X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=bb896aec78254e3e03cafff44688a98cf03947f9;hb=885253f33f05af39d0d529659d534f5a3365159e;hp=2b39eee675407cbbd9e9cd463ba6440b9efb68cd;hpb=0feab495c350ff488c86253826bca4b202c46f4d;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 2b39eee..bb896ae 100644
--- 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;
@@ -927,6 +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() ) );
         }
@@ -1502,6 +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
     }