work on data buffer for aLeaves MAFFT suite + clean up

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index 29a378b..576d952 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -53,8 +53,8 @@ import org.forester.util.ForesterUtil;
 // </applet>
 public class ArchaeopteryxE extends JApplet implements ActionListener {
 
-    private final static String         NAME                  = "ArchaeopteryxE";
-    private static final long           serialVersionUID      = -1220055577935759443L;
+    private final static String         NAME                                 = "ArchaeopteryxE";
+    private static final long           serialVersionUID                     = -1220055577935759443L;
     private Configuration               _configuration;
     private MainPanelApplets            _main_panel;
     private JMenuBar                    _jmenubar;
@@ -121,8 +121,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     private JMenuItem                   _choose_node_size_mi;
     private JCheckBoxMenuItem           _taxonomy_colorize_node_shapes_cbmi;
     private JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
-    private final LinkedList<TextFrame> _textframes           = new LinkedList<TextFrame>();
-    private String                      _ext_node_data_buffer = "";
+    private final LinkedList<TextFrame> _textframes                          = new LinkedList<TextFrame>();
+    private String                      _ext_node_data_buffer                = "";
+    private int                         _ext_node_data_buffer_change_counter = 0;
 
     @Override
     public void actionPerformed( final ActionEvent e ) {
@@ -400,10 +401,18 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         return dataImg;
     }
 
+    public int getExtNodeDataBufferChangeCounter() {
+        return _ext_node_data_buffer_change_counter;
+    }
+
     public Options getOptions() {
         return _options;
     }
 
+    public void increaseExtNodeDataBufferChangeCounter() {
+        _ext_node_data_buffer_change_counter++;
+    }
+
     @Override
     public void init() {
         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
@@ -908,6 +917,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     }
 
     void setCurrentExternalNodesDataBuffer( final String s ) {
+        increaseExtNodeDataBufferChangeCounter();
         if ( !ForesterUtil.isEmpty( s ) ) {
             _ext_node_data_buffer = s.trim();
         }

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index a7c9f18..7a300ff 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -42,8 +42,8 @@ public final class Constants {
     public final static boolean __SYNTH_LF                                                    = false;                                                    // TODO remove me
     public final static boolean ALLOW_DDBJ_BLAST                                              = false;
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
-    final static String         VERSION                                                       = "0.976";
-    final static String         PRG_DATE                                                      = "121205";
+    final static String         VERSION                                                       = "0.977";
+    final static String         PRG_DATE                                                      = "121210";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { "Verdana", "Tahoma",
             "Arial", "Helvetica", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 12710c0..ded33a8 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -232,6 +232,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     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();
@@ -502,6 +503,10 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         return _ext_node_data_buffer;
     }
 
+    public int getExtNodeDataBufferChangeCounter() {
+        return _ext_node_data_buffer_change_counter;
+    }
+
     public InferenceManager getInferenceManager() {
         return _inference_manager;
     }
@@ -518,6 +523,10 @@ 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 ) );
@@ -958,6 +967,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     }
 
     void setCurrentExternalNodesDataBuffer( final String s ) {
+        increaseExtNodeDataBufferChangeCounter();
         if ( !ForesterUtil.isEmpty( s ) ) {
             _ext_node_data_buffer = s.trim();
         }

diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java
index f87d66a..268379b 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterConstants.java
+++ b/forester/java/src/org/forester/util/ForesterConstants.java
@@ -27,8 +27,8 @@ package org.forester.util;
 
 public final class ForesterConstants {
 
-    public final static String  FORESTER_VERSION            = "1.008";
-    public final static String  FORESTER_DATE               = "121205";
+    public final static String  FORESTER_VERSION            = "1.009";
+    public final static String  FORESTER_DATE               = "121210";
     public final static String  PHYLO_XML_VERSION           = "1.10";
     public final static String  PHYLO_XML_LOCATION          = "http://www.phyloxml.org";
     public final static String  PHYLO_XML_XSD               = "phyloxml.xsd";