From 891cca0970ffc3f1091b405164af423353a54bea Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 15 Jan 2013 18:36:58 +0000 Subject: [PATCH] removed clustalo --- .../archaeopteryx/tools/InferenceManager.java | 8 +------- .../archaeopteryx/tools/PhyloInferenceDialog.java | 7 ------- .../archaeopteryx/tools/PhylogeneticInferrer.java | 19 +------------------ 3 files changed, 2 insertions(+), 32 deletions(-) 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 --- 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 --- 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 --- 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 seqs, final List 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; } } -- 1.7.10.2