applet gsdi

[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 7a300ff..e539c54 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -24,7 +24,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.archaeopteryx;
 
@@ -37,19 +37,19 @@ 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                                                       = "0.977";
-    final static String         PRG_DATE                                                      = "121210";
+    final static String         VERSION                                                       = "0.9806 A1ST";
+    final static String         PRG_DATE                                                      = "130308";
     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 boolean        VERBOSE_DEFAULT                                               = false;
     final static int            DOMAIN_STRUCTURE_DEFAULT_WIDTH                                = 200;
-    final static String         AUTHOR_EMAIL                                                  = "phylosoft@gmail.com";
+    final static String         AUTHOR_EMAIL                                                  = "phyloxml@gmail.com";
     final static int            DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP                      = 0;
     final static float          BUTTON_ZOOM_IN_FACTOR                                         = 1.25f;
     final static float          BUTTON_ZOOM_OUT_FACTOR                                        = 1 / Constants.BUTTON_ZOOM_IN_FACTOR;
@@ -59,12 +59,13 @@ 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 );
     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";
@@ -74,11 +75,11 @@ public final class Constants {
     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                                                 = "http://www.phylosoft.org/archaeopteryx/";
+    final static String         APTX_WEB_SITE                                                 = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx";
     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;
@@ -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;
 }