updated jalview reference

diff --git a/help/html/index.html b/help/html/index.html
index adc1fa5..a349349 100755 (executable)
--- a/help/html/index.html
+++ b/help/html/index.html
@@ -6,13 +6,14 @@
 <br><br>
 <strong>Jalview Documentation</strong></font>
 <br><br>
-Jalview (2004) is a fast Java multiple alignment editor and analysis tool. It
+Jalview (2009) is a fast Java multiple alignment editor and analysis tool. It
 features many of the functions of <a href="http://www.compbio.dundee.ac.uk/Software/Amas/amas.html">AMAS</a>,
 for the analysis of sub-families and the prediction of functional sites, but is
 fully interactive. (View the <a href="http://www.jalview.org">Jalview homepage</a>).
 <p></p>
-<p> If you use Jalview in your work, please cite the bioinformatics paper: </p>
-<p>Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), "The Jalview
-  Java Alignment Editor", Bioinformatics, 20, 426-7.</p>
+<p> If you use Jalview in your work, please cite the Jalview 2 paper in Bioinformatics: </p>
+<p>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton, G.J (2009), <br>
+   &quot;Jalview version 2: A Multiple Sequence Alignment and Analysis Workbench,&quot;<br>
+   <em>Bioinformatics</em> doi: 10.1093/bioinformatics/btp033
 </body>
 </html>

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index be84f43..4cdf84c 100755 (executable)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -626,9 +626,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
                     + "\nDevelopment managed by The Barton Group, University of Dundee, Scotland, UK.\n"
                     + "\nFor help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\n"
                     + "\nIf  you use Jalview, please cite:"
-                    + "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\""
-                    + "\nBioinformatics,  2004 20;426-7.");
-
+                    + "\nWaterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+            + "\nJalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+            + "\nBioinformatics doi: 10.1093/bioinformatics/btp033");
     JOptionPane.showInternalMessageDialog(Desktop.desktop,
 
     message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);

diff --git a/src/jalview/gui/SplashScreen.java b/src/jalview/gui/SplashScreen.java
index 6fc4262..f4c5e8e 100755 (executable)
--- a/src/jalview/gui/SplashScreen.java
+++ b/src/jalview/gui/SplashScreen.java
@@ -212,11 +212,9 @@ public class SplashScreen extends JPanel implements Runnable
                     50, y += fontSize + 4);
     g
             .drawString(
-                    "If  you use Jalview, please cite: Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004),",
-                    50, y += fontSize + 4);
-    g
-            .drawString(
-                    "\"The Jalview Java Alignment Editor\" Bioinformatics,  2004 20; 426-7.",
-                    50, y += fontSize + 4);
+                    "If  you use Jalview, please cite: ",50,y+=fontSize+4);
+    g.drawString("Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",50,y+=fontSize+4);
+        g.drawString("Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",50,y+=fontSize+4);
+        g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",50,y+=fontSize+4);
   }
 }