X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConstants.java;h=be02fd7d250b30caa5a6536f85eba783de576730;hb=fbb463a0dc277aa6efa5231f6db554de3696b194;hp=464b428caf8ecf580cfd16f2f402e42d96ea78e6;hpb=a3ab1c26605a4ffaaa5e8fd0927250c53c884bf9;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index 464b428..be02fd7 100644
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -42,15 +42,15 @@ 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                                                       = "0.9809 A1ST";
-    final static String         PRG_DATE                                                      = "130314";
+    final static String         VERSION                                                       = "0.988 SR";
+    final static String         PRG_DATE                                                      = "140418";
     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" };
+    final static String[]       DEFAULT_FONT_CHOICES                                          = { "Arial", "Helvetica",
+            "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans"  };
     final static boolean        VERBOSE_DEFAULT                                               = false;
-    final static int            DOMAIN_STRUCTURE_DEFAULT_WIDTH                                = 200;
+    final static int            DOMAIN_STRUCTURE_DEFAULT_WIDTH                                = 100;
     final static String         AUTHOR_EMAIL                                                  = "phyloxml@gmail.com";
-    final static int            DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP                      = 0;
+    final static int            DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP                      = -3;
     final static float          BUTTON_ZOOM_IN_FACTOR                                         = 1.25f;
     final static float          BUTTON_ZOOM_OUT_FACTOR                                        = 1 / Constants.BUTTON_ZOOM_IN_FACTOR;
     final static float          BUTTON_ZOOM_IN_X_CORRECTION_FACTOR                            = 1.2f;
@@ -82,8 +82,8 @@ public final class Constants {
     final static String         APTX_REFERENCE                                                = "Zmasek...";                                                         //TODO
     final static String         PHYLOXML_REFERENCE                                            = ForesterConstants.PHYLO_XML_REFERENCE;
     final static String         PHYLOXML_REFERENCE_SHORT                                      = "Han MV and Zmasek CM (2009), BMC Bioinformatics, 10:356";
-    final static short          NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT = 2;
-    final static short          NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT    = 1;
+    final static short          NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT = 3;
+    final static short          NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT    = 2;
     public static final boolean NH_PARSING_IGNORE_QUOTES_DEFAULT                              = false;
     static final CLADOGRAM_TYPE CLADOGRAM_TYPE_DEFAULT                                        = CLADOGRAM_TYPE.EXT_NODE_SUM_DEP;
     final static boolean        VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT                  = true;