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 fc679aa..30db176 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java
@@ -1,10 +1,76 @@
 
 package org.forester.archaeopteryx.tools;
 
-public class InferenceManager {
+import java.io.File;
 
-    public static InferenceManager getInstance() {
-        // TODO Auto-generated method stub
+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 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() );
+    }
+
+    public boolean canDoMsa() {
+        return ( getPathToLocalMafft() != null );
+    }
+
+    public File getPathToLocalMafft() {
+        return _path_to_local_mafft;
+    }
+
+    public File getPathToLocalFastme() {
+        return _path_to_local_fastme;
+    }
+
+    public File getPathToLocalRaxml() {
+        return _path_to_local_raxml;
+    }
+
+    private final static File createLocalPath( final File path, final String name ) {
+        if ( ( path != null ) && path.canExecute() && !path.isDirectory() ) {
+            return path;
+        }
+        final File p1 = new File( name );
+        if ( p1.canExecute() && !p1.isDirectory() ) {
+            return p1;
+        }
+        for( final String path_str : DEFAULT_PATHS ) {
+            try {
+                final File p2 = new File( path_str + name );
+                if ( p2.canExecute() && !p2.isDirectory() ) {
+                    return p2;
+                }
+                final File p3 = new File( path_str + name + ".exe" );
+                if ( p3.canExecute() && !p3.isDirectory() ) {
+                    return p3;
+                }
+                final File p4 = new File( path_str + name + ".bat" );
+                if ( p4.canExecute() && !p4.isDirectory() ) {
+                    return p4;
+                }
+            }
+            catch ( final Exception e ) {
+            }
+        }
         return null;
     }
+
+    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 ) {
+        _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" );
+    }
 }