Merge remote-tracking branch 'origin/develop' into

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

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index efb204e..5dc57f9 100644 (file)
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -25,7 +25,7 @@ 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;
@@ -105,8 +105,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
 
     ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
             !nucleotide);
-    pcaModel = new PCAModel(seqstrings, seqs, nucleotide,
- scoreModel,
+    pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
             SimilarityParams.SeqSpace);
 
     rc = new RotatableCanvas(viewport);
@@ -217,6 +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();
       }
     }
@@ -225,6 +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();
       }
     }
@@ -276,7 +281,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     }
     ;
     Object[] alAndColsel = pcaModel.getSeqtrings()
-            .getAlignmentAndColumnSelection(gc);
+            .getAlignmentAndHiddenColumns(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
     {
@@ -284,7 +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]);
     }
   }