X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=7730210dcfebf1de737da9c2ad195e4e96128891;hb=dee97314c8d002df2ec57812bf82f0460ba51dd8;hp=fc1d359c44b813389cbf0697289fc75d2c564796;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index fc1d359..7730210 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);
@@ -145,7 +145,7 @@ public class PCAPanel extends EmbmenuFrame
       top = pcaModel.getTop();
     } catch (OutOfMemoryError x)
     {
-      System.err.println("Out of memory when calculating PCA.");
+      jalview.bin.Console.errPrintln("Out of memory when calculating PCA.");
       return;
     }
     calcSettings.setEnabled(true);
@@ -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)