clean up

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

diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java
index ec63ca6..2bf8471 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -31,9 +31,9 @@ import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.NodeData;
 import org.forester.phylogeny.data.NodeData.NODE_DATA;
-import org.forester.phylogeny.data.NodeVisualization;
-import org.forester.phylogeny.data.NodeVisualization.NodeFill;
-import org.forester.phylogeny.data.NodeVisualization.NodeShape;
+import org.forester.phylogeny.data.NodeVisualData;
+import org.forester.phylogeny.data.NodeVisualData.NodeFill;
+import org.forester.phylogeny.data.NodeVisualData.NodeShape;
 import org.forester.util.ForesterUtil;
 
 /*
@@ -51,8 +51,8 @@ final public class Options {
     private CLADOGRAM_TYPE                    _cladogram_type;
     private boolean                           _color_by_taxonomic_group;
     private boolean                           _color_labels_same_as_parent_branch;
-    private NodeVisualization.NodeFill        _default_node_fill;
-    private NodeVisualization.NodeShape       _default_node_shape;
+    private NodeVisualData.NodeFill           _default_node_fill;
+    private NodeVisualData.NodeShape          _default_node_shape;
     private short                             _default_node_shape_size;
     private boolean                           _editable;
     private NODE_DATA                         _ext_desc_data_to_return;
@@ -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;
+    }
 }