package jalview.gui;

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

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

import javax.swing.JMenuItem;

/**
 * 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 abstract String getStateInfo();

  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;
  }

  public AlignmentPanel[] getAllAlignmentPanels()
  {
    AlignmentPanel[] t, list = new AlignmentPanel[0];
    for (String setid : _aps)
    {
      AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
      if (panels != null)
      {
        t = new AlignmentPanel[list.length + panels.length];
        System.arraycopy(list, 0, t, 0, list.length);
        System.arraycopy(panels, 0, t, list.length, panels.length);
        list = t;
      }
    }
  
    return list;
  }

  /**
   * set the primary alignmentPanel reference and add another alignPanel to the
   * list of ones to use for colouring and aligning
   * 
   * @param nap
   */
  public void addAlignmentPanel(AlignmentPanel nap)
  {
    if (getAlignmentPanel() == null)
    {
      setAlignmentPanel(nap);
    }
    if (!_aps.contains(nap.av.getSequenceSetId()))
    {
      _aps.add(nap.av.getSequenceSetId());
    }
  }

  /**
   * remove any references held to the given alignment panel
   * 
   * @param nap
   */
  public void removeAlignmentPanel(AlignmentPanel nap)
  {
    try
    {
      _alignwith.remove(nap);
      _colourwith.remove(nap);
      if (getAlignmentPanel() == nap)
      {
        setAlignmentPanel(null);
        for (AlignmentPanel aps : getAllAlignmentPanels())
        {
          if (aps != nap)
          {
            setAlignmentPanel(aps);
            break;
          }
        }
      }
    } catch (Exception ex)
    {
    }
    if (getAlignmentPanel() != null)
    {
      buildActionMenu();
    }
  }

  public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
  {
    addAlignmentPanel(nap);
    if (!_alignwith.contains(nap))
    {
      _alignwith.add(nap);
    }
  }

  public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
  {
    if (_alignwith.contains(nap))
    {
      _alignwith.remove(nap);
    }
  }

  public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, boolean enableColourBySeq)
  {
    useAlignmentPanelForColourbyseq(nap);
    getBinding().setColourBySequence(enableColourBySeq);
    seqColour.setSelected(enableColourBySeq);
    viewerColour.setSelected(!enableColourBySeq);
  }

  public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
  {
    addAlignmentPanel(nap);
    if (!_colourwith.contains(nap))
    {
      _colourwith.add(nap);
    }
  }

  public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
  {
    if (_colourwith.contains(nap))
    {
      _colourwith.remove(nap);
    }
  }
}