X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=845e8804b175abf5603dfcc0e865b276e6409fe9;hb=502eab512b790bcee60cefef90b0c46711a4264d;hp=1dd05e0e9afe1f82d92d2554a3cfa8e77c1e98e3;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 1dd05e0..845e880 100755
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -26,86 +26,117 @@ import java.awt.event.*;
 
 import jalview.analysis.*;
 import jalview.datamodel.*;
-import jalview.jbappletgui.*;
+
 
 public class PCAPanel
-    extends GPCAPanel implements Runnable
+    extends Frame implements Runnable, ActionListener, ItemListener
 {
   PCA pca;
   int top;
   RotatableCanvas rc;
   AlignViewport av;
+  SequenceI [] seqs;
+  AlignmentView seqstrings;
 
-  public void run()
-  {
-    // do stuff
-  }
 
-  public PCAPanel(AlignViewport av, SequenceI[] s)
+  public PCAPanel(AlignViewport av)
   {
-
-    this.av = av;
-    if (av.getSelectionGroup().getSize() > 3)
+    try
     {
-      s = new Sequence[av.getSelectionGroup().getSize()];
-      for (int i = 0; i < s.length; i++)
-      {
-        s[i] = av.getSelectionGroup().getSequenceAt(i);
-      }
+      jbInit();
     }
-
-    if (s == null)
+    catch (Exception e)
     {
-      s = new Sequence[av.getAlignment().getHeight()];
-      for (int i = 0; i < av.getAlignment().getHeight(); i++)
-      {
-        s[i] = av.getAlignment().getSequenceAt(i);
-      }
+      e.printStackTrace();
     }
 
-//////////////////////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)
+    for (int i = 1; i < 8; i++)
     {
-      ii++;
+      xCombobox.addItem("dim " + i);
+      yCombobox.addItem("dim " + i);
+      zCombobox.addItem("dim " + i);
     }
 
-    double[][] comps = new double[ii][ii];
+    this.av = av;
+    seqstrings = av.getAlignmentView(av.getSelectionGroup()!=null);
+    if(av.getSelectionGroup()==null)
+    {
+      seqs = av.alignment.getSequencesArray();
+    }
+    else
+    {
+      seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+    }
+    SeqCigar sq[]=seqstrings.getSequences();
+    int length = sq[0].getWidth();
 
-    for (int i = 0; i < ii; i++)
+    for (int i = 0; i < seqs.length; i++)
     {
-      if (pca.getEigenvalue(i) > 1e-4)
+      if (sq[i].getWidth() != length)
       {
-        comps[i] = pca.component(i);
+        System.out.println("Sequences must be equal length for PCA analysis");
+        return;
       }
     }
 
-    //////////////////
 
-    xCombobox.select(0);
-    yCombobox.select(1);
-    zCombobox.select(2);
+    rc = new RotatableCanvas(av);
+    add(rc, BorderLayout.CENTER);
 
-    top = pca.getM().rows - 1;
+    jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",
+                                       400, 400);
 
-    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);
-    }
+    Thread worker = new Thread(this);
+    worker.start();
+  }
 
-    rc = new RotatableCanvas(av, points, pca.getM().rows);
+  /**
+   * DOCUMENT ME!
+   */
+  public void run()
+  {
+              pca = new PCA(seqstrings.getSequenceStrings(' '));
+              pca.run();
 
-    //rc.printPoints();
+              // Now find the component coordinates
+              int ii = 0;
 
-    add(rc, BorderLayout.CENTER);
+              while ((ii < seqs.length) && (seqs[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.select(0);
+              yCombobox.select(1);
+              zCombobox.select(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(seqs[i], scores[i]);
+                  points.addElement(sp);
+              }
+
+              rc.setPoints(points, pca.getM().rows);
+              rc.repaint();
+              seqs = null;
+              this.repaint();
   }
 
   void doDimensionChange()
@@ -131,19 +162,132 @@ public class PCAPanel
     rc.paint(rc.getGraphics());
   }
 
