From 731df4f556602bdfffb0127953c525a38feb0438 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 23 Nov 2016 12:25:32 +0000
Subject: [PATCH] JAL-2325 release notes formatting

---
 help/html/releases.html |  162 +++++++++++++++++++++++++++++++++++++----------
 1 file changed, 127 insertions(+), 35 deletions(-)

diff --git a/help/html/releases.html b/help/html/releases.html
index c958aba..6469c5f 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -52,23 +52,59 @@
         </div>
       </td>
       <td><div align="left">
-	    <em>General</em>
-            <ul>
-	      <li><!-- JAL-98 -->Improved memory usage: sparse arrays used for all consensus calculations</li>
-	      <li><!-- JAL-2177 -->Updated Jmol shipped with applet and desktop to 14.6.4</li>
-          <li><!--  --></li>
-        
+          <em>General</em>
+          <ul>
+            <li>
+              <!-- JAL-98 -->Improved memory usage: sparse arrays used
+              for all consensus calculations
+            </li>
+            <li>
+              <!-- JAL-2177 -->Updated Jmol shipped with applet and
+              desktop to 14.6.4
+            </li>
+            <li>
+              <!--  -->
+            </li>
+
           </ul>
           <em>Application</em>
           <ul>
-        <li><!-- JAL-1723 -->Sequence ID tool tips have been tamed (databases sorted alphabetically, abridged ID sets) </li>
-   	    <li><!-- JAL-2282-->New replacement token for creating URLs <em>just</em> from database cross references. Users with custom links will receive a warning dialog asking them to update their preferences.</li>
-	    <li><!-- JAL-2287-->Cancel button and escape listener on dialog warning user about disconnecting Jalview from a Chimera session</li>
-        <li><!-- JAL-2320-->Jalview's chimera control window closes if the Chimera it is connected to is shut down</li>
-	    <li><!-- JAL-2281-->Custom URL links for database cross-references are matched to database name regardless of case</li>
-	    <li><!-- JAL-1738-->Select highlighted columns menu item and keystroke (B) to mark columns containing highlighted regions from structure selections or results of a Find operation</li>
-        <li><!-- JAL-2284-->Command line option for batch-generation of HTML pages rendering alignment data with the BioJS MSAviewer</li>
-	    
+            <li>
+              <!-- JAL-1723 -->Sequence ID tool tips have been tamed
+              (databases sorted alphabetically, abridged ID sets)
+            </li>
+            <li>
+              <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
+              from database cross references. Users with custom links
+              will receive a warning dialog asking them to update their
+              preferences.
+            </li>
+            <li>
+              <!-- JAL-2287-->Cancel button and escape listener on
+              dialog warning user about disconnecting Jalview from a
+              Chimera session
+            </li>
+            <li>
+              <!-- JAL-2320-->Jalview's chimera control window closes if
+              the Chimera it is connected to is shut down
+            </li>
+            <li>
+              <!-- JAL-2281-->Custom URL links for database
+              cross-references are matched to database name regardless
+              of case
+            </li>
+            <li>
+              <!-- JAL-1738-->Select highlighted columns menu item and
+              keystroke (B) to mark columns containing highlighted
+              regions from structure selections or results of a Find
+              operation
+            </li>
+            <li>
+              <!-- JAL-2284-->Command line option for batch-generation
+              of HTML pages rendering alignment data with the BioJS
+              MSAviewer
+            </li>
+
 
