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package structures;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Locale;
import fileIO.ByteFile;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import shared.Tools;
public abstract class CoverageArray implements Serializable {
/**
*
*/
private static final long serialVersionUID = -7175422489330746676L;
public static final CoverageArray read(String fname){
if(!fname.contains(".ca")){
throw new RuntimeException();
// ca=new CoverageArray2();
// ca.load(new TsvCoverageFile(fname));
// return ca;
}
fname=ReadWrite.findFileExtension(fname);
// System.err.println("Found "+fname);
return ReadWrite.read(CoverageArray.class, fname, true);
// if(fname.endsWith(".ca2") || fname.contains(".ca2.")){return ReadWrite.read(CoverageArray2.class, fname);}
// else if(fname.endsWith(".ca") || fname.contains(".ca.")){return ReadWrite.read(CoverageArray1.class, fname);}
// else{return ReadWrite.read(CoverageArray.class, fname);}
}
public CoverageArray(int chrom){chromosome=chrom;}
/**
* @param loc
* @param amt
*/
public abstract void increment(int loc, int amt);
/**
* @param loc
*/
public abstract void increment(int loc);
public final void incrementRange(int min, int max){incrementRange(min, max, 1);}
public abstract void incrementRange(int min, int max, int amt);
public abstract void incrementRangeSynchronized(int min, int max, int amt);
public void incrementRanges(IntList ranges, int amt){
for(int i=0; i<ranges.size; i+=2){
int a=ranges.get(i), b=ranges.get(i+1);
incrementRange(a, b-1, 1);
}
}
public abstract void set(int loc, int val);
public abstract int get(int loc);
public abstract void resize(int newlen);
public final double[][] toGraph(int blocksize, int min, int max){
min=max(min, minIndex);
max=min(max, maxIndex);
int length=max-min;
ArrayList<double[]> list=new ArrayList<double[]>();
int block;
if(blocksize<=0){
// block=((array.length+62999)/63000);//For Excel
// block=((length+62999)/63000);//For Excel
block=((length+31499)/31500);//For Excel
}else{
block=blocksize;
}
block=max(block, 1);
int current=0;
double[] sum=new double[2];
for(int loc=min; loc<=max; loc++){
if(current==block){
for(int i=0; i<sum.length; i++){
sum[i]=sum[i]/current;
}
sum[0]=Math.round(sum[0]);
list.add(sum);
sum=new double[2];
current=0;
}
sum[0]+=loc;
sum[1]+=get(loc);
current++;
}
return list.toArray(new double[0][]);
}
public static final void print(double[][] data){
// data=stats.Smoother.weightedAveragePlank(data, 24);
assert(false) : "Smoother disabled in this code purely to reduce dependancies.";
StringBuilder sb=new StringBuilder(data.length*20);
for(double[] d : data){
sb.append(String.format(Locale.ROOT, "%d\t%.2f\n",(int)d[0],d[1]));
}
System.out.print(sb);
}
public static CoverageArray makeArray(int num, int size, Class<? extends CoverageArray> c){
if(c==CoverageArray2.class){
return new CoverageArray2(num, size);
}else if(c==CoverageArray3.class){
return new CoverageArray3(num, size);
}else if(c==CoverageArray3A.class){
return new CoverageArray3(num, size);
}
throw new RuntimeException("Unhandled class: "+c);
}
//TODO: Extremely slow due to string processing
public static HashMap<String, CoverageArray> loadDepth(FileFormat ffdepth, Class<? extends CoverageArray> c) {
ByteFile bf=ByteFile.makeByteFile(ffdepth);
HashMap<String, CoverageArray> map=new HashMap<String, CoverageArray>();
String prevName=null;
CoverageArray prevArray=null;
for(byte[] line=bf.nextLine(); line!=null; line=bf.nextLine()){
if(line[0]!='#'){
// ArrayList<byte[]> split=Tools.split(line, 0, (byte)'\t');
String[] split=Tools.tabPattern.split(new String(line));
String name=split[0];
int pos=Integer.parseInt(split[1]);
int depth=Integer.parseInt(split[2]);
CoverageArray current;
if(name.equals(prevName)){
current=prevArray;
}else{
assert(!map.containsKey(name)) : name; //Could do a lookup but should not be needed
current=makeArray(map.size()+1, 64, c);
map.put(name, current);
prevName=name;
prevArray=current;
}
if(depth>0){current.set(pos, depth);}
}
}
return map;
}
@Override
public abstract String toString();
static final long min(long x, long y){return x<y ? x : y;}
static final long max(long x, long y){return x>y ? x : y;}
static final int min(int x, int y){return x<y ? x : y;}
static final int max(int x, int y){return x>y ? x : y;}
public int chromosome;
public int maxIndex=-1;
public int minIndex=Integer.MAX_VALUE;
public int length(){return maxIndex-minIndex+1;}
public abstract int arrayLength();
private static boolean OVERFLOWED=false;
}
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