From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 24 Sep 2012 16:53:09 +0000 (+0100)
Subject: JAL-958 revised applet parameter documentation to standardise on long form 'normalise... 
X-Git-Tag: Jalview_2_9~298
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=37fd8c26efada7832b61e5af5c0d56baa69608c3;p=jalview.git

JAL-958 revised applet parameter documentation to standardise on long form 'normaliseSequenceLogo', but still allow short form for legacy test pages.
---

diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index a03a3e0..106d977 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -512,7 +512,7 @@ pageTracker._trackPageview();
           <td>true of false (default is false)</td>
           <td>When true, shows a sequence logo above the consensus sequence (overlaid above the Consensus Histogram, if visible, with symbols coloured using the alignment's default colourscheme). (<em>since 2.7</em>)</td>
           </tr>
-          <tr><td>normaliseLogo</td>
+          <tr><td>normaliseSequenceLogo</td>
           <td>true of false (default is false)</td>
           <td>When true, all sequence logos will be normalised (all symbol stacks add up to full height of annotation row), rather than being scaled according to the fraction of symbols identical to the consensus. (<em>since 2.8</em>)</td>
           </tr>
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index e0a6a71..64907ac 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -204,7 +204,7 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
 
       showSequenceLogo = applet.getDefaultParameter("showSequenceLogo", showSequenceLogo);
 
-      normaliseSequenceLogo = applet.getDefaultParameter("normaliseSequenceLogo", normaliseSequenceLogo);
+      normaliseSequenceLogo = applet.getDefaultParameter("normaliseSequenceLogo", applet.getDefaultParameter("normaliseLogo", normaliseSequenceLogo));
 
       showGroupConsensus = applet.getDefaultParameter("showGroupConsensus", showGroupConsensus);