From f2560d91ad4d0e4fb8b150f5ebeefb405d669bde Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Mon, 10 Dec 2012 20:43:05 +0000 Subject: [PATCH] work on data buffer for aLeaves MAFFT suite + clean up --- .../org/forester/archaeopteryx/ArchaeopteryxE.java | 18 ++++++++++++++---- .../src/org/forester/archaeopteryx/Constants.java | 4 ++-- .../src/org/forester/archaeopteryx/MainFrame.java | 10 ++++++++++ .../src/org/forester/util/ForesterConstants.java | 4 ++-- 4 files changed, 28 insertions(+), 8 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 29a378b..576d952 100644 --- 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; // 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 _textframes = new LinkedList(); - private String _ext_node_data_buffer = ""; + private final LinkedList _textframes = new LinkedList(); + 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 --- 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 --- 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 --- 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"; -- 1.7.10.2