/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.gui;

import jalview.analysis.AlignmentSorter;
import jalview.analysis.NJTree;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.ViewBasedAnalysisI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.OrderCommand;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.NodeTransformI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.io.NewickFile;
import jalview.jbgui.GTreePanel;
import jalview.util.ImageMaker;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;

import java.awt.Font;
import java.awt.Graphics;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.image.BufferedImage;
import java.beans.PropertyChangeEvent;
import java.io.FileOutputStream;
import java.util.ArrayList;
import java.util.List;

import javax.imageio.ImageIO;
import javax.swing.ButtonGroup;
import javax.swing.JMenuItem;
import javax.swing.JRadioButtonMenuItem;

import org.jibble.epsgraphics.EpsGraphics2D;

/**
 * DOCUMENT ME!
 * 
 * @author $author$
 * @version $Revision$
 */
public class TreePanel extends GTreePanel
{
  String type;

  String pwtype;

  TreeCanvas treeCanvas;

  NJTree tree;

  AlignViewport av;

  /**
   * Creates a new TreePanel object.
   * 
   * @param av
   *          DOCUMENT ME!
   * @param seqVector
   *          DOCUMENT ME!
   * @param type
   *          DOCUMENT ME!
   * @param pwtype
   *          DOCUMENT ME!
   * @param s
   *          DOCUMENT ME!
   * @param e
   *          DOCUMENT ME!
   */
  public TreePanel(AlignmentPanel ap, String type, String pwtype)
  {
    super();
    initTreePanel(ap, type, pwtype, null, null);

    // We know this tree has distances. JBPNote TODO: prolly should add this as
    // a userdefined default
    // showDistances(true);
  }

  /**
   * Creates a new TreePanel object.
   * 
   * @param av
   *          DOCUMENT ME!
   * @param seqVector
   *          DOCUMENT ME!
   * @param newtree
   *          DOCUMENT ME!
   * @param type
   *          DOCUMENT ME!
   * @param pwtype
   *          DOCUMENT ME!
   */
  public TreePanel(AlignmentPanel ap, String type, String pwtype,
          NewickFile newtree)
  {
    super();
    initTreePanel(ap, type, pwtype, newtree, null);
  }

  public TreePanel(AlignmentPanel av, String type, String pwtype,
          NewickFile newtree, AlignmentView inputData)
  {
    super();
    initTreePanel(av, type, pwtype, newtree, inputData);
  }

  public AlignmentI getAlignment()
  {
    return treeCanvas.av.getAlignment();
  }

  public AlignmentViewport getViewPort()
  {
    return treeCanvas.av;
  }

  void initTreePanel(AlignmentPanel ap, String type, String pwtype,
          NewickFile newTree, AlignmentView inputData)
  {

    av = ap.av;
    this.type = type;
    this.pwtype = pwtype;

    treeCanvas = new TreeCanvas(this, ap, scrollPane);
    scrollPane.setViewportView(treeCanvas);

    PaintRefresher.Register(this, ap.av.getSequenceSetId());

    buildAssociatedViewMenu();

    av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
    {
      @Override
      public void propertyChange(PropertyChangeEvent evt)
      {
        if (evt.getPropertyName().equals("alignment"))
        {
          if (tree == null)
          {
            System.out.println("tree is null");
            // TODO: deal with case when a change event is received whilst a
            // tree is still being calculated - should save reference for
            // processing message later.
            return;
          }
          if (evt.getNewValue() == null)
          {
            System.out
                    .println("new alignment sequences vector value is null");
          }

          tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
          treeCanvas.nameHash.clear(); // reset the mapping between canvas
          // rectangles and leafnodes
          repaint();
        }
      }
    });

    TreeLoader tl = new TreeLoader(newTree);
    if (inputData != null)
    {
      tl.odata = inputData;
    }
    tl.start();

