in progress

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

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 72c5753..064fc7d 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -129,7 +129,7 @@ public final class Configuration {
     final static int                        collapse_uncollapse                                    = 1;
     final static int                        reroot                                                 = 2;
     final static int                        subtree                                                = 3;
-    final static int                        swap                                                   = 4;
+    final static int                        swap               = 4;
     final static int                        color_subtree                                          = 5;
     final static int                        open_seq_web                                           = 6;
     final static int                        open_tax_web                                           = 7;
@@ -140,6 +140,9 @@ public final class Configuration {
     final static int                        add_new_node                                           = 12;
     final static int                        edit_node_data                                         = 13;
     final static int                        blast                                                  = 14;
+    final static int                        sort_descendents                                        = 15;
+    
+    
     // ---------------------------
     // Display options for trees
     // ---------------------------
@@ -151,7 +154,7 @@ public final class Configuration {
     String                                  default_config_filename                                = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
     final static String                     display_options[][]                                    = {
             { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
-            { "Annotation", "nodisplay", "no" }, { "Confidence Value", "display", "?" }, { "Event", "display", "?" },
+            { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, { "Event", "display", "?" },
             { "Taxonomy Colorize", "display", "no" }, { "Colorize Branches", "display", "no" },
             { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" },
             { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" },
@@ -167,7 +170,7 @@ public final class Configuration {
             { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
             { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Cut Subtree", "display" },
             { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
-            { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Blast", "nodisplay" } };
+            { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Blast", "nodisplay" }, { "Sort Descendants", "display" } };
     // This option is selected in the dropdown
     int                                     default_clickto                                        = Configuration.display_node_data;
     // --------------
@@ -363,6 +366,9 @@ public final class Configuration {
         else if ( name.equals( "swap" ) ) {
             index = Configuration.swap;
         }
+        else if ( name.equals( "sort_descendants" ) ) {
+            index = Configuration.sort_descendents;
+        }
         else if ( name.equals( "display_sequences" ) ) {
             ForesterUtil
                     .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
@@ -781,6 +787,10 @@ public final class Configuration {
         _cladogram_type = cladogram_type;
     }
 
+    public void setColorizeBranches( final boolean b ) {
+        display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
+    }
+
     public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
         _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
     }
@@ -801,14 +811,62 @@ public final class Configuration {
         _default_node_shape_size = default_node_shape_size;
     }
 
+    public void setDisplayAsPhylogram( final boolean b ) {
+        display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
+    }
+
     public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
         _display_colors = display_colors;
     }
 
+    public void setDisplayConfidenceValues( final boolean b ) {
+        display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
+    }
+
+    public void setDisplayInternalData( final boolean b ) {
+        display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
+    }
+
+    public void setDisplayNodeNames( final boolean b ) {
+        display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
+    }
+
+    public void setDisplaySequenceAcc( final boolean b ) {
+        display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
+    }
+
+    public void setDisplaySequenceNames( final boolean b ) {
+        display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
+    }
+
     public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
         _display_sequence_relations = display_sequence_relations;
     }
 
+    public void setDisplaySequenceSymbols( final boolean b ) {
+        display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no";
+    }
+
+    public void setDisplayTaxonomyCode( final boolean b ) {
+        display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
+    }
+
+    public void setDisplayTaxonomyCommonNames( final boolean b ) {
+        display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
+    }
+
+    public void setDisplayTaxonomyImages( final boolean b ) {
+        display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
+    }
+
+    public void setDisplayTaxonomyScientificNames( final boolean b ) {
+        display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
+    }
+
+    public void setDynamicallyHideData( final boolean b ) {
+        display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
+    }
+
     private void setEditable( final boolean editable ) {
         _editable = editable;
     }
@@ -1418,10 +1476,18 @@ public final class Configuration {
         _show_scale = show_scale;
     }
 
+    public void setTaxonomyColorize( final boolean b ) {
+        display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
+    }
+
     public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
         _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
     }
 
+    public void setUseBranchesWidths( final boolean b ) {
+        display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
+    }
+
     private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
         _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
     }