--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/prok/StatsContainer.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,198 @@
+package prok;
+
+import java.util.Arrays;
+
+import shared.Tools;
+import stream.Read;
+import structures.ByteBuilder;
+import structures.LongHashSet;
+
+class StatsContainer {
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Initialization        ----------------*/
+	/*--------------------------------------------------------------*/
+
+	StatsContainer(int type_, int kInner, int framesInner, int kStart, int framesStart, int offsetStart, int kStop, int framesStop, int offsetStop){
+		type=type_;
+		name=ProkObject.typeStrings[type];
+		setInner(kInner, framesInner);
+		setStart(kStart, framesStart, offsetStart);
+		setStop(kStop, framesStop, offsetStop);
+	}
+
+	StatsContainer(int type_){
+		type=type_;
+		name=ProkObject.typeStrings[type];
+	}
+	
+	void setInner(int kInner, int framesInner){
+		assert(inner==null);
+		statsArray[0]=inner=new FrameStats(name+" inner", kInner, framesInner, 0);
+	}
+	
+	void setStart(int kStart, int framesStart, int offsetStart){
+		assert(start==null);
+		statsArray[1]=start=new FrameStats(name+" start", kStart, framesStart, offsetStart);
+	}
+	
+	void setStop(int kStop, int framesStop, int offsetStop){
+		assert(stop==null);
+		statsArray[2]=stop=new FrameStats(name+" stop", kStop, framesStop, offsetStop);
+	}
+	
+	void setInner(FrameStats fs){
+		assert(inner==null);
+		assert(fs!=null);
+		statsArray[0]=inner=fs;
+	}
+	
+	void setStart(FrameStats fs){
+		assert(start==null);
+		statsArray[1]=start=fs;
+	}
+	
+	void setStop(FrameStats fs){
+		assert(stop==null);
+		statsArray[2]=stop=fs;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------           Methods            ----------------*/
+	/*--------------------------------------------------------------*/
+
+	@Override
+	public String toString(){
+		return appendTo(new ByteBuilder()).toString();
+	}
+	
+	public ByteBuilder appendTo(ByteBuilder bb) {
+		bb.append("#name\t").append(name).nl();
+		bb.append("#type\t").append(type).nl();
+		bb.append("#count\t").append(lengthCount).nl();
+		bb.append("#lengthSum\t").append(lengthSum).nl();
+		//lengths
+		bb.append("#contains\t").append(3).nl();
+		if(ProkObject.processType(type)) {
+			for(FrameStats fs : statsArray){
+				fs.appendTo(bb);
+			}
+		}else{
+			for(FrameStats fs : statsArray){
+				fs.append0(bb);
+			}
+		}
+		return bb;
+	}
+	
+	public void clear(){
+		for(int i=0; i<statsArray.length; i++){
+			if(statsArray[i]!=null){
+				statsArray[i].clear();
+			}
+		}
+
+		assert(inner==statsArray[0]);
+		assert(start==statsArray[1]);
+		assert(stop==statsArray[2]);
+		
+		Arrays.fill(lengths, 0);
+		lengthSum=0;
+		lengthCount=0;
+		calculate();
+	}
+	
+	public void setFrom(StatsContainer sc){
+		assert(sc.name.equals(name));
+		for(int i=0; i<statsArray.length; i++){
+			FrameStats fs=sc.statsArray[i];
+			if(statsArray[i]==null){
+				statsArray[i]=new FrameStats(fs.name, fs.k, fs.frames, fs.leftOffset);
+				statsArray[i].add(fs);
+			}else{
+				statsArray[i].setFrom(fs);
+			}
+		}
+		inner=statsArray[0];
+		start=statsArray[1];
+		stop=statsArray[2];
+		
+		for(int i=0; i<lengths.length; i++){lengths[i]=sc.lengths[i];}
+		lengthSum=sc.lengthSum;
+		lengthCount=sc.lengthCount;
+		calculate();
+	}
+	
+	public void add(StatsContainer sc){
+		assert(sc.name.equals(name));
+		for(int i=0; i<statsArray.length; i++){
+			FrameStats fs=sc.statsArray[i];
+			if(statsArray[i]==null){
+				statsArray[i]=new FrameStats(fs.name, fs.k, fs.frames, fs.leftOffset);
+			}
+			statsArray[i].add(fs);
+		}
+
+		inner=statsArray[0];
+		start=statsArray[1];
+		stop=statsArray[2];
+		
+		Tools.add(lengths, sc.lengths);
+		lengthSum+=sc.lengthSum;
+		lengthCount+=sc.lengthCount;
+		calculate();
+	}
+	
+	public void multiplyBy(double mult) {
+		for(int i=0; i<statsArray.length; i++){
+			FrameStats fs=statsArray[i];
+			fs.multiplyBy(mult);
+		}
+		
+		Tools.multiplyBy(lengths, mult);
+		lengthSum=Math.round(lengthSum*mult);
+		lengthCount=Math.round(lengthCount*mult);
+		calculate();
+	}
+	
+	public void calculate(){
+		for(int i=0; i<statsArray.length; i++){
+			statsArray[i].calculate();
+		}
+		lengthAvg=(int)(lengthSum/Tools.max(1.0, lengthCount));
+		invLengthAvg=1f/Tools.max(1, lengthAvg);
+	}
+	
+	public void addLength(int x){
+		lengthSum+=x;
+		lengthCount++;
+		lengths[Tools.min(x, lengths.length-1)]++;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	FrameStats inner;
+	FrameStats start;
+	FrameStats stop;
+	final FrameStats[] statsArray=new FrameStats[3];
+	
+	int kLongLen(){return ProkObject.kLongLen(type);}
+	LongHashSet kmerSet(){return ProkObject.kmerSet(type);}
+	Read[] consensusSequence(){return ProkObject.consensusReads(type);}
+	float minIdentity(){return ProkObject.minID(type);}
+
+	public int startSlop(){return ProkObject.startSlop(type);}
+	public int stopSlop(){return ProkObject.stopSlop(type);}
+	
+	final String name;
+	long lengthSum=0;
+	long lengthCount=0;
+	int lengthAvg=-1;
+	float invLengthAvg;
+	
+	int[] lengths=new int[5000];
+	public final int type;
+	
+}