Revision as of 14:26, 9 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];

      }

}