// 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.archaeopteryx.tools;
import org.forester.archaeopteryx.AptxUtil;
import org.forester.archaeopteryx.MainFrameApplication;
import org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD;
-import org.forester.sequence.Sequence;
+import org.forester.sequence.MolecularSequence;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.DescriptiveStatistics;
private JTextField _input_seqs_min_length_tf;
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_2.add( _input_seqs_max_length_tf = new JTextField() );
inputfile_pnl_2.add( new JLabel( "Type:" ) );
inputfile_pnl_2.add( _input_seqs_type_tf = new JTextField() );
-
-
- inputfile_pnl_3.add( _mafft_cb = new JCheckBox( "MAFFT") );
+ 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_max_length_tf.setEditable( false );
_input_seqs_number_tf.setEditable( false );
_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 );
_value = JOptionPane.CANCEL_OPTION;
if ( from_unaligned_seqs ) {
updateSeqsItems();
- }
+ }
else {
updateMsaItems();
}
}
private void readInputSeqsFile() {
- getParentFrame().readSeqsFromFile();
+ getParentFrame().readSeqsFromFileforPI();
updateSeqsItems();
}
}
}
- DescriptiveStatistics calcSequenceStats( final List<Sequence> seqs ) {
+ DescriptiveStatistics calcSequenceStats( final List<MolecularSequence> seqs ) {
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
- for( final Sequence s : seqs ) {
+ for( final MolecularSequence s : seqs ) {
stats.addValue( s.getLength() );
}
return stats;