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 2bf8471..ec72006 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -61,6 +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;
@@ -77,8 +78,8 @@ 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;
@@ -100,10 +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;
     }
@@ -256,6 +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;
     }
@@ -272,10 +273,6 @@ final public class Options {
         return _search_case_sensitive;
     }
 
-    final boolean isShowBranchLengthValues() {
-        return _show_branch_length_values;
-    }
-
     boolean isShowConfidenceStddev() {
         return _show_confidence_stddev;
     }
@@ -284,6 +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;
     }
@@ -362,6 +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;
     }
@@ -414,10 +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;
     }
@@ -430,6 +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;
     }
@@ -446,7 +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;
@@ -456,6 +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;
@@ -471,7 +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;
@@ -487,10 +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;
     }
 
@@ -507,7 +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() );
@@ -562,6 +567,7 @@ final public class Options {
             }
             instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() );
             instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() );
+            instance.setShowDefaultNodeShapesForMarkedNodes( configuration.isShowDefaultNodeShapesForMarkedNodes() );
             if ( configuration.getExtDescNodeDataToReturn() != null ) {
                 instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() );
             }