X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa%2FMafft.java;h=ae9fdf11a0ee9bc18240513c58ed0d38d6e2b8e1;hb=fda4b2cd36f7c4d7edf6381268ebcf5fbbc77297;hp=7e4e4c02b39537b20ab36674b57e5d9e3f0ce9cf;hpb=e86d89ccaf293b3e50d16db81d8e151c37c5fdb1;p=jalview.git

diff --git a/forester/java/src/org/forester/msa/Mafft.java b/forester/java/src/org/forester/msa/Mafft.java
index 7e4e4c0..ae9fdf1 100644
--- a/forester/java/src/org/forester/msa/Mafft.java
+++ b/forester/java/src/org/forester/msa/Mafft.java
@@ -21,36 +21,36 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.msa;
 
+import java.io.BufferedWriter;
 import java.io.File;
+import java.io.FileWriter;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
 import org.forester.io.parsers.FastaParser;
-import org.forester.util.ForesterUtil;
+import org.forester.io.writers.SequenceWriter;
+import org.forester.io.writers.SequenceWriter.SEQ_FORMAT;
+import org.forester.sequence.Sequence;
 import org.forester.util.SystemCommandExecutor;
 
-public final class Mafft implements MsaInferrer {
+public final class Mafft extends MsaInferrer {
 
     private final static String DEFAULT_PARAMETERS = "--maxiterate 1000 --localpair";
     private String              _error;
     private int                 _exit_code;
     private final String        _path_to_prg;
 
-   
-
     public static MsaInferrer createInstance( final String path_to_prg ) throws IOException {
         return new Mafft( path_to_prg );
     }
 
-   
-
     private Mafft( final String path_to_prg ) throws IOException {
-        if ( !SystemCommandExecutor.isExecuteableFile( new File( path_to_prg ) ) ) {
+        if ( !isInstalled( path_to_prg ) ) {
             throw new IOException( "cannot execute MAFFT with \"" + path_to_prg + "\"" );
         }
         _path_to_prg = new String( path_to_prg );
@@ -62,11 +62,6 @@ public final class Mafft implements MsaInferrer {
     }
 
     @Override
-    public Object clone() {
-        throw new NoSuchMethodError();
-    }
-
-    @Override
     public String getErrorDescription() {
         return _error;
     }
@@ -77,6 +72,18 @@ public final class Mafft implements MsaInferrer {
     }
 
     @Override
+    public Msa infer( final List<Sequence> seqs, final List<String> opts ) throws IOException, InterruptedException {
+        final File file = File.createTempFile( "__mafft_input_", ".fasta" );
+        file.deleteOnExit();
+        final BufferedWriter writer = new BufferedWriter( new FileWriter( file ) );
+        SequenceWriter.writeSeqs( seqs, writer, SEQ_FORMAT.FASTA, 100 );
+        writer.close();
+        final Msa msa = infer( file, opts );
+        file.delete();
+        return msa;
+    }
+
+    @Override
     public Msa infer( final File path_to_input_seqs, final List<String> opts ) throws IOException, InterruptedException {
         init();
         final List<String> my_opts = new ArrayList<String>();