X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FOptions.java;h=80f0861edbc70c95b5ea370b26e36488c29c15fc;hb=8d6e81da091d432309f2f7034cf93dbc5ba5e82a;hp=727838acc7182d9b4e0a93d9f49d42937498eb06;hpb=bdf2d2a11d720d6457f52866af7ff909afe98db4;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java
index 727838a..80f0861 100644
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -29,8 +29,7 @@ import java.awt.Font;
 
 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.NodeDataField;
 import org.forester.phylogeny.data.NodeVisualData;
 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
@@ -55,12 +54,13 @@ final public class Options {
     private NodeVisualData.NodeShape          _default_node_shape;
     private short                             _default_node_shape_size;
     private boolean                           _editable;
-    private NODE_DATA                         _ext_desc_data_to_return;
+    private NodeDataField                         _ext_desc_data_to_return;
     private boolean                           _graphics_export_using_actual_size;
     private boolean                           _graphics_export_visible_only;
     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;
@@ -78,6 +78,7 @@ final public class Options {
     private boolean                           _search_case_sensitive;
     private boolean                           _show_annotation_ref_source;
     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;
@@ -91,7 +92,7 @@ final public class Options {
         init();
     }
 
-    public NodeData.NODE_DATA getExtDescNodeDataToReturn() {
+    public NodeDataField getExtDescNodeDataToReturn() {
         return _ext_desc_data_to_return;
     }
 
@@ -99,10 +100,6 @@ 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;
     }
@@ -123,7 +120,7 @@ final public class Options {
         _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
     }
 
-    public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
+    public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) {
         _ext_desc_data_to_return = ext_desc_data_to_return;
     }
 
@@ -255,6 +252,10 @@ final public class Options {
         return _match_whole_terms_only;
     }
 
+    final boolean isSearchWithRegex() {
+        return _search_with_regex;
+    }
+
     final boolean isPrintBlackAndWhite() {
         return _print_black_and_white;
     }
@@ -279,6 +280,10 @@ 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;
     }
@@ -357,6 +362,10 @@ 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;
     }
@@ -421,6 +430,10 @@ 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;
     }
@@ -446,6 +459,7 @@ 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;
@@ -461,6 +475,7 @@ 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_with_regex = false;
         _search_case_sensitive = false;
         _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
         _show_overview = true;
@@ -477,10 +492,10 @@ 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;
+        _ext_desc_data_to_return = NodeDataField.UNKNOWN;
+        _line_up_renderable_node_data = true;
         _right_align_domains = false;
     }
 
@@ -551,6 +566,7 @@ final public class Options {
             }
             instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() );
             instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() );
+            instance.setShowDefaultNodeShapesForMarkedNodes( configuration.isShowDefaultNodeShapesForMarkedNodes() );
             if ( configuration.getExtDescNodeDataToReturn() != null ) {
                 instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() );
             }