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.ScoreMatrix;
  25 import jalview.analysis.scoremodels.ScoreModels;
  26 import jalview.analysis.scoremodels.SimilarityParams;
  27 import jalview.api.analysis.DistanceScoreModelI;
  28 import jalview.api.analysis.ScoreModelI;
  29 import jalview.api.analysis.SimilarityParamsI;
  30 import jalview.util.MessageManager;
  31
  32 import java.awt.Color;
  33 import java.awt.FlowLayout;
  34 import java.awt.Font;
  35 import java.awt.GridLayout;
  36 import java.awt.event.ActionEvent;
  37 import java.awt.event.ItemEvent;
  38 import java.awt.event.ItemListener;
  39 import java.beans.PropertyVetoException;
  40
  41 import javax.swing.ButtonGroup;
  42 import javax.swing.JButton;
  43 import javax.swing.JCheckBox;
  44 import javax.swing.JComboBox;
  45 import javax.swing.JInternalFrame;
  46 import javax.swing.JLabel;
  47 import javax.swing.JLayeredPane;
  48 import javax.swing.JPanel;
  49 import javax.swing.JRadioButton;
  50
  51 /**
  52  * A dialog to allow a user to select and action Tree calculation options
  53  */
  54 public class TreeChooser extends JPanel
  55 {
  56   private static final Font VERDANA_11PT = new Font("Verdana", 0, 11);
  57
  58   AlignFrame af;
  59
  60   JRadioButton pca;
  61
  62   JRadioButton tree;
  63
  64   JRadioButton neighbourJoining;
  65
  66   JRadioButton averageDistance;
  67
  68   JComboBox<String> modelNames;
  69
  70   private JInternalFrame frame;
  71
  72   private ButtonGroup treeTypes;
  73
  74   private JCheckBox includeGaps;
  75
  76   private JCheckBox matchGaps;
  77
  78   private JCheckBox includeGappedColumns;
  79
  80   private JCheckBox shorterSequence;
  81
  82   /**
  83    * Constructor
  84    *
  85    * @param af
  86    */
  87   public TreeChooser(AlignFrame alignFrame)
  88   {
  89     this.af = alignFrame;
  90     init();
  91   }
  92
  93   /**
  94    * Lays out the panel and adds it to the desktop
  95    */
  96   void init()
  97   {
  98     frame = new JInternalFrame();
  99     frame.setContentPane(this);
 100     this.setBackground(Color.white);
 101
 102     /*
 103      * Layout consists of 5 panels:
 104      * - first with choice of Tree or PCA
 105      * - second with choice of tree method NJ or AV
 106      * - third with choice of score model
 107      * - fourth with score model parameter options
 108      * - fifth with OK and Cancel
 109      */
 110     tree = new JRadioButton(MessageManager.getString("label.tree"));
 111     tree.setOpaque(false);
 112     pca = new JRadioButton(
 113             MessageManager.getString("label.principal_component_analysis"));
 114     pca.setOpaque(false);
 115     neighbourJoining = new JRadioButton(
 116             MessageManager.getString("label.tree_calc_nj"));
 117     averageDistance = new JRadioButton(
 118             MessageManager.getString("label.tree_calc_av"));
 119     ItemListener listener = new ItemListener()
 120     {
 121       @Override
 122       public void itemStateChanged(ItemEvent e)
 123       {
 124         neighbourJoining.setEnabled(tree.isSelected());
 125         averageDistance.setEnabled(tree.isSelected());
 126       }
 127     };
 128     pca.addItemListener(listener);
 129     tree.addItemListener(listener);
 130     ButtonGroup calcTypes = new ButtonGroup();
 131     calcTypes.add(pca);
 132     calcTypes.add(tree);
 133     JPanel calcChoicePanel = new JPanel();
 134     calcChoicePanel.setOpaque(false);
 135     tree.setSelected(true);
 136     calcChoicePanel.add(tree);
 137     calcChoicePanel.add(pca);
 138
 139     neighbourJoining.setOpaque(false);
 140     treeTypes = new ButtonGroup();
 141     treeTypes.add(neighbourJoining);
 142     treeTypes.add(averageDistance);
 143     neighbourJoining.setSelected(true);
 144     JPanel treeChoicePanel = new JPanel();
 145     treeChoicePanel.setOpaque(false);
 146     treeChoicePanel.add(neighbourJoining);
 147     treeChoicePanel.add(averageDistance);
 148
 149     /*
 150      * score model drop-down
 151      */
 152     modelNames = new JComboBox<String>();
 153     ScoreModels scoreModels = ScoreModels.getInstance();
 154     for (ScoreModelI sm : scoreModels.getModels())
 155     {
 156       boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
 157       if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide)
 158       {
 159         modelNames.addItem(sm.getName());
 160       }
 161     }
 162     modelNames.addItemListener(new ItemListener()
 163     {
 164
 165       @Override
 166       public void itemStateChanged(ItemEvent e)
 167       {
 168         if (e.getStateChange() == ItemEvent.SELECTED)
 169         {
 170           scoreModelChanged((String) e.getItem());
 171         }
 172       }
 173     });
 174     JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
 175     scoreModelPanel.setOpaque(false);
 176     scoreModelPanel.add(modelNames, FlowLayout.LEFT);
 177
 178     /*
 179      * score model parameters
 180      */
 181     JPanel paramsPanel = new JPanel(new GridLayout(5, 1));
 182     paramsPanel.setOpaque(false);
 183     includeGaps = new JCheckBox("Include gaps");
 184     matchGaps = new JCheckBox("Match gaps");
 185     includeGappedColumns = new JCheckBox("Include gapped columns");
 186     shorterSequence = new JCheckBox("Match on shorter sequence");
