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.PIDModel;
  25 import jalview.analysis.scoremodels.ScoreModels;
  26 import jalview.analysis.scoremodels.SimilarityParams;
  27 import jalview.api.analysis.ScoreModelI;
  28 import jalview.api.analysis.SimilarityParamsI;
  29 import jalview.util.MessageManager;
  30
  31 import java.awt.Color;
  32 import java.awt.FlowLayout;
  33 import java.awt.Font;
  34 import java.awt.GridLayout;
  35 import java.awt.event.ActionEvent;
  36 import java.awt.event.ItemEvent;
  37 import java.awt.event.ItemListener;
  38 import java.beans.PropertyVetoException;
  39
  40 import javax.swing.ButtonGroup;
  41 import javax.swing.JButton;
  42 import javax.swing.JCheckBox;
  43 import javax.swing.JComboBox;
  44 import javax.swing.JInternalFrame;
  45 import javax.swing.JLabel;
  46 import javax.swing.JLayeredPane;
  47 import javax.swing.JPanel;
  48 import javax.swing.JRadioButton;
  49
  50 /**
  51  * A dialog to allow a user to select and action Tree calculation options
  52  */
  53 public class TreeChooser extends JPanel
  54 {
  55   private static final Font VERDANA_11PT = new Font("Verdana", 0, 11);
  56
  57   AlignFrame af;
  58
  59   JRadioButton pca;
  60
  61   JRadioButton tree;
  62
  63   JRadioButton neighbourJoining;
  64
  65   JRadioButton averageDistance;
  66
  67   JComboBox<String> modelNames;
  68
  69   private JInternalFrame frame;
  70
  71   private ButtonGroup treeTypes;
  72
  73   private JCheckBox includeGaps;
  74
  75   private JCheckBox matchGaps;
  76
  77   private JCheckBox includeGappedColumns;
  78
  79   private JCheckBox shorterSequence;
  80
  81   /**
  82    * Constructor
  83    *
  84    * @param af
  85    */
  86   public TreeChooser(AlignFrame alignFrame)
  87   {
  88     this.af = alignFrame;
  89     init();
  90   }
  91
  92   /**
  93    * Lays out the panel and adds it to the desktop
  94    */
  95   void init()
  96   {
  97     frame = new JInternalFrame();
  98     frame.setContentPane(this);
  99     this.setBackground(Color.white);
 100
 101     /*
 102      * Layout consists of 4 or 5 panels:
 103      * - first with choice of Tree or PCA
 104      * - second with choice of tree method NJ or AV
 105      * - third with choice of score model
 106      * - fourth with score model parameter options [suppressed]
 107      * - fifth with OK and Cancel
 108      */
 109     tree = new JRadioButton(MessageManager.getString("label.tree"));
 110     tree.setOpaque(false);
 111     pca = new JRadioButton(
 112             MessageManager.getString("label.principal_component_analysis"));
 113     pca.setOpaque(false);
 114     neighbourJoining = new JRadioButton(
 115             MessageManager.getString("label.tree_calc_nj"));
 116     averageDistance = new JRadioButton(
 117             MessageManager.getString("label.tree_calc_av"));
 118     ItemListener listener = new ItemListener()
 119     {
 120       @Override
 121       public void itemStateChanged(ItemEvent e)
 122       {
 123         neighbourJoining.setEnabled(tree.isSelected());
 124         averageDistance.setEnabled(tree.isSelected());
 125       }
 126     };
 127     pca.addItemListener(listener);
 128     tree.addItemListener(listener);
 129     ButtonGroup calcTypes = new ButtonGroup();
 130     calcTypes.add(pca);
 131     calcTypes.add(tree);
 132     JPanel calcChoicePanel = new JPanel();
 133     calcChoicePanel.setOpaque(false);
 134     tree.setSelected(true);
 135     calcChoicePanel.add(tree);
 136     calcChoicePanel.add(pca);
 137
 138     neighbourJoining.setOpaque(false);
 139     treeTypes = new ButtonGroup();
 140     treeTypes.add(neighbourJoining);
 141     treeTypes.add(averageDistance);
 142     neighbourJoining.setSelected(true);
 143     JPanel treeChoicePanel = new JPanel();
 144     treeChoicePanel.setOpaque(false);
 145     treeChoicePanel.add(neighbourJoining);
 146     treeChoicePanel.add(averageDistance);
 147
 148     /*
 149      * score model drop-down
 150      */
 151     modelNames = new JComboBox<String>();
 152     ScoreModels scoreModels = ScoreModels.getInstance();
 153     for (ScoreModelI sm : scoreModels.getModels())
 154     {
 155       boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
 156       if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide)
 157       {
 158         modelNames.addItem(sm.getName());
 159       }
 160     }
 161
 162     JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
 163     scoreModelPanel.setOpaque(false);
 164     scoreModelPanel.add(modelNames, FlowLayout.LEFT);
 165
 166     /*
 167      * score model parameters
 168      */
 169     JPanel paramsPanel = new JPanel(new GridLayout(5, 1));
 170     paramsPanel.setOpaque(false);
 171     includeGaps = new JCheckBox("Include gaps");
 172     matchGaps = new JCheckBox("Match gaps");
 173     includeGappedColumns = new JCheckBox("Include gapped columns");
 174     shorterSequence = new JCheckBox("Match on shorter sequence");
