, function(){ this.construct(16); }); Clazz.makeConstructor(c$, function(capacity){ Clazz.superConstructor(this,java.util.HashMap,[]); if(capacity>=0){ this.elementCount=0; this.elementData=this.newElementArray(capacity==0?1:capacity); this.loadFactor=0.75; this.computeMaxSize(); }else{ throw new IllegalArgumentException(); }},"~N"); Clazz.makeConstructor(c$, function(capacity,loadFactor){ Clazz.superConstructor(this,java.util.HashMap,[]); if(capacity>=0&&loadFactor>0){ this.elementCount=0; this.elementData=this.newElementArray(capacity==0?1:capacity); this.loadFactor=loadFactor; this.computeMaxSize(); }else{ throw new IllegalArgumentException(); }},"~N,~N"); Clazz.makeConstructor(c$, function(map){ this.construct(map.size()<6?11:map.size()*2); Clazz.superCall(this,java.util.HashMap,"putAll",[map]); },"java.util.Map"); Clazz.overrideMethod(c$,"clear", function(){ if(this.elementCount>0){ this.elementCount=0; java.util.Arrays.fill(this.elementData,null); this.modCount++; }}); Clazz.defineMethod(c$,"clone", function(){ try{ var map=Clazz.superCall(this,java.util.HashMap,"clone",[]); map.elementData=this.newElementArray(this.elementData.length); var entry; for(var i=0;i<this.elementData.length;i++){ if((entry=this.elementData[i])!=null){ map.elementData[i]=entry.clone(); }} return map; }catch(e){ if(Clazz.instanceOf(e,CloneNotSupportedException)){ return null; }else{ throw e; } } }); Clazz.defineMethod(c$,"computeMaxSize", ($fz=function(){ this.threshold=Math.round((this.elementData.length*this.loadFactor)); },$fz.isPrivate=true,$fz)); Clazz.overrideMethod(c$,"containsKey", function(key){ return this.getEntry(key)!=null; },"~O"); Clazz.defineMethod(c$,"keysEqual", function(k1,entry){ var k1Hash=k1==null?0:k1.hashCode(); if(k1Hash!=entry.origKeyHash){ return false; }if(k1==null&&entry.key==null){ return true; }return k1.equals(entry.key); },"~O,java.util.HashMap.Entry"); Clazz.overrideMethod(c$,"containsValue", function(value){ if(value!=null){ 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; } } }else{ for(var i=this.elementData.length;--i>=0;){ var entry=this.elementData[i]; while(entry!=null){ if(entry.value==null){ return true; }entry=entry.next; } } }return false; },"~O"); Clazz.overrideMethod(c$,"entrySet", function(){ return new java.util.HashMap.HashMapEntrySet(this); }); Clazz.overrideMethod(c$,"get", function(key){ var m=this.getEntry(key); if(m!=null){ return m.value; }return null; },"~O"); Clazz.defineMethod(c$,"getEntry", function(key){ var index=this.getModuloHash(key); return this.findEntry(key,index); },"~O"); Clazz.defineMethod(c$,"getModuloHash", function(key){ if(key==null){ return 0; }return(key.hashCode()&0x7FFFFFFF)%this.elementData.length; },"~O"); Clazz.defineMethod(c$,"findEntry", function(key,index){ var m; m=this.elementData[index]; if(key!=null){ while(m!=null&&!this.keysEqual(key,m)){ m=m.next; } }else{ while(m!=null&&m.key!=null){ m=m.next; } }return m; },"~O,~N"); Clazz.overrideMethod(c$,"isEmpty", function(){ return this.elementCount==0; }); Clazz.overrideMethod(c$,"keySet", function(){ if(this.$keySet==null){ this.$keySet=((Clazz.isClassDefined("java.util.HashMap$1")?0:java.util.HashMap.$HashMap$1$()),Clazz.innerTypeInstance(java.util.HashMap$1,this,null)); }return this.$keySet; }); Clazz.overrideMethod(c$,"put", function(key,value){ var index=this.getModuloHash(key); var entry=this.findEntry(key,index); if(entry==null){ this.modCount++; if(++this.elementCount>this.threshold){ this.rehash(); index=key==null?0:(key.hashCode()&0x7FFFFFFF)%this.elementData.length; }entry=this.createEntry(key,index,value); return null; }var result=entry.value; entry.value=value; return result; },"~O,~O"); Clazz.defineMethod(c$,"createEntry", function(key,index,value){ var entry=new java.util.HashMap.Entry(key,value); entry.next=this.elementData[index]; this.elementData[index]=entry; return entry; },"~O,~N,~O"); Clazz.overrideMethod(c$,"putAll", function(map){ if(!map.isEmpty()){ var capacity=this.elementCount+map.size(); if(capacity>this.threshold){ this.rehash(capacity); }Clazz.superCall(this,java.util.HashMap,"putAll",[map]); }},"java.util.Map"); Clazz.defineMethod(c$,"rehash", function(capacity){ var length=(capacity==0?1:capacity<<1); var newData=this.newElementArray(length); for(var i=0;i<this.elementData.length;i++){ var entry=this.elementData[i]; while(entry!