package jalview.gui;

import jalview.datamodel.*;

import java.util.*;

public class Selection
{

  Vector selected = new Vector();
  AlignViewport av;

  public Selection(AlignViewport av)
  {
    this.av = av;
  }

  public void addElement(SequenceI seq) {
    selected.addElement(seq);
    SequenceGroup sg = av.getRubberbandGroup();
    if(sg==null)
    {
      sg = new SequenceGroup();
      sg.setEndRes(av.alignment.getWidth()-1);
      av.setRubberbandGroup(sg);
    }

    sg.addSequence(seq);

  }

  public void clear() {
    selected.removeAllElements();
  }

  public void removeElement(SequenceI seq) {
    if (selected.contains(seq))
      selected.removeElement(seq);
    else
      System.err.println("WARNING: Tried to remove SequenceI NOT in Selection");

    SequenceGroup sg = av.getRubberbandGroup();
    if (sg != null)
      sg.deleteSequence(seq);


  }

  public boolean contains(SequenceI seq) {
    return selected.contains(seq);
  }

  public SequenceI sequenceAt(int i) {
    return (SequenceI)selected.elementAt(i);
  }

  public int size() {
    return selected.size();
  }

  public Vector asVector() {
    return selected;
  }

  public void selectAll(AlignmentI align) {
    for (int i=0;i<align.getSequences().size();i++) {
      SequenceI seq = align.getSequenceAt(i);
      if (!contains(seq)) {
        addElement(seq);
      }
    }
  }
}