Merge branch 'kjvdh/features/PhylogenyViewer_tabbedsupport' into merge/2_11_2/kjvdh...

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

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index a32f785..fe9d69b 100644 (file)
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -117,7 +117,7 @@ public class PCAPanel extends EmbmenuFrame
             MessageManager.getString("label.principal_component_analysis"),
             475, 400);
 
-    Thread worker = new Thread(this);
+    Thread worker = new Thread(this, "PCACalcThread");
     worker.start();
   }
 
@@ -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());
   }
 
@@ -220,7 +218,7 @@ public class PCAPanel extends EmbmenuFrame
         ScoreModelI scoreModel = ScoreModels.getInstance()
                 .getDefaultModel(false);
         pcaModel.setScoreModel(scoreModel);
-        new Thread(this).start();
+        new Thread(this, "PCARecalcThread").start();
       }
     }
     else if (evt.getSource() == protSetting)
@@ -231,7 +229,7 @@ public class PCAPanel extends EmbmenuFrame
         ScoreModelI scoreModel = ScoreModels.getInstance()
                 .getDefaultModel(true);
         pcaModel.setScoreModel(scoreModel);
-        new Thread(this).start();
+        new Thread(this, "PCARecalcThread").start();
       }
     }
   }
@@ -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)