From baf4db894c841b22eabbd31a03dd552167d43c60 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 16 Jan 2015 23:02:52 +0000 Subject: [PATCH] in progress --- forester/java/src/org/forester/archaeopteryx/Constants.java | 2 +- forester/java/src/org/forester/archaeopteryx/TreePanel.java | 2 +- forester/java/src/org/forester/test/Test.java | 8 ++++++++ 3 files changed, 10 insertions(+), 2 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java index 1a517c6..a4cf125 100644 --- a/forester/java/src/org/forester/archaeopteryx/Constants.java +++ b/forester/java/src/org/forester/archaeopteryx/Constants.java @@ -43,7 +43,7 @@ public final class Constants { public final static boolean ALLOW_DDBJ_BLAST = false; public final static String PRG_NAME = "Archaeopteryx"; final static String VERSION = "0.9903 beta"; - final static String PRG_DATE = "141224"; + final static String PRG_DATE = "150116"; final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file"; final static String[] DEFAULT_FONT_CHOICES = { "Arial", "Helvetica", "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" }; diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index d0d6ddc..f0ac584 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -176,7 +176,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee private static final BasicStroke STROKE_2 = new BasicStroke( 2f ); private static final double TWO_PI = 2 * Math.PI; private final static int WIGGLE = 2; - private static final String SHOW_ONLY_THIS_CONF_TYPE = "posterior probability"; //TODO remove me + private static final String SHOW_ONLY_THIS_CONF_TYPE = null; //TODO remove me HashMap _nodeid_dist_to_leaf = new HashMap(); final private Arc2D _arc = new Arc2D.Double(); private AffineTransform _at; diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index 607045d..94798ae 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -9450,6 +9450,14 @@ public final class Test { if ( !p11.toNewHampshireX().equals( "(('A: \"':0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) { return false; } + final Phylogeny p12 = factory + .create( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]", + new NHXParser() )[ 0 ]; + if ( !p12.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) { + return false; + } + + } catch ( final Exception e ) { e.printStackTrace( System.out ); -- 1.7.10.2