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=d750a43e2163560d63827c5d04cf2670e9e45fd6;hpb=656be28debec520e0e35a8b311114398a40ea366;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 d750a43..8850d2b 100644
--- a/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java
@@ -48,7 +48,7 @@ import javax.swing.border.LineBorder;
 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;
 
@@ -79,14 +79,12 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
     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;
@@ -132,9 +130,6 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
             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 );
@@ -149,8 +144,6 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
             _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 );
@@ -393,7 +386,7 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
     }
 
     private void readInputSeqsFile() {
-        getParentFrame().readSeqsFromFile();
+        getParentFrame().readSeqsFromFileforPI();
         updateSeqsItems();
     }
 
@@ -484,9 +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;