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     public MainPanel( final Configuration configuration, final MainFrame parent ) {
  74         if ( configuration == null ) {
  75             throw new IllegalArgumentException( "configuration is null" );
  76         }
  77         addComponentListener( this );
  78         _configuration = configuration;
  79         _mainframe = parent;
  80         _treepanels = new ArrayList<TreePanel>();
  81         initialize();
  82         _control_panel = new ControlPanel( this, configuration );
  83         add( _control_panel, BorderLayout.WEST );
  84         setupTreeGraphic( configuration, getControlPanel() );
  85         getControlPanel().showWhole();
  86     }
  87
  88     MainPanel() {
  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     @Override
 147     public void componentHidden( final ComponentEvent e ) {
 148         // Do nothing.
 149     }
 150
 151     @Override
 152     public void componentMoved( final ComponentEvent e ) {
 153         // Do nothing.
 154     }
 155
 156     @Override
 157     public void componentResized( final ComponentEvent e ) {
 158         if ( getCurrentTreePanel() != null ) {
 159             getCurrentTreePanel().updateOvSettings();
 160             getCurrentTreePanel().updateOvSizes();
 161         }
 162     }
 163
 164     @Override
 165     public void componentShown( final ComponentEvent e ) {
 166         // Do nothing.
 167     }
 168
 169     public ControlPanel getControlPanel() {
 170         return _control_panel;
 171     }
 172
 173     public Set<Long> getCopiedAndPastedNodes() {
 174         return _copied_and_pasted_nodes;
 175     }
 176
 177     public TreePanel getCurrentTreePanel() {
 178         final int selected = getTabbedPane().getSelectedIndex();
 179         if ( selected >= 0 ) {
 180             return _treepanels.get( selected );
 181         }
 182         else {
 183             if ( _treepanels.size() == 1 ) {
 184                 return _treepanels.get( 0 );
 185             }
 186             else {
 187                 return null;
 188             }
 189         }
 190     }
 191
 192     public Options getOptions() {
 193         return _mainframe.getOptions();
 194     }
 195
 196     public JTabbedPane getTabbedPane() {
 197         return _tabbed_pane;
 198     }
 199
 200     public TreeFontSet getTreeFontSet() {
 201         return _fontset;
 202     }
 203
 204     public void setArrowCursor() {
 205         setCursor( TreePanel.ARROW_CURSOR );
 206         repaint();
 207     }
 208
 209     public void setCopiedAndPastedNodes( final Set<Long> node_ids ) {
 210         _copied_and_pasted_nodes = node_ids;
 211     }
 212
 213     public void setWaitCursor() {
 214         setCursor( TreePanel.WAIT_CURSOR );
 215         repaint();
 216     }
 217
 218     void addPhylogenyInPanel( final Phylogeny phy, final Configuration config ) {
 219         final TreePanel treepanel = new TreePanel( phy, config, this );
 220         getControlPanel().phylogenyAdded( config );
 221         treepanel.setControlPanel( getControlPanel() );
 222         _treepanels.add( treepanel );
 223         final JScrollPane treegraphic_scroll_pane = new JScrollPane( treepanel );
 224         treegraphic_scroll_pane.getHorizontalScrollBar().addAdjustmentListener( new AdjustmentListener() {
 225
 226             @Override
 227             public void adjustmentValueChanged( final AdjustmentEvent e ) {
 228                 if ( treepanel.isOvOn() || getOptions().isShowScale() ) {
 229                     treepanel.repaint();
 230                 }
 231             }
 232         } );
 233         treegraphic_scroll_pane.getVerticalScrollBar().addAdjustmentListener( new AdjustmentListener() {
 234
 235             @Override
 236             public void adjustmentValueChanged( final AdjustmentEvent e ) {
 237                 if ( treepanel.isOvOn() || getOptions().isShowScale() ) {
 238                     treepanel.repaint();
 239                     //System.out.println( e.getValue() );
