label

[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 e45dfc8..4e445bc 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -47,6 +47,7 @@ import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
 import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE;
 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
+import org.forester.phylogeny.data.NodeData.NODE_DATA;
 import org.forester.phylogeny.data.NodeVisualization;
 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
@@ -145,6 +146,7 @@ public final class Configuration {
     final static int                        add_new_node                                           = 13;
     final static int                        edit_node_data                                         = 14;
     final static int                        sort_descendents                                       = 15;
+    final static int                        get_ext_desc_data                                      = 16;
     // ---------------------------
     // Display options for trees
     // ---------------------------
@@ -173,7 +175,7 @@ public final class Configuration {
             { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" },
             { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" },
             { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" },
-            { "Sort Descendants", "display" }                                                     };
+            { "Sort Descendants", "display" }, { "Get External Node Data", "display" }            };
     // This option is selected in the dropdown
     int                                     default_clickto                                        = Configuration.display_node_data;
     // --------------
@@ -208,6 +210,7 @@ public final class Configuration {
     private Color                           _gui_button_border_color                               = Constants.BUTTON_BORDER_COLOR_DEFAULT;
     private Color                           _domain_structure_font_color                           = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
     private Color                           _domain_structure_base_color                           = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
+    private NODE_DATA                       _ext_desc_data_to_return;
     private static String                   DEFAULT_FONT_FAMILY                                    = "";
     static {
         for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
@@ -372,6 +375,9 @@ public final class Configuration {
         else if ( name.equals( "sort_descendants" ) ) {
             index = Configuration.sort_descendents;
         }
+        else if ( name.equals( "get_ext_descendents_data" ) ) {
+            index = Configuration.get_ext_desc_data;
+        }
         else if ( name.equals( "display_sequences" ) ) {
             ForesterUtil
                     .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
@@ -439,8 +445,6 @@ public final class Configuration {
         return _path_to_local_mafft;
     }
 
-  
-
     public File getPathToLocalFastme() {
         return _path_to_local_fastme;
     }
@@ -823,8 +827,6 @@ public final class Configuration {
         _path_to_local_mafft = path_to_local_mafft;
     }
 
-   
-
     private void setPathToLocalFastme( final File path_to_local_fastme ) {
         _path_to_local_fastme = path_to_local_fastme;
     }
@@ -1063,7 +1065,6 @@ public final class Configuration {
                 setPathToLocalMafft( new File( str ) );
             }
         }
-       
         else if ( key.equals( "fastme_local" ) ) {
             final String str = ( ( String ) st.nextElement() ).trim();
             if ( !ForesterUtil.isEmpty( str ) ) {
@@ -1286,6 +1287,31 @@ public final class Configuration {
         else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
             setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
         }
+        else if ( key.equals( "ext_descendents_data_to_return" ) ) {
+            final String s = ( ( String ) st.nextElement() ).trim();
+            if ( s.equalsIgnoreCase( "node_name" ) ) {
+                setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
+            }
+            else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
+                setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
+            }
+            else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
+                setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
+            }
+            else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
+                setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
+            }
+            else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
+                setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
+            }
+            else {
+                ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
+                        + "] for [ext_descendents_data_to_return]" );
+            }
+        }
+        else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
+           set( ( String ) st.nextElement() ).replaceAll( "_", " " );
+        }
         else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
             // yet retrieved!
             int key_index = -1;
@@ -1574,4 +1600,12 @@ public final class Configuration {
     public enum UI {
         NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
     }
+
+    public NODE_DATA getExtDescNodeDataToReturn() {
+        return _ext_desc_data_to_return;
+    }
+
+    public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
+        _ext_desc_data_to_return = ext_desc_data_to_return;
+    }
 }