Revision as of 14:36, 13 March 2009

DAS workshop March 9th-11th 2009 Genome Campus, Hinxton

BioSapiens Network

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Day3page

Chromsome.java

package myplugins;

import java.util.ArrayList;
import java.util.Iterator;

import org.biojava.servlets.dazzle.Segment;
import org.biojava.servlets.dazzle.datasource.GFFFeature;

/**
 * simple class for demo purposes that returns features from given
segments of a chromosome
 * that has probably been specified in gff type format
 * @author jw12
 *
 */
public class Chromosome {
       private String id="";
       private int start=1;
       private int end;
       ArrayList features;
       public Chromosome(String id, int end){
        this.id=id;
        this.end=end;
        features =new ArrayList();
       }
       public void addFeature(GFFFeature feature){
               this.features.add(feature);
       }
       public GFFFeature[] getFeatures(Segment seg){
               System.out.println("seg in chromosome="+seg);
               ArrayList featuresOnSegment=new ArrayList();
               int start=seg.getStart();
               int stop =seg.getStop();
               //loop over arraylist of features and return a lis
               Iterator it=features.iterator();
            while(it.hasNext()){
                       GFFFeature feature=(GFFFeature)it.next();
                       int fStart=Integer.parseInt(feature.getStart());
                       int fStop=Integer.parseInt(feature.getEnd());
               //if between start and stop then include in returned list
                       if((fStart>=start && fStart<=stop)||(fStop<=stop && fStop>=start)){
                               featuresOnSegment.add(feature);
                       }
               }
               return (GFFFeature[]) featuresOnSegment.toArray(new
GFFFeature[featuresOnSegment.size()]);
               //return new GFFFeature[0];
       }
}