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[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 4573a9d..b9c91cd 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -37,20 +37,20 @@ import org.forester.util.ForesterConstants;
 public final class Constants {
 
     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
+    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
     public final static boolean ALLOW_DDBJ_BLAST                                              = false;
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
-    final static String         VERSION                                                       = "0.9811 A1ST";
-    final static String         PRG_DATE                                                      = "130326";
+    final static String         VERSION                                                       = "0.9899 beta";
+    final static String         PRG_DATE                                                      = "140925";
     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;
@@ -59,7 +59,7 @@ public final class Constants {
     final static float          WHEEL_ZOOM_OUT_FACTOR                                         = 1 / Constants.WHEEL_ZOOM_IN_FACTOR;
     final static float          WHEEL_ZOOM_IN_X_CORRECTION_FACTOR                             = 1.085f;
     final static float          WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR                            = 1 / Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR;
-    static final boolean        SPECIAL_CUSTOM                                                = false;                                                               //TODO remove me
+    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 );
@@ -76,14 +76,15 @@ public final class Constants {
     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_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/";
     final static String         APTX_REFERENCE_URL                                            = "http://www.biomedcentral.com/bmcbioinformatics/";
-    final static String         APTX_REFERENCE                                                = "Zmasek...";                                                         //TODO
+    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;
@@ -104,10 +105,12 @@ public final class Constants {
                                                                                                            255 );
     final static Color          BUTTON_BORDER_COLOR_DEFAULT                                   = new Color( 0, 0, 0 );
     final static Color          TAB_LABEL_FOREGROUND_COLOR_SELECTED                           = new Color( 0, 0, 0 );
-    final static Color          DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT                           = new Color( 32, 32, 32 );
-    final static Color          DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT                           = new Color( 144,
-                                                                                                           144,
-                                                                                                           144 );
     final static String         NCBI_ALL_DATABASE_SEARCH                                      = "http://www.ncbi.nlm.nih.gov/gquery/?term=";
+    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;
 }