bugfix

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 3839128..a1c16c2 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -83,7 +83,7 @@ public final class Configuration {
     private short                           _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
     private boolean                         _editable                                              = true;
     private boolean                         _nh_parsing_replace_underscores                        = false;
-    private TAXONOMY_EXTRACTION             _taxonomy_extraction                                   = TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT;
+    private TAXONOMY_EXTRACTION             _taxonomy_extraction                                   = TAXONOMY_EXTRACTION.NO;
     private boolean                         _internal_number_are_confidence_for_nh_parsing         = false;
     private boolean                         _display_sequence_relations                            = false;
     private boolean                         _validate_against_phyloxml_xsd_schema                  = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index 8dd077f..6beacfa 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -43,7 +43,7 @@ public final class Constants {
     public final static boolean ALLOW_DDBJ_BLAST                                              = false;
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
     final static String         VERSION                                                       = "0.9812 A1ST";
-    final static String         PRG_DATE                                                      = "130401";
+    final static String         PRG_DATE                                                      = "130403";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { "Arial", "Helvetica",
             "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans"  };

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index e4bd6f1..c353213 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -1318,7 +1318,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
         if ( ( _extract_taxonomy_yes_rbmi != null ) && _extract_taxonomy_yes_rbmi.isSelected() ) {
-            options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.AGRESSIVE );
+            options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
         }
         else if ( ( _extract_taxonomy_pfam_rbmi != null ) && _extract_taxonomy_pfam_rbmi.isSelected() ) {
             options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 53ca7cb..977bcbb 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -547,6 +547,9 @@ public final class MainFrameApplication extends MainFrame {
                 }
                 updateOptions( getOptions() );
             }
+            else if ( o == _extract_taxonomy_no_rbmi ) {
+                updateOptions( getOptions() );
+            }
             else if ( o == _inference_from_msa_item ) {
                 executePhyleneticInference( false );
             }

diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java
index e90ae20..f8aa376 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -458,7 +458,7 @@ final public class Options {
         _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
         _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
         _nh_parsing_replace_underscores = false;
-        _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT;
+        _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
         _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
         _show_domain_labels = true;
         setAbbreviateScientificTaxonNames( false );