/**
 * 
 */
package org.vamsas.test.objects;

import org.vamsas.objects.core.Alignment;
import org.vamsas.objects.core.AlignmentSequence;
import org.vamsas.objects.core.DataSet;
import org.vamsas.objects.core.Sequence;
import org.vamsas.objects.core.VAMSAS;

/**
 * @author jim
 * test XSD-Java binding classes in org.vamsas.objects.core
 */
public class Core {
  /**
   * 
   * complete any automatically completable entries in the dataset
   * @param ds
   */
  public static void complete(DataSet ds) {
    Sequence[] q = ds.getSequence();
    for (int i=0,j=q.length; i<j; i++) {
      q[i].setStart(i+1);
      q[i].setEnd(q[i].getSequence().length()+i+1);
    }
  }  
  public static Sequence Sequence(String Name, String Sequence, String Dictionary, int start, int end) {
    Sequence seq= new Sequence();
     seq.setDictionary(Dictionary);
     seq.setName(Name);
     seq.setSequence(Sequence);
     seq.setStart(start);
     if (start<=end) {
       if ((end-start)!=Sequence.length())
         seq.setEnd(start+Sequence.length());
     } else {
       // reverse topology mapping. TODO: VAMSAS: decide if allowed to do start>end on Sequence object
       if ((start-end)!=Sequence.length())
         seq.setEnd(end+Sequence.length());
     }
     return seq;
  }
  public static VAMSAS getDemoVamsas() {
     VAMSAS v=new VAMSAS();
     DataSet ds = new DataSet();
     ds.addSequence(Sequence("Dummy1","ASDFLEQ","info:iubmb.org/aminoacids", 5, 11));
     complete(ds);
     v.addDataSet(ds);
     Alignment al = new Alignment();
     
     al.addAlignmentSequence(new AlignmentSequence());
     return v;
   }
  /**
   * @param args
   */
  public static void main(String[] args) {
    // TODO Auto-generated method stub

  }

}