From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 7 Aug 2017 10:56:46 +0000 (+0100)
Subject: JAL-2418 release notes formatting
X-Git-Tag: Release_2_10_3b1~132^2~15^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=dfdd9065b253d59b628b6b778105979c8e10444b;p=jalview.git

JAL-2418 release notes formatting
---

diff --git a/help/html/releases.html b/help/html/releases.html
index 351b055..d1a1c59 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -152,9 +152,10 @@ li:before {
               superposition.
             </li>
             <li>
-            <!-- JAL-2507 -->More robust per-sequence positional annotation input/output via stockholm flatfile
+              <!-- JAL-2507 -->More robust per-sequence positional
+              annotation input/output via stockholm flatfile
             </li>
-            
+
           </ul>
           <em>Application</em>
           <ul>
@@ -185,7 +186,9 @@ li:before {
               format sequence substitution matrices
             </li>
             <li>
-            <!-- JAL-2375 -->Structure chooser automatically shows Cached Structures rather than querying the PDBe if structures are already available for sequences
+              <!-- JAL-2375 -->Structure chooser automatically shows
+              Cached Structures rather than querying the PDBe if
+              structures are already available for sequences
             </li>
             <li>
               <!-- JAL-2520 -->Structures imported via URL are cached in
@@ -230,11 +233,11 @@ li:before {
                   constants)
                 </li>
                 <li>
-                  <!-- JAL-2228 -->FeatureCounter script refactored for efficiency when counting all displayed features (not backwards compatible with 2.10.1)  
-                </li>
-                <li>
-                
+                  <!-- JAL-2228 -->FeatureCounter script refactored for
+                  efficiency when counting all displayed features (not
+                  backwards compatible with 2.10.1)
                 </li>
+                <li></li>
 
