Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into...

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

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index fc1d359..7730210 100644 (file)
--- 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)