forester/java/src/org/forester/archaeopteryx/MainPanel.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 // Copyright (C) 2000-2001 Washington University School of Medicine
   8 // and Howard Hughes Medical Institute
   9 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
  10 // All rights reserved
  11 //
  12 // This library is free software; you can redistribute it and/or
  13 // modify it under the terms of the GNU Lesser General Public
  14 // License as published by the Free Software Foundation; either
  15 // version 2.1 of the License, or (at your option) any later version.
  16 //
  17 // This library is distributed in the hope that it will be useful,
  18 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  19 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  20 // Lesser General Public License for more details.
  21 //
  22 // You should have received a copy of the GNU Lesser General Public
  23 // License along with this library; if not, write to the Free Software
  24 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  25 //
  26 // Contact: phylosoft @ gmail . com
  27 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  28
  29 package org.forester.archaeopteryx;
  30
  31 import java.awt.BorderLayout;
  32 import java.awt.Dimension;
  33 import java.awt.event.AdjustmentEvent;
  34 import java.awt.event.AdjustmentListener;
  35 import java.awt.event.ComponentEvent;
  36 import java.awt.event.ComponentListener;
  37 import java.awt.image.BufferedImage;
  38 import java.util.ArrayList;
  39 import java.util.HashMap;
  40 import java.util.Hashtable;
  41 import java.util.List;
  42 import java.util.Map;
  43 import java.util.Set;
  44
  45 import javax.swing.JPanel;
  46 import javax.swing.JScrollPane;
  47 import javax.swing.JTabbedPane;
  48 import javax.swing.SwingConstants;
  49 import javax.swing.event.ChangeEvent;
  50 import javax.swing.event.ChangeListener;
  51
  52 import org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture;
  53 import org.forester.phylogeny.Phylogeny;
  54 import org.forester.util.ForesterUtil;
  55
  56 public class MainPanel extends JPanel implements ComponentListener {
  57
  58     private static final long                serialVersionUID = -2682765312661416435L;
  59     MainFrame                                _mainframe;
  60     List<TreePanel>                          _treepanels;
  61     ControlPanel                             _control_panel;
  62     private List<JScrollPane>                _treegraphic_scroll_panes;
  63     private List<JPanel>                     _treegraphic_scroll_pane_panels;
  64     Configuration                            _configuration;
  65     private JTabbedPane                      _tabbed_pane;
  66     private TreeColorSet                     _colorset;
  67     private TreeFontSet                      _fontset;
  68     private Phylogeny                        _cut_or_copied_tree;
  69     private Set<Long>                        _copied_and_pasted_nodes;
  70     private Hashtable<String, BufferedImage> _image_map;
  71     private static Map<String, String>       _lineage_to_rank_map;
  72
  73     MainPanel() {
  74     }
  75
  76     public MainPanel( final Configuration configuration, final MainFrame parent ) {
  77         if ( configuration == null ) {
  78             throw new IllegalArgumentException( "configuration is null" );
  79         }
  80         addComponentListener( this );
  81         _configuration = configuration;
  82         _mainframe = parent;
  83         _treepanels = new ArrayList<TreePanel>();
  84         initialize();
  85         _control_panel = new ControlPanel( this, configuration );
  86         add( _control_panel, BorderLayout.WEST );
  87         setupTreeGraphic( configuration, getControlPanel() );
  88         getControlPanel().showWhole();
  89     }
  90
  91     public void addPhylogenyInNewTab( final Phylogeny phy,
  92                                       final Configuration config,
  93                                       final String default_name,
  94                                       final String full_path ) {
  95         final TreePanel treepanel = new TreePanel( phy, config, this );
  96         getControlPanel().phylogenyAdded( config );
  97         treepanel.setControlPanel( getControlPanel() );
  98         _treepanels.add( treepanel );
  99         String name = "";
 100         if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
 101             name = phy.getName();
 102         }
 103         else if ( phy.getIdentifier() != null ) {
 104             name = phy.getIdentifier().toString();
 105         }
 106         else if ( !ForesterUtil.isEmpty( default_name ) ) {
 107             name = default_name;
 108         }
 109         else {
 110             name = "[" + ( getTabbedPane().getTabCount() + 1 ) + "]";
 111         }
 112         final JScrollPane treegraphic_scroll_pane = new JScrollPane( treepanel );
