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(),
}
public boolean canDoMsa() {
- return ( getPathToLocalMafft() != null ) || ( getPathToLocalClustalo() != null );
+ return ( getPathToLocalMafft() != null );
}
public File getPathToLocalMafft() {
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;
_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" );
}
}
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;
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 );
_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 );
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;
switch ( msa_prg ) {
case MAFFT:
return runMAFFT( _seqs, processMafftOptions() );
- case CLUSTAL_O:
- return runClustalOmega( _seqs, processMafftOptions() );
default:
return null;
}
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 {
}
public enum MSA_PRG {
- MAFFT, CLUSTAL_O;
+ MAFFT;
}
}