X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=b121828c8e5bf3b3b18db3cdfac298f38af0958f;hb=4f1f764c09427cd63c3e355fa729da86735a8194;hp=6465ee839e13046ccf0d41040ba8c903c5992e01;hpb=0c0f58648af5512096275b634158c37c87989eaa;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 6465ee8..b121828 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) 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
@@ -27,7 +27,6 @@ import java.awt.event.*;
 import jalview.analysis.*;
 import jalview.datamodel.*;
 
-
 public class PCAPanel
     extends Frame implements Runnable, ActionListener, ItemListener
 {
@@ -35,8 +34,8 @@ public class PCAPanel
   int top;
   RotatableCanvas rc;
   AlignViewport av;
-  SequenceI [] seqs;
-
+  SequenceI[] seqs;
+  AlignmentView seqstrings;
 
   public PCAPanel(AlignViewport av)
   {
@@ -57,20 +56,24 @@ public class PCAPanel
     }
 
     this.av = av;
-    if (av.getSelectionGroup()!=null && av.getSelectionGroup().getSize(false) > 3)
+    seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
+    if (av.getSelectionGroup() == null)
     {
-      seqs = new Sequence[av.getSelectionGroup().getSize(false)];
-      for (int i = 0; i < av.getSelectionGroup().getSize(false); i++)
-      {
-        seqs[i] = av.getSelectionGroup().getSequenceAt(i);
-      }
+      seqs = av.alignment.getSequencesArray();
     }
     else
     {
-      seqs = new Sequence[av.getAlignment().getHeight()];
-      for (int i = 0; i < av.getAlignment().getHeight(); i++)
+      seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+    }
+    SeqCigar sq[] = seqstrings.getSequences();
+    int length = sq[0].getWidth();
+
+    for (int i = 0; i < seqs.length; i++)
+    {
+      if (sq[i].getWidth() != length)
       {
-        seqs[i] = av.getAlignment().getSequenceAt(i);
+        System.out.println("Sequences must be equal length for PCA analysis");
+        return;
       }
     }
 
@@ -78,8 +81,7 @@ public class PCAPanel
     add(rc, BorderLayout.CENTER);
 
     jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",
-                                       400, 400);
-
+                                     400, 400);
 
     Thread worker = new Thread(this);
     worker.start();
@@ -90,47 +92,47 @@ public class PCAPanel
    */
   public void run()
   {
-              pca = null;//new PCA(seqs);
-              pca.run();
-
-              // Now find the component coordinates
-              int ii = 0;
-
-              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();
+    pca = new PCA(seqstrings.getSequenceStrings(' '));
+    pca.run();
+
+    // Now find the component coordinates
+    int ii = 0;
+
+    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()
@@ -158,20 +160,32 @@ public class PCAPanel
 
   public void actionPerformed(ActionEvent evt)
   {
-    values_actionPerformed();
+    if (evt.getSource() == inputData)
+    {
+      showOriginalData();
+    }
+    else
+    {
+      values_actionPerformed();
+    }
   }
 
   public void itemStateChanged(ItemEvent evt)
   {
-    if(evt.getSource()==xCombobox)
+    if (evt.getSource() == xCombobox)
+    {
       xCombobox_actionPerformed();
-    else if(evt.getSource()==yCombobox)
+    }
+    else if (evt.getSource() == yCombobox)
+    {
       yCombobox_actionPerformed();
-    else if(evt.getSource()==zCombobox)
+    }
+    else if (evt.getSource() == zCombobox)
+    {
       zCombobox_actionPerformed();
+    }
   }
 
-
   protected void xCombobox_actionPerformed()
   {
     doDimensionChange();
@@ -195,13 +209,35 @@ public class PCAPanel
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame, "PCA details", 500, 500);
 
-      cap.setText(pca.getDetails());
+    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() );
+    rc.showLabels(labels.getState());
   }
+
   Panel jPanel2 = new Panel();
   Label jLabel1 = new Label();
   Label jLabel2 = new Label();
@@ -216,6 +252,7 @@ public class PCAPanel
   Menu menu2 = new Menu();
   protected CheckboxMenuItem labels = new CheckboxMenuItem();
   MenuItem values = new MenuItem();
+  MenuItem inputData = new MenuItem();
 
   private void jbInit()
       throws Exception
@@ -242,6 +279,7 @@ public class PCAPanel
     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);
@@ -253,6 +291,8 @@ public class PCAPanel
     menuBar1.add(menu2);
     menu2.add(labels);
     menu1.add(values);
+    menu1.add(inputData);
+    inputData.addActionListener(this);
   }
 
 }