 113         treegraphic_scroll_pane.getHorizontalScrollBar().addAdjustmentListener( new AdjustmentListener() {
 114
 115             @Override
 116             public void adjustmentValueChanged( final AdjustmentEvent e ) {
 117                 if ( treepanel.isOvOn() || getOptions().isShowScale() ) {
 118                     treepanel.repaint();
 119                 }
 120             }
 121         } );
 122         treegraphic_scroll_pane.getVerticalScrollBar().addAdjustmentListener( new AdjustmentListener() {
 123
 124             @Override
 125             public void adjustmentValueChanged( final AdjustmentEvent e ) {
 126                 if ( treepanel.isOvOn() || getOptions().isShowScale() ) {
 127                     treepanel.repaint();
 128                     //System.out.println( e.getValue() );
 129                 }
 130             }
 131         } );
 132         treegraphic_scroll_pane.getHorizontalScrollBar().setUnitIncrement( 10 );
 133         treegraphic_scroll_pane.getHorizontalScrollBar().setBlockIncrement( 200 );
 134         treegraphic_scroll_pane.getVerticalScrollBar().setUnitIncrement( 10 );
 135         treegraphic_scroll_pane.getVerticalScrollBar().setBlockIncrement( 200 );
 136         final JPanel treegraphic_scroll_pane_panel = new JPanel();
 137         treegraphic_scroll_pane_panel.setLayout( new BorderLayout() );
 138         treegraphic_scroll_pane_panel.add( treegraphic_scroll_pane, BorderLayout.CENTER );
 139         _treegraphic_scroll_pane_panels.add( treegraphic_scroll_pane_panel );
 140         _treegraphic_scroll_panes.add( treegraphic_scroll_pane );
 141         getTabbedPane().addTab( name, null, treegraphic_scroll_pane_panel, "" );
 142         getTabbedPane().setSelectedIndex( getTabbedPane().getTabCount() - 1 );
 143         getControlPanel().showWhole();
 144     }
 145
 146     void addPhylogenyInPanel( final Phylogeny phy, final Configuration config ) {
 147         final TreePanel treepanel = new TreePanel( phy, config, this );
 148         getControlPanel().phylogenyAdded( config );
 149         treepanel.setControlPanel( getControlPanel() );
 150         _treepanels.add( treepanel );
 151         final JScrollPane treegraphic_scroll_pane = new JScrollPane( treepanel );
 152         treegraphic_scroll_pane.getHorizontalScrollBar().addAdjustmentListener( new AdjustmentListener() {
 153
 154             @Override
 155             public void adjustmentValueChanged( final AdjustmentEvent e ) {
 156                 if ( treepanel.isOvOn() || getOptions().isShowScale() ) {
 157                     treepanel.repaint();
 158                 }
 159             }
 160         } );
 161         treegraphic_scroll_pane.getVerticalScrollBar().addAdjustmentListener( new AdjustmentListener() {
 162
 163             @Override
 164             public void adjustmentValueChanged( final AdjustmentEvent e ) {
 165                 if ( treepanel.isOvOn() || getOptions().isShowScale() ) {
 166                     treepanel.repaint();
 167                     //System.out.println( e.getValue() );
 168                 }
 169             }
 170         } );
 171         treegraphic_scroll_pane.getHorizontalScrollBar().setUnitIncrement( 20 );
 172         treegraphic_scroll_pane.getHorizontalScrollBar().setBlockIncrement( 50 );
 173         treegraphic_scroll_pane.getVerticalScrollBar().setUnitIncrement( 20 );
 174         treegraphic_scroll_pane.getVerticalScrollBar().setBlockIncrement( 50 );
 175         final JPanel treegraphic_scroll_pane_panel = new JPanel();
 176         treegraphic_scroll_pane_panel.setLayout( new BorderLayout() );
 177         treegraphic_scroll_pane_panel.add( treegraphic_scroll_pane, BorderLayout.CENTER );
 178         _treegraphic_scroll_pane_panels.add( treegraphic_scroll_pane_panel );
 179         _treegraphic_scroll_panes.add( treegraphic_scroll_pane );
 180         add( treegraphic_scroll_pane_panel, BorderLayout.CENTER );
 181     }
 182
 183     void adjustJScrollPane() {
 184         if ( getTabbedPane() != null ) {
 185             getCurrentScrollPanePanel().remove( getCurrentScrollPane() );
 186             getCurrentScrollPanePanel().add( getCurrentScrollPane(), BorderLayout.CENTER );
 187         }
 188         getCurrentScrollPane().revalidate();
 189     }
 190
 191     void closeCurrentPane() {
 192         final int index = getCurrentTabIndex();
 193         if ( ( index >= 0 ) && ( getTabbedPane().getTabCount() > 0 ) ) {
 194             getTabbedPane().remove( index );
 195             getTreePanels().remove( index );
 196             _treegraphic_scroll_panes.remove( index );
 197             _treegraphic_scroll_pane_panels.remove( index );
 198             getControlPanel().phylogenyRemoved( index );
 199         }
 200     }
 201
 202     @Override
 203     public void componentHidden( final ComponentEvent e ) {
 204         // Do nothing.
