domain + go output work begins

[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 4d96164..ec72006 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -35,7 +35,6 @@ 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;
-import org.omg.stub.java.rmi._Remote_Stub;
 
 /*
  * This is to hold changeable options.
@@ -62,6 +61,7 @@ final public class Options {
     private boolean                           _internal_number_are_confidence_for_nh_parsing;
     private boolean                           _inverse_search_result;
     private boolean                           _match_whole_terms_only;
+    private boolean                           _search_with_regex;
     private double                            _min_confidence_value;
     private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style;
     private boolean                           _nh_parsing_replace_underscores;
@@ -78,16 +78,16 @@ final public class Options {
     private double                            _scale_bar_length;
     private boolean                           _search_case_sensitive;
     private boolean                           _show_annotation_ref_source;
-    private boolean                           _show_branch_length_values;
     private boolean                           _show_confidence_stddev;
+    private boolean                           _show_default_node_shapes_for_marked_nodes;
     private boolean                           _show_default_node_shapes_external;
     private boolean                           _show_default_node_shapes_internal;
     private boolean                           _show_domain_labels;
     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 boolean                           _line_up_renderable_node_data;
+    private boolean                           _right_align_domains;
 
     private Options() {
         init();
@@ -101,10 +101,6 @@ final public class Options {
         return _allow_errors_in_distance_to_parent;
     }
 
-    public boolean isAllowFontSizeChange() {
-        return true;
-    }
-
     public final boolean isShowAnnotationRefSource() {
         return _show_annotation_ref_source;
     }
@@ -257,6 +253,10 @@ final public class Options {
         return _match_whole_terms_only;
     }
 
+    final boolean isSearchWithRegex() {
+        return _search_with_regex;
+    }
+
     final boolean isPrintBlackAndWhite() {
         return _print_black_and_white;
     }
@@ -273,10 +273,6 @@ final public class Options {
         return _search_case_sensitive;
     }
 
-    final boolean isShowBranchLengthValues() {
-        return _show_branch_length_values;
-    }
-
     boolean isShowConfidenceStddev() {
         return _show_confidence_stddev;
     }
@@ -285,6 +281,10 @@ final public class Options {
         return _show_default_node_shapes_external;
     }
 
+    boolean isShowDefaultNodeShapesForMarkedNodes() {
+        return _show_default_node_shapes_for_marked_nodes;
+    }
+
     boolean isShowDefaultNodeShapesInternal() {
         return _show_default_node_shapes_internal;
     }
@@ -363,6 +363,10 @@ final public class Options {
         _match_whole_terms_only = search_whole_words_only;
     }
 
+    final void setSearchWithRegex( final boolean search_with_regex ) {
+        _search_with_regex = search_with_regex;
+    }
+
     final void setMinConfidenceValue( final double min_confidence_value ) {
         _min_confidence_value = min_confidence_value;
     }
@@ -415,10 +419,6 @@ final public class Options {
         _search_case_sensitive = search_case_sensitive;
     }
 
-    final void setShowBranchLengthValues( final boolean show_branch_length_values ) {
-        _show_branch_length_values = show_branch_length_values;
-    }
-
     void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
         _show_confidence_stddev = show_confidence_stddev;
     }
@@ -431,6 +431,10 @@ final public class Options {
         _show_default_node_shapes_internal = show_default_node_shapes_internal;
     }
 
+    void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) {
+        _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes;
+    }
+
     final void setShowOverview( final boolean show_overview ) {
         _show_overview = show_overview;
     }
@@ -447,7 +451,6 @@ final public class Options {
         _default_node_shape = NodeShape.CIRCLE;
         _default_node_fill = NodeFill.GRADIENT;
         _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
-        _show_branch_length_values = false;
         _internal_number_are_confidence_for_nh_parsing = false;
         _show_scale = false;
         _antialias_screen = true;
@@ -457,6 +460,7 @@ final public class Options {
         _background_color_gradient = false;
         _show_default_node_shapes_internal = false;
         _show_default_node_shapes_external = false;
+        _show_default_node_shapes_for_marked_nodes = false;
         if ( AptxUtil.isUsOrCanada() ) {
             _print_size_x = Constants.US_LETTER_SIZE_X;
             _print_size_y = Constants.US_LETTER_SIZE_Y;
@@ -472,7 +476,8 @@ final public class Options {
         _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
         _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 );
         _match_whole_terms_only = false;
-        _search_case_sensitive = false;
+        _search_with_regex = false;
+        _search_case_sensitive = true;
         _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
         _show_overview = true;
         _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
@@ -488,10 +493,10 @@ final public class Options {
         _show_annotation_ref_source = true;
         setAbbreviateScientificTaxonNames( false );
         _color_labels_same_as_parent_branch = false;
-        _show_confidence_stddev = true;
+        _show_confidence_stddev = false;
         _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;
+        _line_up_renderable_node_data = true;
         _right_align_domains = false;
     }
 
@@ -508,7 +513,6 @@ final public class Options {
         if ( configuration != null ) {
             instance.setAntialiasScreen( configuration.isAntialiasScreen() );
             instance.setShowScale( configuration.isShowScale() );
-            instance.setShowBranchLengthValues( configuration.isShowBranchLengthValues() );
             instance.setShowOverview( configuration.isShowOverview() );
             instance.setColorByTaxonomicGroup( configuration.isColorByTaxonomicGroup() );
             instance.setCladogramType( configuration.getCladogramType() );
@@ -563,12 +567,12 @@ final public class Options {
             }
             instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() );
             instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() );
+            instance.setShowDefaultNodeShapesForMarkedNodes( configuration.isShowDefaultNodeShapesForMarkedNodes() );
             if ( configuration.getExtDescNodeDataToReturn() != null ) {
                 instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() );
             }
-            
-            instance.setRightLineUpDomains(  configuration.isRightLineUpDomains() );
-            instance.setLineUpRendarableNodeData(  configuration.isLineUpRendarableNodeData() );
+            instance.setRightLineUpDomains( configuration.isRightLineUpDomains() );
+            instance.setLineUpRendarableNodeData( configuration.isLineUpRendarableNodeData() );
             instance.setAllowErrorsInDistanceToParent( false );
         }
         return instance;
@@ -613,23 +617,18 @@ final public class Options {
     }
 
     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 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;
     }
-    
 }