X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2Ftools%2FInferenceManager.java;h=e3e5e65f8f5d5df2732d90ab831dd0853b9b224e;hb=a9cc2cc5c9cda0ab49f26ccfb7a1aa30531e6ecf;hp=688624337705a8fc6304a178366f682cbcab65c4;hpb=e86d89ccaf293b3e50d16db81d8e151c37c5fdb1;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java b/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java
index 6886243..e3e5e65 100644
--- a/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java
@@ -10,32 +10,21 @@ public final class InferenceManager {
     private final static String DEFAULT_PATHS[] = { "C:\\Program Files\\", "C:\\Program Files (x86)\\", "/bin/",
             "/usr/local/bin/", "/usr/bin/"     };
     private final File          _path_to_local_mafft;
-    private final File          _path_to_local_kalign;
     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(),
-                                     c.getPathToLocalKalign(),
-                                     c.getPathToLocalFastme(),
-                                     c.getPathToLocalRaxml(),
-                                     c.getPathToLocalClustalOmega() );
+        return new InferenceManager( c.getpathToLocalMafft(), c.getPathToLocalFastme(), c.getPathToLocalRaxml() );
     }
 
     public boolean canDoMsa() {
-        return ( getPathToLocalMafft() != null ) || ( getPathToLocalKalign() != null )
-                || ( getPathToLocalClustalo() != null );
+        return ( getPathToLocalMafft() != null );
     }
 
     public File getPathToLocalMafft() {
         return _path_to_local_mafft;
     }
 
-    public File getPathToLocalKalign() {
-        return _path_to_local_kalign;
-    }
-
     public File getPathToLocalFastme() {
         return _path_to_local_fastme;
     }
@@ -44,15 +33,11 @@ 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;
         }
-        File p1 = new File(  name );
+        final File p1 = new File( name );
         if ( p1.canExecute() && !p1.isDirectory() ) {
             return p1;
         }
@@ -78,14 +63,10 @@ public final class InferenceManager {
     }
 
     private InferenceManager( final File path_to_local_mafft,
-                              final File path_to_local_kalign,
                               final File path_to_local_fastme,
-                              final File path_to_local_raxml,
-                              final File path_to_local_clustalo ) {
+                              final File path_to_local_raxml ) {
         _path_to_local_mafft = createLocalPath( path_to_local_mafft, "mafft" );
-        _path_to_local_kalign = createLocalPath( path_to_local_kalign, "kalign" );
         _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" );
     }
 }