From d79235eeb9913fa59f5f4e635a2a8c39d80c775b Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 8 Sep 2015 18:00:42 +0100
Subject: [PATCH] JAL-1645 defictionalising release notes

---
 help/html/releases.html |  126 ++++++++++++++++++++++++-----------------------
 1 file changed, 64 insertions(+), 62 deletions(-)

diff --git a/help/html/releases.html b/help/html/releases.html
index 07d05ea..f8b6d29 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -49,53 +49,48 @@
       <td><em>General</em>
         <ul>
           <li>Linked visualisation and analysis of DNA and Protein
-            alignments:<ul>
-          <li>Translated cDNA alignments shown as split protein and
-            DNA alignment views</li>
-          <li>Codon consensus annotation for linked protein and
-            cDNA alignment views</li>
-          <li>Add cDNA or Protein product sequences to Protein or
-            cDNA alignments</li>
-          <li>Reconstruct linked cDNA alignment from aligned
-            protein sequences</i>
-            </ul></li>
-
-          <li>Update Jmol to v14.2n</li>
-
-          <li>BioJSON data exchange</li>
-
+            alignments:
+            <ul>
+              <li>Translated cDNA alignments shown as split protein
+                and DNA alignment views</li>
+              <li>Codon consensus annotation for linked protein and
+                cDNA alignment views</li>
+              <li>Link cDNA or Protein product sequences by loading
+                them onto Protein or cDNA alignments</li>
+              <li>Reconstruct linked cDNA alignment from aligned
+                protein sequences</li>
+            </ul>
+          </li>
+          <li>Jmol integration updated to Jmol v14.2.14</li>
+          <li>Import and export of Jalview alignment views as <a href="">BioJSON</a></li>
           <li>New alignment annotation file statements for
             reference sequences and marking hidden columns</li>
-
-          <li>Alignments can be sorted by number of RNA helices</li>
-            
-          <li>Assign a reference sequence to highlight
-            variation and consensus analysis</li>
-
+          <li>Assign an alignment reference sequence to highlight
+            variation</li>
           <li>Select or hide columns according to alignment
             annotation</li>
           <li>Find option for locating sequences by
             description</li>
-
           <li>Conserved physicochemical properties shown in amino
             acid conservation row</li>
-
-        </ul> <em>Application</em>
+          <li>Alignments can be sorted by number of RNA helices</li>
+        </ul>
+        <em>Application</em>
         <ul>
           <li>Optional embedding of BioJSON data when exporting
             alignment figures to HTML</li>
-          <li>New Export Settings dialog to control hidden region export in flat file
-            generation</li>
-          <li>New cDNA/Protein analysis capabilities<ul>
-          <li>Get Cross-References should open a Split Frame view
-            with cDNA/Protein</li>
-          <li>Detect when nucleotide sequences and protein
-            sequences are placed in the same alignment</li>
-          <li>Split cDNA/Protein views are saved in Jalview
-            projects</li>
-          <li>support '*' in amino acid sequences to indicate stop
-            codon</li>
-            </ul></li>
+          <li>New Export Settings dialog to control hidden region
+            export in flat file generation</li>
+          <li>New cDNA/Protein analysis capabilities
+            <ul>
+              <li>Get Cross-References should open a Split Frame
+                view with cDNA/Protein</li>
+              <li>Detect when nucleotide sequences and protein
+                sequences are placed in the same alignment</li>
+              <li>Split cDNA/Protein views are saved in Jalview
+                projects</li>
+            </ul>
+          </li>
 
           <li>Use REST API to talk to Chimera</li>
           <li>Selected regions in Chimera are highlighted in linked Jalview windows</li>
@@ -109,8 +104,7 @@
           <li>Pseudoknots displayed as Jalview RNA annotation can be shown in VARNA</li>
 
           <li>changed 'View nucleotide structure' submenu to 'View VARNA 2D Structure'</li>
-          <li>change "View protein structure" menu option to "3D
-            Structure ..."</li>
+          <li>change "View protein structure" menu option to "3D Structure ..."</li>
 
           <li>Make groups for selection uses marked columns as well
             as the active selected region</li>
@@ -119,23 +113,27 @@
             tree building and PCA</li>
 
           <li>Export alignment views for display with the <a
-            href="">BioJS MSAViewer</a></li>
-          <li>Scrollable SVG for HTML export</li>
+            href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
+            
+          <li>Export scrollable SVG in HTML page</li>
 
-          <li>Novel data discovery and retrieval mechanism using
-            PDBe Search API</li>
-          <li>Smarter technique for selecting PDB structures to
-            view in Jalview</li>
+          <li>Interactive free text and structured queries with the
+            PDBe Search API for PDB data retrieval</li>
+          <li>PDBe Search API based discovery and selection of PDB structures to
+            view for a sequence set</li>
 
