iterating nh parser

[jalview.git] / forester / java / src / org / forester / archaeopteryx / MainFrame.java

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index ded33a8..dc081fa 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.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;
 
@@ -231,8 +231,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     InferenceManager            _inference_manager;
     final ProcessPool           _process_pool;
     private String              _previous_node_annotation_ref;
-    private String              _ext_node_data_buffer                   = "";
-    private int                 _ext_node_data_buffer_change_counter    = 0;
 
     MainFrame() {
         _process_pool = ProcessPool.createInstance();
@@ -500,11 +498,15 @@ public abstract class MainFrame extends JFrame implements ActionListener {
      * @return current external node data as String
      */
     public String getCurrentExternalNodesDataBuffer() {
-        return _ext_node_data_buffer;
+        return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
     }
 
-    public int getExtNodeDataBufferChangeCounter() {
-        return _ext_node_data_buffer_change_counter;
+    public int getCurrentExternalNodesDataBufferChangeCounter() {
+        return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
+    }
+
+    public int getCurrentExternalNodesDataBufferLength() {
+        return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
     }
 
     public InferenceManager getInferenceManager() {
@@ -523,10 +525,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         return _process_pool;
     }
 
-    public void increaseExtNodeDataBufferChangeCounter() {
-        _ext_node_data_buffer_change_counter++;
-    }
-
     public void showTextFrame( final String s, final String title ) {
         checkTextFrames();
         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
@@ -891,7 +889,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
         sb.append( "\n" );
-        sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
+        sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );
         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
         TextFrame.instantiate( sb.toString(), "Help", _textframes );
     }
@@ -966,16 +964,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         _configuration = configuration;
     }
 
-    void setCurrentExternalNodesDataBuffer( final String s ) {
-        increaseExtNodeDataBufferChangeCounter();
-        if ( !ForesterUtil.isEmpty( s ) ) {
-            _ext_node_data_buffer = s.trim();
-        }
-        else {
-            _ext_node_data_buffer = "";
-        }
-    }
-
     void setInferenceManager( final InferenceManager i ) {
         _inference_manager = i;
     }