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 36d0224..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;
@@ -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;
     }
@@ -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;
     }
@@ -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;