git://source.jalview.org / jalview.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
JAL-2872 Undid inference disabling (done in Jalview instead)
[jalview.git] / forester / java / src / org / forester / archaeopteryx / AptxConstants.java
diff --git a/forester/java/src/org/forester/archaeopteryx/AptxConstants.java b/forester/java/src/org/forester/archaeopteryx/AptxConstants.java
index 8ad9735..8ae324d 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxConstants.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxConstants.java
@@ -36,16 +36,13 @@ import org.forester.util.ForesterConstants;
 
 public final class AptxConstants {
 
-    final static boolean        __ALLOW_PHYLOGENETIC_INFERENCE                                = true;
-    public final static boolean __RELEASE                                                     = false;                                                                             // TODO remove me
-    public final static boolean __SNAPSHOT_RELEASE                                            = false;                                                                             // TODO remove me
-    public final static boolean __SYNTH_LF                                                    = false;                                                                             // TODO remove me
+    final static boolean        __ALLOW_PHYLOGENETIC_INFERENCE                                = true; 
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
-    final static String         VERSION                                                       = "0.9910 beta";
-    final static String         PRG_DATE                                                      = "160623";
+    final static String         VERSION                                                       = "0.9921 beta";
+    final static String         PRG_DATE                                                      = "170712";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { 
-            "SansSerif", "Sans-serif", "Sans", "Dialog", "Lucida Sans", "Tahoma", "Helvetica", "Arial", "Verdana" };
+            "Arial Unicode MS", "Dialog", "SansSerif", "Sans", "Arial", "Helvetica" };
     final static boolean        VERBOSE_DEFAULT                                               = false;
     final static int            DOMAIN_STRUCTURE_DEFAULT_WIDTH                                = 100;
     final static String         AUTHOR_EMAIL                                                  = "phyloxml@gmail.com";
@@ -61,7 +58,7 @@ public final class AptxConstants {
     static final boolean        SPECIAL_CUSTOM                                                = false;                                                                             //TODO remove me
     static final double         EXT_NODE_INFO_LENGTH_MAX_RATIO                                = 0.95;
     static final Dimension      NODE_PANEL_SPLIT_MINIMUM_SIZE                                 = new Dimension( 100, 50 );
-    static final Dimension      NODE_PANEL_SIZE                                               = new Dimension( 500, 600 );
+    static final Dimension      NODE_PANEL_SIZE                                               = new Dimension( 500, 540 );
     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";
@@ -69,12 +66,10 @@ public final class AptxConstants {
     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";
     static final int            MAX_TREES_TO_LOAD                                             = 100;
-    static final int            US_LETTER_SIZE_X                                              = 612;
-    static final int            US_LETTER_SIZE_Y                                              = 792;
-    static final int            A4_SIZE_X                                                     = 595;
-    static final int            A4_SIZE_Y                                                     = 845;
     final static float          PDF_LINE_WIDTH_DEFAULT                                        = 0.5f;
     final static String         APTX_WEB_SITE                                                 = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx";
+    final static String         APTX_JS_WEB_SITE                                              = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx-js";
+    final static String         APTX_MAILING_LIST                                             = "https://groups.google.com/forum/?fromgroups#!forum/archaeopteryx";
     final static String         APTX_DOC_SITE                                                 = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/documentation";
     final static String         PHYLOXML_WEB_SITE                                             = ForesterConstants.PHYLO_XML_LOCATION;
     final static String         PHYLOXML_REFERENCE_URL                                        = "http://www.biomedcentral.com/1471-2105/10/356/";
@@ -85,7 +80,7 @@ public final class AptxConstants {
     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;
+    static final CLADOGRAM_TYPE CLADOGRAM_TYPE_DEFAULT                                        = CLADOGRAM_TYPE.LINED_UP;
     final static boolean        VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT                  = true;
     final static String         BACKUP_FILE_SUFFIX                                            = ".BAK";
     final static double         MIN_NOT_COLLAPSE_DEFAULT                                      = 50;
@@ -108,8 +103,9 @@ public final class AptxConstants {
     public final static Color   DOMAIN_BASE_COLOR_FOR_PDF                                     = new Color( 100,
                                                                                                            100,
                                                                                                            100 );
-    public final static Color   DOMAIN_LABEL_COLOR_FOR_PDF                                    = new Color( 150,
-                                                                                                           150,
-                                                                                                           150 );
-    final static short          DEFAULT_NODE_SHAPE_SIZE_DEFAULT                               = 4;
+    public final static Color   DOMAIN_LABEL_COLOR_FOR_PDF                                    = new Color( 0,
+                                                                                                           0,
+                                                                                                           0 );
+    final static short          DEFAULT_NODE_SHAPE_SIZE_DEFAULT                               = 7;
+    static final int            MAX_LENGTH_FOR_COLLAPSED_NAME = 8;
 }