X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=7c0dfa964c883bede949f6f4c5fe50a357fd8567;hb=7ec3bb005b1dd1621d386b05087ebab33fc47d0f;hp=5dc57f936891dd7a838367f18c2d98ae85895bdc;hpb=3c75c089a56859ec8e7f674d7054e82af41e4b77;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 5dc57f9..7c0dfa9 100644
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -48,8 +48,8 @@ import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 
-public class PCAPanel extends EmbmenuFrame implements Runnable,
-        ActionListener, ItemListener
+public class PCAPanel extends EmbmenuFrame
+        implements Runnable, ActionListener, ItemListener
 {
   RotatableCanvas rc;
 
@@ -88,7 +88,8 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     }
     else
     {
-      seqs = viewport.getSelectionGroup().getSequencesInOrder(viewport.getAlignment());
+      seqs = viewport.getSelectionGroup()
+              .getSequencesInOrder(viewport.getAlignment());
     }
     SeqCigar sq[] = seqstrings.getSequences();
     int length = sq[0].getWidth();
@@ -103,8 +104,8 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
       }
     }
 
-    ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
-            !nucleotide);
+    ScoreModelI scoreModel = ScoreModels.getInstance()
+            .getDefaultModel(!nucleotide);
     pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
             SimilarityParams.SeqSpace);
 
@@ -133,7 +134,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     {
       nuclSetting.setState(pcaModel.isNucleotide());
       protSetting.setState(!pcaModel.isNucleotide());
-      pcaModel.run();
+      pcaModel.calculate();
       // ////////////////
       xCombobox.select(0);
       yCombobox.select(1);
@@ -166,9 +167,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     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());
   }
 
@@ -216,8 +215,8 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
       if (!pcaModel.isNucleotide())
       {
         pcaModel.setNucleotide(true);
-        ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
-                false);
+        ScoreModelI scoreModel = ScoreModels.getInstance()
+                .getDefaultModel(false);
         pcaModel.setScoreModel(scoreModel);
         new Thread(this).start();
       }
@@ -227,8 +226,8 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
       if (pcaModel.isNucleotide())
       {
         pcaModel.setNucleotide(false);
-        ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
-                true);
+        ScoreModelI scoreModel = ScoreModels.getInstance()
+                .getDefaultModel(true);
         pcaModel.setScoreModel(scoreModel);
         new Thread(this).start();
       }
@@ -280,17 +279,17 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     {
     }
     ;
-    Object[] alAndColsel = pcaModel.getSeqtrings()
+    Object[] alAndColsel = pcaModel.getInputData()
             .getAlignmentAndHiddenColumns(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
     {
       Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
-      AlignFrame af = new AlignFrame(al, av.applet,
-              "Original Data for PCA", false);
+      AlignFrame af = new AlignFrame(al, av.applet, "Original Data for PCA",
+              false);
 
-      af.viewport.getAlignment().setHiddenColumns(
-              (HiddenColumns) alAndColsel[1]);
+      af.viewport.getAlignment()
+              .setHiddenColumns((HiddenColumns) alAndColsel[1]);
     }
   }
 
@@ -366,8 +365,8 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     values.setLabel(MessageManager.getString("label.output_values"));
     values.addActionListener(this);
     inputData.setLabel(MessageManager.getString("label.input_data"));
-    nuclSetting.setLabel(MessageManager
-            .getString("label.nucleotide_matrix"));
+    nuclSetting
+            .setLabel(MessageManager.getString("label.nucleotide_matrix"));
     nuclSetting.addItemListener(this);
     protSetting.setLabel(MessageManager.getString("label.protein_matrix"));
     protSetting.addItemListener(this);