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package prok;
import java.util.ArrayList;
import json.JsonObject;
import shared.Tools;
import structures.ByteBuilder;
public class ScoreTracker {
public ScoreTracker(int type_){
type=type_;
}
public void add(ScoreTracker st){
geneStartScoreSum+=st.geneStartScoreSum;
geneStopScoreSum+=st.geneStopScoreSum;
geneInnerScoreSum+=st.geneInnerScoreSum;
lengthSum+=st.lengthSum;
geneStartScoreCount+=st.geneStartScoreCount;
geneStopScoreCount+=st.geneStopScoreCount;
geneInnerScoreCount+=st.geneInnerScoreCount;
lengthCount+=st.lengthCount;
}
public void add(ArrayList<Orf>[] array){
for(ArrayList<Orf> list : array){add(list);}
}
public void add(ArrayList<Orf> list){
if(list==null){return;}
for(Orf orf : list){
if(orf.type==type){add(orf);}
}
}
public void add(Orf orf){
if(orf==null || orf.type!=type){return;}
geneStartScoreSum+=orf.startScore;
geneStopScoreSum+=orf.stopScore;
geneInnerScoreSum+=orf.averageKmerScore();
lengthSum+=orf.length();
geneStartScoreCount++;
geneStopScoreCount++;
geneInnerScoreCount++;
lengthCount++;
}
@Override
public String toString(){
ByteBuilder bb=new ByteBuilder();
bb.append("Start Score: \t ").append(geneStartScoreSum/geneStartScoreCount, 4).nl();
bb.append("Stop Score: \t ").append(geneStopScoreSum/geneStopScoreCount, 4).nl();
bb.append("Inner Score: \t ").append(geneInnerScoreSum/geneInnerScoreCount, 4).nl();
bb.append("Length: \t ").append(lengthSum/(double)lengthCount, 2).nl();
if(genomeSize>0){
bb.append("Approx Genic Fraction:\t ").append(Tools.min(1.0, lengthSum/(double)genomeSize), 4).nl();
}
return bb.toString();
}
public JsonObject toJson(){
JsonObject jo=new JsonObject();
jo.addLiteral("Start Score", geneStartScoreSum/geneStartScoreCount, 4);
jo.addLiteral("Stop Score", geneStopScoreSum/geneStopScoreCount, 4);
jo.addLiteral("Inner Score", geneInnerScoreSum/geneInnerScoreCount, 4);
jo.addLiteral("Length", lengthSum/(double)lengthCount, 2);
if(genomeSize>0){
jo.addLiteral("Approx Genic Fraction", Tools.min(1.0, lengthSum/(double)genomeSize), 4);
}
return jo;
}
long geneStartScoreCount=0;
long geneStopScoreCount=0;
long geneInnerScoreCount=0;
long lengthCount=0;
double geneStartScoreSum=0;
double geneStopScoreSum=0;
double geneInnerScoreSum=0;
long lengthSum=0;
long genomeSize=0;
final int type;
}
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