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package bin;
import java.util.ArrayList;
import dna.Data;
import fileIO.ByteFile;
import shared.LineParser1;
import shared.Tools;
import structures.FloatList;
public class KmerProb {
public static synchronized void load() {
if(matrix!=null) {return;}
String fname=Data.findPath("?shred4merFractions.tsv");
matrix=load(fname);
}
private static float[][] load(String fname){
ArrayList<byte[]> lines=ByteFile.toLines(fname);
ArrayList<FloatList> vectors=new ArrayList<FloatList>();
LineParser1 lp=new LineParser1('\t');
for(byte[] line : lines) {
lp.set(line);
if(!lp.startsWith('#')) {
// System.err.println("Making a vector: "+lp.terms());
FloatList list=new FloatList(lp.terms()-2);
for(int i=2; i<lp.terms(); i++) {
float f=lp.parseFloat(i);
assert(f>=0 && f<=1);
list.add(f);
}
vectors.add(list);
}
}
float[][] data=new float[vectors.size()][];
for(int i=0; i<vectors.size(); i++) {
FloatList list=vectors.get(i);
assert(list.size()==list.array.length);
list.shrink();
data[i]=list.array;
}
// System.err.println("Read "+data.length+" vectors.");
return data;
}
/** Probability that two sequences with this
* kmer frequency cosine difference come from the same genome.
* The length is the length of the shorter sequence.
* Genomes used for this were 5000 bacteria, <95% ANI,
* around 700m pairs.
* @param length
* @param dif
* @return
*/
public static float prob(long length, float dif) {
int idx=quantizeLength(length);
float[] array=matrix[idx];
int idx2=Math.min(array.length-1, (int)(dif*1024));
return array[idx2];
}
//Bins contain everything UP TO that size.
//For example, bin 0 is 256, which contains 1-256.
//Bin 1 is 256-362, then 363-512, etc.
static int quantizeLength(long size) {
size=Tools.mid(size, 200, 200000);
int idx=(int)Math.ceil(2*Tools.log2(size));
return idx-idxOffset;
}
static int dequantizeLength(int idx) {
idx+=idxOffset;
int size=(int)Math.pow(2, idx/2f);
return size;
}
private static final int idxOffset=(int)Math.ceil(2*Tools.log2(200));
public static float[][] matrix;
}
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