inprogress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / Configuration.java

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 1f89033..4aa85f2 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;
@@ -723,8 +723,8 @@ public final class Configuration {
     }
 
     boolean isAntialiasScreen() {
-        if ( AptxUtil.isMac() ) {
-            // Apple Macintosh graphics are slow, turn off anti-alias.
+        if ( ForesterUtil.isMac() ) {
+            //Apple Macintosh graphics are slow, turn off anti-alias.
             return false;
         }
         return _antialias_screen;
@@ -772,7 +772,7 @@ public final class Configuration {
     }
 
     final boolean isUseNativeUI() {
-        if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() ) {
+        if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
             _ui = UI.NATIVE;
         }
         return _ui == UI.NATIVE;
@@ -1307,15 +1307,21 @@ public final class Configuration {
             if ( s.equalsIgnoreCase( "no" ) ) {
                 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
             }
-            else if ( s.equalsIgnoreCase( "yes" ) ) {
+            else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) {
                 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             }
-            else if ( s.equalsIgnoreCase( "pfam" ) ) {
+            else if ( s.equalsIgnoreCase( "pfam_strict" ) ) {
                 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             }
+            else if ( s.equalsIgnoreCase( "aggressive" ) ) {
+                setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
+            }
             else {
-                ForesterUtil.printWarningMessage( Constants.PRG_NAME,
-                                                  "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s );
+                ForesterUtil
+                        .printWarningMessage( Constants.PRG_NAME,
+                                              "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
+                                                      + s
+                                                      + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
             }
             if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
                 ForesterUtil
@@ -1615,7 +1621,8 @@ public final class Configuration {
                     }
                 }
                 else if ( key.equals( "species_color" ) ) {
-                    getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ), Color.decode( ( String ) st.nextElement() ) );
+                    getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
+                                            Color.decode( ( String ) st.nextElement() ) );
                 }
                 else if ( key.equals( "domain_color" ) ) {
                     getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );