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[jalview.git] / src / jalview / gui / PCAPanel.java

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index d1005c2..26f1160 100755 (executable)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -29,6 +29,7 @@ import java.awt.event.*;
 \r
 import java.util.*;\r
 import javax.swing.JOptionPane;\r
+import javax.swing.JInternalFrame;\r
 \r
 \r
 /**\r
@@ -51,31 +52,61 @@ public class PCAPanel extends GPCAPanel implements Runnable
      * @param av DOCUMENT ME!\r
      * @param s DOCUMENT ME!\r
      */\r
-    public PCAPanel(AlignViewport av, SequenceI[] s)\r
+    public PCAPanel(AlignViewport av)\r
     {\r
         this.av = av;\r
 \r
+        boolean sameLength = true;\r
+\r
         if ((av.getSelectionGroup() != null) &&\r
                 (av.getSelectionGroup().getSize() > 3))\r
         {\r
             seqs = new Sequence[av.getSelectionGroup().getSize()];\r
-\r
-            for (int i = 0; i < s.length; i++)\r
+            int length = av.getSelectionGroup().getSequenceAt(0).getLength();\r
+            for (int i = 0; i < av.getSelectionGroup().getSize(); i++)\r
             {\r
                 seqs[i] = av.getSelectionGroup().getSequenceAt(i);\r
+                if(seqs[i].getLength()!=length)\r
+                {\r
+                  sameLength = false;\r
+                  break;\r
+                }\r
             }\r
         }\r
-\r
-        if (s == null)\r
+        else\r
         {\r
             seqs = new Sequence[av.getAlignment().getHeight()];\r
+            int length = av.alignment.getSequenceAt(0).getLength();\r
 \r
             for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
             {\r
                 seqs[i] = av.getAlignment().getSequenceAt(i);\r
+                if(seqs[i].getLength()!=length)\r
+               {\r
+                 sameLength = false;\r
+                 break;\r
+               }\r
+\r
             }\r
         }\r
 \r
+        if (!sameLength)\r
+        {\r
+          JOptionPane.showMessageDialog(Desktop.desktop,\r
+                                        "The sequences must be aligned before calculating PCA.\n" +\r
+                                        "Try using the Pad function in the edit menu,\n" +\r
+                                        "or one of the multiple sequence alignment web services.",\r
+                                        "Sequences not aligned",\r
+                                        JOptionPane.WARNING_MESSAGE);\r
+\r
+          return;\r
+        }\r
+\r
+        JInternalFrame frame = new JInternalFrame();\r
+        frame.setContentPane(this);\r
+        Desktop.addInternalFrame(frame, "Principal component analysis",\r
+                               400, 400);\r
+\r
 \r
         rc = new RotatableCanvas(av);\r
         add(rc, BorderLayout.CENTER);\r
@@ -140,6 +171,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
                                               , "Out of memory",\r
                                               JOptionPane.WARNING_MESSAGE);\r
         System.out.println("PCAPanel: "+er);\r
+        System.gc();\r
 \r
       }\r
 \r