removed clustalo

[jalview.git] / forester / java / src / org / forester / archaeopteryx / tools / InferenceManager.java

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java b/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java
index 2c416b9..30db176 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java
@@ -12,7 +12,6 @@ public final class InferenceManager {
     private final File          _path_to_local_mafft;
     private final File          _path_to_local_fastme;
     private final File          _path_to_local_raxml;
-    private final File          _path_to_local_clustalo;
 
     public static InferenceManager createInstance( final Configuration c ) {
         return new InferenceManager( c.getpathToLocalMafft(),
@@ -22,16 +21,13 @@ public final class InferenceManager {
     }
 
     public boolean canDoMsa() {
-        return ( getPathToLocalMafft() != null ) 
-                || ( getPathToLocalClustalo() != null );
+        return ( getPathToLocalMafft() != null );
     }
 
     public File getPathToLocalMafft() {
         return _path_to_local_mafft;
     }
 
-    
-
     public File getPathToLocalFastme() {
         return _path_to_local_fastme;
     }
@@ -40,10 +36,6 @@ public final class InferenceManager {
         return _path_to_local_raxml;
     }
 
-    public File getPathToLocalClustalo() {
-        return _path_to_local_clustalo;
-    }
-
     private final static File createLocalPath( final File path, final String name ) {
         if ( ( path != null ) && path.canExecute() && !path.isDirectory() ) {
             return path;
@@ -78,9 +70,7 @@ public final class InferenceManager {
                               final File path_to_local_raxml,
                               final File path_to_local_clustalo ) {
         _path_to_local_mafft = createLocalPath( path_to_local_mafft, "mafft" );
-      
         _path_to_local_fastme = createLocalPath( path_to_local_fastme, "fastme" );
         _path_to_local_raxml = createLocalPath( path_to_local_raxml, "raxml" );
-        _path_to_local_clustalo = createLocalPath( path_to_local_clustalo, "clustalo" );
     }
 }