package jalview.gui;

import java.awt.Component;
import java.util.ArrayList;
import java.util.List;
import java.util.Vector;

import javax.swing.JMenuItem;

import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.jbgui.GStructureViewer;

/**
 * Base class with common functionality for JMol, Chimera or other structure
 * viewers.
 * 
 * @author gmcarstairs
 *
 */
public abstract class StructureViewerBase extends GStructureViewer
        implements Runnable, ViewSetProvider
{

  /**
   * list of sequenceSet ids associated with the view
   */
  protected List<String> _aps = new ArrayList<String>();
  /**
   * list of alignment panels to use for superposition
   */
  protected Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
  /**
   * list of alignment panels that are used for colouring structures by aligned
   * sequences
   */
  protected Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
  private String viewId = null;
  private AlignmentPanel ap;

  /**
   * 
   * @param ap2
   * @return true if this Jmol instance is linked with the given alignPanel
   */
  public boolean isLinkedWith(AlignmentPanel ap2)
  {
    return _aps.contains(ap2.av.getSequenceSetId());
  }

  public boolean isUsedforaligment(AlignmentPanel ap2)
  {
  
    return (_alignwith != null) && _alignwith.contains(ap2);
  }

  public boolean isUsedforcolourby(AlignmentPanel ap2)
  {
    return (_colourwith != null) && _colourwith.contains(ap2);
  }

  /**
   * 
   * @return TRUE if the view is NOT being coloured by the alignment colours.
   */
  public boolean isColouredByViewer()
  {
    return !getBinding().isColourBySequence();
  }

  public String getViewId()
  {
    if (viewId == null)
    {
      viewId = System.currentTimeMillis() + "." + this.hashCode();
    }
    return viewId;
  }

  protected void setViewId(String viewId)
  {
    this.viewId = viewId;
  }

  public String getStateInfo()
  {
    return "";
  }

  protected void buildActionMenu()
  {
    if (_alignwith == null)
    {
      _alignwith = new Vector<AlignmentPanel>();
    }
    if (_alignwith.size() == 0 && ap != null)
    {
      _alignwith.add(ap);
    }
    ;
    for (Component c : viewerActionMenu.getMenuComponents())
    {
      if (c != alignStructs)
      {
        viewerActionMenu.remove((JMenuItem) c);
      }
    }
  }

  public AlignmentPanel getAlignmentPanel()
  {
    return ap;
  }

  protected void setAlignmentPanel(AlignmentPanel alp)
  {
    this.ap = alp;
  }
}