X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=3db44f7a8b113188ab4b1a196462c204b7dbb88a;hb=a2e1b38bab7e593d79946c24e653776e6d796e00;hp=f764e7fbd6d9b6676400bfeb90dc0f5f5c35c3d8;hpb=a2be52673716ddf6f158c0831075d47635779e64;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index f764e7f..3db44f7 100644
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -135,7 +135,7 @@ public final class Configuration {
         { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
         { "Properties", "display", "no" }, { "Gene Name", "display", "yes" },
         { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" }
-        , { "Taxonomy Rank", "display", "no" }};
+        , { "Taxonomy Rank", "display", "no" }, { "Show External Data", "display", "yes" }};
     final static int                        display_as_phylogram                                   = 0;
     final static int                        show_node_names                                        = 1;
     final static int                        show_tax_code                                          = 2;
@@ -166,6 +166,7 @@ public final class Configuration {
     final static int                        show_mol_seqs                                          = 27;
     final static int                        write_branch_length_values                             = 28;
     final static int                        show_tax_rank                                          = 29;
+    final static int                        display_external_data                                  = 30;
     
     static final String                     VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA                   = "validate_against_phyloxml_xsd_schema";
     private static Hashtable<String, Color> _sequence_colors;
@@ -526,6 +527,10 @@ public final class Configuration {
     public void setDisplayInternalData( final boolean b ) {
         display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
     }
+    
+    public void setDisplayExternalData( final boolean b ) {
+        display_options[ display_external_data ][ 2 ] = b ? "yes" : "no";
+    }
 
     public void setDisplayMultipleSequenceAlignment( final boolean b ) {
         display_options[ show_mol_seqs ][ 2 ] = b ? "yes" : "no";
@@ -1434,6 +1439,9 @@ public final class Configuration {
             else if ( key.equals( "display_internal_data" ) ) {
                 key_index = Configuration.display_internal_data;
             }
+            else if ( key.equals( "display_external_data" ) ) {
+                key_index = Configuration.display_external_data;
+            }
             else if ( key.equals( "dynamically_hide_data" ) ) {
                 key_index = Configuration.dynamically_hide_data;
             }
@@ -1727,7 +1735,7 @@ public final class Configuration {
         return _species_colors;
     }
 
-    final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+    public final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
         return _taxonomy_extraction;
     }
 
@@ -1756,11 +1764,11 @@ public final class Configuration {
         return _hide_controls_and_menus;
     }
 
-    boolean isInternalNumberAreConfidenceForNhParsing() {
+    public boolean isInternalNumberAreConfidenceForNhParsing() {
         return _internal_number_are_confidence_for_nh_parsing;
     }
 
-    boolean isReplaceUnderscoresInNhParsing() {
+    public boolean isReplaceUnderscoresInNhParsing() {
         return _nh_parsing_replace_underscores;
     }
 
@@ -1787,7 +1795,7 @@ public final class Configuration {
         return _use_tabbed_display;
     }
 
-    boolean isValidatePhyloXmlAgainstSchema() {
+   public boolean isValidatePhyloXmlAgainstSchema() {
         return _validate_against_phyloxml_xsd_schema;
     }
 
@@ -1804,4 +1812,10 @@ public final class Configuration {
     }
 
     
+    public String getConfigFilename() {
+        return config_filename;
+    }
+    
+
+    
 }