src/org/vamsas/test/objects/Core.java

   1 /**
   2  *
   3  */
   4 package org.vamsas.test.objects;
   5
   6 import org.vamsas.objects.core.Alignment;
   7 import org.vamsas.objects.core.AlignmentSequence;
   8 import org.vamsas.objects.core.DataSet;
   9 import org.vamsas.objects.core.Sequence;
  10 import org.vamsas.objects.core.VAMSAS;
  11
  12 /**
  13  * @author jim
  14  * test XSD-Java binding classes in org.vamsas.objects.core
  15  */
  16 public class Core {
  17   /**
  18    *
  19    * complete any automatically completable entries in the dataset
  20    * @param ds
  21    */
  22   public static void complete(DataSet ds) {
  23     Sequence[] q = ds.getSequence();
  24     for (int i=0,j=q.length; i<j; i++) {
  25       q[i].setStart(i+1);
  26       q[i].setEnd(q[i].getSequence().length()+i+1);
  27     }
  28   }
  29   public static Sequence Sequence(String Name, String Sequence, String Dictionary, int start, int end) {
  30     Sequence seq= new Sequence();
  31      seq.setDictionary(Dictionary);
  32      seq.setName(Name);
  33      seq.setSequence(Sequence);
  34      seq.setStart(start);
  35      if (start<=end) {
  36        if ((end-start)!=Sequence.length())
  37          seq.setEnd(start+Sequence.length());
  38      } else {
  39        // reverse topology mapping. TODO: decide if allowed to do start>end on Sequence object
  40        if ((start-end)!=Sequence.length())
  41          seq.setEnd(end+Sequence.length());
  42      }
  43      return seq;
  44   }
  45   public static VAMSAS getDemoVamsas() {
  46      VAMSAS v=new VAMSAS();
  47      DataSet ds = new DataSet();
  48      ds.addSequence(Sequence("Dummy1","ASDFLEQ",
  49      seq.setDictionary("info:iubmb.org/aminoacids");
  50      seq.setName(
  51      ds.addSequence(seq);
  52     seq = new Sequence();
  53      seq.setDictionary("info:iubmb.org/aminoacids");
  54      seq.setName("Dummy1");
  55      seq.setSequence("ASDFLEQ");
  56      complete(ds);
  57      v.addDataSet(ds);
  58      Alignment al = new Alignment();
  59
  60      al.addAlignmentSequence(new AlignmentSequence());
  61      return v;
  62    }
  63   /**
  64    * @param args
  65    */
  66   public static void main(String[] args) {
  67     // TODO Auto-generated method stub
  68
  69   }
  70
  71 }