X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainPanel.java;h=6551f1bd01ee4b3c387d4dc5f7a326eb05073aad;hb=28cf1afacf61a15e72411b1e58c3694f78d6d0dd;hp=7e20578de5d7d7aa865fbec6321e0e3e2d4b4ad3;hpb=bfe6fc2e246794a6845c7c8cf99031c2bcd6281c;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/MainPanel.java b/forester/java/src/org/forester/archaeopteryx/MainPanel.java
index 7e20578..6551f1b 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 +66,14 @@ public class MainPanel extends JPanel implements ComponentListener {
     private TreeColorSet                     _colorset;
     private TreeFontSet                      _fontset;
     private Phylogeny                        _cut_or_copied_tree;
-    private Set<Integer>                     _copied_and_pasted_nodes;
+    private Set<Long>                        _copied_and_pasted_nodes;
     private Hashtable<String, BufferedImage> _image_map;
+    private static Map<String, String>       _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 +88,22 @@ 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 ) {
+    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 {
@@ -136,10 +138,7 @@ public class MainPanel extends JPanel implements ComponentListener {
         treegraphic_scroll_pane_panel.add( treegraphic_scroll_pane, BorderLayout.CENTER );
         _treegraphic_scroll_pane_panels.add( treegraphic_scroll_pane_panel );
         _treegraphic_scroll_panes.add( treegraphic_scroll_pane );
-        getTabbedPane().addTab( name,
-                                null,
-                                treegraphic_scroll_pane_panel,
-                                Util.createDescriptionForTab( phy, full_path ) );
+        getTabbedPane().addTab( name, null, treegraphic_scroll_pane_panel, "" );
         getTabbedPane().setSelectedIndex( getTabbedPane().getTabCount() - 1 );
         getControlPanel().showWhole();
     }
@@ -150,6 +149,25 @@ public class MainPanel extends JPanel implements ComponentListener {
         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 );
@@ -204,15 +222,15 @@ public class MainPanel extends JPanel implements ComponentListener {
         // Do nothing.
     }
 
-    private Configuration getConfiguration() {
+    Configuration getConfiguration() {
         return _configuration;
     }
 
-    ControlPanel getControlPanel() {
+    public ControlPanel getControlPanel() {
         return _control_panel;
     }
 
-    public Set<Integer> getCopiedAndPastedNodes() {
+    public Set<Long> getCopiedAndPastedNodes() {
         return _copied_and_pasted_nodes;
     }
 
@@ -265,7 +283,7 @@ public class MainPanel extends JPanel implements ComponentListener {
         }
     }
 
-    TreePanel getCurrentTreePanel() {
+    public TreePanel getCurrentTreePanel() {
         final int selected = getTabbedPane().getSelectedIndex();
         if ( selected >= 0 ) {
             return _treepanels.get( selected );
@@ -303,7 +321,7 @@ public class MainPanel extends JPanel implements ComponentListener {
         return getCurrentScrollPane().getViewport().getExtentSize();
     }
 
-    JTabbedPane getTabbedPane() {
+    public JTabbedPane getTabbedPane() {
         return _tabbed_pane;
     }
 
@@ -370,7 +388,7 @@ public class MainPanel extends JPanel implements ComponentListener {
         repaint();
     }
 
-    public void setCopiedAndPastedNodes( final Set<Integer> node_ids ) {
+    public void setCopiedAndPastedNodes( final Set<Long> node_ids ) {
         _copied_and_pasted_nodes = node_ids;
     }
 
@@ -391,6 +409,7 @@ 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() );
     }
@@ -413,4 +432,11 @@ public class MainPanel extends JPanel implements ComponentListener {
     synchronized Hashtable<String, BufferedImage> getImageMap() {
         return _image_map;
     }
+
+    public synchronized static Map<String, String> getLineageToRankMap() {
+        if ( _lineage_to_rank_map == null ) {
+            _lineage_to_rank_map = new HashMap<String, String>();
+        }
+        return _lineage_to_rank_map;
+    }
 }