           <li>JPred4 employed for protein secondary structure
             predictions</li>
           <li>Hide Insertions menu option to hide unaligned columns
             for one or a group of sequences</li>
           <li>Automatically hide insertions in alignments imported from the JPred4 web server</li>
+          <li>(Nearly) Native 'Quaqua' dialogs for browsing file
+            system on OSX<br />LGPL libraries courtesy of <a
+            href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
+          </li>
         </ul> <em>Applet</em>
         <ul>
-          <li>Parameter to enable SplitFrame view</li>? check other
-          parameters in applet ?
+          <li>New parameters to enable SplitFrame view (file2, scaleProteinAsCdna)</li>
           <li>New example demonstrating linked viewing of cDNA and
             Protein alignments</li>
           <li>New layout for applet example pages</li>
@@ -147,16 +145,18 @@
         <li>Github project and web URL for storing BioJsMSA
           Templates</li>
         <li>Jalview's unit tests now managed with TestNG</li></td>
-      <td><em>General</em>
+      <td>
+        <!-- <em>General</em>
         <ul>
-        </ul> <!--  issues resolved --> <em>Application</em>
+        </ul>  -->
+        <!--  issues resolved --> <em>Application</em>
         <ul>
           <li>Escape should close any open find dialogs</li>
-          <li>typo in select-by-features status report</li>
+          <li>Typo in select-by-features status report</li>
           <li>Consensus RNA secondary secondary structure
             predictions are not highlighted in amber</li>
-          <li>missing gap character means v2.7 example file appears
-            unaligned REVIEW</li>
+          <li>Missing gap character in v2.7 example file means
+            alignment appears unaligned when pad-gaps is not enabled</li>
           <li>First switch to RNA Helices colouring doesn't colour
             associated structure views</li>
           <li>ID width preference option is greyed out when auto
@@ -181,12 +181,12 @@
             to a grey/invisible alignment window</li>
           <li>Exported Jpred annotation from a sequence region
             imports to different position</li>
-          <li>Space at beginning of sequence feature mouseover
-            tooltip on some platforms</li>
+          <li>Space at beginning of sequence feature tooltips shown
+            on some platforms</li>
           <li>Chimera viewer 'View | Show Chain' menu is not
             populated</li>
-          <li>'New View' fails with a Null Pointer Exception if
-            Chimera has been opened</li>
+          <li>'New View' fails with a Null Pointer Exception in
+            console if Chimera has been opened</li>
           <li>Mouseover to Chimera not working</li>
           <li>Miscellaneous ENA XML feature qualifiers not
             retrieved</li>
@@ -195,18 +195,14 @@
             either sequence shows on first structure</li>
           <li>'Show annotations' options should not make
             non-positional annotations visible</li>
-          <li>subsequence secondary structure annotation not shown
+          <li>Subsequence secondary structure annotation not shown
             in right place after 'view flanking regions'</li>
           <li>File Save As type unset when current file format is
             unknown</li>
-          <li>Native 'Quaqua' dialogs for saving and loading files
-            on OSX</li>
           <li>Save as '.jar' option removed for saving Jalview
             projects</li>
           <li>Colour by Sequence colouring in Chimera more
             responsive</li>
-          <li>Can disable consensus calculation independently of
-            quality and conservation</li>
           <li>Cannot 'add reference annotation' for a sequence in
             several views on same alignment</li>
           <li>Cannot show linked products for EMBL / ENA records</li>
@@ -242,7 +238,8 @@
           <li>Nucleotide ambiguity codes involving R not recognised</li>
         </ul> <em>Deployment and Documentation</em>
         <ul>
-
+          <li>Applet example pages appear different to the rest of
+            www.jalview.org</li>
         </ul> <em>Application Known issues</em>
         <ul>
           <li>Incomplete sequence extracted from PDB entry 3a6s</li>
@@ -260,13 +257,18 @@
             placed above or below non-autocalculated rows</li>
           <li>Jalview dekstop becomes sluggish at full screen in
             ultra-high resolution</li>
+          <li>Cannot disable consensus calculation independently of
+            quality and conservation</li>
+          <li>Mouseover highlighting between cDNA and protein can
+            become sluggish with more than one splitframe shown</li>
         </ul> <em>Applet Known Issues</em>
         <ul>
           <li>Core PDB parsing code requires Jmol</li>
           <li>Sequence canvas panel goes white when alignment
             window is being resized
           <li>
-        </ul></td>
+        </ul>
+      </td>
     </tr>
     <tr>
 			<td width="60" nowrap>
-- 
1.7.10.2