formatting

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 4441eeb..f0b7f16 100755 (executable)
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -46,8 +46,9 @@ public class PCA implements Runnable
   StringBuffer details = new StringBuffer();
 
   /**
-   * Creates a new PCA object.
-   * By default, uses blosum62 matrix to generate sequence similarity matrices
+   * Creates a new PCA object. By default, uses blosum62 matrix to generate
+   * sequence similarity matrices
+   * 
    * @param s
    *          Set of amino acid sequences to perform PCA on
    */
@@ -55,13 +56,16 @@ public class PCA implements Runnable
   {
     this(s, false);
   }
-  
+
   /**
-   * Creates a new PCA object.
-   * By default, uses blosum62 matrix to generate sequence similarity matrices
+   * Creates a new PCA object. By default, uses blosum62 matrix to generate
+   * sequence similarity matrices
+   * 
    * @param s
    *          Set of sequences to perform PCA on
-   *          @param nucleotides if true, uses standard DNA/RNA matrix for sequence similarity calculation.
+   * @param nucleotides
+   *          if true, uses standard DNA/RNA matrix for sequence similarity
+   *          calculation.
    */
   public PCA(String[] s, boolean nucleotides)
   {
@@ -71,7 +75,7 @@ public class PCA implements Runnable
 
     while ((ii < s.length) && (s[ii] != null))
     {
-      bs[ii] = new BinarySequence(s[ii],nucleotides);
+      bs[ii] = new BinarySequence(s[ii], nucleotides);
       bs[ii].encode();
       ii++;
     }
@@ -79,10 +83,10 @@ public class PCA implements Runnable
     BinarySequence[] bs2 = new BinarySequence[s.length];
     ii = 0;
 
-    String sm=nucleotides ? "DNA" : "BLOSUM62";
-    ScoreMatrix smtrx=ResidueProperties.getScoreMatrix(sm);
-    details.append("PCA calculation using "+sm+" sequence similarity matrix\n========\n\n");
-    
+    String sm = nucleotides ? "DNA" : "BLOSUM62";
+    ScoreMatrix smtrx = ResidueProperties.getScoreMatrix(sm);
+    details.append("PCA calculation using " + sm
+            + " sequence similarity matrix\n========\n\n");
     while ((ii < s.length) && (s[ii] != null))
     {
       bs2[ii] = new BinarySequence(s[ii], nucleotides);

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index f951acf..ad7d1fd 100755 (executable)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -35,17 +35,19 @@ import jalview.viewmodel.PCAModel;
  * @author $author$
  * @version $Revision$
  */
-public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
+public class PCAPanel extends GPCAPanel implements Runnable,
+        IProgressIndicator
 {
 
-
   RotatableCanvas rc;
 
   AlignmentPanel ap;
 
   AlignViewport av;
+
   PCAModel pcaModel;
-  int top=0;
+
+  int top = 0;
 
   /**
    * Creates a new PCAPanel object.
@@ -62,8 +64,9 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
 
     boolean sameLength = true;
 
-    AlignmentView seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
-    boolean nucleotide=av.getAlignment().isNucleotide();
+    AlignmentView seqstrings = av
+            .getAlignmentView(av.getSelectionGroup() != null);
+    boolean nucleotide = av.getAlignment().isNucleotide();
     SequenceI[] seqs;
     if (av.getSelectionGroup() == null)
     {
@@ -99,7 +102,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
     }
     pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
     PaintRefresher.Register(this, av.getSequenceSetId());
-    
+
     rc = new RotatableCanvas(ap);
     this.getContentPane().add(rc, BorderLayout.CENTER);
     Thread worker = new Thread(this);
@@ -123,11 +126,12 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
    */
   public void run()
   {
-    long progId=System.currentTimeMillis();
-    IProgressIndicator progress=this;
-    String message="Recalculating PCA";
-    if (getParent()==null) {
-      progress=ap.alignFrame;
+    long progId = System.currentTimeMillis();
+    IProgressIndicator progress = this;
+    String message = "Recalculating PCA";
+    if (getParent() == null)
+    {
+      progress = ap.alignFrame;
       message = "Calculating PCA";
     }
     progress.setProgressBar(message, progId);
@@ -139,45 +143,48 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
       xCombobox.setSelectedIndex(0);
       yCombobox.setSelectedIndex(1);
       zCombobox.setSelectedIndex(2);
-      
+
       pcaModel.updateRc(rc);
       // rc.invalidate();
       nuclSetting.setSelected(pcaModel.isNucleotide());
       protSetting.setSelected(!pcaModel.isNucleotide());
-      top=pcaModel.getTop();
       jvVersionSetting.setSelected(pcaModel.isJvCalcMode());
+      top = pcaModel.getTop();
 
