JAL-1632 dialog to calculate either Tree or PCA

[jalview.git] / src / jalview / appletgui / PCAPanel.java

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 21668d3..efb204e 100644 (file)
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -20,7 +20,9 @@
  */
 package jalview.appletgui;
 
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.analysis.ScoreModelI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
@@ -57,7 +59,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
 
   int top = 0;
 
-  public PCAPanel(AlignViewport av)
+  public PCAPanel(AlignViewport viewport)
   {
     try
     {
@@ -74,19 +76,19 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
       zCombobox.addItem("dim " + i);
     }
 
-    this.av = av;
-    boolean selected = av.getSelectionGroup() != null
-            && av.getSelectionGroup().getSize() > 0;
-    AlignmentView seqstrings = av.getAlignmentView(selected);
-    boolean nucleotide = av.getAlignment().isNucleotide();
+    this.av = viewport;
+    boolean selected = viewport.getSelectionGroup() != null
+            && viewport.getSelectionGroup().getSize() > 0;
+    AlignmentView seqstrings = viewport.getAlignmentView(selected);
+    boolean nucleotide = viewport.getAlignment().isNucleotide();
     SequenceI[] seqs;
     if (!selected)
     {
-      seqs = av.getAlignment().getSequencesArray();
+      seqs = viewport.getAlignment().getSequencesArray();
     }
     else
     {
-      seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
+      seqs = viewport.getSelectionGroup().getSequencesInOrder(viewport.getAlignment());
     }
     SeqCigar sq[] = seqstrings.getSequences();
     int length = sq[0].getWidth();
@@ -100,10 +102,14 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
         return;
       }
     }
+
+    ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
+            !nucleotide);
     pcaModel = new PCAModel(seqstrings, seqs, nucleotide,
+ scoreModel,
             SimilarityParams.SeqSpace);
 
-    rc = new RotatableCanvas(av);
+    rc = new RotatableCanvas(viewport);
     embedMenuIfNeeded(rc);
     add(rc, BorderLayout.CENTER);