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package jgi;
import java.util.Arrays;
import shared.Tools;
import structures.CoverageArray;
/**
* This class is designed to help calculate coverage of ORFs
* @author Brian Bushnell
* @date May 13, 2013
*
*/
public class Orf implements Comparable<Orf>{
public Orf(String name_, int start_, int stop_, byte strand_){
name=name_;
start=start_;
stop=stop_;
strand=strand_;
assert(stop>start || (start==0 && stop==0));
}
@Override
public String toString(){
return name+"\t"+start+"\t"+stop+"\t"+strand;
}
public int length(){return stop-start+1;}
public double avgCoverage(){
int len=length();
return len<=0 ? 0 : baseDepth/(double)len;
}
public double fractionCovered(){
int len=length();
return len<=0 ? 0 : baseCoverage/(double)len;
}
public int[] readCoverageArray(CoverageArray ca){
final int len=length();
if(len<1 || ca==null){return null;}
final int[] array=new int[len];
baseCoverage=0;
baseDepth=0;
minDepth=Integer.MAX_VALUE;
maxDepth=0;
medianDepth=0;
stdevDepth=0;
for(int i=start, j=0; i<=stop; i++, j++){
int cov=ca.get(i);
array[j]=cov;
if(cov>1){
baseCoverage++;
baseDepth+=cov;
minDepth=Tools.min(minDepth, cov);
maxDepth=Tools.max(maxDepth, cov);
}
}
if(baseDepth>0){
Arrays.sort(array);
medianDepth=array[array.length/2];
stdevDepth=Tools.standardDeviation(array);
}
return array;
}
@Override
public int compareTo(Orf o) {
int x=name.compareTo(o.name);
if(x!=0){return x;}
x=o.start-start;
if(x!=0){return x;}
x=o.stop-stop;
if(x!=0){return x;}
return o.strand-strand;
}
@Override
public boolean equals(Object o){return equals((Orf)o);}
public boolean equals(Orf o){return compareTo(o)==0;}
@Override
public int hashCode(){return Integer.rotateLeft(name.hashCode(),16)^(start<<8)^(stop)^strand;}
/** Name of ORF (not necessarily the name of its scaffold) */
public String name;
public int start;
public int stop;
public byte strand;
/** Number of bases with nonzero coverage */
public long baseCoverage;
/** Number of reads mapped to this orf */
public long readDepth=0;
/** Number of bases mapped to this orf */
public long baseDepth=0;
/** Lowest base depth */
public long minDepth=0;
/** Highest base depth */
public long maxDepth=0;
/** Median base depth */
public long medianDepth=0;
/** Standard deviation of depth */
public double stdevDepth=0;
}
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