in progress

[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 1143288..a228d29 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -41,7 +41,7 @@ import org.forester.util.ForesterUtil;
 final public class Options {
 
     public static enum CLADOGRAM_TYPE {
-        EXT_NODE_SUM_DEP, NON_LINED_UP, TOTAL_NODE_SUM_DEP;
+        LINED_UP, NON_LINED_UP;
     }
 
     public static enum NODE_LABEL_DIRECTION {
@@ -51,6 +51,12 @@ final public class Options {
     public static enum PHYLOGENY_GRAPHICS_TYPE {
         CIRCULAR, CONVEX, CURVED, EURO_STYLE, RECTANGULAR, ROUNDED, TRIANGULAR, UNROOTED;
     }
+    
+    static enum PHYLOGENY_DISPLAY_TYPE {
+        CLADOGRAM,
+        ALIGNED_PHYLOGRAM,
+        UNALIGNED_PHYLOGRAM
+    }
 
     static enum OVERVIEW_PLACEMENT_TYPE {
         LOWER_LEFT( "lower left" ),
@@ -73,6 +79,7 @@ final public class Options {
             return toString().replaceAll( " ", "_" );
         }
     }
+   
     static final double                       MIN_CONFIDENCE_DEFAULT = 0.0;
     private boolean                           _abbreviate_scientific_names;
     private boolean                           _allow_errors_in_distance_to_parent;
@@ -119,7 +126,10 @@ final public class Options {
     private boolean                           _line_up_renderable_node_data;
     private boolean                           _right_align_domains;
     private boolean                           _color_all_found_nodes_when_coloring_subtree;
-
+    private boolean                           _parse_beast_style_extended_nexus_tags;
+    private boolean                           _collapsed_with_average_height;
+    private boolean                           _show_abbreviated_labels_for_collapsed_nodes;
+    
     private Options() {
         init();
     }
@@ -195,6 +205,7 @@ final public class Options {
         _show_default_node_shapes_external = false;
         _show_default_node_shapes_for_marked_nodes = false;
         _color_all_found_nodes_when_coloring_subtree = false;
+        _parse_beast_style_extended_nexus_tags= true;
         _min_confidence_value = MIN_CONFIDENCE_DEFAULT;
         _print_black_and_white = false;
         _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
@@ -222,6 +233,8 @@ final public class Options {
         _ext_desc_data_to_return = NodeDataField.UNKNOWN;
         _line_up_renderable_node_data = true;
         _right_align_domains = false;
+        _collapsed_with_average_height = true;
+        _show_abbreviated_labels_for_collapsed_nodes = true;
     }
 
     final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
@@ -591,4 +604,31 @@ final public class Options {
     final void setColorAllFoundNodesWhenColoringSubtree( final boolean color_all_found_nodes_when_coloring_subtree ) {
         _color_all_found_nodes_when_coloring_subtree = color_all_found_nodes_when_coloring_subtree;
     }
+
+    final boolean isParseBeastStyleExtendedNexusTags() {
+        return _parse_beast_style_extended_nexus_tags;
+    }
+
+    final void setParseBeastStyleExtendedNexusTags( final boolean parse_beast_style_extended_nexus_tags ) {
+        _parse_beast_style_extended_nexus_tags = parse_beast_style_extended_nexus_tags;
+    }
+    
+    final boolean isCollapsedWithAverageHeigh() {
+        return _collapsed_with_average_height;
+    }
+
+    final void setCollapsedWithAverageHeigh( final boolean collapsed_with_average_height ) {
+        _collapsed_with_average_height = collapsed_with_average_height;
+    }
+
+    final boolean isShowAbbreviatedLabelsForCollapsedNodes() {
+        return _show_abbreviated_labels_for_collapsed_nodes;
+    }
+    
+    final void setShowAbbreviatedLabelsForCollapsedNodes(final boolean show_abbreviated_labels_for_collapsed_nodes) {
+        _show_abbreviated_labels_for_collapsed_nodes =  show_abbreviated_labels_for_collapsed_nodes;
+    }
+    
+   
+    
 }