  }

  @Override
  public void viewMenu_menuSelected()
  {
    buildAssociatedViewMenu();
  }

  void buildAssociatedViewMenu()
  {
    AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
            .getSequenceSetId());
    if (aps.length == 1 && treeCanvas.ap == aps[0])
    {
      associateLeavesMenu.setVisible(false);
      return;
    }

    associateLeavesMenu.setVisible(true);

    if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
    {
      viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
    }

    associateLeavesMenu.removeAll();

    JRadioButtonMenuItem item;
    ButtonGroup buttonGroup = new ButtonGroup();
    int i, iSize = aps.length;
    final TreePanel thisTreePanel = this;
    for (i = 0; i < iSize; i++)
    {
      final AlignmentPanel ap = aps[i];
      item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
      buttonGroup.add(item);
      item.addActionListener(new ActionListener()
      {
        @Override
        public void actionPerformed(ActionEvent evt)
        {
          treeCanvas.applyToAllViews = false;
          treeCanvas.ap = ap;
          treeCanvas.av = ap.av;
          PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
        }
      });

      associateLeavesMenu.add(item);
    }

    final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
            MessageManager.getString("label.all_views"));
    buttonGroup.add(itemf);
    itemf.setSelected(treeCanvas.applyToAllViews);
    itemf.addActionListener(new ActionListener()
    {
      @Override
      public void actionPerformed(ActionEvent evt)
      {
        treeCanvas.applyToAllViews = itemf.isSelected();
      }
    });
    associateLeavesMenu.add(itemf);

  }

  class TreeLoader extends Thread
  {
    NewickFile newtree;

    jalview.datamodel.AlignmentView odata = null;

    public TreeLoader(NewickFile newtree)
    {
      this.newtree = newtree;
      if (newtree != null)
      {
        // Must be outside run(), as Jalview2XML tries to
        // update distance/bootstrap visibility at the same time
        showBootstrap(newtree.HasBootstrap());
        showDistances(newtree.HasDistances());
      }
    }

    @Override
    public void run()
    {

      if (newtree != null)
      {
        if (odata == null)
        {
          tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
        }
        else
        {
          tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
                  newtree);
        }
        if (!tree.hasOriginalSequenceData())
        {
          allowOriginalSeqData(false);
        }
      }
      else
      {
        int start, end;
        SequenceI[] seqs;
        boolean selview = av.getSelectionGroup() != null
                && av.getSelectionGroup().getSize() > 1;
        AlignmentView seqStrings = av.getAlignmentView(selview);
        if (!selview)
        {
          start = 0;
          end = av.getAlignment().getWidth();
          seqs = av.getAlignment().getSequencesArray();
        }
        else
        {
          start = av.getSelectionGroup().getStartRes();
          end = av.getSelectionGroup().getEndRes() + 1;
          seqs = av.getSelectionGroup().getSequencesInOrder(
                  av.getAlignment());
        }
        ScoreModelI sm = ScoreModels.getInstance().forName(pwtype);
        if (sm instanceof ViewBasedAnalysisI)
        {
          try
          {
            sm = sm.getClass().newInstance();
            ((ViewBasedAnalysisI) sm)
                    .configureFromAlignmentView(treeCanvas.ap);
          } catch (Exception q)
          {
            Cache.log.error("Couldn't create a scoremodel instance for "
                    + sm.getName());
          }
          tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
        }
        else
        {
          tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
                  end);
        }
        showDistances(true);
      }

      tree.reCount(tree.getTopNode());
      tree.findHeight(tree.getTopNode());
      treeCanvas.setTree(tree);
      treeCanvas.repaint();
      av.setCurrentTree(tree);
      if (av.getSortByTree())
      {
        sortByTree_actionPerformed();
      }
    }
  }

  public void showDistances(boolean b)
  {
    treeCanvas.setShowDistances(b);
    distanceMenu.setSelected(b);
  }

  public void showBootstrap(boolean b)
  {
    treeCanvas.setShowBootstrap(b);
    bootstrapMenu.setSelected(b);
  }

  public void showPlaceholders(boolean b)
  {
    placeholdersMenu.setState(b);
    treeCanvas.setMarkPlaceholders(b);
  }

  private void allowOriginalSeqData(boolean b)
  {
    originalSeqData.setVisible(b);
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  public NJTree getTree()
  {
    return tree;
  }

