--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/prok/FrameStats.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,310 @@
+package prok;
+
+import java.util.Arrays;
+
+import dna.AminoAcid;
+import shared.KillSwitch;
+import shared.Parse;
+import shared.Tools;
+import structures.ByteBuilder;
+
+/**
+ * Stores frame-relative kmer counts for a type of genomic feature, such as a coding start site.
+ * @author Brian Bushnell
+ * @date Sep 24, 2018
+ */
+public class FrameStats {
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Initialization        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	public FrameStats(String name_, int k_, int frames_, int leftOffset_){
+		name=name_;
+		k=k_;
+		mask=~((-1)<<(2*k));
+		frames=frames_;
+		kMax=1<<(2*k);
+		invFrames=1.0f/frames;
+		leftOffset=leftOffset_;
+		
+		probs=new float[frames][kMax];
+		countsTrue=new long[frames][kMax];
+		countsFalse=new long[frames][kMax];
+		counts=new long[][][] {countsFalse, countsTrue};
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------           Methods            ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	public void add(int kmer, int frame, int valid){
+		counts[valid][frame][kmer]++;
+		validSums[valid]++;
+	}
+	
+	public boolean compatibleWith(FrameStats fs) {
+		return fs.name.equals(name) && fs.leftOffset==leftOffset && fs.k==k && fs.frames==frames;
+	}
+	
+	public void clear() {
+		Tools.fill(counts, 0);
+		Arrays.fill(validSums, 0);
+	}
+	
+	public void setFrom(FrameStats fs) {
+		assert(compatibleWith(fs)) : name+", "+frames+", "+fs.name+", "+fs.frames;
+		clear();
+		add(fs);
+	}
+	
+	public void add(FrameStats fs){
+		assert(fs.name.equals(name));
+		assert(fs.leftOffset==leftOffset);
+		assert(fs.k==k);
+		assert(fs.frames==frames) : name+", "+frames+", "+fs.name+", "+fs.frames;
+//		for(int x=0; x<counts.length; x++) {
+//			for(int y=0; y<counts[x].length; y++) {
+//				for(int z=0; z<counts[x][y].length; z++) {
+//					assert(fs.counts[x][y][z]>=0) : counts[x][y][z]+", "+fs.counts[x][y][z]+", "+fs.name;
+//					assert(counts[x][y][z]>=0) : counts[x][y][z]+", "+fs.counts[x][y][z];
+//				}
+//			}
+//		}
+
+		Tools.add(counts, fs.counts);
+		Tools.add(validSums, fs.validSums);
+//		for(int x=0; x<counts.length; x++) {
+//			for(int y=0; y<counts[x].length; y++) {
+//				for(int z=0; z<counts[x][y].length; z++) {
+//					assert(fs.counts[x][y][z]>=0) : counts[x][y][z]+", "+fs.counts[x][y][z];
+//					assert(counts[x][y][z]>=0) : counts[x][y][z]+", "+fs.counts[x][y][z];
+//				}
+//			}
+//		}
+//		calculate();
+	}
+	
+	public void multiplyBy(double mult) {
+		Tools.multiplyBy(counts, mult);
+		Tools.multiplyBy(validSums, mult);
+	}
+	
+	void calculate(){
+		average=(float)((validSums[1]+1.0)/(validSums[0]+validSums[1]+1.0));
+		invAvg=1.0f/average;
+		
+		for(int a=0; a<frames; a++){
+			for(int b=0; b<kMax; b++){
+				long t=countsTrue[a][b];
+				long f=countsFalse[a][b];
+				probs[a][b]=(float)(t/(t+f+1.0))*invAvg;
+			}
+		}
+	}
+	
+	public float scorePoint(int point, byte[] bases){
+		final int mask=~((-1)<<(2*k));
+		
+		int kmer=0;
+		int len=0;
+		float score=0;
+
+//		outstream.println("k="+k);
+//		outstream.println("mask="+mask);
+		
+		int start=point-leftOffset;
+		for(int i=start, frame=0-k+1; i<bases.length && frame<frames; i++, frame++){
+			byte b=(i>=0 ? bases[i] : (byte)'A');
+			int x=AminoAcid.baseToNumber[b];
+			kmer=((kmer<<2)|x)&mask;
+			
+//			outstream.println("b="+(char)b+", kmer="+kmer+", len="+(len+1)+", frame="+frame);
+			
+			if(x>=0){
+				len++;
+				if(len>=k){
+					float prob=probs[frame][kmer];
+					float dif=prob-0.99f;
+					score+=dif;
+					
+//					if(name.equals("startStats")){
+//						System.err.println("frame="+frame+" kmer="+AminoAcid.kmerToString(kmer, k)+
+//								String.format(Locale.ROOT, " prob=%.4f\tdif=%.4f\tscore=%.4f", prob, dif, score)+
+//								"\tvalid="+counts[1][frame][kmer]+"\tinvalid="+counts[0][frame][kmer]);
+//					}
+				}
+			}else{len=0;}
+		}
+		
+		return score*invFrames;
+	}
+	
+	void processCDSFrames(byte[] bases, byte[] validFrames){
+		if(!ProkObject.callCDS){return;}
+		int kmer=0;
+		int len=0;
+		
+		for(int i=0; i<bases.length; i++){
+			byte b=bases[i];
+			int x=AminoAcid.baseToNumber[b];
+			kmer=((kmer<<2)|x)&mask;
+			if(x>=0){
+				len++;
+				if(len>=k){
+					int vf=validFrames[i];
+					for(int frame=0; frame<frames; frame++){
+						int valid=vf&1;
+						add(kmer, frame, valid);
+						//For CDS start (0-based) of 189, i=192, j=189, vf=1, frame=0 - all as expected.
