inprogress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / Constants.java

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index 48f7447..be02fd7 100644 (file)
--- 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                                                       = "0.979";
-    final static String         PRG_DATE                                                      = "130104";
+    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;
@@ -65,6 +65,7 @@ public final class Constants {
     static final Dimension      NODE_PANEL_SIZE                                               = new Dimension( 500, 600 );
     static final Dimension      NODE_FRAME_SIZE                                               = new Dimension( 520, 640 );
     static final String         APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD                     = "url_of_tree_to_load";
+    static final String         APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD             = "url_of_species_tree_to_load";
     static final String         APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL                         = "config_file";
     static final String         APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE                  = "homology_type_analysis_query_sequence";
     static final String         APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE          = "homology_type_analysis_initial_relation_type";
@@ -81,8 +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;
@@ -108,5 +109,5 @@ public final class Constants {
                                                                                                            144,
                                                                                                            144 );
     final static String         NCBI_ALL_DATABASE_SEARCH                                      = "http://www.ncbi.nlm.nih.gov/gquery/?term=";
-    final static short          DEFAULT_NODE_SHAPE_SIZE_DEFAULT                               = 6;
+    final static short          DEFAULT_NODE_SHAPE_SIZE_DEFAULT                               = 4;
 }