X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=6559a17521192bb5d50fda8c92d2f4d7434d6565;hb=608832fec5a504b4c56e5837b2b3dfc1993fe734;hp=0368d2a8770e934428a251144fefee9fff219c06;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 0368d2a..6559a17 100755
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -29,13 +29,14 @@ import jalview.datamodel.*;
 
 
 public class PCAPanel
-    extends Frame implements Runnable
+    extends Frame implements Runnable, ActionListener, ItemListener
 {
   PCA pca;
   int top;
   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() > 3)
+    seqstrings = av.getAlignmentView(av.getSelectionGroup()!=null);
+    if(av.getSelectionGroup()==null)
     {
-      seqs = new Sequence[av.getSelectionGroup().getSize()];
-      for (int i = 0; i < av.getSelectionGroup().getSize(); 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 = new PCA(seqs);
+              pca = new PCA(seqstrings.getSequenceStrings(' '));
               pca.run();
 
               // Now find the component coordinates
@@ -156,22 +162,41 @@ 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(ActionEvent actionEvent)
+  public void values_actionPerformed()
   {
 
     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
@@ -182,6 +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() );
@@ -200,6 +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
@@ -214,48 +262,19 @@ public class PCAPanel
     jLabel3.setText("z=");
     jPanel2.setBackground(Color.white);
     zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
-    zCombobox.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        zCombobox_actionPerformed(null);
-      }
-    });
+    zCombobox.addItemListener(this);
     yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
-    yCombobox.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        yCombobox_actionPerformed(null);
-      }
-    });
+    yCombobox.addItemListener(this);
     xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
-    xCombobox.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        xCombobox_actionPerformed(null);
-      }
-    });
+    xCombobox.addItemListener(this);
     this.setMenuBar(menuBar1);
     menu1.setLabel("File");
     menu2.setLabel("View");
     labels.setLabel("Labels");
-    labels.addItemListener(new ItemListener()
-    {
-      public void itemStateChanged(ItemEvent itemEvent)
-      {
-        labels_itemStateChanged(itemEvent);
-      }
-    });
+    labels.addItemListener(this);
     values.setLabel("Output Values...");
-    values.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        values_actionPerformed(actionEvent);
-      }
-    });
+    values.addActionListener(this);
+    inputData.setLabel("Input Data...");
     this.add(jPanel2, BorderLayout.SOUTH);
     jPanel2.add(jLabel1, null);
     jPanel2.add(xCombobox, null);
@@ -267,6 +286,8 @@ public class PCAPanel
     menuBar1.add(menu2);
     menu2.add(labels);
     menu1.add(values);
+    menu1.add(inputData);
+    inputData.addActionListener(this);
   }
 
 }