X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=5dc57f936891dd7a838367f18c2d98ae85895bdc;hb=3b239d86dc3a1bf3aa07c0ad3d38aeca57b54ada;hp=21668d379c60f0df355f473642451aac2ebef1d5;hpb=74c5bd7b1f98214a6d57d7c64d0548013530d397;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 21668d3..5dc57f9 100644
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -20,10 +20,12 @@
  */
 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;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SeqCigar;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
@@ -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 +102,13 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
         return;
       }
     }
-    pcaModel = new PCAModel(seqstrings, seqs, nucleotide,
+
+    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);
 
@@ -211,6 +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();
       }
     }
@@ -219,6 +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();
       }
     }
@@ -270,7 +281,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     }
     ;
     Object[] alAndColsel = pcaModel.getSeqtrings()
-            .getAlignmentAndColumnSelection(gc);
+            .getAlignmentAndHiddenColumns(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
     {
@@ -278,7 +289,8 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
       AlignFrame af = new AlignFrame(al, av.applet,
               "Original Data for PCA", false);
 
-      af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
+      af.viewport.getAlignment().setHiddenColumns(
+              (HiddenColumns) alAndColsel[1]);
     }
   }