+//						assert(valid==0) : "vf="+vf+", frame="+frame+", len="+len+", kmer="+AminoAcid.kmerToString(kmer, k)+", i="+i+", j="+j;
+						vf=(vf>>1);
+					}
+				}
+			}else{len=0;}
+		}
+	}
+	
+	void processPoint(byte[] bases, int point, int valid){
+		
+		//Degenerate cases where the point is at the end, possibly from a truncated gene.
+		if(point<3){return;}
+		if(point>=bases.length-3){return;}
+		
+		int kmer=0;
+		int len=0;
+
+//		outstream.println("k="+k);
+//		outstream.println("mask="+mask);
+		
+		int start=point-leftOffset;
+		
+		int i=start, frame=0-k+1;
+		while(i<0){i++; frame++;}
+		for(; i<bases.length && frame<frames; i++, frame++){
+			byte b=bases[i];
+			int x=AminoAcid.baseToNumber[b];
+			kmer=((kmer<<2)|x)&mask;
+			
+//			outstream.println("b="+(char)b+", kmer="+kmer+", len="+(len+1)+", frame="+frame);
+			
+			if(x>=0){
+				len++;
+				if(len>=k){
+					add(kmer, frame, valid);
+				}
+			}else{len=0;}
+		}
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Text Methods         ----------------*/
+	/*--------------------------------------------------------------*/
+
+	public void parseData(byte[] line) {
+		int a=0, b=0;
+		final int valid, frame;
+		
+		while(b<line.length && line[b]!='\t'){b++;}
+		assert(b>a) : "Missing field 0: "+new String(line);
+		valid=Parse.parseInt(line, a, b);
+		b++;
+		a=b;
+		
+		while(b<line.length && line[b]!='\t'){b++;}
+		assert(b>a) : "Missing field 1: "+new String(line);
+		frame=Parse.parseInt(line, a, b);
+		b++;
+		a=b;
+		
+		assert(valid==0 || valid==1);
+		assert(frame>=0 && frame<frames);
+		try {
+			final long[] row=counts[valid][frame];
+			long sum=0;
+			for(int kmer=0; kmer<row.length; kmer++){
+				while(b<line.length && line[b]!='\t'){b++;}
+				assert(b>a) : "Missing field 1: "+new String(line);
+				long count=Parse.parseLong(line, a, b);
+				b++;
+				a=b;
+				row[kmer]=count;
+				sum+=count;
+			}
+			validSums[valid]+=sum;
+		} catch (Exception e) {
+			System.err.println(new String(line)+"\n"+name);
+			assert(false) : e;
+		}
+	}
+	
+	@Override
+	public String toString(){
+		return appendTo(new ByteBuilder()).toString();
+	}
+	
+	public ByteBuilder appendTo(ByteBuilder bb){
+		bb.append("#name\t").append(name).nl();
+		bb.append("#k\t").append(k).nl();
+		bb.append("#frames\t").append(frames).nl();
+		bb.append("#offset\t").append(leftOffset).nl();
+		bb.append("#valid\tframe");
+		for(int i=0; i<kMax; i++){bb.tab().append(AminoAcid.kmerToString(i, k));}
+		bb.nl();
+		for(int a=0; a<2; a++){//valid
+			for(int b=0; b<frames; b++){
+				bb.append(a);
+				bb.tab().append(b);
+				for(int c=0; c<kMax; c++){
+					bb.tab().append(counts[a][b][c]);
+				}
+				bb.nl();
+			}
+		}
+		return bb;
+	}
+	
+	public ByteBuilder append0(ByteBuilder bb){
+		bb.append("#name\t").append(name).nl();
+		bb.append("#k\t").append(k).nl();
+		bb.append("#frames\t").append(frames).nl();
+		bb.append("#offset\t").append(leftOffset).nl();
+		bb.append("#valid\tframe");
+		for(int i=0; i<kMax; i++){bb.tab().append(AminoAcid.kmerToString(i, k));}
+		bb.nl();
+		for(int a=0; a<2; a++){//valid
+			for(int b=0; b<frames; b++){
+				bb.append(a);
+				bb.tab().append(b);
+				for(int c=0; c<kMax; c++){
+					bb.tab().append(0);
+				}
+				bb.nl();
+			}
+		}
+		return bb;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+
+	public final String name;
+	public final int k;
+	public final int mask;
+	public final int frames;
+	public final int kMax;
+	public final float invFrames;
+	public final int leftOffset;
+	public int rightOffset() {return frames-leftOffset-1;}
+	
+	public final float[][] probs;
+	public final long[][] countsTrue;
+	public final long[][] countsFalse;
+	public final long[][][] counts;
+
+	public final long[] validSums=KillSwitch.allocLong1D(2);
+	private float average=-1;
+	private float invAvg=-1;
+	
+}