// 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 java.awt.Color;
import java.awt.FlowLayout;
+import java.awt.Frame;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.List;
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_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;
public PhyloInferenceDialog( final MainFrameApplication frame,
final PhylogeneticInferenceOptions options,
final boolean from_unaligned_seqs ) {
- super( frame, true );
+ super( (Frame) null, true );
setVisible( false );
_parent_frame = frame;
_opts = options;
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 );
distance_calc_pnl_1.add( _distance_calc_kimura_rb = new JRadioButton( "Kimura correction" ) );
distance_calc_pnl_1.add( _distance_calc_poisson_rb = new JRadioButton( "Poisson" ) );
distance_calc_pnl_1
- .add( _distance_calc_fract_dissimilarity_rb = new JRadioButton( "Fractional dissimilarity" ) );
+ .add( _distance_calc_fract_dissimilarity_rb = new JRadioButton( "Fractional dissimilarity" ) );
final ButtonGroup distance_calc_group_1 = new ButtonGroup();
distance_calc_group_1.add( _distance_calc_kimura_rb );
distance_calc_group_1.add( _distance_calc_poisson_rb );
private void processMsaProcessing() {
getPhylogeneticInferenceOptions().setExecuteMsaProcessing( _execute_msa_processing_cb.isSelected() );
getPhylogeneticInferenceOptions()
- .setMsaProcessingRemoveAllGapColumns( _msa_processing_remove_all_gap_columns_cb.isSelected() );
+ .setMsaProcessingRemoveAllGapColumns( _msa_processing_remove_all_gap_columns_cb.isSelected() );
int min_length = -1;
try {
min_length = Integer.parseInt( _msa_processing_min_allowed_length_tf.getText().trim() );
double msa_processing_max_allowed_gap_ratio = -1.0;
try {
msa_processing_max_allowed_gap_ratio = Double.parseDouble( _msa_processing_max_allowed_gap_ratio_tf
- .getText().trim() );
+ .getText().trim() );
}
catch ( final NumberFormatException e ) {
msa_processing_max_allowed_gap_ratio = -1.0;
}
private void readInputSeqsFile() {
- getParentFrame().readSeqsFromFile();
+ getParentFrame().readSeqsFromFileforPI();
updateSeqsItems();
}
private void updateMsaProcessingItem() {
_execute_msa_processing_cb.setSelected( getPhylogeneticInferenceOptions().isExecuteMsaProcessing() );
_msa_processing_remove_all_gap_columns_cb.setSelected( getPhylogeneticInferenceOptions()
- .isMsaProcessingRemoveAllGapColumns() );
+ .isMsaProcessingRemoveAllGapColumns() );
if ( _opts.getMsaProcessingMaxAllowedGapRatio() > 0 ) {
_msa_processing_max_allowed_gap_ratio_tf.setText( _opts.getMsaProcessingMaxAllowedGapRatio() + "" );
}
}
}
- 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;