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[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 80e73b7..2b7a066 100644 (file)
--- a/forester/java/src/org/forester/msa/ClustalOmega.java
+++ b/forester/java/src/org/forester/msa/ClustalOmega.java
@@ -21,36 +21,37 @@
 // 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;
 
+import java.io.BufferedWriter;
 import java.io.File;
+import java.io.FileWriter;
 import java.io.IOException;
 import java.util.ArrayList;
 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.MolecularSequence;
 import org.forester.util.SystemCommandExecutor;
 
-public final class ClustalOmega implements MsaInferrer {
+public final class ClustalOmega extends MsaInferrer {
 
     private final static String DEFAULT_PARAMETERS = "";
     private String              _error;
     private int                 _exit_code;
     private final String        _path_to_prg;
 
-   
-
     public static MsaInferrer createInstance( final String path_to_prg ) throws IOException {
         return new ClustalOmega( path_to_prg );
     }
 
-   
-
     private ClustalOmega( final String path_to_prg ) throws IOException {
-        if ( !SystemCommandExecutor.isExecuteableFile( new File( path_to_prg ) ) ) {
-            throw new IOException( "cannot execute MAFFT with \"" + path_to_prg + "\"" );
+        if ( !isInstalled( path_to_prg ) ) {
+            throw new IOException( "cannot execute Clustal Omega with \"" + path_to_prg + "\"" );
         }
         _path_to_prg = new String( path_to_prg );
         init();
@@ -61,11 +62,6 @@ public final class ClustalOmega implements MsaInferrer {
     }
 
     @Override
-    public Object clone() {
-        throw new NoSuchMethodError();
-    }
-
-    @Override
     public String getErrorDescription() {
         return _error;
     }
@@ -76,6 +72,19 @@ public final class ClustalOmega implements MsaInferrer {
     }
 
     @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 ) );
+        SequenceWriter.writeSeqs( seqs, writer, SEQ_FORMAT.FASTA, 100 );
+        writer.close();
+        final Msa msa = infer( file, opts );
+        file.delete();
+        return msa;
+    }
+
+    @Override
     public Msa infer( final File path_to_input_seqs, final List<String> opts ) throws IOException, InterruptedException {
         init();
         final List<String> my_opts = new ArrayList<String>();
@@ -90,12 +99,12 @@ public final class ClustalOmega implements 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 );
+            throw new IOException( "Clustal Omega program did not produce any output\nCommand:\n" + my_opts
+                                   + "\nError:\n" + stderr );
         }
         final Msa msa = FastaParser.parseMsa( stdout.toString() );
         return msa;