From 4fe245b8f8ced3dfe7bc225388c6a04202aa1718 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 21 Sep 2005 17:08:56 +0000
Subject: [PATCH] Sequences must be aligned before PCA

---
 src/jalview/appletgui/AlignFrame.java |   18 +++++++++++++++++
 src/jalview/gui/AlignFrame.java       |    8 ++------
 src/jalview/gui/PCAPanel.java         |   34 ++++++++++++++++++++++++++++++++-
 3 files changed, 53 insertions(+), 7 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 1cfddf8..3da1401 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1125,6 +1125,24 @@ public class AlignFrame
 
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
+    //are the sequences aligned?
+    if (!viewport.alignment.isAligned())
+    {
+      SequenceI current;
+      int Width = viewport.getAlignment().getWidth();
+
+      for (int i = 0; i < viewport.getAlignment().getSequences().size();
+           i++)
+      {
+        current = viewport.getAlignment().getSequenceAt(i);
+
+        if (current.getLength() < Width)
+        {
+          current.insertCharAt(Width - 1, viewport.getGapCharacter());
+        }
+      }
+      alignPanel.repaint();
+    }
 
     if ( (viewport.getSelectionGroup() != null &&
           viewport.getSelectionGroup().getSize() < 4 &&
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b6705ad..4d0e1b2 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1149,7 +1149,7 @@ public class AlignFrame
    */
   public void font_actionPerformed(ActionEvent e)
   {
-    FontChooser fc = new FontChooser(alignPanel);
+    new FontChooser(alignPanel);
   }
 
   /**
@@ -1836,11 +1836,7 @@ public class AlignFrame
       return;
     }
 
-      PCAPanel pcaPanel = new PCAPanel(viewport);
-      JInternalFrame frame = new JInternalFrame();
-      frame.setContentPane(pcaPanel);
-      Desktop.addInternalFrame(frame, "Principal component analysis",
-                               400, 400);
+     new PCAPanel(viewport);
   }
 
   /**
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 8685b3e..26f1160 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -29,6 +29,7 @@ import java.awt.event.*;
 
 import java.util.*;
 import javax.swing.JOptionPane;
+import javax.swing.JInternalFrame;
 
 
 /**
@@ -55,26 +56,57 @@ public class PCAPanel extends GPCAPanel implements Runnable
     {
         this.av = av;
 
+        boolean sameLength = true;
+
         if ((av.getSelectionGroup() != null) &&
                 (av.getSelectionGroup().getSize() > 3))
         {
             seqs = new Sequence[av.getSelectionGroup().getSize()];
-
+            int length = av.getSelectionGroup().getSequenceAt(0).getLength();
             for (int i = 0; i < av.getSelectionGroup().getSize(); i++)
             {
                 seqs[i] = av.getSelectionGroup().getSequenceAt(i);
+                if(seqs[i].getLength()!=length)
+                {
+                  sameLength = false;
+                  break;
+                }
             }
         }
         else
         {
             seqs = new Sequence[av.getAlignment().getHeight()];
+            int length = av.alignment.getSequenceAt(0).getLength();
 
             for (int i = 0; i < av.getAlignment().getHeight(); i++)
             {
                 seqs[i] = av.getAlignment().getSequenceAt(i);
+                if(seqs[i].getLength()!=length)
+               {
+                 sameLength = false;
+                 break;
+               }
+
             }
         }
 
+        if (!sameLength)
+        {
+          JOptionPane.showMessageDialog(Desktop.desktop,
+                                        "The sequences must be aligned before calculating PCA.\n" +
+                                        "Try using the Pad function in the edit menu,\n" +
+                                        "or one of the multiple sequence alignment web services.",
+                                        "Sequences not aligned",
+                                        JOptionPane.WARNING_MESSAGE);
+
+          return;
+        }
+
+        JInternalFrame frame = new JInternalFrame();
+        frame.setContentPane(this);
+        Desktop.addInternalFrame(frame, "Principal component analysis",
+                               400, 400);
+
 
         rc = new RotatableCanvas(av);
         add(rc, BorderLayout.CENTER);
-- 
1.7.10.2