X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainPanel.java;h=cc03467d80393cbc7e7bdfa49185da7bbdc7b06b;hb=54d8e3a926c3cf3477199c8b85aca478230e223c;hp=8062491812a5ae979a7692d1581574a2e99fe681;hpb=14957af9a5402acadbd477347006e2b392491403;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainPanel.java b/forester/java/src/org/forester/archaeopteryx/MainPanel.java index 8062491..cc03467 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/MainPanel.java @@ -24,7 +24,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; @@ -36,8 +36,10 @@ import java.awt.event.ComponentEvent; import java.awt.event.ComponentListener; import java.awt.image.BufferedImage; import java.util.ArrayList; +import java.util.HashMap; import java.util.Hashtable; import java.util.List; +import java.util.Map; import java.util.Set; import javax.swing.JPanel; @@ -64,13 +66,11 @@ public class MainPanel extends JPanel implements ComponentListener { private TreeColorSet _colorset; private TreeFontSet _fontset; private Phylogeny _cut_or_copied_tree; - private Set _copied_and_pasted_nodes; + private Set _copied_and_pasted_nodes; private Hashtable _image_map; + private static Map _lineage_to_rank_map; - MainPanel() { - } - - MainPanel( final Configuration configuration, final MainFrame parent ) { + public MainPanel( final Configuration configuration, final MainFrame parent ) { if ( configuration == null ) { throw new IllegalArgumentException( "configuration is null" ); } @@ -85,23 +85,25 @@ public class MainPanel extends JPanel implements ComponentListener { getControlPanel().showWhole(); } - void addPhylogenyInNewTab( final Phylogeny phy, - final Configuration config, - final String default_name, - final String full_path ) { + MainPanel() { + } + + public void addPhylogenyInNewTab( final Phylogeny phy, + final Configuration config, + final String default_name, + final String full_path ) { final TreePanel treepanel = new TreePanel( phy, config, this ); getControlPanel().phylogenyAdded( config ); treepanel.setControlPanel( getControlPanel() ); _treepanels.add( treepanel ); String name = ""; - // if ( !ForesterUtil.isEmpty( phy.getName() ) ) { - // name = phy.getName(); - // } - // else if ( phy.getIdentifier() != null ) { - // name = phy.getIdentifier().toString(); - // } - /* else */ - if ( !ForesterUtil.isEmpty( default_name ) ) { + if ( !ForesterUtil.isEmpty( phy.getName() ) ) { + name = phy.getName(); + } + else if ( phy.getIdentifier() != null ) { + name = phy.getIdentifier().toString(); + } + else if ( !ForesterUtil.isEmpty( default_name ) ) { name = default_name; } else { @@ -141,12 +143,103 @@ public class MainPanel extends JPanel implements ComponentListener { getControlPanel().showWhole(); } + @Override + public void componentHidden( final ComponentEvent e ) { + // Do nothing. + } + + @Override + public void componentMoved( final ComponentEvent e ) { + // Do nothing. + } + + @Override + public void componentResized( final ComponentEvent e ) { + if ( getCurrentTreePanel() != null ) { + getCurrentTreePanel().updateOvSettings(); + getCurrentTreePanel().updateOvSizes(); + } + } + + @Override + public void componentShown( final ComponentEvent e ) { + // Do nothing. + } + + public ControlPanel getControlPanel() { + return _control_panel; + } + + public Set getCopiedAndPastedNodes() { + return _copied_and_pasted_nodes; + } + + public TreePanel getCurrentTreePanel() { + final int selected = getTabbedPane().getSelectedIndex(); + if ( selected >= 0 ) { + return _treepanels.get( selected ); + } + else { + if ( _treepanels.size() == 1 ) { + return _treepanels.get( 0 ); + } + else { + return null; + } + } + } + + public Options getOptions() { + return _mainframe.getOptions(); + } + + public JTabbedPane getTabbedPane() { + return _tabbed_pane; + } + + public TreeFontSet getTreeFontSet() { + return _fontset; + } + + public void setArrowCursor() { + setCursor( TreePanel.ARROW_CURSOR ); + repaint(); + } + + public void setCopiedAndPastedNodes( final Set node_ids ) { + _copied_and_pasted_nodes = node_ids; + } + + public void setWaitCursor() { + setCursor( TreePanel.WAIT_CURSOR ); + repaint(); + } + void addPhylogenyInPanel( final Phylogeny phy, final Configuration config ) { final TreePanel treepanel = new TreePanel( phy, config, this ); getControlPanel().phylogenyAdded( config ); treepanel.setControlPanel( getControlPanel() ); _treepanels.add( treepanel ); final JScrollPane treegraphic_scroll_pane = new JScrollPane( treepanel ); + treegraphic_scroll_pane.getHorizontalScrollBar().addAdjustmentListener( new AdjustmentListener() { + + @Override + public void adjustmentValueChanged( final AdjustmentEvent e ) { + if ( treepanel.isOvOn() || getOptions().isShowScale() ) { + treepanel.repaint(); + } + } + } ); + treegraphic_scroll_pane.getVerticalScrollBar().addAdjustmentListener( new AdjustmentListener() { + + @Override + public void adjustmentValueChanged( final AdjustmentEvent e ) { + if ( treepanel.isOvOn() || getOptions().isShowScale() ) { + treepanel.repaint(); + //System.out.println( e.getValue() ); + } + } + } ); treegraphic_scroll_pane.getHorizontalScrollBar().setUnitIncrement( 20 ); treegraphic_scroll_pane.getHorizontalScrollBar().setBlockIncrement( 50 ); treegraphic_scroll_pane.getVerticalScrollBar().setUnitIncrement( 20 ); @@ -178,41 +271,10 @@ public class MainPanel extends JPanel implements ComponentListener { } } - @Override - public void componentHidden( final ComponentEvent e ) { - // Do nothing. - } - - @Override - public void componentMoved( final ComponentEvent e ) { - // Do nothing. - } - - @Override - public void componentResized( final ComponentEvent e ) { - if ( getCurrentTreePanel() != null ) { - getCurrentTreePanel().updateOvSettings(); - getCurrentTreePanel().updateOvSizes(); - } - } - - @Override - public void componentShown( final ComponentEvent e ) { - // Do nothing. - } - - private Configuration getConfiguration() { + Configuration getConfiguration() { return _configuration; } - ControlPanel getControlPanel() { - return _control_panel; - } - - public Set getCopiedAndPastedNodes() { - return _copied_and_pasted_nodes; - } - Phylogeny getCurrentPhylogeny() { if ( getCurrentTreePanel() == null ) { return null; @@ -255,38 +317,16 @@ public class MainPanel extends JPanel implements ComponentListener { } } - void setTitleOfSelectedTab( final String title ) { - final int selected = getTabbedPane().getSelectedIndex(); - if ( selected >= 0 ) { - getTabbedPane().setTitleAt( selected, title ); - } - } - - TreePanel getCurrentTreePanel() { - final int selected = getTabbedPane().getSelectedIndex(); - if ( selected >= 0 ) { - return _treepanels.get( selected ); - } - else { - if ( _treepanels.size() == 1 ) { - return _treepanels.get( 0 ); - } - else { - return null; - } - } - } - Phylogeny getCutOrCopiedTree() { return _cut_or_copied_tree; } - MainFrame getMainFrame() { - return _mainframe; + synchronized Hashtable getImageMap() { + return _image_map; } - public Options getOptions() { - return _mainframe.getOptions(); + MainFrame getMainFrame() { + return _mainframe; } Phylogeny getPhylogeny( final int index ) { @@ -300,18 +340,10 @@ public class MainPanel extends JPanel implements ComponentListener { return getCurrentScrollPane().getViewport().getExtentSize(); } - JTabbedPane getTabbedPane() { - return _tabbed_pane; - } - TreeColorSet getTreeColorSet() { return _colorset; } - public TreeFontSet getTreeFontSet() { - return _fontset; - } - List getTreePanels() { return _treepanels; } @@ -362,17 +394,19 @@ public class MainPanel extends JPanel implements ComponentListener { add( _tabbed_pane, BorderLayout.CENTER ); } - public void setArrowCursor() { - setCursor( TreePanel.ARROW_CURSOR ); - repaint(); + void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) { + _cut_or_copied_tree = cut_or_copied_tree; } - public void setCopiedAndPastedNodes( final Set node_ids ) { - _copied_and_pasted_nodes = node_ids; + synchronized void setImageMap( final Hashtable image_map ) { + _image_map = image_map; } - void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) { - _cut_or_copied_tree = cut_or_copied_tree; + void setTitleOfSelectedTab( final String title ) { + final int selected = getTabbedPane().getSelectedIndex(); + if ( selected >= 0 ) { + getTabbedPane().setTitleAt( selected, title ); + } } void setTreeColorSet( final TreeColorSet colorset ) { @@ -388,26 +422,21 @@ public class MainPanel extends JPanel implements ComponentListener { void setupTreeGraphic( final Configuration config_settings, final ControlPanel control ) { control.setSpeciesColors( config_settings.getSpeciesColors() ); + control.setSequenceColors( config_settings.getSequenceColors() ); control.setAnnotationColors( config_settings.getAnnotationColors() ); RenderableDomainArchitecture.setColorMap( config_settings.getDomainColors() ); } - public void setWaitCursor() { - setCursor( TreePanel.WAIT_CURSOR ); - repaint(); - } - void terminate() { for( final TreePanel atvtreepanel : _treepanels ) { atvtreepanel.removeAllEditNodeJFrames(); } } - synchronized void setImageMap( final Hashtable image_map ) { - _image_map = image_map; - } - - synchronized Hashtable getImageMap() { - return _image_map; + public synchronized static Map getLineageToRankMap() { + if ( _lineage_to_rank_map == null ) { + _lineage_to_rank_map = new HashMap(); + } + return _lineage_to_rank_map; } }