package jalview.controller;

import java.awt.Color;

import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;

public class AlignViewController implements AlignViewControllerI
{
  AlignViewportI viewport=null;
  AlignmentViewPanel alignPanel=null;
  /**
   * the GUI container that is handling interactions with the user
   */
  private AlignViewControllerGuiI avcg;
  @Override
  protected void finalize() throws Throwable {
    viewport = null;
    alignPanel = null;
    avcg = null;
  };
  
  public AlignViewController(AlignViewControllerGuiI alignFrame, AlignViewportI viewport,
          AlignmentViewPanel alignPanel)
  {
    this.avcg = alignFrame;
    this.viewport=viewport;
    this.alignPanel = alignPanel;
  }
  @Override
  public void setViewportAndAlignmentPanel(AlignViewportI viewport,AlignmentViewPanel alignPanel)
  {
    this.alignPanel = alignPanel;
    this.viewport = viewport;
    
  }
  @Override
  public boolean makeGroupsFromSelection()
  {

    if (viewport.getSelectionGroup() != null)
    {
      SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
              viewport.getSequenceSelection(),
              viewport.getAlignmentView(true).getSequenceStrings(
                      viewport.getGapCharacter()), viewport.getAlignment()
                      .getGroups());
      viewport.getAlignment().deleteAllGroups();
      viewport.clearSequenceColours();
      viewport.setSelectionGroup(null);
      // set view properties for each group
      for (int g = 0; g < gps.length; g++)
      {
        // gps[g].setShowunconserved(viewport.getShowUnconserved());
        gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
        viewport.getAlignment().addGroup(gps[g]);
        Color col = new Color((int) (Math.random() * 255),
                (int) (Math.random() * 255), (int) (Math.random() * 255));
        col = col.brighter();
        for (SequenceI sq : gps[g].getSequences(null))
          viewport.setSequenceColour(sq, col);
      }
      return true;
    }
    return false;
}
  @Override
  public boolean createGroup()
  {

    SequenceGroup sg = viewport.getSelectionGroup();
    if (sg!=null)
    {
        viewport.getAlignment().addGroup(sg);
        return true;
      } 
    return false;
  }
  @Override
  public boolean unGroup()
  {
    SequenceGroup sg = viewport.getSelectionGroup();
    if (sg!=null)
    {
        viewport.getAlignment().deleteGroup(sg);
        return true;
    }
    return false;
  }
  @Override
  public boolean deleteGroups()
  {
    if (viewport.getAlignment().getGroups()!=null && viewport.getAlignment().getGroups().size()>0)
    {
    viewport.getAlignment().deleteAllGroups();
    viewport.clearSequenceColours();
    viewport.setSelectionGroup(null);
    return true;
    }
    return false;
  }
    
  }