X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=f423a43935271495642a5eedea794c66ac8b15ff;hb=59d682209891099d46b960509907c79e3fb276fe;hp=eb7806f136cbb00a5bad662c0dc0998a0c128eec;hpb=55c883270e9f64da9562a24f09dfe5f2f079e59a;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index eb7806f..f423a43 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -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.
@@ -61,11 +63,12 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
     this.ap = ap;
 
     boolean sameLength = true;
-
-    AlignmentView seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
-    boolean nucleotide=av.getAlignment().isNucleotide();
+    boolean selected = av.getSelectionGroup() != null
+            && av.getSelectionGroup().getSize() > 0;
+    AlignmentView seqstrings = av.getAlignmentView(selected);
+    boolean nucleotide = av.getAlignment().isNucleotide();
     SequenceI[] seqs;
-    if (av.getSelectionGroup() == null)
+    if (!selected)
     {
       seqs = av.getAlignment().getSequencesArray();
     }
@@ -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);
@@ -139,51 +143,64 @@ 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);
+      Thread worker = new Thread(this);
+      worker.start();
+    }
+  }
+
+  @Override
+  protected void jvVersionSetting_actionPerfomed(ActionEvent arg0)
+  {
+    pcaModel.setJvCalcMode(jvVersionSetting.isSelected());
     Thread worker = new Thread(this);
     worker.start();
-    }
   }
+
   /**
    * DOCUMENT ME!
    */
@@ -288,7 +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)
     {
@@ -502,7 +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)
     {
@@ -511,8 +531,6 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
     }
   }
 
-  
-
   /*
    * (non-Javadoc)
    * 
@@ -525,7 +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)
@@ -541,7 +561,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
    */
   @Override
@@ -625,7 +645,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
   }
 
   /**
-   *
+   * 
    * @return true if any progress bars are still active
    */
   @Override
@@ -637,14 +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);
   }
 }