 
               </ul>
@@ -265,9 +268,9 @@ li:before {
               restore 2.10.2 mode
             </li>
             <li>
-              <!-- JAL-2424 -->Fixed off-by-one bug that affected scaling
-              of branch lengths for trees computed using Sequence
-              Feature Similarity.
+              <!-- JAL-2424 -->Fixed off-by-one bug that affected
+              scaling of branch lengths for trees computed using
+              Sequence Feature Similarity.
             </li>
             <li>
               <!-- JAL-2346 -->Reopening Colour by annotation dialog
@@ -381,7 +384,8 @@ li:before {
               overview when features overlaid on alignment
             </li>
             <li>
-              <!-- JAL-2473 -->Minimum size set for Jalview windows so widgets don't permanently disappear 
+              <!-- JAL-2473 -->Minimum size set for Jalview windows so
+              widgets don't permanently disappear
             </li>
             <li>
               <!-- JAL-2503 -->Cannot select or filter quantitative
@@ -389,9 +393,13 @@ li:before {
               T-Coffee column reliability scores)
             </li>
             <li>
-              <!-- JAL-2589 -->Gap colours in user-defined colourschemes are not shown   
+              <!-- JAL-2589 -->Gap colours in user-defined colourschemes
+              are not shown
+            </li>
+            <li>
+              <!-- JAL-2594 -->Exception thrown if trying to create a
+              sequence feature on gaps only
             </li>
-            <li><!-- JAL-2594 -->Exception thrown if trying to create a sequence feature on gaps only</li>
             <li>
               <!-- JAL-2544 --> Sort by features includes features to
               right of selected region when gaps present on right-hand
@@ -407,30 +415,40 @@ li:before {
               exporting tree calculated in Jalview
             </li>
             <li>
-            <!-- JAL-2507 -->Per-sequence RNA secondary structures added after a sequence was imported are not written to Stockholm File
+              <!-- JAL-2507 -->Per-sequence RNA secondary structures
+              added after a sequence was imported are not written to
+              Stockholm File
             </li>
             <li>
-            <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost when importing RNA secondary structure via Stockholm 
+              <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
+              when importing RNA secondary structure via Stockholm
             </li>
             <li>
-            <!-- JAL-2509 -->Secondary structure arrows for [] and {} not shown in correct direction for simple pseudoknots 
+              <!-- JAL-2509 -->Secondary structure arrows for [] and {}
+              not shown in correct direction for simple pseudoknots
             </li>
             <li>
-            <!-- JAL-2437 -->Hiding sequences at bottom of alignment and then revealing them reorders sequences on the alignment 
-            </li><li>
-            <!-- JAL-964 -->Group panel in sequence feature settings doesn't update to reflect available set of groups after interactively adding or modifying features
+              <!-- JAL-2437 -->Hiding sequences at bottom of alignment
+              and then revealing them reorders sequences on the
+              alignment
+            </li>
+            <li>
+              <!-- JAL-964 -->Group panel in sequence feature settings
+              doesn't update to reflect available set of groups after
+              interactively adding or modifying features
             </li>
             <li>
-            <!-- JAL-2225 -->Sequence Database chooser unusable on Linux  
+              <!-- JAL-2225 -->Sequence Database chooser unusable on
+              Linux
             </li>
             <li>
-            <!-- JAL --> 
+              <!-- JAL -->
             </li>
             <li>
-            <!-- JAL --> 
+              <!-- JAL -->
             </li>
             <li>
-            <!-- JAL --> 
+              <!-- JAL -->
             </li>
           </ul>
           <strong>Documentation</strong>
@@ -439,15 +457,25 @@ li:before {
               <!-- JAL-2339 -->Release notes reformatted for readibility
               with the built-in Java help viewer
             </li>
-            <li><!-- JAL-1644 -->Find documentation updated with 'search sequence description' option</li>
+            <li>
+              <!-- JAL-1644 -->Find documentation updated with 'search
+              sequence description' option
+            </li>
           </ul>
           <em>Application</em>
           <ul>
             <li>
-            <!-- JAL-2225 -->Sequence Database chooser doesn't show available databases panel on Linux  
+              <!-- JAL-2225 -->Sequence Database chooser doesn't show
+              available databases panel on Linux
+            </li>
+            <li>
+              <!-- JAL-2519 -->EnsemblGenomes example failing after
+              release of Ensembl v.88
+            </li>
+            <li>
+              <!-- JAL-2361 -->User Defined Colours not added to Colour
+              menu
             </li>
-            <li><!-- JAL-2519 -->EnsemblGenomes example failing after release of Ensembl v.88</li>
-            <li><!-- JAL-2361 -->User Defined Colours not added to Colour menu</li>
             <li>
               <!-- JAL-2401 -->Easier creation of colours for all 'Lower
               case' residues (button in colourscheme editor debugged and
@@ -462,9 +490,14 @@ li:before {
               new features are added to alignment
             </li>
             <li>
-            <!-- JAL-2532 -->Cancel in feature settings reverts changes to feature colours via the Amend features dialog
+              <!-- JAL-2532 -->Cancel in feature settings reverts
+              changes to feature colours via the Amend features dialog
+            </li>
+            <li>
+              <!-- JAL-2506 -->Null pointer exception when attempting to
+              edit graduated feature colour via amend features dialog
+              box
             </li>
-            <li><!-- JAL-2506 -->Null pointer exception when attempting to edit graduated feature colour via amend features dialog box</li>
             <li>
               <!-- JAL-2436 -->Structure viewer's View -> Colour By view
               selection menu changes colours of alignment views
@@ -499,10 +532,10 @@ li:before {
               when alignment view imported from project
             </li>
             <li>
-              <!-- JAL-2520,JAL-2465 -->No mappings generated between structure
-              and sequences extracted from structure files imported via
-              URL and viewed in Jmol
-            </li>            
+              <!-- JAL-2520,JAL-2465 -->No mappings generated between
+              structure and sequences extracted from structure files
+              imported via URL and viewed in Jmol
+            </li>
             <li>
               <!-- JAL-2520 -->Structures loaded via URL are saved in
               Jalview Projects rather than fetched via URL again when
@@ -531,7 +564,8 @@ li:before {
               proteins
             </li>
             <li>
-              <!-- JAL-2482 -->SIFTs mappings not created for some structures 
+              <!-- JAL-2482 -->SIFTs mappings not created for some
+              structures
             </li>
 
 
@@ -591,9 +625,10 @@ li:before {
               <!-- JAL-2479 -->Relocated StructureChooserTest and
               ParameterUtilsTest Unit tests to Network suite
             </li>
-            
+
           </ul>
         </div>
+    
     <tr>
       <td width="60" nowrap>
         <div align="center">