X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=b121828c8e5bf3b3b18db3cdfac298f38af0958f;hb=4741fc6fc72b7c5ffd75af5b1bc17070fef448f9;hp=2613df5b506f3d5578fde6b74f62aa02b1fddb2a;hpb=ec955aa655d8320258b91eb079bc57f688cd0a07;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 2613df5..b121828 100755
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -1,101 +1,155 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+
 package jalview.appletgui;
 
-import jalview.datamodel.*;
-import jalview.analysis.PCA;
-import jalview.jbappletgui.*;
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
 
+import jalview.analysis.*;
+import jalview.datamodel.*;
 
-public class PCAPanel extends GPCAPanel implements Runnable
+public class PCAPanel
+    extends Frame implements Runnable, ActionListener, ItemListener
 {
   PCA pca;
   int top;
   RotatableCanvas rc;
   AlignViewport av;
+  SequenceI[] seqs;
+  AlignmentView seqstrings;
 
-  public void run()
+  public PCAPanel(AlignViewport av)
   {
-    // do stuff
-  }
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
 
-  public PCAPanel(AlignViewport av, SequenceI[] s) {
+    for (int i = 1; i < 8; i++)
+    {
+      xCombobox.addItem("dim " + i);
+      yCombobox.addItem("dim " + i);
+      zCombobox.addItem("dim " + i);
+    }
 
     this.av = av;
-    if(av.getSelectionGroup().getSize()>3)
+    seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
+    if (av.getSelectionGroup() == null)
     {
-      s = new Sequence[av.getSelectionGroup().getSize()];
-      for(int i=0; i<s.length; i++)
-        s[i] = av.getSelectionGroup().getSequenceAt(i);
+      seqs = av.alignment.getSequencesArray();
     }
+    else
+    {
+      seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+    }
+    SeqCigar sq[] = seqstrings.getSequences();
+    int length = sq[0].getWidth();
 
-
-    if(s==null)
+    for (int i = 0; i < seqs.length; i++)
     {
-      s = new Sequence[av.getAlignment().getHeight()];
-      for (int i = 0; i < av.getAlignment().getHeight(); i++)
-        s[i] = av.getAlignment().getSequenceAt(i);
-     }
+      if (sq[i].getWidth() != length)
+      {
+        System.out.println("Sequences must be equal length for PCA analysis");
+        return;
+      }
+    }
+
+    rc = new RotatableCanvas(av);
+    add(rc, BorderLayout.CENTER);
+
+    jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",
+                                     400, 400);
 
-//////////////////////This part was done in PCATHread originally. Is it too slow???
-    pca = new PCA(s);
+    Thread worker = new Thread(this);
+    worker.start();
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void run()
+  {
+    pca = new PCA(seqstrings.getSequenceStrings(' '));
     pca.run();
 
     // Now find the component coordinates
-    int ii=0;
-    while (ii < s.length && s[ii] != null)
+    int ii = 0;
+
+    while ( (ii < seqs.length) && (seqs[ii] != null))
     {
       ii++;
     }
 
     double[][] comps = new double[ii][ii];
 
-    for (int i=0; i < ii; i++ )
+    for (int i = 0; i < ii; i++)
     {
       if (pca.getEigenvalue(i) > 1e-4)
       {
-        comps[i]  = pca.component(i);
+        comps[i] = pca.component(i);
       }
     }
 
     //////////////////
-
     xCombobox.select(0);
     yCombobox.select(1);
     zCombobox.select(2);
 
-    top = pca.getM().rows-1;
+    top = pca.getM().rows - 1;
 
     Vector points = new Vector();
-    float[][] scores = pca.getComponents(top-1,top-2,top-3,100);
+    float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
 
-    for (int i =0; i < pca.getM().rows; i++ )
+    for (int i = 0; i < pca.getM().rows; i++)
     {
-      SequencePoint sp = new SequencePoint(s[i],scores[i]);
+      SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
       points.addElement(sp);
     }
 
-    rc = new RotatableCanvas(av,points,pca.getM().rows);
-
-    //rc.printPoints();
-
-    add(rc, BorderLayout.CENTER);
+    rc.setPoints(points, pca.getM().rows);
+    rc.repaint();
+    seqs = null;
+    this.repaint();
   }
 
-
   void doDimensionChange()
   {
-    if(top==0)
+    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];
+    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;
@@ -104,19 +158,141 @@ public class PCAPanel extends GPCAPanel implements Runnable
     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);
+  }
+
 }