 175     paramsPanel.add(new JLabel("Pairwise sequence scoring options"));
 176     paramsPanel.add(includeGaps);
 177     paramsPanel.add(matchGaps);
 178     paramsPanel.add(includeGappedColumns);
 179     paramsPanel.add(shorterSequence);
 180
 181     /*
 182      * OK / Cancel buttons
 183      */
 184     JButton ok = new JButton(MessageManager.getString("action.ok"));
 185     ok.setFont(VERDANA_11PT);
 186     ok.addActionListener(new java.awt.event.ActionListener()
 187     {
 188       @Override
 189       public void actionPerformed(ActionEvent e)
 190       {
 191         ok_actionPerformed();
 192       }
 193     });
 194     JButton cancel = new JButton(MessageManager.getString("action.cancel"));
 195     cancel.setFont(VERDANA_11PT);
 196     cancel.addActionListener(new java.awt.event.ActionListener()
 197     {
 198       @Override
 199       public void actionPerformed(ActionEvent e)
 200       {
 201         cancel_actionPerformed(e);
 202       }
 203     });
 204     JPanel actionPanel = new JPanel();
 205     actionPanel.setOpaque(false);
 206     actionPanel.add(ok);
 207     actionPanel.add(cancel);
 208
 209     boolean includeParams = false;
 210     this.add(calcChoicePanel);
 211     this.add(treeChoicePanel);
 212     this.add(scoreModelPanel);
 213     if (includeParams)
 214     {
 215       this.add(paramsPanel);
 216     }
 217     this.add(actionPanel);
 218
 219     int width = 380;
 220     int height = includeParams ? 400 : 220;
 221     Desktop.addInternalFrame(frame,
 222             MessageManager.getString("label.choose_tree"), width, height,
 223             false);
 224
 225     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 226   }
 227
 228   /**
 229    * Open and calculate the selected tree on 'OK'
 230    */
 231   protected void ok_actionPerformed()
 232   {
 233     boolean doPCA = pca.isSelected();
 234     ScoreModelI sm = ScoreModels.getInstance().forName(
 235             modelNames.getSelectedItem().toString());
 236     SimilarityParamsI params = getSimilarityParameters(doPCA, sm);
 237
 238     if (doPCA)
 239     {
 240       AlignViewport viewport = af.getViewport();
 241       if (((viewport.getSelectionGroup() != null)
 242               && (viewport.getSelectionGroup().getSize() < 4) && (viewport
 243               .getSelectionGroup().getSize() > 0))
 244               || (viewport.getAlignment().getHeight() < 4))
 245       {
 246         JvOptionPane
 247                 .showInternalMessageDialog(
 248                         this,
 249                         MessageManager
 250                                 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
 251                         MessageManager
 252                                 .getString("label.sequence_selection_insufficient"),
 253                         JvOptionPane.WARNING_MESSAGE);
 254         return;
 255       }
 256       new PCAPanel(af.alignPanel, sm, params);
 257     }
 258     else
 259     {
 260       String treeType = neighbourJoining.isSelected() ? NJTree.NEIGHBOUR_JOINING
 261               : NJTree.AVERAGE_DISTANCE;
 262       af.newTreePanel(treeType, sm, params);
 263     }
 264
 265     // closeFrame();
 266   }
 267
 268   /**
 269    *
 270    */
 271   protected void closeFrame()
 272   {
 273     try
 274     {
 275       frame.setClosed(true);
 276     } catch (PropertyVetoException ex)
 277     {
 278     }
 279   }
 280
 281   /**
 282    * Returns a data bean holding parameters for similarity (or distance) model
 283    * calculation
 284    *
 285    * @param doPCA
 286    * @param sm
 287    * @return
 288    */
 289   protected SimilarityParamsI getSimilarityParameters(boolean doPCA,
 290           ScoreModelI sm)
 291   {
 292     // commented out: parameter choices read from gui widgets
 293     // SimilarityParamsI params = new SimilarityParams(
 294     // includeGappedColumns.isSelected(), matchGaps.isSelected(),
 295     // includeGaps.isSelected(), shorterSequence.isSelected());
 296
 297     /*
 298      * for now we want
 299      * includeGappedColumns = true
 300      * includeGaps = true
 301      * matchOnShortestSequence = false
 302      * matchGaps = true except false for PCA by PID (to match SeqSpace)
 303      */
 304     boolean includeGapGap = true;
 305     boolean includeGapResidue = true;
 306     boolean matchOnShortestLength = false;
 307     boolean matchGap = true;
 308     if (doPCA && (sm instanceof PIDModel))
 309     {
 310       matchGap = false;
 311     }
 312     return new SimilarityParams(includeGapGap, matchGap, includeGapResidue, matchOnShortestLength);
 313   }
 314
 315   /**
 316    * Closes dialog on cancel
 317    *
 318    * @param e
 319    */
 320   protected void cancel_actionPerformed(ActionEvent e)
 321   {
 322     try
 323     {
 324       frame.setClosed(true);
 325     } catch (Exception ex)
 326     {
 327     }
 328   }
 329 }