X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainPanel.java;h=59fda587f01a08555760282e8f57c970decf36ad;hb=bfc7a76aa65c3fafda5602bfff43b3e3222a04f7;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..59fda58 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainPanel.java
@@ -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;
@@ -66,11 +68,12 @@ public class MainPanel extends JPanel implements ComponentListener {
     private Phylogeny                        _cut_or_copied_tree;
     private Set<Integer>                     _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 {
@@ -205,7 +207,7 @@ public class MainPanel extends JPanel implements ComponentListener {
         return _configuration;
     }
 
-    ControlPanel getControlPanel() {
+    public ControlPanel getControlPanel() {
         return _control_panel;
     }
 
@@ -262,7 +264,7 @@ public class MainPanel extends JPanel implements ComponentListener {
         }
     }
 
-    TreePanel getCurrentTreePanel() {
+    public TreePanel getCurrentTreePanel() {
         final int selected = getTabbedPane().getSelectedIndex();
         if ( selected >= 0 ) {
             return _treepanels.get( selected );
@@ -300,7 +302,7 @@ public class MainPanel extends JPanel implements ComponentListener {
         return getCurrentScrollPane().getViewport().getExtentSize();
     }
 
-    JTabbedPane getTabbedPane() {
+    public JTabbedPane getTabbedPane() {
         return _tabbed_pane;
     }
 
@@ -410,4 +412,11 @@ 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;
+    }
 }