/********************
 * 2004 Jalview Reengineered
 * Barton Group
 * Dundee University
 *
 * AM Waterhouse
 *******************/




package jalview.gui;

import jalview.jbgui.GAlignFrame;
import jalview.schemes.*;
import jalview.datamodel.*;
import jalview.analysis.*;
import jalview.io.*;
import java.awt.event.*;
import java.awt.*;
import javax.swing.*;

public class AlignFrame extends GAlignFrame
{
  AlignmentPanel alignPanel;
  AlignViewport viewport;
  public AlignFrame(AlignmentI al)
  {
    super();
    viewport = new AlignViewport(al,true,true,true,false);
    alignPanel = new AlignmentPanel(this, viewport);
    getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
    fontNameMenuItem.setText(viewport.getFont().getName());
    fontSizeMenuItem.setText(viewport.getFont().getSize()+"");
  }

  protected void saveAs_actionPerformed(ActionEvent e)
  {
    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);
    chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
    chooser.setToolTipText("Save");
    int value = chooser.showSaveDialog(this);
    if(value == JFileChooser.APPROVE_OPTION)
    {
      String choice =  chooser.getSelectedFile().getPath();
      jalview.bin.Cache.LAST_DIRECTORY = choice;
      String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
      try{
        java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );
        out.println(output);
        out.close();
      }
      catch(Exception ex){}
    }

  }

  protected void outputText_actionPerformed(ActionEvent e)
  {
     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
     JInternalFrame frame = new JInternalFrame();
     cap.formatForOutput();
     frame.setContentPane(cap);
     Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
     cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
  }

  protected void htmlMenuItem_actionPerformed(ActionEvent e)
  {
    HTMLOutput htmlOutput = new HTMLOutput(viewport.getAlignment(), alignPanel.seqPanel.getColourScheme());
    htmlOutput = null;
  }

  public void saveAsPostscriptMenuItem_actionPerformed(ActionEvent e)
  {

  }

  public void closeMenuItem_actionPerformed(ActionEvent e)
  {
    try{
      this.setClosed(true);
    }catch(Exception ex){}
  }

  public void groupsMenuItem_actionPerformed(ActionEvent e)
  {

  }

  public void groupEditingMenuItem_actionPerformed(ActionEvent e)
  {

  }

  public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
  {
    Selection sel = viewport.getSelection();
    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
      sel.addElement( viewport.getAlignment().getSequenceAt(i));
    PaintRefresher.Refresh(null);
  }

  public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.getSelection().clear();
    PaintRefresher.Refresh(null);
  }

  public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
  {
    Selection sel = viewport.getSelection();
    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
    {
      if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
        sel.removeElement(viewport.getAlignment().getSequenceAt(i));
      else
        sel.addElement(viewport.getAlignment().getSequenceAt(i));
    }
    PaintRefresher.Refresh(null);
  }

  public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)
  {
    for (int i=0;i < viewport.getSelection().size(); i++)
            viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));

    viewport.getSelection().clear();
    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
    alignPanel.RefreshPanels();
  }

  public void moveSelectedMenuItem_actionPerformed(ActionEvent e)
  {
    copySelectedMenuItem_actionPerformed(null);
    deleteSelectedMenuItem_actionPerformed(null);
    alignPanel.repaint();
  }

  public void copySelectedMenuItem_actionPerformed(ActionEvent e)
  {
    if(viewport.getSelection().size()==0)
      return;

