X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=c1a109674befcc44c220168bb754d895dbaa7e1b;hb=bf4f34e0511813622f68e54ffb783e4e6d92bfa4;hp=271bdfa73ca6a9d685dc6939682deda7f06a1d88;hpb=9e1353590a88991e7593d38c8e307f713a0f3d5b;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 271bdfa..c1a1096 100644
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -220,6 +220,9 @@ public final class Configuration {
     private Color                           _vector_data_mean_color                                = Color.WHITE;
     private double                          _vector_data_height                                    = 12;
     private int                             _vector_data_width                                     = 120;
+    private boolean _line_up_renderable_node_data;
+    private boolean _right_align_domains;
+    
     static {
         for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
             if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
@@ -1492,7 +1495,7 @@ public final class Configuration {
                         + "] for [ext_descendents_data_to_return_on]" );
             }
         }
-        //
+       
         else if ( key.equals( "vector_data_min_color" ) ) {
             _vector_data_min_color = Color.decode( ( String ) st.nextElement() );
         }
@@ -1502,7 +1505,7 @@ public final class Configuration {
         else if ( key.equals( "vector_data_mean_color" ) ) {
             _vector_data_mean_color = Color.decode( ( String ) st.nextElement() );
         }
-        //
+      
         else if ( key.equals( "vector_data_width" ) ) {
             _vector_data_width = parseShort( ( String ) st.nextElement() );
             if ( _vector_data_width < 1 ) {
@@ -1515,7 +1518,16 @@ public final class Configuration {
                 _vector_data_height = 12;
             }
         }
-        //
+       
+        else if ( key.equals( "line_up_renderable_data" ) ) {
+            setLineUpRendarableNodeData( parseBoolean( ( String ) st.nextElement() ) );
+        }
+        
+        else if ( key.equals( "right_align_domain_architectures" ) ) {
+            setRightLineUpDomains( parseBoolean( ( String ) st.nextElement() ) );
+        }
+        
+        
         else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
             // yet retrieved!
             int key_index = -1;
@@ -1747,4 +1759,26 @@ public final class Configuration {
     public int getVectorDataWidth() {
         return _vector_data_width;
     }
+    
+    final public boolean isLineUpRendarableNodeData() {
+        
+        return _line_up_renderable_node_data;
+    }
+    
+    final public boolean isRightLineUpDomains() {
+        
+        return _right_align_domains;
+    }
+    
+    final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data) {
+        
+         _line_up_renderable_node_data = line_up_renderable_node_data;
+    }
+    
+    final public void setRightLineUpDomains( final boolean right_align_domains ) {
+        
+        _right_align_domains = right_align_domains;
+    }
+    
+    
 }