Merge remote-tracking branch 'origin/releases/Release_2_10_2b1_Branch'

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

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index d8e6b06..f861a7c 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -59,8 +59,8 @@ import javax.swing.event.InternalFrameEvent;
  * @author $author$
  * @version $Revision$
  */
-public class PCAPanel extends GPCAPanel implements Runnable,
-        IProgressIndicator
+public class PCAPanel extends GPCAPanel
+        implements Runnable, IProgressIndicator
 {
 
   private IProgressIndicator progressBar;
@@ -86,9 +86,12 @@ public class PCAPanel extends GPCAPanel implements Runnable,
    */
   public PCAPanel(AlignmentPanel alignPanel)
   {
-    this(alignPanel, ScoreModels.getInstance()
-            .getDefaultModel(!alignPanel.av.getAlignment().isNucleotide())
-            .getName(), SimilarityParams.SeqSpace);
+    this(alignPanel,
+            ScoreModels.getInstance()
+                    .getDefaultModel(
+                            !alignPanel.av.getAlignment().isNucleotide())
+                    .getName(),
+            SimilarityParams.SeqSpace);
   }
 
   /**
@@ -131,8 +134,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
     }
 
-    ScoreModelI scoreModel = ScoreModels.getInstance().getScoreModel(
-            modelName, ap);
+    ScoreModelI scoreModel = ScoreModels.getInstance()
+            .getScoreModel(modelName, ap);
     pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
             params);
     PaintRefresher.Register(this, av.getSequenceSetId());
@@ -189,8 +192,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
           {
             if (!pcaModel.getScoreModelName().equals(name))
             {
-              ScoreModelI sm2 = ScoreModels.getInstance().getScoreModel(
-                      name, ap);
+              ScoreModelI sm2 = ScoreModels.getInstance()
+                      .getScoreModel(name, ap);
               pcaModel.setScoreModel(sm2);
               Thread worker = new Thread(PCAPanel.this);
               worker.start();
@@ -271,8 +274,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     if (!pcaModel.isNucleotide())
     {
       pcaModel.setNucleotide(true);
-      pcaModel.setScoreModel(ScoreModels.getInstance().getDefaultModel(
-              false));
+      pcaModel.setScoreModel(
+              ScoreModels.getInstance().getDefaultModel(false));
       Thread worker = new Thread(this);
       worker.start();
     }
@@ -286,8 +289,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     if (pcaModel.isNucleotide())
     {
       pcaModel.setNucleotide(false);
-      pcaModel.setScoreModel(ScoreModels.getInstance()
-              .getDefaultModel(true));
+      pcaModel.setScoreModel(
+              ScoreModels.getInstance().getDefaultModel(true));
       Thread worker = new Thread(this);
       worker.start();
     }
@@ -385,8 +388,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     // make this an abstract function of all jalview analysis windows
     if (pcaModel.getSeqtrings() == null)
     {
-      jalview.bin.Cache.log
-              .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+      jalview.bin.Cache.log.info(
+              "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
       return;
     }
     // decide if av alignment is sufficiently different to original data to
@@ -413,8 +416,9 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
 
       AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
-      AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
-              .getAlignment().getDataset() : null;
+      AlignmentI dataset = (av != null && av.getAlignment() != null)
+              ? av.getAlignment().getDataset()
+              : null;
       if (dataset != null)
       {
         al.setDataset(dataset);
@@ -424,8 +428,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       {
         // make a new frame!
         AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
-                AlignFrame.DEFAULT_WIDTH,
-                AlignFrame.DEFAULT_HEIGHT);
+                AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 
         // >>>This is a fix for the moment, until a better solution is
         // found!!<<<
@@ -435,8 +438,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
         // msaorder);
 
         Desktop.addInternalFrame(af, MessageManager.formatMessage(
-                "label.original_data_for_params",
-                new String[] { this.title }), AlignFrame.DEFAULT_WIDTH,
+                "label.original_data_for_params", new String[]
+                { this.title }), AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
       }
     }
@@ -567,8 +570,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
 
   void buildAssociatedViewMenu()
   {
-    AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
-            .getSequenceSetId());
+    AlignmentPanel[] aps = PaintRefresher
+            .getAssociatedPanels(av.getSequenceSetId());
     if (aps.length == 1 && rc.av == aps[0].av)
     {
       associateViewsMenu.setVisible(false);
@@ -577,7 +580,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
 
     associateViewsMenu.setVisible(true);
 
-    if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+    if ((viewMenu
+            .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
     {
       viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
     }
@@ -608,7 +612,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       associateViewsMenu.add(item);
     }
 
-    final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+    final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
+            "All Views");
 
     buttonGroup.add(itemf);
 
@@ -641,9 +646,9 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       cap.setText(pcaModel.getPointsasCsv(false,
               xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
               zCombobox.getSelectedIndex()));
-      Desktop.addInternalFrame(cap, MessageManager.formatMessage(
-              "label.points_for_params", new String[] { this.getTitle() }),
-              500, 500);
+      Desktop.addInternalFrame(cap, MessageManager
+              .formatMessage("label.points_for_params", new String[]
+              { this.getTitle() }), 500, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning("exporting PCA points", oom);
@@ -668,8 +673,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
               xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
               zCombobox.getSelectedIndex()));
       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
-              "label.transformed_points_for_params",
-              new String[] { this.getTitle() }), 500, 500);
+              "label.transformed_points_for_params", new String[]
+              { this.getTitle() }), 500, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning("exporting transformed PCA points", oom);