X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=845e8804b175abf5603dfcc0e865b276e6409fe9;hb=174230b4233d9ce80f94527768d2cd2f76da11ab;hp=6465ee839e13046ccf0d41040ba8c903c5992e01;hpb=0c0f58648af5512096275b634158c37c87989eaa;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 6465ee8..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
@@ -36,6 +36,7 @@ public class PCAPanel
   RotatableCanvas rc;
   AlignViewport av;
   SequenceI [] seqs;
+  AlignmentView seqstrings;
 
 
   public PCAPanel(AlignViewport av)
@@ -57,23 +58,28 @@ 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;
       }
     }
 
+
     rc = new RotatableCanvas(av);
     add(rc, BorderLayout.CENTER);
 
@@ -90,7 +96,7 @@ public class PCAPanel
    */
   public void run()
   {
-              pca = null;//new PCA(seqs);
+              pca = new PCA(seqstrings.getSequenceStrings(' '));
               pca.run();
 
               // Now find the component coordinates
@@ -158,7 +164,10 @@ public class PCAPanel
 
   public void actionPerformed(ActionEvent evt)
   {
-    values_actionPerformed();
+    if(evt.getSource()==inputData)
+      showOriginalData();
+    else
+      values_actionPerformed();
   }
 
   public void itemStateChanged(ItemEvent evt)
@@ -198,6 +207,28 @@ public class PCAPanel
       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() );
@@ -216,6 +247,7 @@ 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 +274,7 @@ 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 +286,8 @@ public class PCAPanel
     menuBar1.add(menu2);
     menu2.add(labels);
     menu1.add(values);
+    menu1.add(inputData);
+    inputData.addActionListener(this);
   }
 
 }