in progress...

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

diff --git a/forester/java/src/org/forester/msa/ClustalOmega.java b/forester/java/src/org/forester/msa/ClustalOmega.java
index 72db9d3..2b7a066 100644 (file)
--- a/forester/java/src/org/forester/msa/ClustalOmega.java
+++ b/forester/java/src/org/forester/msa/ClustalOmega.java
@@ -21,17 +21,21 @@
 // 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.sequence.Sequence;
+import org.forester.io.writers.SequenceWriter;
+import org.forester.io.writers.SequenceWriter.SEQ_FORMAT;
+import org.forester.sequence.MolecularSequence;
 import org.forester.util.SystemCommandExecutor;
 
 public final class ClustalOmega extends MsaInferrer {
@@ -68,6 +72,19 @@ public final class ClustalOmega extends MsaInferrer {
     }
 
     @Override
+    public Msa infer( final List<MolecularSequence> 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>();
@@ -82,12 +99,12 @@ public final class ClustalOmega extends MsaInferrer {
         _error = stderr.toString();
         if ( _exit_code != 0 ) {
             throw new IOException( "Clustal Omega program failed, exit code: " + _exit_code + "\nCommand:\n" + my_opts
-                    + "\nError:\n" + stderr );
+                                   + "\nError:\n" + stderr );
         }
         final StringBuilder stdout = command_executor.getStandardOutputFromCommand();
         if ( ( stdout == null ) || ( stdout.length() < 2 ) ) {
             throw new IOException( "Clustal Omega program did not produce any output\nCommand:\n" + my_opts
-                    + "\nError:\n" + stderr );
+                                   + "\nError:\n" + stderr );
         }
         final Msa msa = FastaParser.parseMsa( stdout.toString() );
         return msa;
@@ -97,10 +114,4 @@ 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;
-    }
 }