X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa%2FClustalOmega.java;h=2b7a0669b1a7ab1274ea0600c6b7cf7714155ee1;hb=0b39293d1577083551ba528d0ac7afcacbf69dde;hp=f6d4f6516c923d3eeb0b1be5c3bf627d76fd19a1;hpb=def5f3c9ca461176f1188d0adfd744726a56e6ed;p=jalview.git

diff --git a/forester/java/src/org/forester/msa/ClustalOmega.java b/forester/java/src/org/forester/msa/ClustalOmega.java
index f6d4f65..2b7a066 100644
--- 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();
@@ -99,12 +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;
@@ -114,6 +114,4 @@ public final class ClustalOmega extends MsaInferrer {
         _error = null;
         _exit_code = -100;
     }
-
-  
 }