jpayne@68: package clump;
jpayne@68: 
jpayne@68: import java.io.Serializable;
jpayne@68: 
jpayne@68: import hiseq.FlowcellCoordinate;
jpayne@68: import shared.KillSwitch;
jpayne@68: import shared.Tools;
jpayne@68: import stream.Read;
jpayne@68: import structures.IntList;
jpayne@68: 
jpayne@68: class ReadKey implements Serializable, Comparable<ReadKey> {
jpayne@68: 	
jpayne@68: //	public static ReadKey makeKeyIfNeeded(Read r){
jpayne@68: //		if(r.obj==null){
jpayne@68: //			return makeKey(r, true);
jpayne@68: //		}
jpayne@68: //		return (ReadKey)r.obj;
jpayne@68: //	}
jpayne@68: 	
jpayne@68: 	public static ReadKey makeKey(Read r, boolean setObject){
jpayne@68: 		assert(r.obj==null);
jpayne@68: 		try {
jpayne@68: 			ReadKey rk=new ReadKey(r);
jpayne@68: 			if(setObject){r.obj=rk;}
jpayne@68: 			return rk;
jpayne@68: 		} catch (OutOfMemoryError e) {
jpayne@68: 			KillSwitch.memKill(e);
jpayne@68: 			throw new RuntimeException(e);
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private ReadKey(Read r){
jpayne@68: 		this(r, 0, 0, true);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private ReadKey(Read r, long kmer_, int position_, boolean plus_){
jpayne@68: 		kmer=kmer_;
jpayne@68: 		position=position_;
jpayne@68: 		clump=null;
jpayne@68: 		assert(!r.swapped());
jpayne@68: 		flipped=false;
jpayne@68: 		kmerMinusStrand=!plus_;
jpayne@68: 		
jpayne@68: 		if(Clump.opticalOnly){
jpayne@68: 			FlowcellCoordinate fc=FlowcellCoordinate.getFC();
jpayne@68: 			fc.setFrom(r.id);
jpayne@68: 			lane=fc.lane;
jpayne@68: 			tile=fc.tile;
jpayne@68: 			x=fc.x;
jpayne@68: 			y=fc.y;
jpayne@68: 		}
jpayne@68: //		expectedErrors=r.expectedErrorsIncludingMate(true);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	protected ReadKey(){}
jpayne@68: 	
jpayne@68: 	public void set(long kmer_, int position_, boolean minus_){
jpayne@68: 		setKmer(kmer_);
jpayne@68: 		setPosition(position_);
jpayne@68: //		setClump(null);
jpayne@68: 		kmerMinusStrand=minus_;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private long setKmer(long kmer_){
jpayne@68: 		return kmer=kmer_;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private int setPosition(int position_){
jpayne@68: 		return position=position_;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public Clump setClump(Clump clump_){
jpayne@68: 		return clump=clump_;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private boolean setFlipped(boolean flipped_){
jpayne@68: 		assert(flipped!=flipped_);
jpayne@68: 		return flipped=flipped_;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public void clear(){
jpayne@68: 		setKmer(0);
jpayne@68: 		setPosition(0);
jpayne@68: 		setClump(null);
jpayne@68: 		kmerMinusStrand=false;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public void flip(Read r, int k){
jpayne@68: 		assert(r.swapped()==flipped);
jpayne@68: 		r.reverseComplement();
jpayne@68: 		r.setSwapped(!r.swapped());
jpayne@68: 		setFlipped(!flipped);
jpayne@68: 		if(r.length()>=k){setPosition(r.length()-position+k-2);}
jpayne@68: 		assert(r.swapped()==flipped);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public int compareTo(ReadKey b){
jpayne@68: 		if(kmer!=b.kmer){return kmer>b.kmer ? -1 : 1;} //Bigger kmers first...
jpayne@68: 		if(kmerMinusStrand!=b.kmerMinusStrand){return kmerMinusStrand ? 1 : -1;}
jpayne@68: 		if(position!=b.position){return position<b.position ? 1 : -1;}
jpayne@68: 		if(Clump.opticalOnly){
jpayne@68: 			if(lane!=b.lane){return lane-b.lane;}
jpayne@68: 			if(!spanTiles()){
jpayne@68: 				if(tile!=b.tile){return tile-b.tile;}
jpayne@68: 			}
jpayne@68: 			if(Clump.sortYEarly()){ //Improves speed slightly
jpayne@68: 				if(y!=b.y){return y-b.y;}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: //		if(expectedErrors!=b.expectedErrors){
jpayne@68: //			return expectedErrors>b.expectedErrors ? 1 : -1;//Higher quality first
jpayne@68: //		}
jpayne@68: 		return 0;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public boolean equals(Object b){
jpayne@68: 		return equals((ReadKey)b, false);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public int hashCode() {
jpayne@68: 		int x=(int)((kmer^position)&0xFFFFFFFFL);
jpayne@68: 		return kmerMinusStrand ? -x : x;
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	/** True if this physically contains b (ignoring mismatches) */
jpayne@68: 	public boolean physicallyContains(ReadKey b, int aLen, int bLen){
jpayne@68: 		if(bLen>aLen){return false;}
jpayne@68: 		if(kmer!=b.kmer){return false;}
jpayne@68: 		final int dif=position-b.position;
jpayne@68: 		int bStart=dif, bStop=dif+bLen;
jpayne@68: 		return bStart>=0 && bStop<=aLen;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** True if this physically contains b as a prefix or suffix (ignoring mismatches).
