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biojs-vis-pdbviewer

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A BioJS 2.0 component to view protein structures

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/* http://j2s.sf.net/ */Clazz.load(null,"java.lang.AbstractStringBuilder",["java.io.InvalidObjectException","java.lang.ArrayIndexOutOfBoundsException","$.IndexOutOfBoundsException","$.NegativeArraySizeException","$.NullPointerException","$.StringIndexOutOfBoundsException"],function(){ c$=Clazz.decorateAsClass(function(){ this.value=null; this.count=0; this.shared=false; Clazz.instantialize(this,arguments); },java.lang,"AbstractStringBuilder"); Clazz.defineMethod(c$,"getValue", function(){ return this.value; }); Clazz.defineMethod(c$,"shareValue", function(){ this.shared=true; return this.value; }); Clazz.defineMethod(c$,"set", function(val,len){ if(val==null)val=Clazz.newArray(0,'\0'); if(val.length<len)throw new java.io.InvalidObjectException(("K0199")); this.shared=false; this.value=val; this.count=len; },"~A,~N"); Clazz.makeConstructor(c$, function(){ this.value=Clazz.newArray(16,'\0'); }); Clazz.makeConstructor(c$, function(capacity){ if(capacity<0)throw new NegativeArraySizeException(); this.value=Clazz.newArray(capacity,'\0'); },"~N"); Clazz.makeConstructor(c$, function(string){ this.count=string.length; this.shared=false; this.value=Clazz.newArray(this.count+16,'\0'); string.getChars(0,this.count,this.value,0); },"~S"); Clazz.defineMethod(c$,"enlargeBuffer", ($fz=function(min){ var twice=(this.value.length<<1)+2; var newData=Clazz.newArray(min>twice?min:twice,'\0'); System.arraycopy(this.value,0,newData,0,this.count); this.value=newData; this.shared=false; },$fz.isPrivate=true,$fz),"~N"); Clazz.defineMethod(c$,"appendNull", function(){ var newSize=this.count+4; if(newSize>this.value.length){ this.enlargeBuffer(newSize); }else if(this.shared){ this.value=this.value.clone(); this.shared=false; }this.value[this.count++]='n'; this.value[this.count++]='u'; this.value[this.count++]='l'; this.value[this.count++]='l'; }); Clazz.defineMethod(c$,"append0", function(chars){ var newSize=this.count+chars.length; if(newSize>this.value.length){ this.enlargeBuffer(newSize); }else if(this.shared){ this.value=this.value.clone(); this.shared=false; }System.arraycopy(chars,0,this.value,this.count,chars.length); this.count=newSize; },"~A"); Clazz.defineMethod(c$,"append0", function(chars,start,length){ if(chars==null){ throw new NullPointerException(); }if(start>=0&&0<=length&&length<=chars.length-start){ var newSize=this.count+length; if(newSize>this.value.length){ this.enlargeBuffer(newSize); }else if(this.shared){ this.value=this.value.clone(); this.shared=false; }System.arraycopy(chars,start,this.value,this.count,length); this.count=newSize; }else{ throw new ArrayIndexOutOfBoundsException(); }},"~A,~N,~N"); Clazz.defineMethod(c$,"append0", function(ch){ if(this.count==this.value.length){ this.enlargeBuffer(this.count+1); }if(this.shared){ this.value=this.value.clone(); this.shared=false; }this.value[this.count++]=ch; },"~N"); Clazz.defineMethod(c$,"append0", function(string){ if(string==null){ this.appendNull(); return; }var adding=string.length; var newSize=this.count+adding; if(newSize>this.value.length){ this.enlargeBuffer(newSize); }else if(this.shared){ this.value=this.value.clone(); this.shared=false; }string.getChars(0,adding,this.value,this.count); this.count=newSize; },"~S"); Clazz.defineMethod(c$,"append0", function(s,start,end){ if(s==null)s="null"; if(start<0||end<0||start>end||end>s.length())throw new IndexOutOfBoundsException(); this.append0(s.subSequence(start,end).toString()); },"CharSequence,~N,~N"); Clazz.defineMethod(c$,"capacity", function(){ return this.value.length; }); Clazz.defineMethod(c$,"charAt", function(index){ if(index<0||index>=this.count)throw new StringIndexOutOfBoundsException(index); return this.value[index]; },"~N"); Clazz.defineMethod(c$,"delete0", function(start,end){ if(start>=0){ if(end>this.count){ end=this.count; }if(end==start){ return; }if(end>start){ var length=this.count-end; if(length>0){ if(!this.shared){ System.arraycopy(this.value,end,this.value,start,length); }else{ var newData=Clazz.newArray(this.value.length,'\0'); System.arraycopy(this.value,0,newData,0,start); System.arraycopy(this.value,end,newData,start,length); this.value=newData; this.shared=false; }}this.count-=end-start; return; }}throw new StringIndexOutOfBoundsException(); },"~N,~N"); Clazz.defineMethod(c$,"deleteCharAt0", function(location){ if(0>location||location>=this.count)throw new StringIndexOutOfBoundsException(location); var length=this.count-location-1; if(length>0){ if(!this.shared){ System.arraycopy(this.value,location+1,this.value,location,length); }else{ var newData=Clazz.newArray(this.value.length,'\0'); System.arraycopy(this.value,0,newData,0,location); System.arraycopy(this.value,location+1,newData,location,length); this.value=newData; this.shared=false; }}this.count--; },"~N"); Clazz.defineMethod(c$,"ensureCapacity", function(min){ if(min>this.value.length){ this.enlargeBuffer(min); }},"~N"); Clazz.defineMethod(c$,"getChars", function(start,end,dest,destStart){ if(start>this.count||end>this.count||start>end){ throw new StringIndexOutOfBoundsException(); }System.arraycopy(this.value,start,dest,destStart,end-start); },"~N,~N,~A,~N"); Clazz.defineMethod(c$,"insert0", function(index,chars){ if(0>index||index>this.count){ throw new StringIndexOutOfBoundsException(index); }if(chars.length!=0){ this.move(chars.length,index); System.arraycopy(chars,0,this.value,index,chars.length); this.count+=chars.length; }},"~N,~A"); Clazz.defineMethod(c$,"insert0", function(index,chars,start,length){ if(0<=index&&index<=this.count){ if(start>=0&&0<=length&&length<=chars.length-start){ if(length!=0){ this.move(length,index); System.arraycopy(chars,start,this.value,index,length); this.count+=length; }return; }throw new StringIndexOutOfBoundsException("offset "+start+", len "+length+", array.length "+chars.length); }throw new StringIndexOutOfBoundsException(index); },"~N,~A,~N,~N"); Clazz.defineMethod(c$,"insert0", function(index,ch){ if(0>index||index>this.count){ throw new ArrayIndexOutOfBoundsException(index); }this.move(1,index); this.value[index]=ch; this.count++; },"~N,~N"); Clazz.defineMethod(c$,"insert0", function(index,string){ if(0<=index&&index<=this.count){ if(string==null)string="null"; var min=string.length; if(min!=0){ this.move(min,index); string.getChars(0,min,this.value,index); this.count+=min; }}else{ throw new StringIndexOutOfBoundsException(index); }},"~N,~S"); Clazz.defineMethod(c$,"insert0", function(index,s,start,end){ if(s==null)s="null"; if(index<0||index>this.count||start<0||end<0||start>end||end>s.length())throw new IndexOutOfBoundsException(); this.insert0(index,s.subSequence(start,end).toString()); },"~N,CharSequence,~N,~N"); Clazz.defineMethod(c$,"length", function(){ return this.count; }); Clazz.defineMethod(c$,"move", ($fz=function(size,index){ var newSize; if(this.value.length-this.count>=size){ if(!this.shared){ System.arraycopy(this.value,index,this.value,index+size,this.count-index); return; }newSize=this.value.length; }else{ var a=this.count+size; var b=(this.value.length<<1)+2; newSize=a>b?a:b; }var newData=Clazz.newArray(newSize,'\0'); System.arraycopy(this.value,0,newData,0,index); System.arraycopy(this.value,index,newData,index+size,this.count-index); this.value=newData; this.shared=false; },$fz.isPrivate=true,$fz),"~N,~N"); Clazz.defineMethod(c$,"replace0", function(start,end,string){ if(start>=0){ if(end>this.count)end=this.count; if(end>start){ var stringLength=string.length; var diff=end-start-stringLength; if(diff>0){ if(!this.shared){ System.arraycopy(this.value,end,this.value,start+stringLength,this.count-end); }else{ var