in progress

diff --git a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
index 46ac48c..7f96bdd 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
+++ b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
@@ -125,8 +125,12 @@ public final class Archaeopteryx {
         if ( f != null ) {
             title = f.getName();
         }
+        File current_dir = null;
+        if ( ( phylogenies != null ) && ( phylogenies.length > 0 ) ) {
+            current_dir = new File( "." );
+        }
         try {
-            MainFrameApplication.createInstance( phylogenies, conf, title );
+            MainFrameApplication.createInstance( phylogenies, conf, title, current_dir );
         }
         catch ( final Exception ex ) {
             AptxUtil.unexpectedException( ex );

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index 451d04c..4650f9c 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -41,8 +41,8 @@ public final class Constants {
     public final static boolean __SNAPSHOT_RELEASE                                            = true;                                                     // TODO remove me
     public final static boolean __SYNTH_LF                                                    = false;                                                    // TODO remove me
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
-    final static String         VERSION                                                       = "0.969 demo BG";
-    final static String         PRG_DATE                                                      = "2012.02.13";
+    final static String         VERSION                                                       = "0.969 NM";
+    final static String         PRG_DATE                                                      = "2012.03.05";
     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/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index f717323..b1688a3 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -234,6 +234,13 @@ public final class MainFrameApplication extends MainFrame {
     JMenuItem                                _read_values_jmi;
 
     private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
+        this( phys, config, title, null );
+    }
+
+    private MainFrameApplication( final Phylogeny[] phys,
+                                  final Configuration config,
+                                  final String title,
+                                  final File current_dir ) {
         _configuration = config;
         if ( _configuration == null ) {
             throw new IllegalArgumentException( "configuration is null" );
@@ -279,6 +286,9 @@ public final class MainFrameApplication extends MainFrame {
         catch ( final Exception e ) {
             AptxUtil.dieWithSystemError( e.toString() );
         }
+        if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
+            setCurrentDir( current_dir );
+        }
         // hide until everything is ready
         setVisible( false );
         setOptions( Options.createInstance( _configuration ) );
@@ -2609,6 +2619,13 @@ public final class MainFrameApplication extends MainFrame {
         return new MainFrameApplication( phys, config_file_name, title );
     }
 
+    public static MainFrame createInstance( final Phylogeny[] phys,
+                                            final Configuration config,
+                                            final String title,
+                                            final File current_dir ) {
+        return new MainFrameApplication( phys, config, title, current_dir );
+    }
+
     static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
         mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
                 + o.getPrintSizeY() + ")" );

diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java
index 02ba6ea..156c65a 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java
+++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java
@@ -95,6 +95,7 @@ public final class PhyloXmlUtil {
         TAXONOMY_RANKS_LIST.add( "species" );
         TAXONOMY_RANKS_LIST.add( "subspecies" );
         TAXONOMY_RANKS_LIST.add( "variety" );
+        TAXONOMY_RANKS_LIST.add( "varietas" );
         TAXONOMY_RANKS_LIST.add( "subvariety" );
         TAXONOMY_RANKS_LIST.add( "form" );
         TAXONOMY_RANKS_LIST.add( "subform" );
@@ -149,6 +150,7 @@ public final class PhyloXmlUtil {
         TAXONOMY_RANKS_SET.add( "species" );
         TAXONOMY_RANKS_SET.add( "subspecies" );
         TAXONOMY_RANKS_SET.add( "variety" );
+        TAXONOMY_RANKS_SET.add( "varietas" );
         TAXONOMY_RANKS_SET.add( "subvariety" );
         TAXONOMY_RANKS_SET.add( "form" );
         TAXONOMY_RANKS_SET.add( "subform" );