   SequenceI[] s = new Sequence[viewport.getSelection().size()];
   for (int i=0; i < viewport.getSelection().size(); i++) {
     s[i] = new Sequence(viewport.getSelection().sequenceAt(i));
    }
    AlignFrame af = new AlignFrame(new Alignment(s));

    int newHeight = s.length * af.viewport.getCharHeight() + 200;
    if(newHeight>500)
      newHeight=500;
    Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
  }

  public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.getColumnSelection().clear();
    repaint();
  }

  public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
  {
    ColumnSelection colSel = viewport.getColumnSelection();
    if (colSel.size() > 0)
    {
      int min = colSel.getMin();
      viewport.getAlignment().trimLeft(min);
      colSel.compensateForEdit(0,min);
      alignPanel.RefreshPanels();
    }
  }

  public void remove2RightMenuItem_actionPerformed(ActionEvent e)
  {
    ColumnSelection colSel = viewport.getColumnSelection();
    if (colSel.size() > 0)
    {
      int max = colSel.getMax();
      if(max>1)
        viewport.getAlignment().trimRight(max);

      alignPanel.RefreshPanels();
    }

  }

  public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.getAlignment().removeGaps();
    alignPanel.RefreshPanels();
  }

  public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
  {
    SequenceI current;
    int jSize;
    for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
    {
      current = viewport.getAlignment().getSequenceAt(i);
      jSize = current.getLength();
      for (int j=0; j < jSize; j++)
        if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')
        {
          current.deleteCharAt(j);
          j--;
          jSize--;
        }
    }

    alignPanel.RefreshPanels();
  }

  public void setGapCharMenuItem_actionPerformed(ActionEvent e)
  {
    String thisChar = "-";
    String nextChar = ".";
    if(viewport.getGapCharacter().equals("-"))
    {
      thisChar = ".";
      nextChar = "-";
    }
    setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
    viewport.setGapCharacter(thisChar);
  }


  public void fontNameMenuItem_actionPerformed(ActionEvent e)
  {
    String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();


    String selection = JOptionPane.showInputDialog(this,
                                "Select font",
                                "Font selection",
                                JOptionPane.QUESTION_MESSAGE,
                                null,fonts
                                ,fontNameMenuItem.getText()).toString();
    if(selection!=null)
    {
       fontNameMenuItem.setText(selection);
       SetFont();
     }

  }

  public void fontSizeMenuItem_actionPerformed(ActionEvent e)
  {
    String selection = JOptionPane.showInputDialog(this,
                                "Select font size",
                                "Font size",
                                JOptionPane.QUESTION_MESSAGE,
                                null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
                                ,fontSizeMenuItem.getText()).toString();
    if(selection!=null)
     {
       fontSizeMenuItem.setText(selection);
       SetFont();
     }
  }

  public void fontStyleMenuItem_actionPerformed(ActionEvent e)
  {
    String selection = JOptionPane.showInputDialog(this,
                                "Select font style",
                                "Font style",
                                JOptionPane.QUESTION_MESSAGE,
                                null, new String[]{"plain", "bold", "italic"}
                                ,fontStyleMenuItem.getText()).toString();
    if(selection!=null)
    {
      fontStyleMenuItem.setText(selection);
      SetFont();
    }

  }

  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setColourText( colourTextMenuItem.isSelected() );
    alignPanel.RefreshPanels();
  }

  void SetFont()
  {
      int style = java.awt.Font.PLAIN;
      if(fontStyleMenuItem.getText().equals("bold"))
        style = java.awt.Font.BOLD;
      else if(fontStyleMenuItem.getText().equals("italic"))
        style = java.awt.Font.ITALIC;

      viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
                                           style,
                                           Integer.parseInt(fontSizeMenuItem.getText())));
      alignPanel.RefreshPanels();
  }

  public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
    alignPanel.RefreshPanels();
  }

  public void viewTextMenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setShowText( viewTextMenuItem.isSelected() );
    alignPanel.RefreshPanels();
  }


  public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
  {
    alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
  }


  public void clustalColour_actionPerformed(ActionEvent e)
  {
   // alignPanel.seqPanel.setColourScheme( new ClustalxColourScheme() );
  }

  public void zappoColour_actionPerformed(ActionEvent e)
  {
    alignPanel.seqPanel.setColourScheme( new ZappoColourScheme() );
  }

  public void taylorColour_actionPerformed(ActionEvent e)
  {
    alignPanel.seqPanel.setColourScheme( new TaylorColourScheme() );
  }


