/*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.analysis.NJTree;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.util.MessageManager;
import java.awt.Color;
import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.beans.PropertyVetoException;
import javax.swing.ButtonGroup;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
/**
* A dialog to allow a user to select and action Tree calculation options
*/
public class TreeChooser extends JPanel
{
private static final Font VERDANA_11PT = new Font("Verdana", 0, 11);
AlignFrame af;
JRadioButton neighbourJoining;
JRadioButton averageDistance;
JComboBox matrixNames;
private JInternalFrame frame;
private ButtonGroup treeTypes;
private JCheckBox includeGaps;
private JCheckBox matchGaps;
private JCheckBox includeGappedColumns;
private JCheckBox shorterSequence;
/**
* Constructor
*
* @param af
*/
public TreeChooser(AlignFrame alignFrame)
{
this.af = alignFrame;
init();
}
/**
* Lays out the panel and adds it to the desktop
*/
void init()
{
frame = new JInternalFrame();
frame.setContentPane(this);
this.setBackground(Color.white);
/*
* Layout consists of 4 panels:
* - first with choice of tree method NJ or AV
* - second with choice of score model
* - third with score model parameter options
* - fourth with OK and Cancel
*/
neighbourJoining = new JRadioButton(
MessageManager.getString("label.tree_calc_nj"));
neighbourJoining.setOpaque(false);
averageDistance = new JRadioButton(
MessageManager.getString("label.tree_calc_av"));
treeTypes = new ButtonGroup();
treeTypes.add(neighbourJoining);
treeTypes.add(averageDistance);
neighbourJoining.setSelected(true);
JPanel treeChoicePanel = new JPanel();
treeChoicePanel.setOpaque(false);
treeChoicePanel.add(neighbourJoining);
treeChoicePanel.add(averageDistance);
/*
* score model drop-down
*/
matrixNames = new JComboBox();
ScoreModels scoreModels = ScoreModels.getInstance();
for (ScoreModelI sm : scoreModels.getModels())
{
boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide)
{
matrixNames.addItem(sm.getName());
}
}
JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
scoreModelPanel.setOpaque(false);
scoreModelPanel.add(matrixNames, FlowLayout.LEFT);
/*
* score model parameters
*/
JPanel paramsPanel = new JPanel(new GridLayout(5, 1));
paramsPanel.setOpaque(false);
includeGaps = new JCheckBox("Include gaps");
matchGaps = new JCheckBox("Match gaps");
includeGappedColumns = new JCheckBox("Include gapped columns");
shorterSequence = new JCheckBox("Match on shorter sequence");
paramsPanel.add(new JLabel("Pairwise sequence scoring options"));
paramsPanel.add(includeGaps);
paramsPanel.add(matchGaps);
paramsPanel.add(includeGappedColumns);
paramsPanel.add(shorterSequence);
/*
* OK / Cancel buttons
*/
JButton ok = new JButton(MessageManager.getString("action.ok"));
ok.setFont(VERDANA_11PT);
ok.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
ok_actionPerformed(e);
}
});
JButton cancel = new JButton(MessageManager.getString("action.cancel"));
cancel.setFont(VERDANA_11PT);
cancel.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
cancel_actionPerformed(e);
}
});
JPanel actionPanel = new JPanel();
actionPanel.setOpaque(false);
actionPanel.add(ok);
actionPanel.add(cancel);
this.add(treeChoicePanel);
this.add(scoreModelPanel);
this.add(paramsPanel);
this.add(actionPanel);
Desktop.addInternalFrame(frame,
MessageManager.getString("label.choose_tree"), 400, 400, false);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
}
/**
* Open and calculate the selected tree on 'OK'
*
* @param e
*/
protected void ok_actionPerformed(ActionEvent e)
{
String treeType = neighbourJoining.isSelected() ? NJTree.NEIGHBOUR_JOINING
: NJTree.AVERAGE_DISTANCE;
ScoreModelI sm = ScoreModels.getInstance().forName(
matrixNames.getSelectedItem().toString());
SimilarityParamsI params = getSimilarityParameters();
af.newTreePanel(treeType, sm, params);
try
{
frame.setClosed(true);
} catch (PropertyVetoException ex)
{
}
}
private SimilarityParamsI getSimilarityParameters()
{
SimilarityParamsI params = new SimilarityParams(
includeGappedColumns.isSelected(), matchGaps.isSelected(),
includeGaps.isSelected(), shorterSequence.isSelected());
return params;
}
/**
* Closes dialog on cancel
*
* @param e
*/
protected void cancel_actionPerformed(ActionEvent e)
{
try
{
frame.setClosed(true);
} catch (Exception ex)
{
}
}
}