removed clustalo

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java b/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java
index 24ec184..30db176 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java
@@ -12,7 +12,6 @@ public final class InferenceManager {
     private final File          _path_to_local_mafft;
     private final File          _path_to_local_fastme;
     private final File          _path_to_local_raxml;
-    private final File          _path_to_local_clustalo;
 
     public static InferenceManager createInstance( final Configuration c ) {
         return new InferenceManager( c.getpathToLocalMafft(),
@@ -22,7 +21,7 @@ public final class InferenceManager {
     }
 
     public boolean canDoMsa() {
-        return ( getPathToLocalMafft() != null ) || ( getPathToLocalClustalo() != null );
+        return ( getPathToLocalMafft() != null );
     }
 
     public File getPathToLocalMafft() {
@@ -37,10 +36,6 @@ public final class InferenceManager {
         return _path_to_local_raxml;
     }
 
-    public File getPathToLocalClustalo() {
-        return _path_to_local_clustalo;
-    }
-
     private final static File createLocalPath( final File path, final String name ) {
         if ( ( path != null ) && path.canExecute() && !path.isDirectory() ) {
             return path;
@@ -77,6 +72,5 @@ public final class InferenceManager {
         _path_to_local_mafft = createLocalPath( path_to_local_mafft, "mafft" );
         _path_to_local_fastme = createLocalPath( path_to_local_fastme, "fastme" );
         _path_to_local_raxml = createLocalPath( path_to_local_raxml, "raxml" );
-        _path_to_local_clustalo = createLocalPath( path_to_local_clustalo, "clustalo" );
     }
 }

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java b/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java
index d750a43..6a27016 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java
@@ -79,14 +79,12 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
     private JTextField                         _input_seqs_max_length_tf;
     private JTextField                         _input_seqs_type_tf;
     private JTextField                         _mafft_paramenters_tf;
-    private JTextField                         _clustalo_paramenters_tf;
     private JTextField                         _msa_processing_max_allowed_gap_ratio_tf;
     private JTextField                         _msa_processing_min_allowed_length_tf;
     private JTextField                         _random_seed_tf;
     private JCheckBox                          _execute_msa_processing_cb;
     private JCheckBox                          _msa_processing_remove_all_gap_columns_cb;
     private JCheckBox                          _mafft_cb;
-    private JCheckBox                          _clustalo_cb;
     private JCheckBox                          _save_pwd_file_cb;
     private JCheckBox                          _save_processed_msa_cb;
     private JCheckBox                          _save_original_msa_cb;
@@ -132,9 +130,6 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
             inputfile_pnl_3.add( _mafft_cb = new JCheckBox( "MAFFT" ) );
             inputfile_pnl_3.add( new JLabel( "Parameters: " ) );
             inputfile_pnl_3.add( _mafft_paramenters_tf = new JTextField() );
-            inputfile_pnl_4.add( _clustalo_cb = new JCheckBox( "ClustalO" ) );
-            inputfile_pnl_4.add( new JLabel( "Parameters: " ) );
-            inputfile_pnl_4.add( _clustalo_paramenters_tf = new JTextField() );
             _input_seqs_median_length_tf.setColumns( 4 );
             _input_seqs_min_length_tf.setColumns( 4 );
             _input_seqs_max_length_tf.setColumns( 4 );
@@ -149,8 +144,6 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
             _input_seqs_type_tf.setEditable( false );
             _mafft_paramenters_tf.setColumns( 26 );
             _mafft_paramenters_tf.setText( "--maxiterate 1000 --localpair" );
-            _clustalo_paramenters_tf.setColumns( 26 );
-            _clustalo_paramenters_tf.setText( "clustalo options" );
             _select_input_seqs_btn.addActionListener( this );
             _pnl.add( inputfile_pnl_1 );
             _pnl.add( inputfile_pnl_2 );

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
index 10bc95e..1144fcb 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
@@ -41,7 +41,6 @@ import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
 import org.forester.evoinference.tools.BootstrapResampler;
 import org.forester.io.parsers.FastaParser;
 import org.forester.msa.BasicMsa;
-import org.forester.msa.ClustalOmega;
 import org.forester.msa.Mafft;
 import org.forester.msa.Msa;
 import org.forester.msa.Msa.MSA_FORMAT;
@@ -98,8 +97,6 @@ public class PhylogeneticInferrer extends RunnableProcess {
         switch ( msa_prg ) {
             case MAFFT:
                 return runMAFFT( _seqs, processMafftOptions() );
-            case CLUSTAL_O:
-                return runClustalOmega( _seqs, processMafftOptions() );
             default:
                 return null;
         }
@@ -279,20 +276,6 @@ public class PhylogeneticInferrer extends RunnableProcess {
         return msa;
     }
 
-    private Msa runClustalOmega( final List<Sequence> seqs, final List<String> opts ) throws IOException,
-            InterruptedException {
-        Msa msa = null;
-        final MsaInferrer clustalo = ClustalOmega.createInstance( _mf.getInferenceManager().getPathToLocalClustalo()
-                .getCanonicalPath() );
-        try {
-            msa = clustalo.infer( seqs, opts );
-        }
-        catch ( final IOException e ) {
-            System.out.println( clustalo.getErrorDescription() );
-        }
-        return msa;
-    }
-
     private void writeToFiles( final BasicSymmetricalDistanceMatrix m ) {
         if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) {
             try {
@@ -344,6 +327,6 @@ public class PhylogeneticInferrer extends RunnableProcess {
     }
 
     public enum MSA_PRG {
-        MAFFT, CLUSTAL_O;
+        MAFFT;
     }
 }