src/jalview/gui/TreeChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.NJTree;
  24 import jalview.analysis.scoremodels.ScoreModels;
  25 import jalview.analysis.scoremodels.SimilarityParams;
  26 import jalview.api.analysis.ScoreModelI;
  27 import jalview.api.analysis.SimilarityParamsI;
  28 import jalview.util.MessageManager;
  29
  30 import java.awt.Color;
  31 import java.awt.FlowLayout;
  32 import java.awt.Font;
  33 import java.awt.GridLayout;
  34 import java.awt.event.ActionEvent;
  35 import java.beans.PropertyVetoException;
  36
  37 import javax.swing.ButtonGroup;
  38 import javax.swing.JButton;
  39 import javax.swing.JCheckBox;
  40 import javax.swing.JComboBox;
  41 import javax.swing.JInternalFrame;
  42 import javax.swing.JLabel;
  43 import javax.swing.JLayeredPane;
  44 import javax.swing.JPanel;
  45 import javax.swing.JRadioButton;
  46
  47 /**
  48  * A dialog to allow a user to select and action Tree calculation options
  49  */
  50 public class TreeChooser extends JPanel
  51 {
  52   private static final Font VERDANA_11PT = new Font("Verdana", 0, 11);
  53
  54   AlignFrame af;
  55
  56   JRadioButton neighbourJoining;
  57
  58   JRadioButton averageDistance;
  59
  60   JComboBox<String> matrixNames;
  61
  62   private JInternalFrame frame;
  63
  64   private ButtonGroup treeTypes;
  65
  66   private JCheckBox includeGaps;
  67
  68   private JCheckBox matchGaps;
  69
  70   private JCheckBox includeGappedColumns;
  71
  72   private JCheckBox shorterSequence;
  73
  74   /**
  75    * Constructor
  76    *
  77    * @param af
  78    */
  79   public TreeChooser(AlignFrame alignFrame)
  80   {
  81     this.af = alignFrame;
  82     init();
  83   }
  84
  85   /**
  86    * Lays out the panel and adds it to the desktop
  87    */
  88   void init()
  89   {
  90     frame = new JInternalFrame();
  91     frame.setContentPane(this);
  92     this.setBackground(Color.white);
  93
  94     /*
  95      * Layout consists of 4 panels:
  96      * - first with choice of tree method NJ or AV
  97      * - second with choice of score model
  98      * - third with score model parameter options
  99      * - fourth with OK and Cancel
 100      */
 101     neighbourJoining = new JRadioButton(
 102             MessageManager.getString("label.tree_calc_nj"));
 103     neighbourJoining.setOpaque(false);
 104     averageDistance = new JRadioButton(
 105             MessageManager.getString("label.tree_calc_av"));
 106     treeTypes = new ButtonGroup();
 107     treeTypes.add(neighbourJoining);
 108     treeTypes.add(averageDistance);
 109     neighbourJoining.setSelected(true);
 110     JPanel treeChoicePanel = new JPanel();
 111     treeChoicePanel.setOpaque(false);
 112     treeChoicePanel.add(neighbourJoining);
 113     treeChoicePanel.add(averageDistance);
 114
 115     /*
 116      * score model drop-down
 117      */
 118     matrixNames = new JComboBox<String>();
 119     ScoreModels scoreModels = ScoreModels.getInstance();
 120     for (ScoreModelI sm : scoreModels.getModels())
 121     {
 122       boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
 123       if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide)
 124       {
 125         matrixNames.addItem(sm.getName());
 126       }
 127     }
 128     JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
 129     scoreModelPanel.setOpaque(false);
 130     scoreModelPanel.add(matrixNames, FlowLayout.LEFT);
 131
 132     /*
 133      * score model parameters
 134      */
 135     JPanel paramsPanel = new JPanel(new GridLayout(5, 1));
 136     paramsPanel.setOpaque(false);
 137     includeGaps = new JCheckBox("Include gaps");
 138     matchGaps = new JCheckBox("Match gaps");
 139     includeGappedColumns = new JCheckBox("Include gapped columns");
 140     shorterSequence = new JCheckBox("Match on shorter sequence");
 141     paramsPanel.add(new JLabel("Pairwise sequence scoring options"));
 142     paramsPanel.add(includeGaps);
 143     paramsPanel.add(matchGaps);
 144     paramsPanel.add(includeGappedColumns);
 145     paramsPanel.add(shorterSequence);
 146
 147     /*
 148      * OK / Cancel buttons
 149      */
 150     JButton ok = new JButton(MessageManager.getString("action.ok"));
 151     ok.setFont(VERDANA_11PT);
 152     ok.addActionListener(new java.awt.event.ActionListener()
 153     {
 154       @Override
 155       public void actionPerformed(ActionEvent e)
 156       {
 157         ok_actionPerformed(e);
 158       }
 159     });
 160     JButton cancel = new JButton(MessageManager.getString("action.cancel"));
 161     cancel.setFont(VERDANA_11PT);
 162     cancel.addActionListener(new java.awt.event.ActionListener()
 163     {
 164       @Override
 165       public void actionPerformed(ActionEvent e)
 166       {
 167         cancel_actionPerformed(e);
 168       }
 169     });
 170     JPanel actionPanel = new JPanel();
 171     actionPanel.setOpaque(false);
 172     actionPanel.add(ok);
 173     actionPanel.add(cancel);
 174
 175     this.add(treeChoicePanel);
 176     this.add(scoreModelPanel);
 177     this.add(paramsPanel);
 178     this.add(actionPanel);
 179
 180     Desktop.addInternalFrame(frame,
 181             MessageManager.getString("label.choose_tree"), 400, 400, false);
 182
 183     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 184   }
 185
 186   /**
 187    * Open and calculate the selected tree on 'OK'
 188    *
 189    * @param e
 190    */
 191   protected void ok_actionPerformed(ActionEvent e)
 192   {
 193     String treeType = neighbourJoining.isSelected() ? NJTree.NEIGHBOUR_JOINING
 194             : NJTree.AVERAGE_DISTANCE;
 195     ScoreModelI sm = ScoreModels.getInstance().forName(
 196             matrixNames.getSelectedItem().toString());
 197     SimilarityParamsI params = getSimilarityParameters();
 198     af.newTreePanel(treeType, sm, params);
 199
 200     try
 201     {
 202       frame.setClosed(true);
 203     } catch (PropertyVetoException ex)
 204     {
 205     }
 206   }
 207
 208   private SimilarityParamsI getSimilarityParameters()
 209   {
 210     SimilarityParamsI params = new SimilarityParams(
 211             includeGappedColumns.isSelected(), matchGaps.isSelected(),
 212             includeGaps.isSelected(), shorterSequence.isSelected());
 213     return params;
 214   }
 215
 216   /**
 217    * Closes dialog on cancel
 218    *
 219    * @param e
 220    */
 221   protected void cancel_actionPerformed(ActionEvent e)
 222   {
 223     try
 224     {
 225       frame.setClosed(true);
 226     } catch (Exception ex)
 227     {
 228     }
 229   }
 230 }