Merge branch 'master' of https://github.com/cmzmasek/forester.git into JalviewIntegration

[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 30db176..c673f76 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java
@@ -7,17 +7,14 @@ import org.forester.archaeopteryx.Configuration;
 
 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 static String DEFAULT_PATHS[] = {"C:\\Program Files\\mafft-win\\", "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_fastme;
     private final File          _path_to_local_raxml;
 
     public static InferenceManager createInstance( final Configuration c ) {
-        return new InferenceManager( c.getpathToLocalMafft(),
-                                     c.getPathToLocalFastme(),
-                                     c.getPathToLocalRaxml(),
-                                     c.getPathToLocalClustalOmega() );
+        return new InferenceManager( c.getPathToLocalMafft(), c.getPathToLocalFastme(), c.getPathToLocalRaxml() );
     }
 
     public boolean canDoMsa() {
@@ -67,8 +64,7 @@ public final class InferenceManager {
 
     private InferenceManager( final File path_to_local_mafft,
                               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_fastme = createLocalPath( path_to_local_fastme, "fastme" );
         _path_to_local_raxml = createLocalPath( path_to_local_raxml, "raxml" );