X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=4aa85f218febc6efa58bc7049d27eb0fbfa1bfa7;hb=663daba455e534e015bd56bae070e9248e3a4533;hp=c578e05d66214e3a99da0ac7f905a2a574dc4980;hpb=64dc04c28918adc0b9b3752cdccd3df1c8c4cb92;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index c578e05..4aa85f2 100644
--- 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;
@@ -217,6 +217,7 @@ public final class Configuration {
     private EXT_NODE_DATA_RETURN_ON         _ext_node_data_return_on                               = EXT_NODE_DATA_RETURN_ON.WINODW;
     private int                             _frame_x_size;
     private int                             _frame_y_size;
+    private boolean                         _midpoint_root                                         = false;
     private static String                   DEFAULT_FONT_FAMILY                                    = "";
     static {
         for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
@@ -722,8 +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;
@@ -771,7 +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;
@@ -869,10 +870,6 @@ public final class Configuration {
         else if ( name.equals( "color_subtree" ) ) {
             index = Configuration.color_subtree;
         }
-        else if ( name.equals( "go_to_swiss_prot" ) ) {
-            ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" );
-            return DEPRECATED;
-        }
         return index;
     }
 
@@ -1310,15 +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
@@ -1409,6 +1412,9 @@ public final class Configuration {
         else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
             setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
         }
+        else if ( key.equals( "midpoint_reroot" ) ) {
+            setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
+        }
         else if ( key.equals( "ext_descendents_data_to_return" ) ) {
             final String s = ( ( String ) st.nextElement() ).trim();
             if ( s.equalsIgnoreCase( "node_name" ) ) {
@@ -1524,18 +1530,6 @@ public final class Configuration {
             else if ( key.equals( "width_branches" ) ) {
                 key_index = Configuration.width_branches;
             }
-            else if ( key.equals( "color_orthologous" ) ) {
-                ForesterUtil.printWarningMessage( Constants.PRG_NAME,
-                                                  "configuration key [color_orthologous] is deprecated" );
-            }
-            else if ( key.equals( "color_subtree_neighbors" ) ) {
-                ForesterUtil.printWarningMessage( Constants.PRG_NAME,
-                                                  "configuration key [color_subtree_neighbors] is deprecated" );
-            }
-            else if ( key.equals( "color_super_orthologous" ) ) {
-                ForesterUtil.printWarningMessage( Constants.PRG_NAME,
-                                                  "configuration key [color_super_orthologous] is deprecated" );
-            }
             else if ( key.equals( "mark_nodes_with_box" ) ) {
                 ForesterUtil.printWarningMessage( Constants.PRG_NAME,
                                                   "configuration key [mark_nodes_with_box] is deprecated" );
@@ -1627,7 +1621,8 @@ public final class Configuration {
                     }
                 }
                 else if ( key.equals( "species_color" ) ) {
-                    getSpeciesColors().put( ( String ) st.nextElement(), 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() ) );
@@ -1706,4 +1701,12 @@ public final class Configuration {
     static enum TRIPLET {
         TRUE, FALSE, UNKNOWN
     }
+
+    public boolean isMidpointReroot() {
+        return _midpoint_root;
+    }
+
+    public void setMidpointReroot( final boolean midpoint_root ) {
+        _midpoint_root = midpoint_root;
+    }
 }