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=6a270163b0c58fa2c8139d5eca5bcbac08459eee;hpb=891cca0970ffc3f1091b405164af423353a54bea;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 6a27016..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;
 
@@ -386,7 +386,7 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener {
     }
 
     private void readInputSeqsFile() {
-        getParentFrame().readSeqsFromFile();
+        getParentFrame().readSeqsFromFileforPI();
         updateSeqsItems();
     }
 
@@ -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;