X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa%2FMafft.java;h=5a96bc38642aecf51034abec14847f498ddc2287;hb=7ae646b73c00d1458582858319ec62f05e40c71a;hp=ae9fdf11a0ee9bc18240513c58ed0d38d6e2b8e1;hpb=656be28debec520e0e35a8b311114398a40ea366;p=jalview.git

diff --git a/forester/java/src/org/forester/msa/Mafft.java b/forester/java/src/org/forester/msa/Mafft.java
index ae9fdf1..5a96bc3 100644
--- a/forester/java/src/org/forester/msa/Mafft.java
+++ b/forester/java/src/org/forester/msa/Mafft.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 Mafft extends MsaInferrer {
@@ -72,7 +72,8 @@ public final class Mafft 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( "__mafft_input_", ".fasta" );
         file.deleteOnExit();
         final BufferedWriter writer = new BufferedWriter( new FileWriter( file ) );
@@ -98,7 +99,7 @@ public final class Mafft extends MsaInferrer {
         _error = stderr.toString();
         if ( _exit_code != 0 ) {
             throw new IOException( "MAFFT 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 ) ) {