  /**
   * DOCUMENT ME!
   * 
   * @param e
   *          DOCUMENT ME!
   */
  @Override
  public void textbox_actionPerformed(ActionEvent e)
  {
    CutAndPasteTransfer cap = new CutAndPasteTransfer();

    StringBuffer buffer = new StringBuffer();

    if (type.equals(NJTree.AVERAGE_DISTANCE))
    {
      buffer.append("Average distance tree using ");
    }
    else
    {
      buffer.append("Neighbour joining tree using ");
    }

    ScoreModelI sm = ScoreModels.getInstance().forName(pwtype);
    buffer.append(sm.getName());

    NewickFile fout = new NewickFile(tree.getTopNode());
    try
    {
      cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
              tree.isHasRootDistance()));
      Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
    } catch (OutOfMemoryError oom)
    {
      new OOMWarning("generating newick tree file", oom);
      cap.dispose();
    }

  }

  /**
   * DOCUMENT ME!
   * 
   * @param e
   *          DOCUMENT ME!
   */
  @Override
  public void saveAsNewick_actionPerformed(ActionEvent e)
  {
    JalviewFileChooser chooser = new JalviewFileChooser(
            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
    chooser.setFileView(new JalviewFileView());
    chooser.setDialogTitle(MessageManager
            .getString("label.save_tree_as_newick"));
    chooser.setToolTipText(MessageManager.getString("action.save"));

    int value = chooser.showSaveDialog(null);

    if (value == JalviewFileChooser.APPROVE_OPTION)
    {
      String choice = chooser.getSelectedFile().getPath();
      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
              .getSelectedFile().getParent());

      try
      {
        jalview.io.NewickFile fout = new jalview.io.NewickFile(
                tree.getTopNode());
        String output = fout.print(tree.isHasBootstrap(),
                tree.isHasDistances(), tree.isHasRootDistance());
        java.io.PrintWriter out = new java.io.PrintWriter(
                new java.io.FileWriter(choice));
        out.println(output);
        out.close();
      } catch (Exception ex)
      {
        ex.printStackTrace();
      }
    }
  }

  /**
   * DOCUMENT ME!
   * 
   * @param e
   *          DOCUMENT ME!
   */
  @Override
  public void printMenu_actionPerformed(ActionEvent e)
  {
    // Putting in a thread avoids Swing painting problems
    treeCanvas.startPrinting();
  }

  @Override
  public void originalSeqData_actionPerformed(ActionEvent e)
  {
    if (!tree.hasOriginalSequenceData())
    {
      jalview.bin.Cache.log
              .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
      return;
    }
    // decide if av alignment is sufficiently different to original data to
    // warrant a new window to be created
    // create new alignmnt window with hidden regions (unhiding hidden regions
    // yields unaligned seqs)
    // or create a selection box around columns in alignment view
    // test Alignment(SeqCigar[])
    char gc = '-';
    try
    {
      // we try to get the associated view's gap character
      // but this may fail if the view was closed...
      gc = av.getGapCharacter();

    } catch (Exception ex)
    {
    }
    ;
    Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);

    if (alAndColsel != null && alAndColsel[0] != null)
    {
      // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);

      AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
      AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
              .getAlignment().getDataset() : null;
      if (dataset != null)
      {
        al.setDataset(dataset);
      }

      if (true)
      {
        // make a new frame!
        AlignFrame af = new AlignFrame(al,
                (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
                AlignFrame.DEFAULT_HEIGHT);