jpayne@68: 	 * More restrictive than physicallyContains. */
jpayne@68: 	public boolean physicalAffix(ReadKey b, int aLen, int bLen){
jpayne@68: 		if(bLen>aLen){return false;}
jpayne@68: 		if(kmer!=b.kmer){return false;}
jpayne@68: 		final int dif=position-b.position;
jpayne@68: 		int bStart=dif, bStop=dif+bLen;
jpayne@68: 		return (bStart==0 || bStop==aLen) && bStart>=0 && bStop<=aLen;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Note that this is different than compareTo()==0
jpayne@68: 	 * That's to prevent sortYEarly comparison making things unequal.
jpayne@68: 	 * @param b
jpayne@68: 	 * @return True if equal
jpayne@68: 	 */
jpayne@68: 	public boolean equals(ReadKey b, boolean containment){
jpayne@68: 		if(b==null){return false;}
jpayne@68: 		if(kmer!=b.kmer){return false;}
jpayne@68: 		if(!containment && (kmerMinusStrand!=b.kmerMinusStrand || position!=b.position)){return false;}
jpayne@68: 		if(Clump.opticalOnly){
jpayne@68: 			if(lane!=b.lane){return false;}
jpayne@68: 			if(!spanTiles()){
jpayne@68: 				if(tile!=b.tile){return false;}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		return true;
jpayne@68: 	}
jpayne@68: 	public boolean equals(ReadKey b){
jpayne@68: 		return equals(b, false);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public String toString(){
jpayne@68: 		return position+","+(kmerMinusStrand ? ",t" : ",f")+","+kmer+"\t"+lane+","+tile+","+x+","+y;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public float distance(ReadKey rkb){
jpayne@68: 		if(lane!=rkb.lane){return FlowcellCoordinate.big;}
jpayne@68: 		
jpayne@68: 		long a=Tools.absdif(x, rkb.x), b=Tools.absdif(y, rkb.y);
jpayne@68: 		if(tile!=rkb.tile){
jpayne@68: 			if(spanTiles()){
jpayne@68: 				if(spanAdjacentOnly && Tools.absdif(tile, rkb.tile)>1){return FlowcellCoordinate.big;}
jpayne@68: 				if(spanTilesX && spanTilesY){
jpayne@68: 					return Tools.min(a, b);
jpayne@68: 				}else if(spanTilesX){
jpayne@68: 					return a;
jpayne@68: 				}else{
jpayne@68: 					return b;
jpayne@68: 				}
jpayne@68: 			}else{
jpayne@68: 				return FlowcellCoordinate.big;
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		return (float)Math.sqrt(a*a+b*b);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public boolean near(ReadKey rkb, float dist){
jpayne@68: 		return distance(rkb)<dist;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public boolean nearXY(ReadKey rkb, float dist){
jpayne@68: 		if(lane!=rkb.lane){return false;}
jpayne@68: 		
jpayne@68: 		long a=Tools.absdif(x, rkb.x), b=Tools.absdif(y, rkb.y);
jpayne@68: 		return Tools.min(a,b)<=dist;
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	public int flag;
jpayne@68: 	
jpayne@68: 	public long kmer;
jpayne@68: 	/** Position of rightmost base of kmer */
jpayne@68: 	public int position;
jpayne@68: 	public boolean flipped;
jpayne@68: 	public boolean kmerMinusStrand;
jpayne@68: 	public Clump clump;
jpayne@68: 	public IntList vars;
jpayne@68: //	public float expectedErrors;
jpayne@68: 	
jpayne@68: 	public int lane, tile, x, y;
jpayne@68: 	
jpayne@68: 	public static final int overhead=overhead();
jpayne@68: 	private static int overhead(){
jpayne@68: 		return 16+ //self
jpayne@68: 				1*(8)+ //kmer
jpayne@68: 				1*(4)+ //int fields
jpayne@68: 				2*(4)+ //booleans
jpayne@68: 				2*(8)+ //pointers
jpayne@68: 				4*(4); //flowcell coordinate
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static boolean spanTiles(){return spanTilesX || spanTilesY;}
jpayne@68: 	public static boolean spanTilesX=false;
jpayne@68: 	public static boolean spanTilesY=false;
jpayne@68: 	public static boolean spanAdjacentOnly=false;
jpayne@68: 	
jpayne@68: 	/**
jpayne@68: 	 * 
jpayne@68: 	 */
jpayne@68: 	private static final long serialVersionUID = 1L;
jpayne@68: 	
jpayne@68: }