Changed list to set in search0 and 1.

[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 36d0224..80f0861 100644 (file)
--- 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;
@@ -92,7 +92,7 @@ final public class Options {
         init();
     }
 
-    public NodeData.NODE_DATA getExtDescNodeDataToReturn() {
+    public NodeDataField getExtDescNodeDataToReturn() {
         return _ext_desc_data_to_return;
     }
 
@@ -100,10 +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;
     }
@@ -124,7 +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;
     }
 
@@ -256,6 +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;
     }
@@ -362,6 +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;
     }
@@ -471,6 +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;
@@ -489,7 +494,7 @@ final public class Options {
         _color_labels_same_as_parent_branch = false;
         _show_confidence_stddev = false;
         _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
-        _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
+        _ext_desc_data_to_return = NodeDataField.UNKNOWN;
         _line_up_renderable_node_data = true;
         _right_align_domains = false;
     }