  public void hydrophobicityColour_actionPerformed(ActionEvent e)
  {
    alignPanel.seqPanel.setColourScheme( new HydrophobicColourScheme() );
  }

  public void helixColour_actionPerformed(ActionEvent e)
  {
    alignPanel.seqPanel.setColourScheme( new HelixColourScheme() );
  }

  public void strandColour_actionPerformed(ActionEvent e)
  {
    alignPanel.seqPanel.setColourScheme( new StrandColourScheme() );
  }

  public void turnColour_actionPerformed(ActionEvent e)
  {
    alignPanel.seqPanel.setColourScheme( new TurnColourScheme() );
  }

  public void buriedColour_actionPerformed(ActionEvent e)
  {
    alignPanel.seqPanel.setColourScheme( new BuriedColourScheme() );
  }

  public void conservationColour_actionPerformed(ActionEvent e)
  {

  }

  public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
 {

 }


  public void abovePIDColour_actionPerformed(ActionEvent e)
  {
    alignPanel.seqPanel.setColourScheme( new PIDColourScheme() );
  }


  public void userDefinedColour_actionPerformed(ActionEvent e)
  {
    JInternalFrame frame = new JInternalFrame();
    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel.seqPanel );
    frame.setContentPane(chooser);
    Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
    frame.setResizable(false);
    frame.setIconifiable(false);
    frame.setMaximizable(false);
  }

  public void PIDColour_actionPerformed(ActionEvent e)
  {
    alignPanel.seqPanel.setColourScheme( new PIDColourScheme() );
  }

  public void BLOSUM62Colour_actionPerformed(ActionEvent e)
  {
    alignPanel.seqPanel.setColourScheme( new Blosum62ColourScheme(viewport) );
  }


  protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
  {
    ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );
    Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
  }


  public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
  {
    AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
    alignPanel.RefreshPanels();
  }

  public void sortIDMenuItem_actionPerformed(ActionEvent e)
  {
    AlignmentSorter.sortByID( viewport.getAlignment() );
    alignPanel.RefreshPanels();
  }

  public void sortGroupMenuItem_actionPerformed(ActionEvent e)
  {
    AlignmentSorter.sortGroups(viewport.getAlignment());
    AlignmentSorter.sortGroups(viewport.getAlignment());
    alignPanel.RefreshPanels();
  }

  public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
  {
    if(viewport.getCurrentTree()==null)
      return;

    AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
    alignPanel.RefreshPanels();
  }

  public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
  {

  }

  public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
  {
    if(viewport.getSelection().size()<2)
      JOptionPane.showMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
    else
    {
      JInternalFrame frame = new JInternalFrame();
      frame.setContentPane(new PairwiseAlignPanel(viewport));
      Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
    }
  }

  public void PCAMenuItem_actionPerformed(ActionEvent e)
  {
    PCAPanel pcaPanel = new PCAPanel(viewport, null);
    JInternalFrame frame = new JInternalFrame();
    frame.setContentPane(pcaPanel);
    Desktop.addInternalFrame(frame, "Principal component analysis", 400,400);
  }

  public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
  {
    NewTreePanel("AV", "PID", "Average distance tree using PID");
  }

  public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
  {
    NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
  }


  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
  {
    NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
  }

  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
  {
    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
  }

  void NewTreePanel(String type, String pwType, String title)
  {
    JInternalFrame frame = new javax.swing.JInternalFrame();
    TreePanel tp=null;
   if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
   {
     tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
                         viewport.getStartRes(), viewport.getEndRes());
   }
   else
   {
     tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
                         type, pwType, viewport.getStartRes(),
                         viewport.getEndRes());
   }

   frame.setContentPane(tp);
   Desktop.addInternalFrame(frame, title, 600, 500);
  }



  public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
  {
    JOptionPane.showMessageDialog(this, "Jalview is currently being reengineered"
                                  +"\nwithin the Barton Group, Dundee University."
                                  +"\nThis will be available as a web service 2005",
                                  "Web service", JOptionPane.INFORMATION_MESSAGE);
  }

}