From 733a217d66ba90128f3de972ff2729b73bfbfb0f Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 10 Aug 2017 10:19:29 +0100
Subject: [PATCH 1/1] JAL-2418 reorganised release notes to topic sections
 rather than General/Application/Applet

---
 help/html/releases.html |  478 +++++++++++++++++++++++------------------------
 1 file changed, 230 insertions(+), 248 deletions(-)

diff --git a/help/html/releases.html b/help/html/releases.html
index d2d27db..dc96392 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -74,8 +74,17 @@ li:before {
         </div>
       </td>
       <td><div align="left">
-          <em>General</em>
+          <em>Calculations</em>
           <ul>
+
+            <li>
+              <!-- JAL-1933 -->Occupancy annotation row shows number of
+              ungapped positions in each column of the alignment.
+            </li>
+            <li>
+              <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
+              a calculation dialog box
+            </li>
             <li>
               <!-- JAL-2379 -->Revised implementation of PCA for speed
               and memory efficiency (~30x faster)
@@ -84,22 +93,20 @@ li:before {
               <!-- JAL-2403 -->Revised implementation of sequence
               similarity scores as used by Tree, PCA, Shading Consensus
               and other calculations
-              <ul>
-                <li>
-                  <!-- JAL-2416 -->Score matrices are stored as resource
-                  files within the Jalview codebase
-                <li>
-                  <!-- JAL-2500 -->Trees computed on Sequence Feature
-                  Similarity may have different topology due to
-                  increased precision
-                </li>
-              </ul>
             </li>
             <li>
-              <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
-              a calculation dialog box
+              <!-- JAL-2416 -->Score matrices are stored as resource
+              files within the Jalview codebase
             </li>
             <li>
+              <!-- JAL-2500 -->Trees computed on Sequence Feature
+              Similarity may have different topology due to increased
+              precision
+            </li>
+          </ul>
+          <em>Rendering</em>
+          <ul>
+            <li>
               <!-- JAL-2360,JAL-2371, -->More robust colours and shader
               model for alignments and groups
             </li>
@@ -107,69 +114,52 @@ li:before {
               <!--  JAL-384 -->Custom shading schemes created via groovy
               scripts
             </li>
-            <li>Improved overview window
-              <ul>
-                <li>
-                  <!--  JAL-2526 -->Efficiency improvements for
-                  interacting with alignment and overview windows
-                </li>
-                <li>
-                  <!--  JAL-2491 -->Linked scrolling of CDS/Protein
-                  views via Overview or sequence motif search operations
-                </li>
-                <li>
-                  <!-- JAL-2514 -->Scrolling of wrapped alignment views
-                  via overview
-                </li>
-                <li>
-                  <!-- JAL-2388 -->Hidden columns and sequences can be
-                  omitted in Overview
-                </li>
-                <li>
-                  <!-- JAL-2611 -->Click-drag in visible area allows
-                  fine adjustment of visible position
-                </li>
-              </ul>
+          </ul>
+          <em>Overview</em>
+          <ul>
+            <li>
+              <!--  JAL-2526 -->Efficiency improvements for interacting
+              with alignment and overview windows
             </li>
             <li>
-              <!-- JAL-2535 -->Posterior probability annotation from
-              Stockholm files imported as sequence associated annotation
+              <!--  JAL-2491 -->Linked scrolling of CDS/Protein views
+              via Overview or sequence motif search operations
             </li>
             <li>
-              <!-- JAL-2533 -->Sequence names don't include file
-              extension when importing structure files without embedded
-              names or PDB accessions
+              <!-- JAL-2514 -->Scrolling of wrapped alignment views via
+              overview
             </li>
             <li>
-              <!-- JAL-2547 -->Amend sequence features dialog box can be
-              opened by double clicking gaps within sequence feature
-              extent
+              <!-- JAL-2388 -->Hidden columns and sequences can be
+              omitted in Overview
             </li>
             <li>
-              <!-- JAL-2631 -->Graduated feature colour style example
-              included in the example feature file
+              <!-- JAL-2611 -->Click-drag in visible area allows fine
+              adjustment of visible position
             </li>
+          </ul>
+
+          <em>Data import/export</em>
+          <ul>
             <li>
-              <!-- JAL-1933 -->Occupancy annotation row shows number of
-              ungapped positions in each column of the alignment.