newData=Clazz.newArray(this.value.length,'\0'); System.arraycopy(this.value,0,newData,0,start); System.arraycopy(this.value,end,newData,start+stringLength,this.count-end); this.value=newData; this.shared=false; }}else if(diff<0){ this.move(-diff,end); }else if(this.shared){ this.value=this.value.clone(); this.shared=false; }string.getChars(0,stringLength,this.value,start); this.count-=diff; return; }if(start==end){ if(string==null)throw new NullPointerException(); this.insert0(start,string); return; }}throw new StringIndexOutOfBoundsException(); },"~N,~N,~S"); Clazz.defineMethod(c$,"reverse0", function(){ if(this.count<2){ return; }if(!this.shared){ for(var i=0,end=this.count,mid=Math.floor(this.count/2);i<mid;i++){ var temp=this.value[--end]; this.value[end]=this.value[i]; this.value[i]=temp; } }else{ var newData=Clazz.newArray(this.value.length,'\0'); for(var i=0,end=this.count;i<this.count;i++){ newData[--end]=this.value[i]; } this.value=newData; this.shared=false; }}); Clazz.defineMethod(c$,"setCharAt", function(index,ch){ if(0>index||index>=this.count){ throw new StringIndexOutOfBoundsException(index); }if(this.shared){ this.value=this.value.clone(); this.shared=false; }this.value[index]=ch; },"~N,~N"); Clazz.defineMethod(c$,"setLength", function(length){ if(length<0)throw new StringIndexOutOfBoundsException(length); if(this.count<length){ if(length>this.value.length){ this.enlargeBuffer(length); }else{ if(this.shared){ var newData=Clazz.newArray(this.value.length,'\0'); System.arraycopy(this.value,0,newData,0,this.count); this.value=newData; this.shared=false; }else{ for(var i=this.count;i<length;i++){ this.value[i]=String.fromCharCode(0); } }}}this.count=length; },"~N"); Clazz.defineMethod(c$,"substring", function(start){ if(0<=start&&start<=this.count){ if(start==this.count)return""; this.shared=true; return String.instantialize(start,this.count-start,this.value); }throw new StringIndexOutOfBoundsException(start); },"~N"); Clazz.defineMethod(c$,"substring", function(start,end){ if(0<=start&&start<=end&&end<=this.count){ if(start==end)return""; this.shared=true; return String.instantialize(this.value,start,end-start); }throw new StringIndexOutOfBoundsException(); },"~N,~N"); Clazz.overrideMethod(c$,"toString", function(){ if(this.count==0)return""; if(this.count>=256&&this.count<=(this.value.length>>1))return String.instantialize(this.value,0,this.count); this.shared=true; return String.instantialize(0,this.count,this.value); }); Clazz.defineMethod(c$,"subSequence", function(start,end){ return this.substring(start,end); },"~N,~N"); Clazz.defineMethod(c$,"indexOf", function(string){ return this.indexOf(string,0); },"~S"); Clazz.defineMethod(c$,"indexOf", function(subString,start){ if(start<0)start=0; var subCount=subString.length; if(subCount>0){ if(subCount+start>this.count)return-1; var firstChar=subString.charAt(0); while(true){ var i=start; var found=false; for(;i<this.count;i++)if((this.value[i]).charCodeAt(0)==(firstChar).charCodeAt(0)){ found=true; break; } if(!found||subCount+i>this.count)return-1; var o1=i; var o2=0; while(++o2<subCount&&(this.value[++o1]).charCodeAt(0)==(subString.charAt(o2)).charCodeAt(0)){ } if(o2==subCount)return i; start=i+1; } }return(start<this.count||start==0)?start:this.count; },"~S,~N"); Clazz.defineMethod(c$,"lastIndexOf", function(string){ return this.lastIndexOf(string,this.count); },"~S"); Clazz.defineMethod(c$,"lastIndexOf", function(subString,start){ var subCount=subString.length; if(subCount<=this.count&&start>=0){ if(subCount>0){ if(start>this.count-subCount)start=this.count-subCount; var firstChar=subString.charAt(0); while(true){ var i=start; var found=false; for(;i>=0;--i)if((this.value[i]).charCodeAt(0)==(firstChar).charCodeAt(0)){ found=true; break; } if(!found)return-1; var o1=i; var o2=0; while(++o2<subCount&&(this.value[++o1]).charCodeAt(0)==(subString.charAt(o2)).charCodeAt(0)){ } if(o2==subCount)return i; start=i-1; } }return start<this.count?start:this.count; }return-1; },"~S,~N"); Clazz.defineMethod(c$,"trimToSize", function(){ if(this.count<this.value.length){ var newValue=Clazz.newArray(this.count,'\0'); System.arraycopy(this.value,0,newValue,0,this.count); this.value=newValue; this.shared=false; }}); Clazz.defineStatics(c$, "INITIAL_CAPACITY",16); }); Clazz.load(["java.lang.AbstractStringBuilder","$.Appendable"],"java.lang.StringBuilder",["java.lang.Double","$.Float","$.Long"],function(){ c$=Clazz.declareType(java.lang,"StringBuilder",AbstractStringBuilder,[Appendable,CharSequence,java.io.Serializable]); Clazz.makeConstructor(c$, function(seq){ Clazz.superConstructor(this,StringBuilder,[seq.toString()]); },"CharSequence"); Clazz.defineMethod(c$,"append", function(b){ this.append0(b?"true":"false"); return this; },"~B"); Clazz.defineMethod(c$,"append", function(c){ this.append0(c); return this; },"~N"); Clazz.defineMethod(c$,"append", function(i){ this.append0(Integer.toString(i)); return this; },"~N"); Clazz.defineMethod(c$,"append", function(lng){ this.append0(Long.toString(lng)); return this; },"~N"); Clazz.defineMethod(c$,"append", function(f){ this.append0(Float.toString(f)); return this; },"~N"); Clazz.defineMethod(c$,"append", function(d){ this.append0(Double.toString(d)); return this; },"~N"); Clazz.defineMethod(c$,"append", function(obj){ if(obj==null){ this.appendNull(); }else{ this.append0(obj.toString()); }return this; },"~O"); Clazz.defineMethod(c$,"append", function(str){ this.append0(str); return this; },"~S"); Clazz.defineMethod(c$,"append", function(sb){ if(sb==null){ this.appendNull(); }else{ this.append0(sb.getValue(),0,sb.length()); }return this; },"StringBuffer"); Clazz.defineMethod(c$,"append", function(ch){ this.append0(ch); return this; },"~A"); Clazz.defineMethod(c$,"append", function(str,offset,len){ this.append0(str,offset,len); return this; },"~A,~N,~N"); Clazz.defineMethod(c$,"append", function(csq){ if(csq==null){ this.appendNull(); }else{ this.append0(csq.toString()); }return this; },"CharSequence"); Clazz.defineMethod(c$,"append", function(csq,start,end){ this.append0(csq,start,end); return this; },"CharSequence,~N,~N"); Clazz.defineMethod(c$,"$delete", function(start,end){ this.delete0(start,end); return this; },"~N,~N"); Clazz.defineMethod(c$,"deleteCharAt", function(index){ this.deleteCharAt0(index); return this; },"~N"); Clazz.defineMethod(c$,"insert", function(offset,b){ this.insert0(offset,b?"true":"false"); return this; },"~N,~B"); Clazz.defineMethod(c$,"insert", function(offset,c){ this.insert0(offset,c); return this; },"~N,~N"); Clazz.defineMethod(c$,"insert", function(offset,i){ this.insert0(offset,Integer.toString(i)); return this; },"~N,~N"); Clazz.defineMethod(c$,"insert", function(offset,l){ this.insert0(offset,Long.toString(l)); return this; },"~N,~N"); Clazz.defineMethod(c$,"insert", function(offset,f){ this.insert0(offset,Float.toString(f)); return this; },"~N,~N"); Clazz.defineMethod(c$,"insert", function(offset,d){ this.insert0(offset,Double.toString(d)); return this; },"~N,~N"); Clazz.defineMethod(c$,"insert", function(offset,obj){ this.insert0(offset,obj==null?"null":obj.toString()); return this; },"~N,~O"); Clazz.defineMethod(c$,"insert", function(offset,str){ this.insert0(offset,str); return this; },"~N,~S"); Clazz.defineMethod(c$,"insert", function(offset,ch){ this.insert0(offset,ch); return this; },"~N,~A"); Clazz.defineMethod(c$,"insert", function(offset,str,strOffset,strLen){ this.insert0(offset,str,strOffset,strLen); return this; },"~N,~A,~N,~N"); Clazz.defineMethod(c$,"insert", function(offset,s){ this.insert0(offset,s==null?"null":s.toString()); return this; },"~N,CharSequence"); Clazz.defineMethod(c$,"insert", function(offset,s,start,end){ this.insert0(offset,s,start,end); return this; },"~N,CharSequence,~N,~N"); Clazz.defineMethod(c$,"replace", function(start,end,str){ this.replace0(start,end,str); return this; },"~N,~N,~S"); Clazz.defineMethod(c$,"reverse", function(){ this.reverse0(); return this; }); });