JAL-2388 Hidden cols separated from column selection (almost complete)

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

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index c5ec0c1..2ef7d10 100644 (file)
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -22,7 +22,7 @@ package jalview.appletgui;
 
 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;
@@ -116,6 +116,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void run()
   {
     // TODO progress indicator
@@ -164,6 +165,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     rc.paint(rc.getGraphics());
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == inputData)
@@ -183,6 +185,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     }
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == xCombobox)
@@ -265,7 +268,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     }
     ;
     Object[] alAndColsel = pcaModel.getSeqtrings()
-            .getAlignmentAndColumnSelection(gc);
+            .getAlignmentAndHiddenColumns(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
     {
@@ -273,7 +276,8 @@ 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]);
     }
   }