+              <!-- JAL-2535 -->Posterior probability annotation from
+              Stockholm files imported as sequence associated annotation
             </li>
             <li>
-              <!-- JAL-2533 -->File extension pruned from Sequence ID
-              for sequences derived from structure files without
-              embedded database accession
+              <!-- JAL-2507 -->More robust per-sequence positional
+              annotation input/output via stockholm flatfile
             </li>
             <li>
-              <!-- JAL-1476 -->Status bar message shown when not enough
-              aligned positions were available to create a 3D structure
-              superposition.
+              <!-- JAL-2533 -->Sequence names don't include file
+              extension when importing structure files without embedded
+              names or PDB accessions
             </li>
             <li>
-              <!-- JAL-2507 -->More robust per-sequence positional
-              annotation input/output via stockholm flatfile
+              <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
+              format sequence substitution matrices
             </li>
-
           </ul>
-          <em>Application</em>
+          <em>User Interface</em>
           <ul>
             <li>
               <!-- JAL-2447 --> Experimental Features Checkbox in
@@ -177,25 +167,21 @@ li:before {
               the application.
             </li>
             <li>
-              <!-- JAL-1476 -->Warning in alignment status bar when
-              there are not enough columns to superimpose structures in
-              Chimera
-            </li>
-            <li>
-              <!-- JAL-1596 -->Faster Chimera/Jalview communication by
-              file-based command exchange
-            </li>
-            <li>
-              <!-- JAL-2316, -->URLs for viewing database
-              cross-references provided by identifiers.org and the
-              EMBL-EBI's MIRIAM DB
+              <!-- JAL-2547 -->Amend sequence features dialog box can be
+              opened by double clicking gaps within sequence feature
+              extent
             </li>
             <li>
-              <!-- JAL-2549 -->Updated JABAWS client to v2.2
+              <!-- JAL-1476 -->Status bar message shown when not enough
+              aligned positions were available to create a 3D structure
+              superposition.
             </li>
+          </ul>
+          <em>3D Structure</em>
+          <ul>
             <li>
-              <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
-              format sequence substitution matrices
+              <!-- JAL-1596 -->Faster Chimera/Jalview communication by
+              file-based command exchange
             </li>
             <li>
               <!-- JAL-2375 -->Structure chooser automatically shows
@@ -207,56 +193,72 @@ li:before {
               the Jalview project rather than downloaded again when the
               project is reopened.
             </li>
-
-          </ul>
-          <em>Experimental features</em>
-          <ul>
             <li>
               <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
               to transfer Chimera's structure attributes as Jalview
-              features, and vice-versa.
+              features, and vice-versa (<strong>Experimental
+                Feauture</strong>)
             </li>
           </ul>
-          <em>Applet</em>
+          <em>Web Services</em>
           <ul>
             <li>
-              <!--  -->
+              <!-- JAL-2549 -->Updated JABAWS client to v2.2
+            </li>
+            <li>
+              <!-- JAL-2316, -->URLs for viewing database
+              cross-references provided by identifiers.org and the
+              EMBL-EBI's MIRIAM DB
             </li>
           </ul>
-          <em>Test Suite</em>
+
+          <em>Scripting</em>
           <ul>
             <li>
-              <!--  JAL-2474 -->Added PrivilegedAccessor to test suite
+              <!-- JAL-2344 -->FileFormatI interface for describing and
+              identifying file formats (instead of String constants)
             </li>
             <li>
-              <!-- JAL-2326 -->Prevent or clear modal dialogs raised
-              during tests
+              <!-- JAL-2228 -->FeatureCounter script refactored for
+              efficiency when counting all displayed features (not
+              backwards compatible with 2.10.1)
+            </li>
+          </ul>
+          <em>Example files</em>
+          <ul>
+            <li>
+              <!-- JAL-2631 -->Graduated feature colour style example
+              included in the example feature file
+            </li>
+          </ul>
+          <em>Documentation</em>
+          <ul>
+            <li>
+              <!-- 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>
+          </ul>
+          <em>Test Suite</em>
+          <ul>
+            <li>
               <!-- JAL-2485, -->External service integration tests for
               Uniprot REST Free Text Search Client
             </li>
             <li>
-              <!--  --> <em>Scripting</em>
-              <ul>
-                <li>
-                  <!-- JAL-2344 -->FileFormatI interface for describing
-                  and identifying file formats (instead of String
-                  constants)
-                </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>
+              <!--  JAL-2474 -->Added PrivilegedAccessor to test suite
+            </li>
+            <li>
+              <!-- JAL-2326 -->Prevent or clear modal dialogs raised
+              during tests
+            </li>
           </ul>
         </div></td>
       <td><div align="left">
-          <em>General</em>
+          <em>Calculations</em>
           <ul>
             <li>
               <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
@@ -285,15 +287,24 @@ li:before {
               Sequence Feature Similarity.