 187     paramsPanel.add(new JLabel("Pairwise sequence scoring options"));
 188     paramsPanel.add(includeGaps);
 189     paramsPanel.add(matchGaps);
 190     paramsPanel.add(includeGappedColumns);
 191     paramsPanel.add(shorterSequence);
 192     // configure initial state of options
 193     scoreModelChanged(modelNames.getItemAt(0));
 194
 195     /*
 196      * OK / Cancel buttons
 197      */
 198     JButton ok = new JButton(MessageManager.getString("action.ok"));
 199     ok.setFont(VERDANA_11PT);
 200     ok.addActionListener(new java.awt.event.ActionListener()
 201     {
 202       @Override
 203       public void actionPerformed(ActionEvent e)
 204       {
 205         ok_actionPerformed(e);
 206       }
 207     });
 208     JButton cancel = new JButton(MessageManager.getString("action.cancel"));
 209     cancel.setFont(VERDANA_11PT);
 210     cancel.addActionListener(new java.awt.event.ActionListener()
 211     {
 212       @Override
 213       public void actionPerformed(ActionEvent e)
 214       {
 215         cancel_actionPerformed(e);
 216       }
 217     });
 218     JPanel actionPanel = new JPanel();
 219     actionPanel.setOpaque(false);
 220     actionPanel.add(ok);
 221     actionPanel.add(cancel);
 222
 223     this.add(calcChoicePanel);
 224     this.add(treeChoicePanel);
 225     this.add(scoreModelPanel);
 226     this.add(paramsPanel);
 227     this.add(actionPanel);
 228
 229     Desktop.addInternalFrame(frame,
 230             MessageManager.getString("label.choose_tree"), 400, 400, false);
 231
 232     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 233   }
 234
 235   /**
 236    * Action on selection of score model
 237    *
 238    * @param item
 239    */
 240   protected void scoreModelChanged(String modelName)
 241   {
 242     /*
 243      * enable/disable options appropriate to score model
 244      * NB this is temporary - will get score models to provide
 245      * their own parameters
 246      */
 247     includeGaps.setEnabled(true);
 248     matchGaps.setEnabled(true);
 249     includeGappedColumns.setEnabled(true);
 250     shorterSequence.setEnabled(true);
 251
 252     ScoreModelI sm = ScoreModels.getInstance().forName(modelName);
 253     if (sm instanceof DistanceScoreModelI)
 254     {
 255       matchGaps.setEnabled(false);
 256       includeGappedColumns.setEnabled(false);
 257       shorterSequence.setEnabled(false);
 258     }
 259     if (sm instanceof ScoreMatrix)
 260     {
 261       matchGaps.setEnabled(false);
 262     }
 263     if (tree.isSelected())
 264     {
 265       // ?? tree requires specific parameter settings??
 266       includeGaps.setSelected(true);
 267       includeGaps.setEnabled(false);
 268       matchGaps.setSelected(true);
 269       includeGappedColumns.setSelected(true);
 270       includeGappedColumns.setEnabled(false);
 271       shorterSequence.setSelected(false);
 272       shorterSequence.setEnabled(false);
 273     }
 274   }
 275
 276   /**
 277    * Open and calculate the selected tree on 'OK'
 278    *
 279    * @param e
 280    */
 281   protected void ok_actionPerformed(ActionEvent e)
 282   {
 283     ScoreModelI sm = ScoreModels.getInstance().forName(
 284             modelNames.getSelectedItem().toString());
 285     SimilarityParamsI params = getSimilarityParameters();
 286
 287     if (pca.isSelected())
 288     {
 289       AlignViewport viewport = af.getViewport();
 290       if (((viewport.getSelectionGroup() != null)
 291               && (viewport.getSelectionGroup().getSize() < 4) && (viewport
 292               .getSelectionGroup().getSize() > 0))
 293               || (viewport.getAlignment().getHeight() < 4))
 294       {
 295         JvOptionPane
 296                 .showInternalMessageDialog(
 297                         this,
 298                         MessageManager
 299                                 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
 300                         MessageManager
 301                                 .getString("label.sequence_selection_insufficient"),
 302                         JvOptionPane.WARNING_MESSAGE);
 303         return;
 304       }
 305       new PCAPanel(af.alignPanel, sm, params);
 306     }
 307     else
 308     {
 309       String treeType = neighbourJoining.isSelected() ? NJTree.NEIGHBOUR_JOINING
 310               : NJTree.AVERAGE_DISTANCE;
 311       af.newTreePanel(treeType, sm, params);
 312     }
 313
 314     // closeFrame();
 315   }
 316
 317   /**
 318    *
 319    */
 320   protected void closeFrame()
 321   {
 322     try
 323     {
 324       frame.setClosed(true);
 325     } catch (PropertyVetoException ex)
 326     {
 327     }
 328   }
 329
 330   private SimilarityParamsI getSimilarityParameters()
 331   {
 332     SimilarityParamsI params = new SimilarityParams(
 333             includeGappedColumns.isSelected(), matchGaps.isSelected(),
 334             includeGaps.isSelected(), shorterSequence.isSelected());
 335     return params;
 336   }
 337
 338   /**
 339    * Closes dialog on cancel
 340    *
 341    * @param e
 342    */
 343   protected void cancel_actionPerformed(ActionEvent e)
 344   {
 345     try
 346     {
 347       frame.setClosed(true);
 348     } catch (Exception ex)
 349     {
 350     }
 351   }
 352 }