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package hiseq;
import shared.Tools;
public class FlowcellCoordinate implements Comparable<FlowcellCoordinate> {
public FlowcellCoordinate() {}
public FlowcellCoordinate(String id) {
setFrom(id);
}
// public float distance(FlowcellCoordinate fc){ //Comment out due to being unused
// assert(isSet());
// assert(fc.isSet());
//
// if(lane!=fc.lane){return big;}
//
// long a=Tools.absdif(x, fc.x), b=Tools.absdif(y, fc.y);
// if(tile!=fc.tile){
// return spanTiles ? Tools.min(a, b) : big;
// }
// return (float)Math.sqrt(a*a+b*b);
//
// //Hard to say... could consider adjacent tiles?
//// if(tile!=fc.tile){
//// if(allowAdjacentTiles && Tools.absdif(tile, fc.tile)<2){return Tools.min(x-fc.x, y-fc.y);}
//// return big;
//// }
////
//// long a=x-fc.x, b=y-fc.y;
//// return (float)Math.sqrt(a*a+b*b);
// }
//2402:6:1101:6337:2237/1
//MISEQ08:172:000000000-ABYD0:1:1101:18147:1925 1:N:0:TGGATATGCGCCAATT
//HISEQ07:419:HBFNEADXX:1:1101:1238:2072
public void setFrom(String id){
final int lim=id.length();
int i=0;
int current=0;
while(i<lim && id.charAt(i)!=' ' && id.charAt(i)!='/'){i++;}
if(i>=lim){i--;}
for(int semis=0; i>=0; i--){
if(id.charAt(i)==':'){
semis++;
if(semis==4){break;}
}
}
i++;
assert(Tools.isDigit(id.charAt(i))) : id;
while(i<lim && Tools.isDigit(id.charAt(i))){
current=current*10+(id.charAt(i)-'0');
i++;
}
lane=current;
current=0;
i++;
if(!Tools.isDigit(id.charAt(i))){//Hiseq 3000?
while(i<lim && id.charAt(i)!=':'){i++;}
i++;
assert(Tools.isDigit(id.charAt(i))) : id;
while(i<lim && Tools.isDigit(id.charAt(i))){
current=current*10+(id.charAt(i)-'0');
i++;
}
lane=current;
current=0;
i++;
}
assert(Tools.isDigit(id.charAt(i))) : id;
while(i<lim && Tools.isDigit(id.charAt(i))){
current=current*10+(id.charAt(i)-'0');
i++;
}
tile=current;
current=0;
i++;
assert(Tools.isDigit(id.charAt(i))) : id;
while(i<lim && Tools.isDigit(id.charAt(i))){
current=current*10+(id.charAt(i)-'0');
i++;
}
x=current;
current=0;
i++;
assert(Tools.isDigit(id.charAt(i))) : id;
while(i<lim && Tools.isDigit(id.charAt(i))){
current=current*10+(id.charAt(i)-'0');
i++;
}
y=current;
current=0;
i++;
}
public boolean isSet(){
return lane>=0 && tile>=0 && x>=0 && y>=0;
}
@Override
public int compareTo(FlowcellCoordinate b) {
if(lane!=b.lane){return lane-b.lane;}
if(tile!=b.tile){return tile-b.tile;}
if(y!=b.y){return y-b.y;}
if(x!=b.x){return x-b.x;}
return 0;
}
public int lane=-1;
public int tile=-1;
public int x=-1;
public int y=-1;
public static final float big=10000000;
// public static boolean spanTiles=false;
public static FlowcellCoordinate getFC(){
FlowcellCoordinate fc=localFC.get();
if(fc==null){
fc=new FlowcellCoordinate();
localFC.set(fc);
}
return fc;
}
private static final ThreadLocal<FlowcellCoordinate> localFC=new ThreadLocal<FlowcellCoordinate>();
}
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