             </li>
             <li>
+              <!-- JAL-2377 -->PCA calculation could hang when
+              generating output report when working with highly
+              redundant alignments
+            </li>
+            <li>
+              <!-- JAL-2544 --> Sort by features includes features to
+              right of selected region when gaps present on right-hand
+              boundary
+            </li>
+          </ul>
+          <em>User Interface</em>
+          <ul>
+            <li>
               <!-- JAL-2346 -->Reopening Colour by annotation dialog
               doesn't reselect a specific sequence's associated
               annotation after it was used for colouring a view
             </li>
             <li>
-              <!-- JAL-2430 -->Hidden regions in alignment views are not
-              coloured in linked structure views
-            </li>
-            <li>
               <!-- JAL-2419 -->Current selection lost if popup menu
               opened on a region of alignment without groups
             </li>
@@ -310,38 +321,11 @@ li:before {
               hidden regions results in incorrect hidden regions
             </li>
             <li>
-              <!-- JAL-2377 -->PCA calculation could hang when
-              generating output report when working with highly
-              redundant alignments
-            </li>
-            <li>
-              <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours with
-              lightGray or darkGray via features file (but can specify lightgray)
-            </li>
-            <li>
-              <!-- JAL-2421 -->Overview window visible region moves
-              erratically when hidden rows or columns are present
-            </li>
-            <li>
-              <!-- JAL-2362 -->Per-residue colourschemes applied via the
-              Structure Viewer's colour menu don't correspond to
-              sequence colouring
-            </li>
-            <li>
-              <!-- JAL-2405 -->Protein specific colours only offered in
-              colour and group colour menu for protein alignments
-            </li>
-            <li>
               <!-- JAL-2386 -->'Apply to all groups' setting when
               changing colour does not apply Conservation slider value
               to all groups
             </li>
             <li>
-              <!-- JAL-2385 -->Colour threshold slider doesn't update to
-              reflect currently selected view or group's shading
-              thresholds
-            </li>
-            <li>
               <!-- JAL-2373 -->Percentage identity and conservation menu
               items do not show a tick or allow shading to be disabled
             </li>
@@ -354,17 +338,12 @@ li:before {
               gaps before start of features
             </li>
             <li>
-              <!-- JAL-2576 -->Very large alignments take a long time to
-              load
-            </li>
-            <li>
               <!-- JAL-2623 -->Graduated feature colour threshold not
               restored to UI when feature colour is edited
             </li>
             <li>
-              <!-- JAL-2624 -->Feature colour thresholds not respected
-              when rendered on overview and structures when opacity at
-              100%
+              <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
+              a time when scrolling vertically in wrapped mode.
             </li>
             <li>
               <!-- JAL-2630 -->Structure and alignment overview update
@@ -372,10 +351,6 @@ li:before {
               dialog box
             </li>
             <li>
-              <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
-              a time when scrolling vertically in wrapped mode.
