X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2Ftools%2FPhyloInferenceDialog.java;h=8850d2b5c4804d319c89120ce5ae13c91bc1b082;hb=4cc856b8c526a8b82bef79901739d9330206921a;hp=767a41760e8adb76ae5d36db8e773bd2b77cd851;hpb=0f295917c869b17a9322af3e738e3527ba9b31d4;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java b/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java
index 767a417..8850d2b 100644
--- a/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java
@@ -21,7 +21,7 @@
 // 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;
 
@@ -45,10 +45,10 @@ import javax.swing.JTextField;
 import javax.swing.border.Border;
 import javax.swing.border.LineBorder;
 
+import org.forester.archaeopteryx.AptxUtil;
 import org.forester.archaeopteryx.MainFrameApplication;
-import org.forester.archaeopteryx.Util;
 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;
 
@@ -78,13 +78,13 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
     private JTextField                         _input_seqs_min_length_tf;
     private JTextField                         _input_seqs_max_length_tf;
     private JTextField                         _input_seqs_type_tf;
-    private JTextField                         _input_seqs_msa_program_name_tf;
-    private JTextField                         _input_seqs_msa_paramenters_tf;
+    private JTextField                         _mafft_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                          _save_pwd_file_cb;
     private JCheckBox                          _save_processed_msa_cb;
     private JCheckBox                          _save_original_msa_cb;
@@ -108,9 +108,11 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
             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_4 = new JPanel();
             inputfile_pnl_1.setLayout( new FlowLayout() );
             inputfile_pnl_2.setLayout( new FlowLayout() );
             inputfile_pnl_3.setLayout( new FlowLayout() );
+            inputfile_pnl_4.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" ) );
@@ -125,11 +127,9 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
             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" ) );
             inputfile_pnl_3.add( new JLabel( "Parameters: " ) );
-            inputfile_pnl_3.add( _input_seqs_msa_paramenters_tf = new JTextField() );
+            inputfile_pnl_3.add( _mafft_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 );
@@ -142,12 +142,13 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
             _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 );
+            _pnl.add( inputfile_pnl_4 );
         }
         else {
             setTitle( "Phylogenetic Inference (from already aligned sequences) " );
@@ -213,7 +214,7 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
         bootstrap_pnl.setLayout( new FlowLayout() );
         bootstrap_pnl.add( _bootstrap_cb = new JCheckBox( "Perform Bootstrap Resampling" ) );
         bootstrap_pnl.add( new JLabel( "Number of Bootstrap Samples:" ) );
-        bootstrap_pnl.add( _bootstrap_tf = new JFormattedTextField( Util.createMaskFormatter( "###" ) ) );
+        bootstrap_pnl.add( _bootstrap_tf = new JFormattedTextField( AptxUtil.createMaskFormatter( "###" ) ) );
         _bootstrap_tf.setColumns( 4 );
         // TODO see
         // http://download.oracle.com/javase/tutorial/uiswing/components/formattedtextfield.html
@@ -273,8 +274,6 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
         _value = JOptionPane.CANCEL_OPTION;
         if ( from_unaligned_seqs ) {
             updateSeqsItems();
-            _input_seqs_msa_program_name_tf.setText( getPhylogeneticInferenceOptions().getMsaPrg() );
-            _input_seqs_msa_paramenters_tf.setText( getPhylogeneticInferenceOptions().getMsaPrgParameters() );
         }
         else {
             updateMsaItems();
@@ -376,8 +375,8 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
     }
 
     private void processMsaPrgParameters() {
-        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() );
         }
     }
 
@@ -387,7 +386,7 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
     }
 
     private void readInputSeqsFile() {
-        getParentFrame().readSeqsFromFile();
+        getParentFrame().readSeqsFromFileforPI();
         updateSeqsItems();
     }
 
@@ -478,9 +477,9 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
         }
     }
 
-    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;