// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
import org.forester.archaeopteryx.AptxUtil;
import org.forester.archaeopteryx.MainFrameApplication;
import org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD;
import org.forester.archaeopteryx.AptxUtil;
import org.forester.archaeopteryx.MainFrameApplication;
import org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD;
private JTextField _input_seqs_min_length_tf;
private JTextField _input_seqs_max_length_tf;
private JTextField _input_seqs_type_tf;
private JTextField _input_seqs_min_length_tf;
private JTextField _input_seqs_max_length_tf;
private JTextField _input_seqs_type_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 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 _save_pwd_file_cb;
private JCheckBox _save_processed_msa_cb;
private JCheckBox _save_original_msa_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 ) {
public PhyloInferenceDialog( final MainFrameApplication frame,
final PhylogeneticInferenceOptions options,
final boolean from_unaligned_seqs ) {
final JPanel inputfile_pnl_1 = new JPanel();
final JPanel inputfile_pnl_2 = new JPanel();
final JPanel inputfile_pnl_3 = new JPanel();
final JPanel inputfile_pnl_1 = new JPanel();
final JPanel inputfile_pnl_2 = new JPanel();
final JPanel inputfile_pnl_3 = new JPanel();
inputfile_pnl_1.setLayout( new FlowLayout() );
inputfile_pnl_2.setLayout( new FlowLayout() );
inputfile_pnl_3.setLayout( new FlowLayout() );
inputfile_pnl_1.setLayout( new FlowLayout() );
inputfile_pnl_2.setLayout( new FlowLayout() );
inputfile_pnl_3.setLayout( new FlowLayout() );
inputfile_pnl_1.add( new JLabel( "Input Sequence File:" ) );
inputfile_pnl_1.add( _input_seqs_tf = new JTextField() );
inputfile_pnl_1.add( _select_input_seqs_btn = new JButton( "Select Input File" ) );
inputfile_pnl_1.add( new JLabel( "Input Sequence File:" ) );
inputfile_pnl_1.add( _input_seqs_tf = new JTextField() );
inputfile_pnl_1.add( _select_input_seqs_btn = new JButton( "Select Input File" ) );
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_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( new JLabel( "Mutiple Sequence Alignment: " ) );
- inputfile_pnl_3.add( new JLabel( "Program: " ) );
- inputfile_pnl_3.add( _input_seqs_msa_program_name_tf = new JTextField() );
+ inputfile_pnl_3.add( _mafft_cb = new JCheckBox( "MAFFT" ) );
_input_seqs_median_length_tf.setColumns( 4 );
_input_seqs_min_length_tf.setColumns( 4 );
_input_seqs_max_length_tf.setColumns( 4 );
_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 );
_input_seqs_max_length_tf.setEditable( false );
_input_seqs_number_tf.setEditable( false );
_input_seqs_type_tf.setEditable( false );
- _input_seqs_msa_program_name_tf.setEditable( false );
- _input_seqs_msa_paramenters_tf.setColumns( 26 );
+ _mafft_paramenters_tf.setColumns( 26 );
+ _mafft_paramenters_tf.setText( "--maxiterate 1000 --localpair" );
_select_input_seqs_btn.addActionListener( this );
_pnl.add( inputfile_pnl_1 );
_pnl.add( inputfile_pnl_2 );
_pnl.add( inputfile_pnl_3 );
_select_input_seqs_btn.addActionListener( this );
_pnl.add( inputfile_pnl_1 );
_pnl.add( inputfile_pnl_2 );
_pnl.add( inputfile_pnl_3 );
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
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
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 );
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()
private void processMsaProcessing() {
getPhylogeneticInferenceOptions().setExecuteMsaProcessing( _execute_msa_processing_cb.isSelected() );
getPhylogeneticInferenceOptions()
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
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
- if ( _input_seqs_msa_paramenters_tf != null ) {
- getPhylogeneticInferenceOptions().setMsaPrgParameters( _input_seqs_msa_paramenters_tf.getText() );
+ if ( _mafft_paramenters_tf != null ) {
+ getPhylogeneticInferenceOptions().setMsaPrgParameters( _mafft_paramenters_tf.getText() );
private void updateMsaProcessingItem() {
_execute_msa_processing_cb.setSelected( getPhylogeneticInferenceOptions().isExecuteMsaProcessing() );
_msa_processing_remove_all_gap_columns_cb.setSelected( getPhylogeneticInferenceOptions()
private void updateMsaProcessingItem() {
_execute_msa_processing_cb.setSelected( getPhylogeneticInferenceOptions().isExecuteMsaProcessing() );
_msa_processing_remove_all_gap_columns_cb.setSelected( getPhylogeneticInferenceOptions()
if ( _opts.getMsaProcessingMaxAllowedGapRatio() > 0 ) {
_msa_processing_max_allowed_gap_ratio_tf.setText( _opts.getMsaProcessingMaxAllowedGapRatio() + "" );
}
if ( _opts.getMsaProcessingMaxAllowedGapRatio() > 0 ) {
_msa_processing_max_allowed_gap_ratio_tf.setText( _opts.getMsaProcessingMaxAllowedGapRatio() + "" );
}