-            </li>
-            <li>
               <!-- JAL-2034 -->Overview window doesn't always update
               when a group defined on the alignment is resized
             </li>
@@ -383,19 +358,16 @@ li:before {
               <!-- JAL-2605 -->Mouseovers on left/right scale region in
               wrapped view result in positional status updates
             </li>
+
             <li>
-              <!-- JAL-2563 -->Status bar shows position for ambiguous
-              amino acid and nucleotide symbols
+              <!-- JAL-2563 -->Status bar doesn't show position for
+              ambiguous amino acid and nucleotide symbols
             </li>
             <li>
               <!-- JAL-2602 -->Copy consensus sequence failed if
               alignment included gapped columns
             </li>
             <li>
-              <!-- JAL-2589 -->User defined gap colour not shown in
-              overview when features overlaid on alignment
-            </li>
-            <li>
               <!-- JAL-2473 -->Minimum size set for Jalview windows so
               widgets don't permanently disappear
             </li>
@@ -405,19 +377,10 @@ li:before {
               T-Coffee column reliability scores)
             </li>
             <li>
-              <!-- 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-2544 --> Sort by features includes features to
-              right of selected region when gaps present on right-hand
-              boundary
-            </li>
-            <li>
               <!-- JAL-2504 -->Features created with 'New feature'
               button from a Find inherit previously defined feature type
               rather than the Find query string
@@ -427,19 +390,6 @@ 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
-            </li>
-            <li>
-              <!-- 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
-            </li>
-            <li>
               <!-- JAL-2437 -->Hiding sequences at bottom of alignment
               and then revealing them reorders sequences on the
               alignment
@@ -454,37 +404,113 @@ li:before {
               Linux
             </li>
             <li>
-              <!-- JAL -->
+              <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
+              only excluded gaps in current sequence and ignored
+              selection.
             </li>
+          </ul>
+          <em>Rendering</em>
+          <ul>
             <li>
-              <!-- JAL -->
+              <!-- JAL-2430 -->Hidden regions in alignment views are not
+              coloured in linked structure views
             </li>
             <li>
-              <!-- JAL -->
+              <!-- JAL-2421 -->Overview window visible region moves
+              erratically when hidden rows or columns are present
             </li>
-          </ul>
-          <strong>Documentation</strong>
-          <ul>
             <li>
-              <!-- JAL-2339 -->Release notes reformatted for readibility
-              with the built-in Java help viewer
+              <!-- JAL-2362 -->Per-residue colourschemes applied via the
+              Structure Viewer's colour menu don't correspond to
+              sequence colouring
             </li>
             <li>
-              <!-- JAL-1644 -->Find documentation updated with 'search
-              sequence description' option
+              <!-- JAL-2405 -->Protein specific colours only offered in
+              colour and group colour menu for protein alignments
+            </li>
+            <li>
+              <!-- JAL-2385 -->Colour threshold slider doesn't update to
+              reflect currently selected view or group's shading
+              thresholds
+            </li>
+            <li>
+              <!-- JAL-2624 -->Feature colour thresholds not respected
+              when rendered on overview and structures when opacity at
+              100%
+            </li>
+            <li>
+              <!-- JAL-2589 -->User defined gap colour not shown in
+              overview when features overlaid on alignment
             </li>
           </ul>
-          <em>Application</em>
+          <em>Data import/export</em>
           <ul>
             <li>
-              <!-- JAL-2225 -->Sequence Database chooser doesn't show
-              available databases panel on Linux
+              <!-- JAL-2576 -->Very large alignments take a long time to
+              load
+            </li>
+            <li>
+              <!-- 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
+            </li>
+            <li>
+              <!-- JAL-2509 -->Secondary structure arrows for [] and {}
+              not shown in correct direction for simple pseudoknots
+            </li>
+            <li>
+              <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
+              with lightGray or darkGray via features file (but can
+              specify lightgray)
+            </li>
+            <li>
+              <!--  JAL-2383 -->Above PID colour threshold not recovered
+              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>
+            <li>
+              <!-- JAL-2520 -->Structures loaded via URL are saved in
+              Jalview Projects rather than fetched via URL again when
+              the project is loaded and the structure viewed
             </li>
+          </ul>
+          <em>Web Services</em>
+          <ul>
             <li>
               <!-- JAL-2519 -->EnsemblGenomes example failing after
               release of Ensembl v.88
             </li>
             <li>
+              <!--  JAL-2366 -->Proxy server address and port always
+              appear enabled in Preferences->Connections
+            </li>
+            <li>
+              <!--  JAL-2461 -->DAS registry not found exceptions
+              removed from console output
+            </li>
+            <li>
+              <!-- JAL-2582 -->Cannot retrieve protein products from
+              Ensembl by Peptide ID
+            </li>
+            <li>
+              <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
+              created from SIFTs, and spurious 'Couldn't open structure
+              in Chimera' errors raised after April 2017 update (problem
+              due to 'null' string rather than empty string used for
+              residues with no corresponding PDB mapping).
