X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FControlPanel.java;h=8c80f0c01b9d7acabda5a43467bbfdf01343c9c4;hb=25e80a3f3c5c5c957fbf8879fdeb3a022d98b057;hp=f7e6dbab4afa517a2e584f2fe04d395a9c4af698;hpb=ebabb46561f996b5fcd59bd202defd7b189ea5b6;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index f7e6dba..8c80f0c 100644
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -20,7 +20,7 @@
 // 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;
 
@@ -432,6 +432,13 @@ final class ControlPanel extends JPanel implements ActionListener {
         _return_to_super_tree.setEnabled( true );
     }
 
+    void showAnnotations() {
+        _show_annotation.setSelected( true );
+        _color_according_to_annotation.setSelected( true );
+        _color_acc_species.setSelected( false );
+        _mainpanel.getCurrentTreePanel().repaint();
+    }
+
     /**
      * Add zoom and quick edit buttons. (Last modified 8/9/04)
      */
@@ -1270,17 +1277,17 @@ final class ControlPanel extends JPanel implements ActionListener {
         _mainpanel.getCurrentTreePanel().updateOvSettings();
         _mainpanel.getCurrentTreePanel().validate();
         _mainpanel.validate();
-        _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getSizeOfViewport().width,
-                                                                   _mainpanel.getSizeOfViewport().height,
-                                                                   true );
+        _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
+                                                                    _mainpanel.getSizeOfViewport().height,
+                                                                    true );
         _mainpanel.getCurrentTreePanel().resetPreferredSize();
         _mainpanel.adjustJScrollPane();
         _mainpanel.getCurrentTreePanel().repaint();
         _mainpanel.getCurrentTreePanel().validate();
         _mainpanel.validate();
-        _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getSizeOfViewport().width,
-                                                                   _mainpanel.getSizeOfViewport().height,
-                                                                   true );
+        _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
+                                                                    _mainpanel.getSizeOfViewport().height,
+                                                                    true );
         _mainpanel.getCurrentTreePanel().resetPreferredSize();
         _mainpanel.adjustJScrollPane();
         _mainpanel.getCurrentTreePanel().repaint();
@@ -1291,9 +1298,9 @@ final class ControlPanel extends JPanel implements ActionListener {
         for( final TreePanel tree_panel : _mainpanel.getTreePanels() ) {
             if ( tree_panel != null ) {
                 tree_panel.validate();
-                tree_panel.setParametersForPainting( _mainpanel.getSizeOfViewport().width,
-                                                     _mainpanel.getSizeOfViewport().height,
-                                                     true );
+                tree_panel.calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
+                                                      _mainpanel.getSizeOfViewport().height,
+                                                      true );
                 tree_panel.resetPreferredSize();
                 tree_panel.repaint();
             }
@@ -1608,7 +1615,7 @@ final class ControlPanel extends JPanel implements ActionListener {
             }
         }
         if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
-            main_panel.getCurrentTreePanel().setFoundNodes( new HashSet<Integer>() );
+            main_panel.getCurrentTreePanel().setFoundNodes( new HashSet<Long>() );
             for( final PhylogenyNode node : nodes ) {
                 main_panel.getCurrentTreePanel().getFoundNodes().add( node.getId() );
             }
@@ -1739,6 +1746,9 @@ final class ControlPanel extends JPanel implements ActionListener {
                     case SEQUENCE_MOL_SEQ:
                         s = "Molecular Sequence";
                         break;
+                    case SEQUENCE_MOL_SEQ_FASTA:
+                        s = "Molecular Sequence (Fasta)";
+                        break;
                     case SEQUENCE_NAME:
                         s = "Sequence Names";
                         break;