=null){ var key=entry.key; var index=key==null?0:(key.hashCode()&0x7FFFFFFF)%length; var next=entry.next; entry.next=newData[index]; newData[index]=entry; entry=next; } } this.elementData=newData; this.computeMaxSize(); },"~N"); Clazz.defineMethod(c$,"rehash", function(){ this.rehash(this.elementData.length); }); Clazz.overrideMethod(c$,"remove", function(key){ var entry=this.removeEntry(key); if(entry!=null){ return entry.value; }return null; },"~O"); Clazz.defineMethod(c$,"removeEntry", function(key){ var index=0; var entry; var last=null; if(key!=null){ index=(key.hashCode()&0x7FFFFFFF)%this.elementData.length; entry=this.elementData[index]; while(entry!=null&&!this.keysEqual(key,entry)){ last=entry; entry=entry.next; } }else{ entry=this.elementData[0]; while(entry!=null&&entry.key!=null){ last=entry; entry=entry.next; } }if(entry==null){ return null; }if(last==null){ this.elementData[index]=entry.next; }else{ last.next=entry.next; }this.modCount++; this.elementCount--; return entry; },"~O"); Clazz.overrideMethod(c$,"size", function(){ return this.elementCount; }); Clazz.overrideMethod(c$,"values", function(){ if(this.valuesCollection==null){ this.valuesCollection=((Clazz.isClassDefined("java.util.HashMap$2")?0:java.util.HashMap.$HashMap$2$()),Clazz.innerTypeInstance(java.util.HashMap$2,this,null)); }return this.valuesCollection; }); c$.$HashMap$1$=function(){ Clazz.pu$h(self.c$); c$=Clazz.declareAnonymous(java.util,"HashMap$1",java.util.AbstractSet); Clazz.overrideMethod(c$,"contains", function(object){ return this.b$["java.util.HashMap"].containsKey(object); },"~O"); Clazz.overrideMethod(c$,"size", function(){ return this.b$["java.util.HashMap"].size(); }); Clazz.overrideMethod(c$,"clear", function(){ this.b$["java.util.HashMap"].clear(); }); Clazz.overrideMethod(c$,"remove", function(key){ if(this.b$["java.util.HashMap"].containsKey(key)){ this.b$["java.util.HashMap"].remove(key); return true; }return false; },"~O"); Clazz.overrideMethod(c$,"iterator", function(){ return new java.util.HashMap.HashMapIterator(((Clazz.isClassDefined("java.util.HashMap$1$1")?0:java.util.HashMap.$HashMap$1$1$()),Clazz.innerTypeInstance(java.util.HashMap$1$1,this,null)),this.b$["java.util.HashMap"]); }); c$=Clazz.p0p(); }; c$.$HashMap$1$1$=function(){ Clazz.pu$h(self.c$); c$=Clazz.declareAnonymous(java.util,"HashMap$1$1",null,java.util.MapEntry.Type); Clazz.overrideMethod(c$,"get", function(entry){ return entry.key; },"java.util.MapEntry"); c$=Clazz.p0p(); }; c$.$HashMap$2$=function(){ Clazz.pu$h(self.c$); c$=Clazz.declareAnonymous(java.util,"HashMap$2",java.util.AbstractCollection); Clazz.overrideMethod(c$,"contains", function(object){ return this.b$["java.util.HashMap"].containsValue(object); },"~O"); Clazz.overrideMethod(c$,"size", function(){ return this.b$["java.util.HashMap"].size(); }); Clazz.overrideMethod(c$,"clear", function(){ this.b$["java.util.HashMap"].clear(); }); Clazz.overrideMethod(c$,"iterator", function(){ return new java.util.HashMap.HashMapIterator(((Clazz.isClassDefined("java.util.HashMap$2$1")?0:java.util.HashMap.$HashMap$2$1$()),Clazz.innerTypeInstance(java.util.HashMap$2$1,this,null)),this.b$["java.util.HashMap"]); }); c$=Clazz.p0p(); }; c$.