 205     }
 206
 207     @Override
 208     public void componentMoved( final ComponentEvent e ) {
 209         // Do nothing.
 210     }
 211
 212     @Override
 213     public void componentResized( final ComponentEvent e ) {
 214         if ( getCurrentTreePanel() != null ) {
 215             getCurrentTreePanel().updateOvSettings();
 216             getCurrentTreePanel().updateOvSizes();
 217         }
 218     }
 219
 220     @Override
 221     public void componentShown( final ComponentEvent e ) {
 222         // Do nothing.
 223     }
 224
 225     Configuration getConfiguration() {
 226         return _configuration;
 227     }
 228
 229     public ControlPanel getControlPanel() {
 230         return _control_panel;
 231     }
 232
 233     public Set<Long> getCopiedAndPastedNodes() {
 234         return _copied_and_pasted_nodes;
 235     }
 236
 237     Phylogeny getCurrentPhylogeny() {
 238         if ( getCurrentTreePanel() == null ) {
 239             return null;
 240         }
 241         return getCurrentTreePanel().getPhylogeny();
 242     }
 243
 244     JScrollPane getCurrentScrollPane() {
 245         if ( _treegraphic_scroll_panes.size() > 0 ) {
 246             final int selected = getTabbedPane().getSelectedIndex();
 247             if ( selected >= 0 ) {
 248                 return _treegraphic_scroll_panes.get( selected );
 249             }
 250             else {
 251                 return _treegraphic_scroll_panes.get( 0 );
 252             }
 253         }
 254         else {
 255             return null;
 256         }
 257     }
 258
 259     JPanel getCurrentScrollPanePanel() {
 260         final int selected = getTabbedPane().getSelectedIndex();
 261         if ( selected >= 0 ) {
 262             return _treegraphic_scroll_pane_panels.get( selected );
 263         }
 264         else {
 265             return _treegraphic_scroll_pane_panels.get( 0 );
 266         }
 267     }
 268
 269     int getCurrentTabIndex() {
 270         final int selected = getTabbedPane().getSelectedIndex();
 271         if ( selected >= 0 ) {
 272             return selected;
 273         }
 274         else {
 275             return 0;
 276         }
 277     }
 278
 279     void setTitleOfSelectedTab( final String title ) {
 280         final int selected = getTabbedPane().getSelectedIndex();
 281         if ( selected >= 0 ) {
 282             getTabbedPane().setTitleAt( selected, title );
 283         }
 284     }
 285
 286     public TreePanel getCurrentTreePanel() {
 287         final int selected = getTabbedPane().getSelectedIndex();
 288         if ( selected >= 0 ) {
 289             return _treepanels.get( selected );
 290         }
 291         else {
 292             if ( _treepanels.size() == 1 ) {
 293                 return _treepanels.get( 0 );
 294             }
 295             else {
 296                 return null;
 297             }
 298         }
 299     }
 300
 301     Phylogeny getCutOrCopiedTree() {
 302         return _cut_or_copied_tree;
 303     }
 304
 305     MainFrame getMainFrame() {
 306         return _mainframe;
 307     }
 308
 309     public Options getOptions() {
 310         return _mainframe.getOptions();
 311     }
 312
 313     Phylogeny getPhylogeny( final int index ) {
 314         if ( getCurrentTreePanel() == null ) {
 315             return null;
 316         }
 317         return _treepanels.get( index ).getPhylogeny();
 318     }
 319
 320     Dimension getSizeOfViewport() {
 321         return getCurrentScrollPane().getViewport().getExtentSize();
 322     }
 323
 324     public JTabbedPane getTabbedPane() {
 325         return _tabbed_pane;
 326     }
 327
 328     TreeColorSet getTreeColorSet() {
 329         return _colorset;
 330     }
 331
 332     public TreeFontSet getTreeFontSet() {
 333         return _fontset;
 334     }
 335
 336     List<TreePanel> getTreePanels() {
 337         return _treepanels;
 338     }
 339
 340     void initialize() {
 341         if ( !getConfiguration().isUseNativeUI() ) {
 342             setBackground( getConfiguration().getGuiBackgroundColor() );
 343         }
 344         setTreeFontSet( new TreeFontSet( this ) );
 345         getTreeFontSet().setBaseFont( getOptions().getBaseFont() );
