X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=7c0dfa964c883bede949f6f4c5fe50a357fd8567;hb=e3e0829f9fb59144a1ce6e3ae99f25dc2641ecb2;hp=fc1d359c44b813389cbf0697289fc75d2c564796;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index fc1d359..7c0dfa9 100644
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -134,7 +134,7 @@ public class PCAPanel extends EmbmenuFrame
     {
       nuclSetting.setState(pcaModel.isNucleotide());
       protSetting.setState(!pcaModel.isNucleotide());
-      pcaModel.run();
+      pcaModel.calculate();
       // ////////////////
       xCombobox.select(0);
       yCombobox.select(1);
@@ -167,9 +167,7 @@ public class PCAPanel extends EmbmenuFrame
     int dim2 = top - yCombobox.getSelectedIndex();
     int dim3 = top - zCombobox.getSelectedIndex();
     pcaModel.updateRcView(dim1, dim2, dim3);
-    rc.img = null;
-    rc.rotmat.setIdentity();
-    rc.initAxes();
+    rc.resetView();
     rc.paint(rc.getGraphics());
   }
 
@@ -281,7 +279,7 @@ public class PCAPanel extends EmbmenuFrame
     {
     }
     ;
-    Object[] alAndColsel = pcaModel.getSeqtrings()
+    Object[] alAndColsel = pcaModel.getInputData()
             .getAlignmentAndHiddenColumns(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)