+            </li>
+          </ul>
+          <em>Application UI</em>
+          <ul>
+            <li>
               <!-- JAL-2361 -->User Defined Colours not added to Colour
               menu
             </li>
@@ -515,10 +541,6 @@ li:before {
               selection menu changes colours of alignment views
             </li>
             <li>
-              <!--  JAL-2366 -->Proxy server address and port always
-              appear enabled in Preferences->Connections
-            </li>
-            <li>
               <!-- JAL-2426 -->Spurious exceptions in console raised
               from alignment calculation workers after alignment has
               been closed
@@ -536,24 +558,6 @@ li:before {
               shown again after pressing 'Cancel'
             </li>
             <li>
-              <!--  JAL-2461 -->DAS registry not found exceptions
-              removed from console output
-            </li>
-            <li>
-              <!--  JAL-2383 -->Above PID colour threshold not recovered
-              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>
-            <li>
-              <!-- JAL-2520 -->Structures loaded via URL are saved in
-              Jalview Projects rather than fetched via URL again when
-              the project is loaded and the structure viewed
-            </li>
-            <li>
               <!-- JAL-1256 -->Trackpad horizontal scroll gesture
               adjusts start position in wrap mode
             </li>
@@ -562,37 +566,18 @@ li:before {
               ambiguous amino acids
             </li>
             <li>
-              <!-- JAL-2291 -->Hide insertions in PopUp menu excludes
-              gaps in selection, current sequence and only within
-              selected columns
-            </li>
-            <li>
-              <!-- JAL-2582 -->Cannot retrieve protein products from
-              Ensembl by Peptide ID
-            </li>
-            <li>
               <!-- JAL-2431 -->cDNA Consensus annotation not shown in
               CDS/Protein view after CDS sequences added for aligned
               proteins
             </li>
             <li>
-              <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
-              created from SIFTs, and spurious 'Couldn't open structure
-              in Chimera' errors raised after April 2017 update (problem
-              due to 'null' string rather than empty string used for
-              residues with no corresponding PDB mapping).
+              <!-- JAL-2592 -->User defined colourschemes called 'User
+              Defined' don't appear in Colours menu
             </li>
-            <li><!-- JAL-2592 -->User defined colourschemes called 'User Defined' don't appear in Colours menu</li>
-            <li>
-
-
           </ul>
           <em>Applet</em>
           <ul>
             <li>
-              <!-- JAL- -->
-            </li>
-            <li>
               <!-- JAL-2468 -->Switching between Nucleotide and Protein
               score models doesn't always result in an updated PCA plot
             </li>
@@ -610,6 +595,23 @@ li:before {
               colourscheme
             </li>
           </ul>
+          <em>Test Suite</em>
+          <ul>
+            <li>
+              <!-- JAL-2314 -->Unit test failure:
+              jalview.ws.jabaws.RNAStructExportImport setup fails
+            </li>
+            <li>
+              <!-- JAL-2307 -->Unit test failure:
+              jalview.ws.sifts.SiftsClientTest due to compatibility
+              problems with deep array comparison equality asserts in
+              successive versions of TestNG
+            </li>
+            <li>
+              <!-- JAL-2479 -->Relocated StructureChooserTest and
+              ParameterUtilsTest Unit tests to Network suite
+            </li>
+          </ul>
           <em>New Known Issues</em>
           <ul>
             <li>
@@ -631,27 +633,7 @@ li:before {
               to mark columns containing highlighted regions.
             </li>
           </ul>
-          <em>Test Suite</em>
-          <ul>
-            <li>
-              <!-- JAL-2314 -->Unit test failure:
-              jalview.ws.jabaws.RNAStructExportImport setup fails
-            </li>
-            <li>
-              <!-- JAL-2307 -->Unit test failure:
-              jalview.ws.sifts.SiftsClientTest due to compatibility
-              problems with deep array comparison equality asserts in
-              successive versions of TestNG
-            </li>
-            <li>
-              <!-- JAL-2479 -->Relocated StructureChooserTest and
-              ParameterUtilsTest Unit tests to Network suite
-            </li>
-
-          </ul>
-        </div>
-    
-    <tr>
+        </div><tr>
       <td width="60" nowrap>
         <div align="center">
           <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
-- 
1.7.10.2