inprogress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / MainFrame.java

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index e4bd6f1..cc2c9eb 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -111,6 +111,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";
     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";
     static final String         SHOW_DOMAIN_LABELS_LABEL                = "Show Domain Labels";
+    static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Show Seq Annotation Ref Sources";
     static final String         COLOR_LABELS_TIP                        = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";
     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";
@@ -135,7 +136,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JMenuItem                   _gsdi_item;
     JMenuItem                   _gsdir_item;
     JMenuItem                   _lineage_inference;
-    JMenuItem                   _function_analysis;
     // file menu:
     JMenuItem                   _open_item;
     JMenuItem                   _open_url_item;
@@ -179,6 +179,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                             //TODO fix me
     JCheckBoxMenuItem           _show_overview_cbmi;
     JCheckBoxMenuItem           _show_domain_labels;
+    JCheckBoxMenuItem           _show_annotation_ref_source;
     JCheckBoxMenuItem           _abbreviate_scientific_names;
     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
     JMenuItem                   _overview_placment_mi;
@@ -201,8 +202,9 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     // _  parsing
     JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;
     JRadioButtonMenuItem        _extract_taxonomy_no_rbmi;
-    JRadioButtonMenuItem        _extract_taxonomy_yes_rbmi;
-    JRadioButtonMenuItem        _extract_taxonomy_pfam_rbmi;
+    JRadioButtonMenuItem        _extract_taxonomy_agressive_rbmi;
+    JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;
+    JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;
     JCheckBoxMenuItem           _replace_underscores_cbmi;
     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;
     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;
@@ -387,6 +389,9 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         else if ( o == _show_domain_labels ) {
             updateOptions( getOptions() );
         }
+        else if ( o == _show_annotation_ref_source ) {
+            updateOptions( getOptions() );
+        }
         else if ( o == _abbreviate_scientific_names ) {
             updateOptions( getOptions() );
         }
@@ -1259,6 +1264,8 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
                 && _background_gradient_cbmi.isSelected() );
         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
+        options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
+                && _show_annotation_ref_source.isSelected() );
         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
                 && _abbreviate_scientific_names.isSelected() );
         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
@@ -1317,14 +1324,17 @@ public abstract class MainFrame extends JFrame implements ActionListener {
                 && _print_black_and_white_cbmi.isSelected() );
         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
-        if ( ( _extract_taxonomy_yes_rbmi != null ) && _extract_taxonomy_yes_rbmi.isSelected() ) {
-            options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.AGRESSIVE );
+        if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
+            options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+        }
+        else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
+            options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
         }
-        else if ( ( _extract_taxonomy_pfam_rbmi != null ) && _extract_taxonomy_pfam_rbmi.isSelected() ) {
-            options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+        else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
+            options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
         }
         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
-            options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.NO );
+            options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
         }
         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
                 && _replace_underscores_cbmi.isSelected() );