JAL-2805 JAL-281 JAL-2847 set tree file made public as well (heh)

[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 417e889..2b7a066 100644 (file)
--- 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;