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.awt.event.ItemEvent;
  36 import java.awt.event.ItemListener;
  37 import java.beans.PropertyVetoException;
  38
  39 import javax.swing.ButtonGroup;
  40 import javax.swing.JButton;
  41 import javax.swing.JCheckBox;
  42 import javax.swing.JComboBox;
  43 import javax.swing.JInternalFrame;
  44 import javax.swing.JLabel;
  45 import javax.swing.JLayeredPane;
  46 import javax.swing.JPanel;
  47 import javax.swing.JRadioButton;
  48
  49 /**
  50  * A dialog to allow a user to select and action Tree calculation options
  51  */
  52 public class TreeChooser extends JPanel
  53 {
  54   private static final Font VERDANA_11PT = new Font("Verdana", 0, 11);
  55
  56   AlignFrame af;
  57
  58   JRadioButton pca;
  59
  60   JRadioButton tree;
  61
  62   JRadioButton neighbourJoining;
  63
  64   JRadioButton averageDistance;
  65
  66   JComboBox<String> matrixNames;
  67
  68   private JInternalFrame frame;
  69
  70   private ButtonGroup treeTypes;
  71
  72   private JCheckBox includeGaps;
  73
  74   private JCheckBox matchGaps;
  75
  76   private JCheckBox includeGappedColumns;
  77
  78   private JCheckBox shorterSequence;
  79
  80   /**
  81    * Constructor
  82    *
  83    * @param af
  84    */
  85   public TreeChooser(AlignFrame alignFrame)
  86   {
  87     this.af = alignFrame;
  88     init();
  89   }
  90
  91   /**
  92    * Lays out the panel and adds it to the desktop
  93    */
  94   void init()
  95   {
  96     frame = new JInternalFrame();
  97     frame.setContentPane(this);
  98     this.setBackground(Color.white);
  99
 100     /*
 101      * Layout consists of 5 panels:
 102      * - first with choice of Tree or PCA
 103      * - second with choice of tree method NJ or AV
 104      * - third with choice of score model
 105      * - fourth with score model parameter options
 106      * - fifth with OK and Cancel
 107      */
 108     tree = new JRadioButton(MessageManager.getString("label.tree"));
 109     tree.setOpaque(false);
 110     pca = new JRadioButton(
 111             MessageManager.getString("label.principal_component_analysis"));
 112     pca.setOpaque(false);
 113     neighbourJoining = new JRadioButton(
 114             MessageManager.getString("label.tree_calc_nj"));
 115     averageDistance = new JRadioButton(
 116             MessageManager.getString("label.tree_calc_av"));
 117     ItemListener listener = new ItemListener()
 118     {
 119       @Override
 120       public void itemStateChanged(ItemEvent e)
 121       {
 122         neighbourJoining.setEnabled(tree.isSelected());
 123         averageDistance.setEnabled(tree.isSelected());
 124       }
 125     };
 126     pca.addItemListener(listener);
 127     tree.addItemListener(listener);
 128     ButtonGroup calcTypes = new ButtonGroup();
 129     calcTypes.add(pca);
 130     calcTypes.add(tree);
 131     JPanel calcChoicePanel = new JPanel();
 132     calcChoicePanel.setOpaque(false);
 133     tree.setSelected(true);
 134     calcChoicePanel.add(tree);
 135     calcChoicePanel.add(pca);
 136
 137     neighbourJoining.setOpaque(false);
 138     treeTypes = new ButtonGroup();
 139     treeTypes.add(neighbourJoining);
 140     treeTypes.add(averageDistance);
 141     neighbourJoining.setSelected(true);
 142     JPanel treeChoicePanel = new JPanel();
 143     treeChoicePanel.setOpaque(false);
 144     treeChoicePanel.add(neighbourJoining);
 145     treeChoicePanel.add(averageDistance);
 146
 147     /*
 148      * score model drop-down
 149      */
 150     matrixNames = new JComboBox<String>();
 151     ScoreModels scoreModels = ScoreModels.getInstance();
 152     for (ScoreModelI sm : scoreModels.getModels())
 153     {
 154       boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
 155       if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide)
 156       {
 157         matrixNames.addItem(sm.getName());
 158       }
 159     }
 160     JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
 161     scoreModelPanel.setOpaque(false);
 162     scoreModelPanel.add(matrixNames, FlowLayout.LEFT);
 163
 164     /*
 165      * score model parameters
 166      */