        // >>>This is a fix for the moment, until a better solution is
        // found!!<<<
        // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());

        // af.addSortByOrderMenuItem(ServiceName + " Ordering",
        // msaorder);

        Desktop.addInternalFrame(af, MessageManager.formatMessage(
                "label.original_data_for_params",
                new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH,
                AlignFrame.DEFAULT_HEIGHT);
      }
    }
  }

  /**
   * DOCUMENT ME!
   * 
   * @param e
   *          DOCUMENT ME!
   */
  @Override
  public void fitToWindow_actionPerformed(ActionEvent e)
  {
    treeCanvas.fitToWindow = fitToWindow.isSelected();
    repaint();
  }

  /**
   * sort the associated alignment view by the current tree.
   * 
   * @param e
   */
  @Override
  public void sortByTree_actionPerformed()
  {

    if (treeCanvas.applyToAllViews)
    {
      final ArrayList<CommandI> commands = new ArrayList<CommandI>();
      for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
              .getSequenceSetId()))
      {
        commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
      }
      av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
      {

        @Override
        public void undoCommand(AlignmentI[] views)
        {
          for (CommandI tsort : commands)
          {
            tsort.undoCommand(views);
          }
        }

        @Override
        public int getSize()
        {
          return commands.size();
        }

        @Override
        public String getDescription()
        {
          return "Tree Sort (many views)";
        }

        @Override
        public void doCommand(AlignmentI[] views)
        {

          for (CommandI tsort : commands)
          {
            tsort.doCommand(views);
          }
        }
      });
      for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
              .getSequenceSetId()))
      {
        // ensure all the alignFrames refresh their GI after adding an undo item
        ap.alignFrame.updateEditMenuBar();
      }
    }
    else
    {
      treeCanvas.ap.alignFrame
              .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
    }

  }

  public CommandI sortAlignmentIn(AlignmentPanel ap)
  {
    AlignmentViewport av = ap.av;
    SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
    AlignmentSorter.sortByTree(av.getAlignment(), tree);
    CommandI undo;
    undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());

    ap.paintAlignment(true);
    return undo;
  }

  /**
   * DOCUMENT ME!
   * 
   * @param e
   *          DOCUMENT ME!
   */
  @Override
  public void font_actionPerformed(ActionEvent e)
  {
    if (treeCanvas == null)
    {
      return;
    }

    new FontChooser(this);
  }

  public Font getTreeFont()
  {
    return treeCanvas.font;
  }

  public void setTreeFont(Font font)
  {
    if (treeCanvas != null)
    {
      treeCanvas.setFont(font);
    }
  }

  /**
   * DOCUMENT ME!
   * 
   * @param e
   *          DOCUMENT ME!
   */
  @Override
  public void distanceMenu_actionPerformed(ActionEvent e)
  {
    treeCanvas.setShowDistances(distanceMenu.isSelected());
  }

  /**
   * DOCUMENT ME!
   * 
   * @param e
   *          DOCUMENT ME!
   */
  @Override
  public void bootstrapMenu_actionPerformed(ActionEvent e)
  {
    treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
  }

  /**
   * DOCUMENT ME!
   * 
   * @param e
   *          DOCUMENT ME!
   */
  @Override
  public void placeholdersMenu_actionPerformed(ActionEvent e)
  {
    treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
  }

  /**
   * DOCUMENT ME!
   * 
   * @param e
   *          DOCUMENT ME!
   */
  @Override
  public void epsTree_actionPerformed(ActionEvent e)
  {
    boolean accurateText = true;

    String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
            "Prompt each time");