 240                 }
 241             }
 242         } );
 243         treegraphic_scroll_pane.getHorizontalScrollBar().setUnitIncrement( 20 );
 244         treegraphic_scroll_pane.getHorizontalScrollBar().setBlockIncrement( 50 );
 245         treegraphic_scroll_pane.getVerticalScrollBar().setUnitIncrement( 20 );
 246         treegraphic_scroll_pane.getVerticalScrollBar().setBlockIncrement( 50 );
 247         final JPanel treegraphic_scroll_pane_panel = new JPanel();
 248         treegraphic_scroll_pane_panel.setLayout( new BorderLayout() );
 249         treegraphic_scroll_pane_panel.add( treegraphic_scroll_pane, BorderLayout.CENTER );
 250         _treegraphic_scroll_pane_panels.add( treegraphic_scroll_pane_panel );
 251         _treegraphic_scroll_panes.add( treegraphic_scroll_pane );
 252         add( treegraphic_scroll_pane_panel, BorderLayout.CENTER );
 253     }
 254
 255     void adjustJScrollPane() {
 256         if ( getTabbedPane() != null ) {
 257             getCurrentScrollPanePanel().remove( getCurrentScrollPane() );
 258             getCurrentScrollPanePanel().add( getCurrentScrollPane(), BorderLayout.CENTER );
 259         }
 260         getCurrentScrollPane().revalidate();
 261     }
 262
 263     void closeCurrentPane() {
 264         final int index = getCurrentTabIndex();
 265         if ( ( index >= 0 ) && ( getTabbedPane().getTabCount() > 0 ) ) {
 266             getTabbedPane().remove( index );
 267             getTreePanels().remove( index );
 268             _treegraphic_scroll_panes.remove( index );
 269             _treegraphic_scroll_pane_panels.remove( index );
 270             getControlPanel().phylogenyRemoved( index );
 271         }
 272     }
 273
 274     Configuration getConfiguration() {
 275         return _configuration;
 276     }
 277
 278     Phylogeny getCurrentPhylogeny() {
 279         if ( getCurrentTreePanel() == null ) {
 280             return null;
 281         }
 282         return getCurrentTreePanel().getPhylogeny();
 283     }
 284
 285     JScrollPane getCurrentScrollPane() {
 286         if ( _treegraphic_scroll_panes.size() > 0 ) {
 287             final int selected = getTabbedPane().getSelectedIndex();
 288             if ( selected >= 0 ) {
 289                 return _treegraphic_scroll_panes.get( selected );
 290             }
 291             else {
 292                 return _treegraphic_scroll_panes.get( 0 );
 293             }
 294         }
 295         else {
 296             return null;
 297         }
 298     }
 299
 300     JPanel getCurrentScrollPanePanel() {
 301         final int selected = getTabbedPane().getSelectedIndex();
 302         if ( selected >= 0 ) {
 303             return _treegraphic_scroll_pane_panels.get( selected );
 304         }
 305         else {
 306             return _treegraphic_scroll_pane_panels.get( 0 );
 307         }
 308     }
 309
 310     int getCurrentTabIndex() {
 311         final int selected = getTabbedPane().getSelectedIndex();
 312         if ( selected >= 0 ) {
 313             return selected;
 314         }
 315         else {
 316             return 0;
 317         }
 318     }
 319
 320     Phylogeny getCutOrCopiedTree() {
 321         return _cut_or_copied_tree;
 322     }
 323
 324     synchronized Hashtable<String, BufferedImage> getImageMap() {
 325         return _image_map;
 326     }
 327
 328     MainFrame getMainFrame() {
 329         return _mainframe;
 330     }
 331
 332     Phylogeny getPhylogeny( final int index ) {
 333         if ( getCurrentTreePanel() == null ) {
 334             return null;
 335         }
 336         return _treepanels.get( index ).getPhylogeny();
 337     }
 338
 339     Dimension getSizeOfViewport() {
 340         return getCurrentScrollPane().getViewport().getExtentSize();
 341     }
 342
 343     TreeColorSet getTreeColorSet() {
 344         return _colorset;
 345     }
 346
 347     List<TreePanel> getTreePanels() {
 348         return _treepanels;
 349     }
 350
 351     void initialize() {