$HashMap$2$1$=function(){ Clazz.pu$h(self.c$); c$=Clazz.declareAnonymous(java.util,"HashMap$2$1",null,java.util.MapEntry.Type); Clazz.overrideMethod(c$,"get", function(entry){ return entry.value; },"java.util.MapEntry"); c$=Clazz.p0p(); }; Clazz.pu$h(self.c$); c$=Clazz.decorateAsClass(function(){ this.origKeyHash=0; this.next=null; Clazz.instantialize(this,arguments); },java.util.HashMap,"Entry",java.util.MapEntry); Clazz.makeConstructor(c$, function(a,b){ Clazz.superConstructor(this,java.util.HashMap.Entry,[a,b]); this.origKeyHash=(a==null?0:a.hashCode()); },"~O,~O"); Clazz.defineMethod(c$,"clone", function(){ var a=Clazz.superCall(this,java.util.HashMap.Entry,"clone",[]); if(this.next!=null){ a.next=this.next.clone(); }return a; }); c$=Clazz.p0p(); Clazz.pu$h(self.c$); c$=Clazz.decorateAsClass(function(){ this.position=0; this.expectedModCount=0; this.type=null; this.canRemove=false; this.entry=null; this.lastEntry=null; this.associatedMap=null; Clazz.instantialize(this,arguments); },java.util.HashMap,"HashMapIterator",null,java.util.Iterator); Clazz.makeConstructor(c$, function(a,b){ this.associatedMap=b; this.type=a; this.expectedModCount=b.modCount; },"java.util.MapEntry.Type,java.util.HashMap"); Clazz.overrideMethod(c$,"hasNext", function(){ if(this.entry!=null){ return true; }while(this.position<this.associatedMap.elementData.length){ if(this.associatedMap.elementData[this.position]==null){ this.position++; }else{ return true; }} return false; }); Clazz.defineMethod(c$,"checkConcurrentMod", function(){ if(this.expectedModCount!=this.associatedMap.modCount){ throw new java.util.ConcurrentModificationException(); }}); Clazz.overrideMethod(c$,"next", function(){ this.checkConcurrentMod(); if(!this.hasNext()){ throw new java.util.NoSuchElementException(); }var a; if(this.entry==null){ a=this.lastEntry=this.associatedMap.elementData[this.position++]; this.entry=this.lastEntry.next; }else{ if(this.lastEntry.next!==this.entry){ this.lastEntry=this.lastEntry.next; }a=this.entry; this.entry=this.entry.next; }this.canRemove=true; return this.type.get(a); }); Clazz.overrideMethod(c$,"remove", function(){ this.checkConcurrentMod(); if(!this.canRemove){ throw new IllegalStateException(); }this.canRemove=false; this.associatedMap.modCount++; if(this.lastEntry.next===this.entry){ while(this.associatedMap.elementData[--this.position]==null){ ;} this.associatedMap.elementData[this.position]=this.associatedMap.elementData[this.position].next; this.entry=null; }else{ this.lastEntry.next=this.entry; }this.associatedMap.elementCount--; this.expectedModCount++; }); c$=Clazz.p0p(); Clazz.pu$h(self.c$); c$=Clazz.decorateAsClass(function(){ this.associatedMap=null; Clazz.instantialize(this,arguments); },java.util.HashMap,"HashMapEntrySet",java.util.AbstractSet); Clazz.makeConstructor(c$, function(a){ Clazz.superConstructor(this,java.util.HashMap.HashMapEntrySet,[]); this.associatedMap=a; },"java.util.HashMap"); Clazz.defineMethod(c$,"hashMap", function(){ return this.associatedMap; }); Clazz.overrideMethod(c$,"size", function(){ return this.associatedMap.elementCount; }); Clazz.overrideMethod(c$,"clear", function(){ this.associatedMap.clear(); }); Clazz.overrideMethod(c$,"remove", function(a){ if(this.contains(a)){ this.associatedMap.remove((a).getKey()); return true; }return false; },"~O"); Clazz.overrideMethod(c$,"contains", function(a){ if(Clazz.instanceOf(a,java.util.Map.Entry)){ var b=this.associatedMap.getEntry((a).getKey()); return a.equals(b); }return false; },"~O"); Clazz.overrideMethod(c$,"iterator", function(){ return new java.util.HashMap.HashMapIterator(((Clazz.isClassDefined("java.util.HashMap$HashMapEntrySet$1")?0:java.util.HashMap.HashMapEntrySet.$HashMap$HashMapEntrySet$1$()),Clazz.innerTypeInstance(java.util.HashMap$HashMapEntrySet$1,this,null)),this.associatedMap); }); c$.$HashMap$HashMapEntrySet$1$=function(){ Clazz.pu$h(self.c$); c$=Clazz.declareAnonymous(java.util,"HashMap$HashMapEntrySet$1",null,java.util.MapEntry.Type); Clazz.overrideMethod(c$,"get", function(a){ return a; },"java.util.MapEntry"); c$=Clazz.p0p(); }; c$=Clazz.p0p(); Clazz.defineStatics(c$, "DEFAULT_SIZE",16); });