in progress

[jalview.git] / forester / java / src / org / forester / msa / MsaInferrer.java

diff --git a/forester/java/src/org/forester/msa/MsaInferrer.java b/forester/java/src/org/forester/msa/MsaInferrer.java
index 801c247..8c839f9 100644 (file)
--- a/forester/java/src/org/forester/msa/MsaInferrer.java
+++ b/forester/java/src/org/forester/msa/MsaInferrer.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2010 Christian M Zmasek
 // Copyright (C) 2010 Sanford-Burnham Medical Research Institute
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -15,7 +15,7 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
@@ -29,11 +29,26 @@ import java.io.File;
 import java.io.IOException;
 import java.util.List;
 
-public interface MsaInferrer {
+import org.forester.sequence.Sequence;
+import org.forester.util.SystemCommandExecutor;
+
+public abstract class MsaInferrer {
+
+    public abstract String getErrorDescription();
+
+    public abstract int getExitCode();
+
+    public static boolean isInstalled( final String path_to_prg ) {
+        return SystemCommandExecutor.isExecuteableFile( new File( path_to_prg ) );
+    }
 
-    public String getErrorDescription();
+    @Override
+    public Object clone() {
+        throw new NoSuchMethodError();
+    }
 
-    public int getExitCode();
+    public abstract Msa infer( File path_to_input_seqs, List<String> opts ) throws IOException, InterruptedException;
 
-    public Msa infer( File path_to_input_seqs, List<String> opts ) throws IOException, InterruptedException;
+    public abstract Msa infer( final List<Sequence> seqs, final List<String> opts ) throws IOException,
+            InterruptedException;
 }