X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=7bda65a597613aeac4e41f4ab5ae531b6f4bb862;hb=97c00be1121a6758439b73ded035c4edbacfa2bc;hp=ebde9cb058698b75ddfe28ff9aab769631c0a625;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index ebde9cb..7bda65a 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -18,133 +18,168 @@
  */
 package jalview.gui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
 import jalview.analysis.*;
+
 import jalview.datamodel.*;
-import jalview.jbgui.*;
 
-public class PCAPanel
-    extends GPCAPanel implements Runnable
-{
-  PCA pca;
-  int top;
-  RotatableCanvas rc;
-  AlignViewport av;
+import jalview.jbgui.*;
 
-  public PCAPanel(AlignViewport av, SequenceI[] s)
-  {
-    this.av = av;
+import java.awt.*;
+import java.awt.event.*;
 
-    if ( (av.getSelectionGroup() != null) &&
-        (av.getSelectionGroup().getSize() > 3))
-    {
-      s = new Sequence[av.getSelectionGroup().getSize()];
+import java.util.*;
 
-      for (int i = 0; i < s.length; i++)
-      {
-        s[i] = av.getSelectionGroup().getSequenceAt(i);
-      }
-    }
 
-    if (s == null)
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PCAPanel extends GPCAPanel implements Runnable
+{
+    PCA pca;
+    int top;
+    RotatableCanvas rc;
+    AlignViewport av;
+
+    /**
+     * Creates a new PCAPanel object.
+     *
+     * @param av DOCUMENT ME!
+     * @param s DOCUMENT ME!
+     */
+    public PCAPanel(AlignViewport av, SequenceI[] s)
     {
-      s = new Sequence[av.getAlignment().getHeight()];
-
-      for (int i = 0; i < av.getAlignment().getHeight(); i++)
-      {
-        s[i] = av.getAlignment().getSequenceAt(i);
-      }
+        this.av = av;
+
+        if ((av.getSelectionGroup() != null) &&
+                (av.getSelectionGroup().getSize() > 3))
+        {
+            s = new Sequence[av.getSelectionGroup().getSize()];
+
+            for (int i = 0; i < s.length; i++)
+            {
+                s[i] = av.getSelectionGroup().getSequenceAt(i);
+            }
+        }
+
+        if (s == null)
+        {
+            s = new Sequence[av.getAlignment().getHeight()];
+
+            for (int i = 0; i < av.getAlignment().getHeight(); i++)
+            {
+                s[i] = av.getAlignment().getSequenceAt(i);
+            }
+        }
+
+        //////////////////////This part was done in PCATHread originally. Is it too slow???
+        pca = new PCA(s);
+        pca.run();
+
+        // Now find the component coordinates
+        int ii = 0;
+
+        while ((ii < s.length) && (s[ii] != null))
+        {
+            ii++;
+        }
+
+        double[][] comps = new double[ii][ii];
+
+        for (int i = 0; i < ii; i++)
+        {
+            if (pca.getEigenvalue(i) > 1e-4)
+            {
+                comps[i] = pca.component(i);
+            }
+        }
+
+        //////////////////
+        xCombobox.setSelectedIndex(0);
+        yCombobox.setSelectedIndex(1);
+        zCombobox.setSelectedIndex(2);
+
+        top = pca.getM().rows - 1;
+
+        Vector points = new Vector();
+        float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
+
+        for (int i = 0; i < pca.getM().rows; i++)
+        {
+            SequencePoint sp = new SequencePoint(s[i], scores[i]);
+            points.addElement(sp);
+        }
+
+        rc = new RotatableCanvas(av, points, pca.getM().rows);
+
+        //rc.printPoints();
+        add(rc, BorderLayout.CENTER);
     }
 
-    //////////////////////This part was done in PCATHread originally. Is it too slow???
-    pca = new PCA(s);
-    pca.run();
-
-    // Now find the component coordinates
-    int ii = 0;
-
-    while ( (ii < s.length) && (s[ii] != null))
+    /**
+     * DOCUMENT ME!
+     */
+    public void run()
     {
-      ii++;
+        // do stuff
     }
 
-    double[][] comps = new double[ii][ii];
-
-    for (int i = 0; i < ii; i++)
+    /**
+     * DOCUMENT ME!
+     */
+    void doDimensionChange()
     {
-      if (pca.getEigenvalue(i) > 1e-4)
-      {
-        comps[i] = pca.component(i);
-      }
+        if (top == 0)
+        {
+            return;
+        }
+
+        int dim1 = top - xCombobox.getSelectedIndex();
+        int dim2 = top - yCombobox.getSelectedIndex();
+        int dim3 = top - zCombobox.getSelectedIndex();
+
+        float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
+
+        for (int i = 0; i < pca.getM().rows; i++)
+        {
+            ((SequencePoint) rc.points.elementAt(i)).coord = scores[i];
+        }
+
+        rc.img = null;
+        rc.rotmat.setIdentity();
+        rc.initAxes();
+        rc.paint(rc.getGraphics());
     }
 
-    //////////////////
-    xCombobox.setSelectedIndex(0);
-    yCombobox.setSelectedIndex(1);
-    zCombobox.setSelectedIndex(2);
-
-    top = pca.getM().rows - 1;
-
-    Vector points = new Vector();
-    float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
-
-    for (int i = 0; i < pca.getM().rows; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void xCombobox_actionPerformed(ActionEvent e)
     {
-      SequencePoint sp = new SequencePoint(s[i], scores[i]);
-      points.addElement(sp);
+        doDimensionChange();
     }
 
-    rc = new RotatableCanvas(av, points, pca.getM().rows);
-
-    //rc.printPoints();
-    add(rc, BorderLayout.CENTER);
-  }
-
-  public void run()
-  {
-    // do stuff
-  }
-
-  void doDimensionChange()
-  {
-    if (top == 0)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void yCombobox_actionPerformed(ActionEvent e)
     {
-      return;
+        doDimensionChange();
     }
 
-    int dim1 = top - xCombobox.getSelectedIndex();
-    int dim2 = top - yCombobox.getSelectedIndex();
-    int dim3 = top - zCombobox.getSelectedIndex();
-
-    float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
-
-    for (int i = 0; i < pca.getM().rows; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void zCombobox_actionPerformed(ActionEvent e)
     {
-      ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i];
+        doDimensionChange();
     }
-
-    rc.img = null;
-    rc.rotmat.setIdentity();
-    rc.initAxes();
-    rc.paint(rc.getGraphics());
-  }
-
-  protected void xCombobox_actionPerformed(ActionEvent e)
-  {
-    doDimensionChange();
-  }
-
-  protected void yCombobox_actionPerformed(ActionEvent e)
-  {
-    doDimensionChange();
-  }
-
-  protected void zCombobox_actionPerformed(ActionEvent e)
-  {
-    doDimensionChange();
-  }
 }