    // If we need to prompt, and if the GUI is visible then
    // Prompt for EPS rendering style
    if (renderStyle.equalsIgnoreCase("Prompt each time")
            && !(System.getProperty("java.awt.headless") != null && System
                    .getProperty("java.awt.headless").equals("true")))
    {
      EPSOptions eps = new EPSOptions();
      renderStyle = eps.getValue();

      if (renderStyle == null || eps.cancelled)
      {
        return;
      }

    }

    if (renderStyle.equalsIgnoreCase("text"))
    {
      accurateText = false;
    }

    int width = treeCanvas.getWidth();
    int height = treeCanvas.getHeight();

    try
    {
      JalviewFileChooser chooser = new JalviewFileChooser(
              ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
      chooser.setFileView(new JalviewFileView());
      chooser.setDialogTitle(MessageManager
              .getString("label.create_eps_from_tree"));
      chooser.setToolTipText(MessageManager.getString("action.save"));

      int value = chooser.showSaveDialog(this);

      if (value != JalviewFileChooser.APPROVE_OPTION)
      {
        return;
      }

      Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile()
              .getParent());

      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
      EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);

      pg.setAccurateTextMode(accurateText);

      treeCanvas.draw(pg, width, height);

      pg.flush();
      pg.close();
    } catch (Exception ex)
    {
      ex.printStackTrace();
    }
  }

  /**
   * DOCUMENT ME!
   * 
   * @param e
   *          DOCUMENT ME!
   */
  @Override
  public void pngTree_actionPerformed(ActionEvent e)
  {
    int width = treeCanvas.getWidth();
    int height = treeCanvas.getHeight();

    try
    {
      JalviewFileChooser chooser = new JalviewFileChooser(
              ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);

      chooser.setFileView(new jalview.io.JalviewFileView());
      chooser.setDialogTitle(MessageManager
              .getString("label.create_png_from_tree"));
      chooser.setToolTipText(MessageManager.getString("action.save"));

      int value = chooser.showSaveDialog(this);

      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
      {
        return;
      }

      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
              .getSelectedFile().getParent());

      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());

      BufferedImage bi = new BufferedImage(width, height,
              BufferedImage.TYPE_INT_RGB);
      Graphics png = bi.getGraphics();

      treeCanvas.draw(png, width, height);

      ImageIO.write(bi, "png", out);
      out.close();
    } catch (Exception ex)
    {
      ex.printStackTrace();
    }
  }

  /**
   * change node labels to the annotation referred to by labelClass TODO:
   * promote to a datamodel modification that can be undone TODO: make argument
   * one case of a generic transformation function ie { undoStep = apply(Tree,
   * TransformFunction)};
   * 
   * @param labelClass
   */
  public void changeNames(final String labelClass)
  {
    tree.applyToNodes(new NodeTransformI()
    {

      @Override
      public void transform(BinaryNode node)
      {
        if (node instanceof SequenceNode
                && !((SequenceNode) node).isPlaceholder()
                && !((SequenceNode) node).isDummy())
        {
          String newname = null;
          SequenceI sq = (SequenceI) ((SequenceNode) node).element();
          if (sq != null)
          {
            // search dbrefs, features and annotation
            DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
                    sq.getDBRefs(),
                    new String[] { labelClass.toUpperCase() });
            if (refs != null)
            {
              for (int i = 0; i < refs.length; i++)
              {
                if (newname == null)
                {
                  newname = new String(refs[i].getAccessionId());
                }
                else
                {
                  newname = newname + "; " + refs[i].getAccessionId();
                }
              }
            }
            if (newname == null)
            {
              SequenceFeature sf[] = sq.getSequenceFeatures();
              for (int i = 0; sf != null && i < sf.length; i++)
              {
                if (sf[i].getType().equals(labelClass))
                {
                  if (newname == null)
                  {
                    newname = new String(sf[i].getDescription());
                  }
                  else
                  {
                    newname = newname + "; " + sf[i].getDescription();
                  }
                }
              }
            }
          }
          if (newname != null)
          {
            String oldname = ((SequenceNode) node).getName();
            // TODO : save in the undo object for this modification.
            ((SequenceNode) node).setName(newname);
          }
        }
      }
    });
  }
}