jpayne@68: package prok;
jpayne@68: 
jpayne@68: import java.util.Arrays;
jpayne@68: 
jpayne@68: import shared.Tools;
jpayne@68: import stream.Read;
jpayne@68: import structures.ByteBuilder;
jpayne@68: import structures.LongHashSet;
jpayne@68: 
jpayne@68: class StatsContainer {
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------        Initialization        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	StatsContainer(int type_, int kInner, int framesInner, int kStart, int framesStart, int offsetStart, int kStop, int framesStop, int offsetStop){
jpayne@68: 		type=type_;
jpayne@68: 		name=ProkObject.typeStrings[type];
jpayne@68: 		setInner(kInner, framesInner);
jpayne@68: 		setStart(kStart, framesStart, offsetStart);
jpayne@68: 		setStop(kStop, framesStop, offsetStop);
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	StatsContainer(int type_){
jpayne@68: 		type=type_;
jpayne@68: 		name=ProkObject.typeStrings[type];
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	void setInner(int kInner, int framesInner){
jpayne@68: 		assert(inner==null);
jpayne@68: 		statsArray[0]=inner=new FrameStats(name+" inner", kInner, framesInner, 0);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	void setStart(int kStart, int framesStart, int offsetStart){
jpayne@68: 		assert(start==null);
jpayne@68: 		statsArray[1]=start=new FrameStats(name+" start", kStart, framesStart, offsetStart);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	void setStop(int kStop, int framesStop, int offsetStop){
jpayne@68: 		assert(stop==null);
jpayne@68: 		statsArray[2]=stop=new FrameStats(name+" stop", kStop, framesStop, offsetStop);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	void setInner(FrameStats fs){
jpayne@68: 		assert(inner==null);
jpayne@68: 		assert(fs!=null);
jpayne@68: 		statsArray[0]=inner=fs;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	void setStart(FrameStats fs){
jpayne@68: 		assert(start==null);
jpayne@68: 		statsArray[1]=start=fs;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	void setStop(FrameStats fs){
jpayne@68: 		assert(stop==null);
jpayne@68: 		statsArray[2]=stop=fs;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------           Methods            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	@Override
jpayne@68: 	public String toString(){
jpayne@68: 		return appendTo(new ByteBuilder()).toString();
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public ByteBuilder appendTo(ByteBuilder bb) {
jpayne@68: 		bb.append("#name\t").append(name).nl();
jpayne@68: 		bb.append("#type\t").append(type).nl();
jpayne@68: 		bb.append("#count\t").append(lengthCount).nl();
jpayne@68: 		bb.append("#lengthSum\t").append(lengthSum).nl();
jpayne@68: 		//lengths
jpayne@68: 		bb.append("#contains\t").append(3).nl();
jpayne@68: 		if(ProkObject.processType(type)) {
jpayne@68: 			for(FrameStats fs : statsArray){
jpayne@68: 				fs.appendTo(bb);
jpayne@68: 			}
jpayne@68: 		}else{
jpayne@68: 			for(FrameStats fs : statsArray){
jpayne@68: 				fs.append0(bb);
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		return bb;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public void clear(){
jpayne@68: 		for(int i=0; i<statsArray.length; i++){
jpayne@68: 			if(statsArray[i]!=null){
jpayne@68: 				statsArray[i].clear();
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		assert(inner==statsArray[0]);
jpayne@68: 		assert(start==statsArray[1]);
jpayne@68: 		assert(stop==statsArray[2]);
jpayne@68: 		
jpayne@68: 		Arrays.fill(lengths, 0);