 352         if ( !getConfiguration().isUseNativeUI() ) {
 353             setBackground( getConfiguration().getGuiBackgroundColor() );
 354         }
 355         setTreeFontSet( new TreeFontSet( this ) );
 356         getTreeFontSet().setBaseFont( getOptions().getBaseFont() );
 357         setLayout( new BorderLayout() );
 358         setTreeColorSet( TreeColorSet.createInstance( getConfiguration() ) );
 359         _treegraphic_scroll_panes = new ArrayList<JScrollPane>();
 360         _treegraphic_scroll_pane_panels = new ArrayList<JPanel>();
 361         _tabbed_pane = new JTabbedPane( SwingConstants.TOP );
 362         if ( !getConfiguration().isUseNativeUI() ) {
 363             _tabbed_pane.setBackground( getConfiguration().getGuiBackgroundColor() );
 364             _tabbed_pane.setForeground( getConfiguration().getGuiBackgroundColor() );
 365         }
 366         _tabbed_pane.addChangeListener( new ChangeListener() {
 367
 368             // This method is called whenever the selected tab changes
 369             @Override
 370             public void stateChanged( final ChangeEvent evt ) {
 371                 final JTabbedPane pane = ( JTabbedPane ) evt.getSource();
 372                 getControlPanel().tabChanged();
 373                 // Get current tab
 374                 final int sel = pane.getSelectedIndex();
 375                 if ( sel >= 0 ) {
 376                     if ( !getConfiguration().isUseNativeUI() ) {
 377                         if ( _tabbed_pane.getTabCount() > 0 ) {
 378                             _tabbed_pane.setForegroundAt( sel, Constants.TAB_LABEL_FOREGROUND_COLOR_SELECTED );
 379                             for( int i = 0; i < _tabbed_pane.getTabCount(); ++i ) {
 380                                 if ( i != sel ) {
 381                                     _tabbed_pane.setBackgroundAt( i, getConfiguration().getGuiBackgroundColor() );
 382                                     _tabbed_pane.setForegroundAt( i, getConfiguration().getGuiCheckboxTextColor() );
 383                                 }
 384                             }
 385                         }
 386                     }
 387                 }
 388             }
 389         } );
 390         if ( !getConfiguration().isUseNativeUI() ) {
 391             _tabbed_pane.setFont( ControlPanel.jcb_font );
 392         }
 393         _tabbed_pane.setTabLayoutPolicy( JTabbedPane.SCROLL_TAB_LAYOUT );
 394         add( _tabbed_pane, BorderLayout.CENTER );
 395     }
 396
 397     void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
 398         _cut_or_copied_tree = cut_or_copied_tree;
 399     }
 400
 401     synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
 402         _image_map = image_map;
 403     }
 404
 405     void setTitleOfSelectedTab( final String title ) {
 406         final int selected = getTabbedPane().getSelectedIndex();
 407         if ( selected >= 0 ) {
 408             getTabbedPane().setTitleAt( selected, title );
 409         }
 410     }
 411
 412     void setTreeColorSet( final TreeColorSet colorset ) {
 413         _colorset = colorset;
 414         for( final TreePanel p : getTreePanels() ) {
 415             p.setBackground( colorset.getBackgroundColor() );
 416         }
 417     }
 418
 419     void setTreeFontSet( final TreeFontSet fontset ) {
 420         _fontset = fontset;
 421     }
 422
 423     void setupTreeGraphic( final Configuration config_settings, final ControlPanel control ) {
 424         control.setSpeciesColors( config_settings.getSpeciesColors() );
 425         control.setSequenceColors( config_settings.getSequenceColors() );
 426         control.setAnnotationColors( config_settings.getAnnotationColors() );
 427         RenderableDomainArchitecture.setColorMap( config_settings.getDomainColors() );
 428     }
 429
 430     void terminate() {
 431         for( final TreePanel atvtreepanel : _treepanels ) {
 432             atvtreepanel.removeAllEditNodeJFrames();
 433         }
 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 }