in progress (special coloring is still true)

[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 f6d4f65..de57797 100644 (file)
--- a/forester/java/src/org/forester/msa/ClustalOmega.java
+++ b/forester/java/src/org/forester/msa/ClustalOmega.java
@@ -21,7 +21,7 @@
 // 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;
 
@@ -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 {
@@ -71,8 +71,9 @@ public final class ClustalOmega extends MsaInferrer {
         return _exit_code;
     }
 
-    
-    public Msa infer( final List<Sequence> seqs, final List<String> opts ) throws IOException, InterruptedException {
+    @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 ) );
@@ -82,8 +83,7 @@ public final class ClustalOmega extends MsaInferrer {
         file.delete();
         return msa;
     }
-    
-    
+
     @Override
     public Msa infer( final File path_to_input_seqs, final List<String> opts ) throws IOException, InterruptedException {
         init();
@@ -114,6 +114,4 @@ public final class ClustalOmega extends MsaInferrer {
         _error = null;
         _exit_code = -100;
     }
-
-  
 }