 346         setLayout( new BorderLayout() );
 347         setTreeColorSet( TreeColorSet.createInstance( getConfiguration() ) );
 348         _treegraphic_scroll_panes = new ArrayList<JScrollPane>();
 349         _treegraphic_scroll_pane_panels = new ArrayList<JPanel>();
 350         _tabbed_pane = new JTabbedPane( SwingConstants.TOP );
 351         if ( !getConfiguration().isUseNativeUI() ) {
 352             _tabbed_pane.setBackground( getConfiguration().getGuiBackgroundColor() );
 353             _tabbed_pane.setForeground( getConfiguration().getGuiBackgroundColor() );
 354         }
 355         _tabbed_pane.addChangeListener( new ChangeListener() {
 356
 357             // This method is called whenever the selected tab changes
 358             @Override
 359             public void stateChanged( final ChangeEvent evt ) {
 360                 final JTabbedPane pane = ( JTabbedPane ) evt.getSource();
 361                 getControlPanel().tabChanged();
 362                 // Get current tab
 363                 final int sel = pane.getSelectedIndex();
 364                 if ( sel >= 0 ) {
 365                     if ( !getConfiguration().isUseNativeUI() ) {
 366                         if ( _tabbed_pane.getTabCount() > 0 ) {
 367                             _tabbed_pane.setForegroundAt( sel, Constants.TAB_LABEL_FOREGROUND_COLOR_SELECTED );
 368                             for( int i = 0; i < _tabbed_pane.getTabCount(); ++i ) {
 369                                 if ( i != sel ) {
 370                                     _tabbed_pane.setBackgroundAt( i, getConfiguration().getGuiBackgroundColor() );
 371                                     _tabbed_pane.setForegroundAt( i, getConfiguration().getGuiCheckboxTextColor() );
 372                                 }
 373                             }
 374                         }
 375                     }
 376                 }
 377             }
 378         } );
 379         if ( !getConfiguration().isUseNativeUI() ) {
 380             _tabbed_pane.setFont( ControlPanel.jcb_font );
 381         }
 382         _tabbed_pane.setTabLayoutPolicy( JTabbedPane.SCROLL_TAB_LAYOUT );
 383         add( _tabbed_pane, BorderLayout.CENTER );
 384     }
 385
 386     public void setArrowCursor() {
 387         setCursor( TreePanel.ARROW_CURSOR );
 388         repaint();
 389     }
 390
 391     public void setCopiedAndPastedNodes( final Set<Long> node_ids ) {
 392         _copied_and_pasted_nodes = node_ids;
 393     }
 394
 395     void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
 396         _cut_or_copied_tree = cut_or_copied_tree;
 397     }
 398
 399     void setTreeColorSet( final TreeColorSet colorset ) {
 400         _colorset = colorset;
 401         for( final TreePanel p : getTreePanels() ) {
 402             p.setBackground( colorset.getBackgroundColor() );
 403         }
 404     }
 405
 406     void setTreeFontSet( final TreeFontSet fontset ) {
 407         _fontset = fontset;
 408     }
 409
 410     void setupTreeGraphic( final Configuration config_settings, final ControlPanel control ) {
 411         control.setSpeciesColors( config_settings.getSpeciesColors() );
 412         control.setSequenceColors( config_settings.getSequenceColors() );
 413         control.setAnnotationColors( config_settings.getAnnotationColors() );
 414         RenderableDomainArchitecture.setColorMap( config_settings.getDomainColors() );
 415     }
 416
 417     public void setWaitCursor() {
 418         setCursor( TreePanel.WAIT_CURSOR );
 419         repaint();
 420     }
 421
 422     void terminate() {
 423         for( final TreePanel atvtreepanel : _treepanels ) {
 424             atvtreepanel.removeAllEditNodeJFrames();
 425         }
 426     }
 427
 428     synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
 429         _image_map = image_map;
 430     }
 431
 432     synchronized Hashtable<String, BufferedImage> getImageMap() {
 433         return _image_map;
 434     }
 435
 436     public synchronized static Map<String, String> getLineageToRankMap() {
 437         if ( _lineage_to_rank_map == null ) {
 438             _lineage_to_rank_map = new HashMap<String, String>();
 439         }
 440         return _lineage_to_rank_map;
 441     }
 442 }