inprogress

[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 9857b51..a4c15b3 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -42,6 +42,7 @@ import org.forester.util.ForesterUtil;
 final public class Options {
 
     static final double                       MIN_CONFIDENCE_DEFAULT = 0.0;
+    private boolean                           _color_by_taxonomic_group;
     private boolean                           _show_branch_length_values;
     private boolean                           _internal_number_are_confidence_for_nh_parsing;
     private boolean                           _show_scale;
@@ -72,12 +73,12 @@ final public class Options {
     private boolean                           _editable;
     private boolean                           _background_color_gradient;
     private boolean                           _show_domain_labels;
+    private boolean                           _show_annotation_ref_source;
     private boolean                           _color_labels_same_as_parent_branch;
     private boolean                           _abbreviate_scientific_names;
     private NodeVisualization.NodeShape       _default_node_shape;
     private NodeVisualization.NodeFill        _default_node_fill;
     private short                             _default_node_shape_size;
-    private boolean                           _taxonomy_colorize_node_shapes;
     private boolean                           _show_default_node_shapes_internal;
     private boolean                           _show_default_node_shapes_external;
     private boolean                           _show_confidence_stddev;
@@ -96,6 +97,14 @@ final public class Options {
         return _show_domain_labels;
     }
 
+    public final boolean isShowAnnotationRefSource() {
+        return _show_annotation_ref_source;
+    }
+
+    public final void setShowAnnotationRefSource( final boolean show_annotation_ref_source ) {
+        _show_annotation_ref_source = show_annotation_ref_source;
+    }
+
     public void setBackgroundColorGradient( final boolean background_color_gradient ) {
         _background_color_gradient = background_color_gradient;
     }
@@ -248,6 +257,10 @@ final public class Options {
         return _show_branch_length_values;
     }
 
+    final boolean isColorByTaxonomicGroup() {
+        return _color_by_taxonomic_group;
+    }
+
     boolean isShowConfidenceStddev() {
         return _show_confidence_stddev;
     }
@@ -268,10 +281,6 @@ final public class Options {
         return _show_scale;
     }
 
-    boolean isTaxonomyColorizeNodeShapes() {
-        return _taxonomy_colorize_node_shapes;
-    }
-
     final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
         _abbreviate_scientific_names = abbreviate_scientific_names;
     }
@@ -390,6 +399,10 @@ final public class Options {
         _show_branch_length_values = show_branch_length_values;
     }
 
+    final void setColorByTaxonomicGroup( final boolean color_by_taxonomic_group ) {
+        _color_by_taxonomic_group = color_by_taxonomic_group;
+    }
+
     void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
         _show_confidence_stddev = show_confidence_stddev;
     }
@@ -410,11 +423,7 @@ final public class Options {
         _show_scale = show_scale;
     }
 
-    void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
-        _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
-    }
-
-    final void setTaxonomyExtractio( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+    final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
         _taxonomy_extraction = taxonomy_extraction;
     }
 
@@ -422,7 +431,6 @@ final public class Options {
         _default_node_shape = NodeShape.CIRCLE;
         _default_node_fill = NodeFill.GRADIENT;
         _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
-        _taxonomy_colorize_node_shapes = false;
         _show_branch_length_values = false;
         _internal_number_are_confidence_for_nh_parsing = false;
         _show_scale = false;
@@ -458,9 +466,10 @@ final public class Options {
         _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
         _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
         _nh_parsing_replace_underscores = false;
-        _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
+        _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
         _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
         _show_domain_labels = true;
+        _show_annotation_ref_source = true;
         setAbbreviateScientificTaxonNames( false );
         _color_labels_same_as_parent_branch = false;
         _show_confidence_stddev = true;
@@ -483,6 +492,7 @@ final public class Options {
             instance.setShowScale( configuration.isShowScale() );
             instance.setShowBranchLengthValues( configuration.isShowBranchLengthValues() );
             instance.setShowOverview( configuration.isShowOverview() );
+            instance.setColorByTaxonomicGroup( configuration.isColorByTaxonomicGroup() );
             instance.setCladogramType( configuration.getCladogramType() );
             instance.setOvPlacement( configuration.getOvPlacement() );
             instance.setPrintLineWidth( configuration.getPrintLineWidth() );
@@ -496,13 +506,14 @@ final public class Options {
                 instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration
                         .getNumberOfDigitsAfterCommaForConfidenceValues() );
             }
-            instance.setTaxonomyExtractio( configuration.getTaxonomyExtraction() );
+            instance.setTaxonomyExtraction( configuration.getTaxonomyExtraction() );
             instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() );
             instance.setInternalNumberAreConfidenceForNhParsing( configuration
                     .isInternalNumberAreConfidenceForNhParsing() );
             instance.setEditable( configuration.isEditable() );
             instance.setColorLabelsSameAsParentBranch( configuration.isColorLabelsSameAsParentBranch() );
             instance.setShowDomainLabels( configuration.isShowDomainLabels() );
+            instance.setShowAnnotationRefSource( configuration.isShowAnnotationRefSource() );
             instance.setAbbreviateScientificTaxonNames( configuration.isAbbreviateScientificTaxonNames() );
             if ( configuration.getMinConfidenceValue() != MIN_CONFIDENCE_DEFAULT ) {
                 instance.setMinConfidenceValue( configuration.getMinConfidenceValue() );
@@ -532,7 +543,6 @@ final public class Options {
             if ( configuration.getDefaultNodeShapeSize() >= 0 ) {
                 instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() );
             }
-            instance.setTaxonomyColorizeNodeShapes( configuration.isTaxonomyColorizeNodeShapes() );
             instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() );
             instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() );
             if ( configuration.getExtDescNodeDataToReturn() != null ) {