 167     JPanel paramsPanel = new JPanel(new GridLayout(5, 1));
 168     paramsPanel.setOpaque(false);
 169     includeGaps = new JCheckBox("Include gaps");
 170     matchGaps = new JCheckBox("Match gaps");
 171     includeGappedColumns = new JCheckBox("Include gapped columns");
 172     shorterSequence = new JCheckBox("Match on shorter sequence");
 173     paramsPanel.add(new JLabel("Pairwise sequence scoring options"));
 174     paramsPanel.add(includeGaps);
 175     paramsPanel.add(matchGaps);
 176     paramsPanel.add(includeGappedColumns);
 177     paramsPanel.add(shorterSequence);
 178
 179     /*
 180      * OK / Cancel buttons
 181      */
 182     JButton ok = new JButton(MessageManager.getString("action.ok"));
 183     ok.setFont(VERDANA_11PT);
 184     ok.addActionListener(new java.awt.event.ActionListener()
 185     {
 186       @Override
 187       public void actionPerformed(ActionEvent e)
 188       {
 189         ok_actionPerformed(e);
 190       }
 191     });
 192     JButton cancel = new JButton(MessageManager.getString("action.cancel"));
 193     cancel.setFont(VERDANA_11PT);
 194     cancel.addActionListener(new java.awt.event.ActionListener()
 195     {
 196       @Override
 197       public void actionPerformed(ActionEvent e)
 198       {
 199         cancel_actionPerformed(e);
 200       }
 201     });
 202     JPanel actionPanel = new JPanel();
 203     actionPanel.setOpaque(false);
 204     actionPanel.add(ok);
 205     actionPanel.add(cancel);
 206
 207     this.add(calcChoicePanel);
 208     this.add(treeChoicePanel);
 209     this.add(scoreModelPanel);
 210     this.add(paramsPanel);
 211     this.add(actionPanel);
 212
 213     Desktop.addInternalFrame(frame,
 214             MessageManager.getString("label.choose_tree"), 400, 400, false);
 215
 216     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 217   }
 218
 219   /**
 220    * Open and calculate the selected tree on 'OK'
 221    *
 222    * @param e
 223    */
 224   protected void ok_actionPerformed(ActionEvent e)
 225   {
 226     ScoreModelI sm = ScoreModels.getInstance().forName(
 227             matrixNames.getSelectedItem().toString());
 228     SimilarityParamsI params = getSimilarityParameters();
 229
 230     if (pca.isSelected())
 231     {
 232       AlignViewport viewport = af.getViewport();
 233       if (((viewport.getSelectionGroup() != null)
 234               && (viewport.getSelectionGroup().getSize() < 4) && (viewport
 235               .getSelectionGroup().getSize() > 0))
 236               || (viewport.getAlignment().getHeight() < 4))
 237       {
 238         JvOptionPane
 239                 .showInternalMessageDialog(
 240                         this,
 241                         MessageManager
 242                                 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
 243                         MessageManager
 244                                 .getString("label.sequence_selection_insufficient"),
 245                         JvOptionPane.WARNING_MESSAGE);
 246         return;
 247       }
 248       new PCAPanel(af.alignPanel, sm, params);
 249     }
 250     else
 251     {
 252       String treeType = neighbourJoining.isSelected() ? NJTree.NEIGHBOUR_JOINING
 253               : NJTree.AVERAGE_DISTANCE;
 254       af.newTreePanel(treeType, sm, params);
 255     }
 256
 257     // closeFrame();
 258   }
 259
 260   /**
 261    *
 262    */
 263   protected void closeFrame()
 264   {
 265     try
 266     {
 267       frame.setClosed(true);
 268     } catch (PropertyVetoException ex)
 269     {
 270     }
 271   }
 272
 273   private SimilarityParamsI getSimilarityParameters()
 274   {
 275     SimilarityParamsI params = new SimilarityParams(
 276             includeGappedColumns.isSelected(), matchGaps.isSelected(),
 277             includeGaps.isSelected(), shorterSequence.isSelected());
 278     return params;
 279   }
 280
 281   /**
 282    * Closes dialog on cancel
 283    *
 284    * @param e
 285    */
 286   protected void cancel_actionPerformed(ActionEvent e)
 287   {
 288     try
 289     {
 290       frame.setClosed(true);
 291     } catch (Exception ex)
 292     {
 293     }
 294   }
 295 }