X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2FappletParameters.html;h=c880a84c5b30383041cbe2bde6a22a23b1cdd78c;hb=80f48b214af181a923d116e4fa5aa83c32f40bbc;hp=fe29b2e4a0c20dc278423a6136f6fb6a7768c78f;hpb=a22e69eeaf0b0447dc31baaf3ba24ec45a42af18;p=jalview.git

diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index fe29b2e..c880a84 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -187,6 +187,12 @@ the applet can be interacted with <em>via</em> its
             <td>The file to open, must be on same server as the applet.</td>
           </tr>
           <tr> 
+            <td>file2</td>
+            <td>fileName</td>
+            <td>A second file to open. If one file is nucleotide and the other peptide, and at least one peptide sequence
+            is the translation of one of the nucleotide sequences, then alignments will be displayed linked in a split frame (<em>since 2.9</em>).</td>
+          </tr>
+          <tr> 
             <td>sequence1,<br>
               sequence2,<br>
               sequence3</td>
@@ -393,11 +399,14 @@ the applet can be interacted with <em>via</em> its
           <td>1.0 or greater</td>
           <td>Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font. (<em>since 2.5.1</em>)</td>
           </tr>
+          <tr><td>scaleProteinAsCdna</td><td>true or false (default is false)</td>
+          <td>Set true to shown protein residues the same width as their encoding codons. 
+          For use with parameter file2 when showing a split frame of cDNA and protein. (<em>since 2.9</em>)</td></tr>
           <tr><td>centrecolumnlabels</td>
-          <td>true of false (default is false)</td>
+          <td>true or false (default is false)</td>
           <td>When true, text labels associated with a column in the alignment will be shown centered with respect to the column. (<em>since 2.4</em>)</td>
           <tr><td>showUnconserved</td>
-          <td>true of false (default is false)</td>
+          <td>true or false (default is false)</td>
           <td>When true, only gaps and symbols different to the consensus sequence for a column will be shown. Useful for visualizing alignments exhibiting low sequence variation, where it is important to highlight mutations. (<em>since 2.5</em>)</td>
           </tr>
           <tr><td>upperCase</td>
@@ -405,29 +414,29 @@ the applet can be interacted with <em>via</em> its
           <td>Indicate a text style to apply to uppercase sequence symbols. Currently, only <strong>bold</strong> is supported.</td>
           </tr>
           <tr><td>automaticScrolling</td>
-          <td>true of false (default is true)</td>
+          <td>true or false (default is true)</td>
           <td>When true, alignment panels will automatically scroll to show any regions of the alignment highlighted due to javascript events or when mousing over a position in an associated structure. (<em>since 2.6</em>)</td>
           </tr>
           
           <tr><td>showGroupConsensus</td>
-          <td>true of false (default is false)</td>
+          <td>true or false (default is false)</td>
           <td>When true, shows consensus annotation row for any groups on the alignment. (<em>since 2.7</em>)</td>
           </tr>
           
           <tr><td>showGroupConservation</td>
-          <td>true of false (default is false)</td>
+          <td>true or false (default is false)</td>
           <td>When true, shows amino-acid property conservation annotation row for any groups on the alignment. (<em>since 2.7</em>)</td>
           </tr>
           <tr><td>showConsensusHistogram</td>
-          <td>true of false (default is true)</td>
+          <td>true or false (default is true)</td>
           <td>When true, shows the percentage occurence of the consensus symbol for each column as a histogram above the consensus sequence row. (<em>since 2.7</em>)</td>
           </tr>
           <tr><td>showSequenceLogo</td>
-          <td>true of false (default is false)</td>
+          <td>true or 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>normaliseSequenceLogo</td>
-          <td>true of false (default is false)</td>
+          <td>true or 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>
           <tr><td>oninit</td>
