changed Mainframe from JFrame to JInternalFrame

[jalview.git] / forester / java / src / org / forester / archaeopteryx / tools / PhyloInferenceDialog.java

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java b/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java
index 6a27016..b1cd8b6 100644 (file)
--- 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;
 
@@ -203,7 +203,7 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
         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 );
@@ -333,7 +333,7 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
     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() );
@@ -347,7 +347,7 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
         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;
@@ -386,7 +386,7 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
     }
 
     private void readInputSeqsFile() {
-        getParentFrame().readSeqsFromFile();
+        getParentFrame().readSeqsFromFileforPI();
         updateSeqsItems();
     }
 
@@ -409,7 +409,7 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
     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() + "" );
         }
@@ -477,9 +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;