From 3e9eba89979511361b51f1c78882c9877874f2ba Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 15 Jun 2012 17:52:37 +0100
Subject: [PATCH] JAL-1125 option to switch between Jalview and SeqSpace PCA
 calculation modes

---
 src/jalview/analysis/PCA.java       |   18 ++++++++++++++++--
 src/jalview/gui/PCAPanel.java       |   12 +++++++++++-
 src/jalview/jbgui/GPCAPanel.java    |   20 +++++++++++++++++++-
 src/jalview/viewmodel/PCAModel.java |   15 ++++++++++++++-
 4 files changed, 60 insertions(+), 5 deletions(-)

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index b001549..4441eeb 100755
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -232,11 +232,18 @@ public class PCA implements Runnable
    */
   public void run()
   {
+    details.append("PCA Calculation Mode is "+(jvCalcMode ? "Jalview variant" : "Original SeqSpace")+"\n");
     Matrix mt = m.transpose();
 
     details.append(" --- OrigT * Orig ---- \n");
-    // eigenvector = mt.preMultiply(m); // standard seqspace comparison matrix
-    eigenvector = mt.preMultiply(m2); // jalview variation on seqsmace method
+    if (!jvCalcMode)
+    {
+      eigenvector = mt.preMultiply(m); // standard seqspace comparison matrix
+    }
+    else
+    {
+      eigenvector = mt.preMultiply(m2); // jalview variation on seqsmace method
+    }
 
     PrintStream ps = new PrintStream(System.out)
     {
@@ -280,4 +287,11 @@ public class PCA implements Runnable
      * ps.print(","+component(seq, ev)); } ps.println(); }
      */
   }
+
+  boolean jvCalcMode = true;
+
+  public void setJvCalcMode(boolean calcMode)
+  {
+    this.jvCalcMode = calcMode;
+  }
 }
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index eb7806f..f951acf 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -145,6 +145,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
       nuclSetting.setSelected(pcaModel.isNucleotide());
       protSetting.setSelected(!pcaModel.isNucleotide());
       top=pcaModel.getTop();
+      jvVersionSetting.setSelected(pcaModel.isJvCalcMode());
 
     } catch (OutOfMemoryError er)
     {
@@ -180,10 +181,19 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
     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!
    */
diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index c0905a8..15d4b3e 100755
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -76,6 +76,7 @@ public class GPCAPanel extends JInternalFrame
   protected JMenu calcSettings=new JMenu();
   protected JCheckBoxMenuItem nuclSetting=new JCheckBoxMenuItem();
   protected JCheckBoxMenuItem protSetting=new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem jvVersionSetting=new JCheckBoxMenuItem();
   
   protected JLabel statusBar = new JLabel();
   protected GridLayout statusPanelLayout = new GridLayout();
@@ -257,7 +258,18 @@ public class GPCAPanel extends JInternalFrame
       {
         protSetting_actionPerfomed(arg0);
       }
-    });calcSettings.add(nuclSetting);
+    });
+    jvVersionSetting.setText("Jalview PCA Calculation");
+    jvVersionSetting.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        jvVersionSetting_actionPerfomed(arg0);
+      }
+    });
+    calcSettings.add(jvVersionSetting);
+    calcSettings.add(nuclSetting);
     calcSettings.add(protSetting);
     statusPanel.setLayout(statusPanelLayout);
     statusBar.setFont(new java.awt.Font("Verdana",0,12));
@@ -372,4 +384,10 @@ public class GPCAPanel extends JInternalFrame
   {
 
   }
+
+  protected void jvVersionSetting_actionPerfomed(ActionEvent arg0)
+  {
+    // TODO Auto-generated method stub
+    
+  }
 }
diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index 6002c8a..64f2497 100644
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -19,7 +19,7 @@ public class PCAModel
     nucleotide=nucleotide2;
   }
 
-  PCA pca;
+  private volatile PCA pca;
   
   int top;
   
@@ -34,10 +34,18 @@ public class PCAModel
 
   private Vector<SequencePoint> points;
 
+  private boolean jvCalcMode=true;
+
+  public boolean isJvCalcMode()
+  {
+    return jvCalcMode;
+  }
+
   public void run()
   {
     
     pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide);
+    pca.setJvCalcMode(jvCalcMode);
     pca.run();
 
     // Now find the component coordinates
@@ -188,4 +196,9 @@ public class PCAModel
     return pts;
   }
 
+  public void setJvCalcMode(boolean state)
+  {
+    jvCalcMode=state;
+  }
+
 }
-- 
1.7.10.2