X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=2d77c59beefdafdd537183d2d8ef4d0044de7004;hb=567c2595554096f10feab130153f97286f3f7d80;hp=b0b8c9c502e0888982111e4bb0af87e25d1006eb;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index b0b8c9c..2d77c59 100644
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +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;
@@ -56,7 +59,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
 
   int top = 0;
 
-  public PCAPanel(AlignViewport av)
+  public PCAPanel(AlignViewport viewport)
   {
     try
     {
@@ -73,19 +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();
@@ -99,9 +102,13 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
         return;
       }
     }
-    pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
 
-    rc = new RotatableCanvas(av);
+    ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
+            !nucleotide);
+    pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
+            SimilarityParams.SeqSpace);
+
+    rc = new RotatableCanvas(viewport);
     embedMenuIfNeeded(rc);
     add(rc, BorderLayout.CENTER);
 
@@ -116,6 +123,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void run()
   {
     // TODO progress indicator
@@ -164,6 +172,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     rc.paint(rc.getGraphics());
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == inputData)
@@ -183,6 +192,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     }
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == xCombobox)
@@ -206,6 +216,9 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
       if (!pcaModel.isNucleotide())
       {
         pcaModel.setNucleotide(true);
+        ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
+                false);
+        pcaModel.setScoreModel(scoreModel);
         new Thread(this).start();
       }
     }
@@ -214,6 +227,9 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
       if (pcaModel.isNucleotide())
       {
         pcaModel.setNucleotide(false);
+        ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
+                true);
+        pcaModel.setScoreModel(scoreModel);
         new Thread(this).start();
       }
     }