X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa%2FClustalOmega.java;h=938fc7849c53dab506f2f2c64807e4708e4b83b0;hb=877d1e4a2f3e2a937197dc57253ba2cead14a4d6;hp=72db9d3f84d780ba8601f50a53608e133cdeea87;hpb=b1a74bd076c917d428002284a53a2c6f390226fb;p=jalview.git

diff --git a/forester/java/src/org/forester/msa/ClustalOmega.java b/forester/java/src/org/forester/msa/ClustalOmega.java
index 72db9d3..938fc78 100644
--- a/forester/java/src/org/forester/msa/ClustalOmega.java
+++ b/forester/java/src/org/forester/msa/ClustalOmega.java
@@ -25,12 +25,16 @@
 
 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.io.writers.SequenceWriter;
+import org.forester.io.writers.SequenceWriter.SEQ_FORMAT;
 import org.forester.sequence.Sequence;
 import org.forester.util.SystemCommandExecutor;
 
@@ -68,6 +72,18 @@ public final class ClustalOmega extends MsaInferrer {
     }
 
     @Override
+    public Msa infer( final List<Sequence> seqs, final List<String> opts ) throws IOException, InterruptedException {
+        final File file = File.createTempFile( "__clustalo_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>();
@@ -97,10 +113,4 @@ public final class ClustalOmega extends MsaInferrer {
         _error = null;
         _exit_code = -100;
     }
-
-    @Override
-    public Msa infer( final List<Sequence> seqs, final List<String> opts ) throws IOException, InterruptedException {
-        // TODO Auto-generated method stub
-        return null;
-    }
 }