From f2a2cbbd1ca5fcd27f810a3353821791f240212d Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 27 Mar 2012 18:18:45 +0000 Subject: [PATCH] in progress --- .../src/org/forester/archaeopteryx/Archaeopteryx.java | 6 +++++- .../src/org/forester/archaeopteryx/Constants.java | 4 ++-- .../forester/archaeopteryx/MainFrameApplication.java | 17 +++++++++++++++++ .../forester/io/parsers/phyloxml/PhyloXmlUtil.java | 2 ++ 4 files changed, 26 insertions(+), 3 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java index 46ac48c..7f96bdd 100644 --- 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 --- 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 --- 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 --- 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" ); -- 1.7.10.2