X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FOptions.java;h=2bf84713fff66f14ca323c102555eb8e2fe2d9fc;hb=226d82be9b70ce0c67b5b1055654d484073ea184;hp=fdaeacb2657618a5f877dd6efd414cce49d39cc4;hpb=081ab5f646bcae3f5192e9c1786e2d68ce015ed8;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java
index fdaeacb..2bf8471 100644
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -85,6 +85,8 @@ final public class Options {
     private boolean                           _show_overview;
     private boolean                           _show_scale;
     private TAXONOMY_EXTRACTION               _taxonomy_extraction;
+    private boolean                           _line_up_renderable_node_data;
+    private boolean                           _right_align_domains;
 
     private Options() {
         init();
@@ -464,7 +466,7 @@ final public class Options {
         }
         _min_confidence_value = MIN_CONFIDENCE_DEFAULT;
         _print_black_and_white = false;
-        _print_using_actual_size = false;
+        _print_using_actual_size = true;
         _graphics_export_using_actual_size = true;
         _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
         _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 );
@@ -488,6 +490,8 @@ final public class Options {
         _show_confidence_stddev = true;
         _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
         _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
+        _line_up_renderable_node_data = false;
+        _right_align_domains = false;
     }
 
     final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
@@ -561,6 +565,8 @@ final public class Options {
             if ( configuration.getExtDescNodeDataToReturn() != null ) {
                 instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() );
             }
+            instance.setRightLineUpDomains( configuration.isRightLineUpDomains() );
+            instance.setLineUpRendarableNodeData( configuration.isLineUpRendarableNodeData() );
             instance.setAllowErrorsInDistanceToParent( false );
         }
         return instance;
@@ -603,4 +609,20 @@ final public class Options {
             return toString().replaceAll( " ", "_" );
         }
     }
+
+    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;
+    }
 }