X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa%2FClustalOmega.java;h=2b7a0669b1a7ab1274ea0600c6b7cf7714155ee1;hb=5642da5f473ab9ae57fee86c0cb3b33525a2e916;hp=417e889867bf4645ce6b2c9fc0739513028cfb94;hpb=656be28debec520e0e35a8b311114398a40ea366;p=jalview.git

diff --git a/forester/java/src/org/forester/msa/ClustalOmega.java b/forester/java/src/org/forester/msa/ClustalOmega.java
index 417e889..2b7a066 100644
--- a/forester/java/src/org/forester/msa/ClustalOmega.java
+++ b/forester/java/src/org/forester/msa/ClustalOmega.java
@@ -35,7 +35,7 @@ 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.sequence.MolecularSequence;
 import org.forester.util.SystemCommandExecutor;
 
 public final class ClustalOmega extends MsaInferrer {
@@ -72,7 +72,8 @@ public final class ClustalOmega extends MsaInferrer {
     }
 
     @Override
-    public Msa infer( final List<Sequence> seqs, final List<String> opts ) throws IOException, InterruptedException {
+    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 ) );
@@ -98,12 +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;