X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=7fe383523a67470c53b9d704d77bab6151b7572a;hb=017eb4e099ff9c7c8982886ece642da1cecb1061;hp=97df517069289c26c848c64a0743eaead955827c;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 97df517..7fe3835 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -23,6 +23,14 @@ public class PCAPanel extends GPCAPanel implements Runnable
   public PCAPanel(AlignViewport av, SequenceI[] s) {
 
     this.av = av;
+    if(av.getSelection().size()>3)
+    {
+      s = new Sequence[av.getSelection().size()];
+      for(int i=0; i<s.length; i++)
+        s[i] = av.getSelection().sequenceAt(i);
+    }
+
+
     if(s==null)
     {
       s = new Sequence[av.getAlignment().getHeight()];
@@ -62,10 +70,12 @@ public class PCAPanel extends GPCAPanel implements Runnable
     Vector points = new Vector();
     float[][] scores = pca.getComponents(top-1,top-2,top-3,100);
 
-    for (int i =0; i < pca.getM().rows; i++ ) {
+    for (int i =0; i < pca.getM().rows; i++ )
+    {
       SequencePoint sp = new SequencePoint(s[i],scores[i]);
       points.addElement(sp);
     }
+
     rc = new RotatableCanvas(av,points,pca.getM().rows);
 
     //rc.printPoints();