jpayne@68: 		lengthSum=0;
jpayne@68: 		lengthCount=0;
jpayne@68: 		calculate();
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public void setFrom(StatsContainer sc){
jpayne@68: 		assert(sc.name.equals(name));
jpayne@68: 		for(int i=0; i<statsArray.length; i++){
jpayne@68: 			FrameStats fs=sc.statsArray[i];
jpayne@68: 			if(statsArray[i]==null){
jpayne@68: 				statsArray[i]=new FrameStats(fs.name, fs.k, fs.frames, fs.leftOffset);
jpayne@68: 				statsArray[i].add(fs);
jpayne@68: 			}else{
jpayne@68: 				statsArray[i].setFrom(fs);
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		inner=statsArray[0];
jpayne@68: 		start=statsArray[1];
jpayne@68: 		stop=statsArray[2];
jpayne@68: 		
jpayne@68: 		for(int i=0; i<lengths.length; i++){lengths[i]=sc.lengths[i];}
jpayne@68: 		lengthSum=sc.lengthSum;
jpayne@68: 		lengthCount=sc.lengthCount;
jpayne@68: 		calculate();
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public void add(StatsContainer sc){
jpayne@68: 		assert(sc.name.equals(name));
jpayne@68: 		for(int i=0; i<statsArray.length; i++){
jpayne@68: 			FrameStats fs=sc.statsArray[i];
jpayne@68: 			if(statsArray[i]==null){
jpayne@68: 				statsArray[i]=new FrameStats(fs.name, fs.k, fs.frames, fs.leftOffset);
jpayne@68: 			}
jpayne@68: 			statsArray[i].add(fs);
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		inner=statsArray[0];
jpayne@68: 		start=statsArray[1];
jpayne@68: 		stop=statsArray[2];
jpayne@68: 		
jpayne@68: 		Tools.add(lengths, sc.lengths);
jpayne@68: 		lengthSum+=sc.lengthSum;
jpayne@68: 		lengthCount+=sc.lengthCount;
jpayne@68: 		calculate();
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public void multiplyBy(double mult) {
jpayne@68: 		for(int i=0; i<statsArray.length; i++){
jpayne@68: 			FrameStats fs=statsArray[i];
jpayne@68: 			fs.multiplyBy(mult);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		Tools.multiplyBy(lengths, mult);
jpayne@68: 		lengthSum=Math.round(lengthSum*mult);
jpayne@68: 		lengthCount=Math.round(lengthCount*mult);
jpayne@68: 		calculate();
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public void calculate(){
jpayne@68: 		for(int i=0; i<statsArray.length; i++){
jpayne@68: 			statsArray[i].calculate();
jpayne@68: 		}
jpayne@68: 		lengthAvg=(int)(lengthSum/Tools.max(1.0, lengthCount));
jpayne@68: 		invLengthAvg=1f/Tools.max(1, lengthAvg);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public void addLength(int x){
jpayne@68: 		lengthSum+=x;
jpayne@68: 		lengthCount++;
jpayne@68: 		lengths[Tools.min(x, lengths.length-1)]++;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------            Fields            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	FrameStats inner;
jpayne@68: 	FrameStats start;
jpayne@68: 	FrameStats stop;
jpayne@68: 	final FrameStats[] statsArray=new FrameStats[3];
jpayne@68: 	
jpayne@68: 	int kLongLen(){return ProkObject.kLongLen(type);}
jpayne@68: 	LongHashSet kmerSet(){return ProkObject.kmerSet(type);}
jpayne@68: 	Read[] consensusSequence(){return ProkObject.consensusReads(type);}
jpayne@68: 	float minIdentity(){return ProkObject.minID(type);}
jpayne@68: 
jpayne@68: 	public int startSlop(){return ProkObject.startSlop(type);}
jpayne@68: 	public int stopSlop(){return ProkObject.stopSlop(type);}
jpayne@68: 	
jpayne@68: 	final String name;
jpayne@68: 	long lengthSum=0;
jpayne@68: 	long lengthCount=0;
jpayne@68: 	int lengthAvg=-1;
jpayne@68: 	float invLengthAvg;
jpayne@68: 	
jpayne@68: 	int[] lengths=new int[5000];
jpayne@68: 	public final int type;
jpayne@68: 	
jpayne@68: }