           </ul>
           <em>Applet</em>
@@ -76,47 +112,103 @@
           </ul>
           <em>Build and deployment</em>
           <ul>
-            <li>Updated Jalview's Certum code signing certificate for 2016-2017</li>
+            <li>Updated Jalview's Certum code signing certificate
+              for 2016-2017</li>
           </ul>
-	  </div>
-      </td>
+        </div></td>
       <td>
         <div align="left">
           <em>General</em>
           <ul>
-	    <li><!-- JAL-2286 -->Columns with more than one modal residue are not coloured or thresholded according to percent identity (first observed in Jalview 2.8.2)</li>
-	    <li><!-- JAL-2301 -->Threonine incorrectly reported as not hydrophobic</li>
-	    <li><!-- JAL-2318 -->Updates to documentation pages (above PID threshold, amino acid properties)</li>
-	    <li><!-- JAL-2292 -->Lower case residues in sequences are not reported as mapped to residues in a structure file in the View Mapping report</li>
-        <li><!--JAL-2324 -->Identical features with non-numeric scores could be added multiple times to a sequence</li>
-        
+            <li>
+              <!-- JAL-2286 -->Columns with more than one modal residue
+              are not coloured or thresholded according to percent
+              identity (first observed in Jalview 2.8.2)
+            </li>
+            <li>
+              <!-- JAL-2301 -->Threonine incorrectly reported as not
+              hydrophobic
+            </li>
+            <li>
+              <!-- JAL-2318 -->Updates to documentation pages (above PID
+              threshold, amino acid properties)
+            </li>
+            <li>
+              <!-- JAL-2292 -->Lower case residues in sequences are not
+              reported as mapped to residues in a structure file in the
+              View Mapping report
+            </li>
+            <li>
+              <!--JAL-2324 -->Identical features with non-numeric scores
+              could be added multiple times to a sequence
+            </li>
+
           </ul>
           <em>Application</em>
           <ul>
-	    <li><!-- JAL-2282-->Custom URL links for specific database names without regular expressions also offer links from Sequence ID</li>
-	    <li><!-- JAL-2315-->Removing a single configured link in the URL links pane in Connections preferences doesn't actually update Jalview configuration</li>
-	    <li><!-- JAL-2272-->CTRL-Click on a selected region to open the alignment area popup menu doesn't work on El-Capitan</li>
-	    <li><!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF files with similarly named sequences if dropped onto the alignment</li>
-	    <li><!-- JAL-2312 -->Additional mappings are shown for PDB entries where more chains exist in the PDB accession than are reported in the SIFTS file</li>
-	    <li><!-- JAL-2317-->Certain structures do not get mapped to the structure view when displayed with Chimera</li>
-	    <li><!-- JAL-2317-->No chains shown in the Chimera view panel's View->Show Chains submenu</li>
-        <li><!--JAL-2277 -->Export as HTML with embedded SVG doesn't work for wrapped alignment views</li>
+            <li>
+              <!-- JAL-2282-->Custom URL links for specific database
+              names without regular expressions also offer links from
+              Sequence ID
+            </li>
+            <li>
+              <!-- JAL-2315-->Removing a single configured link in the
+              URL links pane in Connections preferences doesn't actually
+              update Jalview configuration
+            </li>
+            <li>
+              <!-- JAL-2272-->CTRL-Click on a selected region to open
+              the alignment area popup menu doesn't work on El-Capitan
+            </li>
+            <li>
+              <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
+              files with similarly named sequences if dropped onto the
+              alignment
+            </li>
+            <li>
+              <!-- JAL-2312 -->Additional mappings are shown for PDB
+              entries where more chains exist in the PDB accession than
+              are reported in the SIFTS file
+            </li>
+            <li>
+              <!-- JAL-2317-->Certain structures do not get mapped to
+              the structure view when displayed with Chimera
+            </li>
+            <li>
+              <!-- JAL-2317-->No chains shown in the Chimera view
+              panel's View->Show Chains submenu
+            </li>
+            <li>
+              <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
+              work for wrapped alignment views
+            </li>
             <li>
               <!--JAL-2335 -->Disulphide bond features shown as two
               highlighted residues rather than a range in linked
               structure views, and treated correctly when selecting and
               computing trees from features
             </li>
-        <li><!--JAL-2197 -->Rename UI components for running JPred predictions from 'JNet' to 'JPred'</li>
-        <li><!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is corrupted when annotation panel vertical scroll is not at first annotation row</li>
-        <li><!--JAL- --></li>
+            <li>
+              <!--JAL-2197 -->Rename UI components for running JPred
+              predictions from 'JNet' to 'JPred'
+            </li>
+            <li>
+              <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
+              corrupted when annotation panel vertical scroll is not at
+              first annotation row
+            </li>
+            <li>
+              <!--JAL- -->
+            </li>
           </ul>
           <em>Applet</em>
           <ul>
           </ul>
           <em>Build and deployment</em>
           <ul>
-            <li><!-- JAL-2308, -->Failing/passing unit tests</li>
+            <li>
+              <!-- JAL-2308, -->Failing/passing unit tests
+            </li>
           </ul>
           <em>New Known Issues</em>
           <ul>
-- 
1.7.10.2