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 0b8b7fc..bb896ae 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -62,6 +62,10 @@ public final class Configuration {
     private boolean                         _use_tabbed_display                                    = false;
     private boolean                         _hide_controls_and_menus                               = false;
     private CLADOGRAM_TYPE                  _cladogram_type                                        = Constants.CLADOGRAM_TYPE_DEFAULT;
+    private File _mafft = null;
+    private File _clustalo = null;
+    private File _fastme = null;
+    
     private SortedMap<String, WebLink>      _weblinks                                              = null;
     private SortedMap<String, Color>        _display_colors                                        = null;
     private boolean                         _antialias_screen                                      = true;
@@ -122,7 +126,6 @@ public final class Configuration {
     final static int                        show_vector_data                                       = 23;
     final static int                        show_taxonomy_images                                   = 24;
     final static int                        show_properties                                        = 25;
-    final static int                        write_confidence_values_sd                             = 26;
     // ------------------
     // Click-to options
     // ------------------
@@ -134,13 +137,14 @@ public final class Configuration {
     final static int                        color_subtree                                          = 5;
     final static int                        open_seq_web                                           = 6;
     final static int                        open_tax_web                                           = 7;
-    final static int                        cut_subtree                                            = 8;
-    final static int                        copy_subtree                                           = 9;
-    final static int                        paste_subtree                                          = 10;
-    final static int                        delete_subtree_or_node                                 = 11;
-    final static int                        add_new_node                                           = 12;
-    final static int                        edit_node_data                                         = 13;
-    final static int                        blast                                                  = 14;
+    final static int                        blast                                                  = 8;
+    final static int                        cut_subtree                                            = 9;
+    final static int                        copy_subtree                                           = 10;
+    final static int                        paste_subtree                                          = 11;
+    final static int                        delete_subtree_or_node                                 = 12;
+    final static int                        add_new_node                                           = 13;
+    final static int                        edit_node_data                                         = 14;
+    final static int                        sort_descendents                                       = 15;
     // ---------------------------
     // Display options for trees
     // ---------------------------
@@ -162,14 +166,14 @@ public final class Configuration {
             { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" },
             { "Prot/Gene Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
             { "Relation Confidence", "display", "no" }, { "Vector Data", "display", "no" },
-            { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" },
-            { "Confidence StdDev", "display", "no" }                                              };
+            { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" }             };
     final static String                     clickto_options[][]                                    = {
             { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
             { "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" } };
+            { "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" }                                                     };
     // This option is selected in the dropdown
     int                                     default_clickto                                        = Configuration.display_node_data;
     // --------------
@@ -365,6 +369,9 @@ 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" );
@@ -376,6 +383,9 @@ public final class Configuration {
         else if ( name.equals( "open_tax_web" ) ) {
             index = Configuration.open_tax_web;
         }
+        else if ( name.equals( "blast" ) ) {
+            index = Configuration.blast;
+        }
         else if ( name.equals( "cut_subtree" ) ) {
             index = Configuration.cut_subtree;
         }
@@ -921,6 +931,18 @@ public final class Configuration {
                 _ui = UI.UNKNOWN;
             }
         }
+        else if ( key.equals( "path_to_mafft" ) ) {
+            setPathToMafft( new File( (String) st.nextElement() ) );
+        }
+        else if ( key.equals( "path_to_clustalo" ) ) {
+            setPathToClustalOmega( new File( (String) st.nextElement() ) );
+        }
+        else if ( key.equals( "path_to_fastme" ) ) {
+            setPathToFastME( new File( (String) st.nextElement() ) );
+        }
+        else if ( key.equals( "path_to_mafft" ) ) {
+            setPathToMafft( new File( (String) st.nextElement() ) );
+        }
         else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
             setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
         }
@@ -1496,6 +1518,38 @@ public final class Configuration {
         return DEFAULT_FONT_FAMILY;
     }
 
+   
+    public File getPathToMafft() {
+        return _mafft;
+    }
+
+    
+
+    public File getPathToClustalOmega() {
+        return _clustalo;
+    }
+
+   
+    public File getPathToFastME() {
+        return _fastme;
+    }
+    
+    
+    public void setPathToMafft( final File mafft ) {
+        _mafft = mafft;
+    }
+
+    
+
+    public void setPathToClustalOmega(  final File clustalo ) {
+         _clustalo = clustalo ;
+    }
+
+   
+    public void setPathToFastME( final File fastme ) {
+         _fastme = fastme;
+    }
+
     static enum TRIPLET {
         TRUE, FALSE, UNKNOWN
     }