     } catch (OutOfMemoryError er)
     {
       new OOMWarning("calculating PCA", er);
       return;
-    }
-    finally {
+    } finally
+    {
       progress.setProgressBar("", progId);
     }
     calcSettings.setEnabled(true);
     repaint();
-    if (getParent()==null)
+    if (getParent() == null)
     {
       addKeyListener(rc);
-      Desktop.addInternalFrame(this, "Principal component analysis", 475, 450);
+      Desktop.addInternalFrame(this, "Principal component analysis", 475,
+              450);
     }
   }
+
   @Override
   protected void nuclSetting_actionPerfomed(ActionEvent arg0)
   {
     if (!pcaModel.isNucleotide())
     {
       pcaModel.setNucleotide(true);
-    Thread worker = new Thread(this);
-    worker.start();
+      Thread worker = new Thread(this);
+      worker.start();
     }
-    
+
   }
+
   @Override
   protected void protSetting_actionPerfomed(ActionEvent arg0)
   {
-    
+
     if (pcaModel.isNucleotide())
     {
       pcaModel.setNucleotide(false);
@@ -298,7 +305,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
     {
     }
     ;
-    Object[] alAndColsel = pcaModel.getSeqtrings().getAlignmentAndColumnSelection(gc);
+    Object[] alAndColsel = pcaModel.getSeqtrings()
+            .getAlignmentAndColumnSelection(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
     {
@@ -512,7 +520,9 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     try
     {
-      cap.setText(pcaModel.getPointsasCsv(false, xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), zCombobox.getSelectedIndex()));
+      cap.setText(pcaModel.getPointsasCsv(false,
+              xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
+              zCombobox.getSelectedIndex()));
       Desktop.addInternalFrame(cap, "Points for " + getTitle(), 500, 500);
     } catch (OutOfMemoryError oom)
     {
@@ -521,8 +531,6 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
     }
   }
 
-  
-
   /*
    * (non-Javadoc)
    * 
@@ -535,7 +543,9 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     try
     {
-      cap.setText(pcaModel.getPointsasCsv(true, xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), zCombobox.getSelectedIndex()));
+      cap.setText(pcaModel.getPointsasCsv(true,
+              xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
+              zCombobox.getSelectedIndex()));
       Desktop.addInternalFrame(cap, "Transformed points for " + getTitle(),
               500, 500);
     } catch (OutOfMemoryError oom)
@@ -551,7 +561,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
    */
   @Override
@@ -635,7 +645,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
   }
 
   /**
-   *
+   * 
    * @return true if any progress bars are still active
    */
   @Override
@@ -647,14 +657,15 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
     }
     return false;
   }
+
   @Override
   protected void resetButton_actionPerformed(ActionEvent e)
   {
-    int t=top;
-    top=0; // ugly - prevents dimensionChanged events from being processed
+    int t = top;
+    top = 0; // ugly - prevents dimensionChanged events from being processed
     xCombobox.setSelectedIndex(0);
     yCombobox.setSelectedIndex(1);
-    top=t;
+    top = t;
     zCombobox.setSelectedIndex(2);
   }
 }