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import java.lang.reflect.Array;
import java.util.ArrayList;
import java.util.Collections;
import javax.swing.JCheckBox;
import javax.swing.JPanel;
public class AlignementMap extends JPanel{
ArrayList _mapResults;
AlignMapParamSet _param;
MapMain _parent;
private static final long serialVersionUID = 49L;
AlignementMap(AlignMapParamSet param, MapMain parent)
{
_param = param;
_parent = parent;
MapCalcul();
}
private void MapCalcul()
{
_mapResults = new ArrayList();
int period;
System.out.println(System.currentTimeMillis());
int i = 0 ;
while( i< 60)
{
period = 100;
ArrayList distribution = createDistribution(period);
_mapResults.add(distibutionResults(distribution, period));
i++;
}
System.out.println(System.currentTimeMillis());
}
private ArrayList createDistribution(int period)
{
ArrayList genes = _parent.getGeneList();
ArrayList distribution = new ArrayList();
for (int i = 0; i< genes.size(); i++)
{
int modulo = ((GenePoint)genes.get(i)).getPosition() % period;
distribution.add(modulo/(double)period);
}
return distribution;
}
private BestAlignementParamSet[] distibutionResults(ArrayList distribution, int period)
{
double error = 0.01;
BestAlignementParamSet[] errorsBA = new BestAlignementParamSet[100];
for (int i = 0; i<99 ; i++)
{
score best = BestAlignementfor(distribution, error);
ArrayList baArea = new ArrayList();
double pValue = pValue(best._score,_parent.getGeneList().size(), error );
float phase = (float)(best._position+ error/2);
baArea.add(new BAAreaParam(_param.getStart(),_param.getEnd(), (float)error, phase, pValue ));
if (phase > 1) phase = phase - 1;
errorsBA[i] = new BestAlignementParamSet(period, _param.getStart(), _param.getEnd() ,pValue, false, phase, _param.getStart(), baArea, period+"/"+error);
error = error + 0.01;
}
return errorsBA;
}
private score BestAlignementfor(ArrayList distribution, double error)
{
ArrayList sumList = new ArrayList();
ArrayList scoreList = new ArrayList();
int sum = 0;
for (int i = 0 ; i< distribution.size(); i++)
{
double pos = (Double)distribution.get(i);
sumList.add(new score(pos,-1));
sumList.add(new score(pos - error, 1));
if (pos <= error) sum++; // initilization with the gene in the first error window
}
Collections.sort(sumList);
scoreList.add(new score(0, sum));
double medPosition;
int max = sum;
int maxIndice = 0;
for (int i = 1 ; i < sumList.size(); i ++)
{
sum = sum + ((score)sumList.get(i-1))._score;
medPosition = ((score)sumList.get(i-1))._position + (((score)sumList.get(i))._position - ((score)sumList.get(i-1))._position)/2;
scoreList.add(new score(medPosition, sum));
if (sum> max)
{
max = sum;
maxIndice = i;
}
}
sum = sum + ((score)sumList.get( sumList.size()-1))._score;
medPosition = ((score)sumList.get( sumList.size()-1))._position + (1 - ((score)sumList.get( sumList.size()-1))._position)/2;
scoreList.add(new score(medPosition, sum));
if (sum> max)
{
max = sum;
maxIndice = sumList.size();
}
return (score)scoreList.get(maxIndice);
}
private double pValue(int nbGenes, int nbGenesIn, double error)
{
double logPVal = 0;
double sum = 0;
for (int i = 1 ; i<= nbGenes; i++)
{
sum = sum + i;
}
logPVal = sum;
sum = 0;
for (int i = 1 ; i<= nbGenesIn; i++)
{
sum = sum + i;
}
logPVal = logPVal - sum;
sum = 0;
for (int i = 1 ; i<= (nbGenes - nbGenesIn); i++)
{
sum = sum + i;
}
logPVal = logPVal - sum;
logPVal = logPVal+nbGenesIn* Math.log(error) + (nbGenes - nbGenesIn) * Math.log(1 - error);
return Math.exp(logPVal);
}
private class score implements Comparable
{
double _position;
int _score;
score(double position, int score)
{
if (position < 0) position = 1 + position;
_position = position;
_score = score;
}
public int compareTo(Object o) {
return( Double.compare(_position, ((score)o)._position));
}
}
} |
