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 0aecc53..a228d29 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -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;
@@ -122,7 +129,6 @@ final public class Options {
     private boolean                           _parse_beast_style_extended_nexus_tags;
     private boolean                           _collapsed_with_average_height;
     private boolean                           _show_abbreviated_labels_for_collapsed_nodes;
-    private boolean                           _align_ext_labels_in_phylogram;
     
     private Options() {
         init();
@@ -229,7 +235,6 @@ final public class Options {
         _right_align_domains = false;
         _collapsed_with_average_height = true;
         _show_abbreviated_labels_for_collapsed_nodes = true;
-        _align_ext_labels_in_phylogram = true;
     }
 
     final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
@@ -624,13 +629,6 @@ final public class Options {
         _show_abbreviated_labels_for_collapsed_nodes =  show_abbreviated_labels_for_collapsed_nodes;
     }
     
-    final boolean isAlignExtLabelsInPhylogram() {
-        return _align_ext_labels_in_phylogram;
-    }
-
-    final void setAlignExtLabelsInPhylogram( final boolean align_ext_labels_in_phylogram ) {
-        _align_ext_labels_in_phylogram = align_ext_labels_in_phylogram;
-    }
-    
+   
     
 }