make PH, aPH, CL selection

[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 f2e803a..775f5e6 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxConstants.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxConstants.java
@@ -37,11 +37,9 @@ 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 String  PRG_NAME                                                      = "Archaeopteryx";
-    final static String         VERSION                                                       = "0.9912 beta";
-    final static String         PRG_DATE                                                      = "160631";
+    final static String         VERSION                                                       = "0.9918 beta";
+    final static String         PRG_DATE                                                      = "161019";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { 
             "Arial Unicode MS", "Dialog", "SansSerif", "Sans", "Arial", "Helvetica" };
@@ -68,12 +66,9 @@ 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_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/";
@@ -84,7 +79,7 @@ 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;
@@ -111,4 +106,5 @@ public final class AptxConstants {
                                                                                                            150,
                                                                                                            150 );
     final static short          DEFAULT_NODE_SHAPE_SIZE_DEFAULT                               = 4;
+    static final int            MAX_LENGTH_FOR_COLLAPSED_NAME = 8;
 }