-  protected void xCombobox_actionPerformed(ActionEvent e)
+  public void actionPerformed(ActionEvent evt)
+  {
+    if(evt.getSource()==inputData)
+      showOriginalData();
+    else
+      values_actionPerformed();
+  }
+
+  public void itemStateChanged(ItemEvent evt)
+  {
+    if(evt.getSource()==xCombobox)
+      xCombobox_actionPerformed();
+    else if(evt.getSource()==yCombobox)
+      yCombobox_actionPerformed();
+    else if(evt.getSource()==zCombobox)
+      zCombobox_actionPerformed();
+  }
+
+
+  protected void xCombobox_actionPerformed()
   {
     doDimensionChange();
   }
 
-  protected void yCombobox_actionPerformed(ActionEvent e)
+  protected void yCombobox_actionPerformed()
   {
     doDimensionChange();
   }
 
-  protected void zCombobox_actionPerformed(ActionEvent e)
+  protected void zCombobox_actionPerformed()
   {
     doDimensionChange();
   }
 
+  public void values_actionPerformed()
+  {
+
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
+    Frame frame = new Frame();
+    frame.add(cap);
+    jalview.bin.JalviewLite.addFrame(frame, "PCA details", 500, 500);
+
+      cap.setText(pca.getDetails());
+  }
+
+  void showOriginalData()
+  {
+    // decide if av alignment is sufficiently different to original data to warrant a new window to be created
+    // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+    // or create a selection box around columns in alignment view
+    // test Alignment(SeqCigar[])
+    Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av.
+        getGapCharacter());
+
+
+    if (alAndColsel != null && alAndColsel[0]!=null)
+     {
+       Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);
+       AlignFrame af = new AlignFrame(al,
+             av.applet,
+             "Original Data for PCA",
+             false);
+
+      af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1] );
+     }
+  }
+
+  public void labels_itemStateChanged(ItemEvent itemEvent)
+  {
+    rc.showLabels( labels.getState() );
+  }
+  Panel jPanel2 = new Panel();
+  Label jLabel1 = new Label();
+  Label jLabel2 = new Label();
+  Label jLabel3 = new Label();
+  protected Choice xCombobox = new Choice();
+  protected Choice yCombobox = new Choice();
+  protected Choice zCombobox = new Choice();
+  FlowLayout flowLayout1 = new FlowLayout();
+  BorderLayout borderLayout1 = new BorderLayout();
+  MenuBar menuBar1 = new MenuBar();
+  Menu menu1 = new Menu();
+  Menu menu2 = new Menu();
+  protected CheckboxMenuItem labels = new CheckboxMenuItem();
+  MenuItem values = new MenuItem();
+  MenuItem inputData = new MenuItem();
+
+  private void jbInit()
+      throws Exception
+  {
+    this.setLayout(borderLayout1);
+    jPanel2.setLayout(flowLayout1);
+    jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel1.setText("x=");
+    jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel2.setText("y=");
+    jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel3.setText("z=");
+    jPanel2.setBackground(Color.white);
+    zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+    zCombobox.addItemListener(this);
+    yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+    yCombobox.addItemListener(this);
+    xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+    xCombobox.addItemListener(this);
+    this.setMenuBar(menuBar1);
+    menu1.setLabel("File");
+    menu2.setLabel("View");
+    labels.setLabel("Labels");
+    labels.addItemListener(this);
+    values.setLabel("Output Values...");
+    values.addActionListener(this);
+    inputData.setLabel("Input Data...");
+    this.add(jPanel2, BorderLayout.SOUTH);
+    jPanel2.add(jLabel1, null);
+    jPanel2.add(xCombobox, null);
+    jPanel2.add(jLabel2, null);
+    jPanel2.add(yCombobox, null);
+    jPanel2.add(jLabel3, null);
+    jPanel2.add(zCombobox, null);
+    menuBar1.add(menu1);
+    menuBar1.add(menu2);
+    menu2.add(labels);
+    menu1.add(values);
+    menu1.add(inputData);
+    inputData.addActionListener(this);
+  }
+
 }