X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=9339b33d5644db3785b74ec41187bc1f4bbb51c7;hb=0d50ab3cdf86523b239e7dcccc551164ed197467;hp=7f1b627d25ed950ac0666d0266d1ae6b48ccbfca;hpb=3ee1b42bc43d39be3978078ac8c6529649665097;p=jalview.git

diff --git a/help/html/releases.html b/help/html/releases.html
index 7f1b627..9339b33 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -47,47 +47,180 @@
     <tr>
       <td width="60" nowrap>
         <div align="center">
-          <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
-            <em>6/10/2015</em></strong>
+          <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>27/9/2016</em></strong>
         </div>
       </td>
+      <td><em>General</em>
+        <ul>
+            <li><!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.</li>
+            <li><!-- JAL-192 --->Alignment ruler shows positions relative to reference sequence</li>
+            <li><!-- JAL-2202 -->Position/residue shown in status bar when mousing over sequence associated annotation</li>
+            <li><!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket' for manual entry</li>
+            <li><!-- JAL-2214 -->RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column</li>
+            <li><!-- JAL-2092 -->Feature settings popup menu options for showing or hiding columns containing a feature</li>
+            <li><!-- JAL-1557 -->Edit selected group by double clicking on group and sequence associated annotation labels</li>
+            <li><!-- JAL-2236 -->Sequence name added to annotation label in select/hide columns by annotation and colour by annotation dialogs</li>
+        </ul> <em>Application</em>
+        <ul>
+            <li><!-- JAL---></li>
+            <li><!-- JAL---></li>
+            <li><!-- JAL---></li>
+            <li><!-- JAL---></li>
+            <li><!--  JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein structure mappings with the EMBL-EBI PDBe SIFTS database</li>          
+            <li><!-- JAL-2079 -->Updated download sites used for Rfam and Pfam sources to xfam.org</li>
+            <li><!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher</li>
+            <li><!-- JAL-2123 -->Show residue labels in Chimera when mousing over sequences in Jalview</li>
+            <li><!-- JAL-2027-->Support for reverse-complement coding regions in ENA and EMBL</li>
+            <li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for ENA record retrieval</li>
+            <li><!-- JAL-2027 -->Support for ENA CDS records with reverse complement operator</li>
+            <li><!--  JAL-1812 -->New 'execute Groovy script' option in an alignment window's Calculate menu</li>
+            <li><!--  JAL-1812 -->Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode</li>
+            <li><!--  JAL-2068 -->Support for creating new alignment calculation workers from groovy scripts</li>
+            <li><!-- JAL-1369 --->Store/restore reference sequence in Jalview projects</li>
+            <li><!-- JAL-1803 -->Chain codes for a sequence's PDB associations are now saved/restored from project</li>
+            <li><!-- JAL-2183 -->Double click on an entry in Jalview's database chooser opens a sequence fetcher</li>
+            <li><!-- JAL-1563 -->Free-text search client for UniProt using the UniProt REST API</li>
+            <li><!-- JAL-2168 -->-nonews command line parameter to prevent the news reader opening</li>
+                    
+             
+        </ul> <em>Applet</em>
+        <ul>
+            <li><!-- JAL---></li>
+        </ul></td>
       <td>
-      <em>General</em>
-      <ul>
-            <li>Updated Spanish translations of localized text for 2.9</li>
-      </ul>
-      <em>Application</em><ul>
-      <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
-      <li>Signed OSX InstallAnywhere installer</li></ul>
-        <em>Applet</em>
-        <ul><li>Split frame example added to applet examples page</li>
-            </ul>
+        <div align="left">
+          <em>General</em>
+          <ul>
+            <li><!-- JAL-2077 -->reinstate CTRL-click for opening pop-up menu on OSX</li>
+            <li><!-- JAL-2018-->Export features in Jalview format (again) includes graduated colourschemes</li>
+            <li><!-- JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
+            <li><!-- JAL-2053-->Hidden column markers not always rendered at right of alignment window</li>
+            <li><!-- JAL-2067, JAL-  -->Tidied up links in help file table of contents</li>
+            <li><!-- JAL-2072  -->Feature based tree calculation not shown for DNA alignments</li>
+            <li><!-- JAL-2075  -->Hidden columns ignored during feature based tree calculation</li>
+            <li><!-- JAL-2065  -->Alignment view stops updating when show unconserved enabled for group on alignment</li>
+            <li><!--  JAL-2086  -->Cannot insert gaps into sequence when set as reference</li>
+            <li><!-- JAL-2146 -->Alignment column in status incorrectly shown as &quot;Sequence position&quot; when mousing over annotation</li>
+            <li><!--  JAL-2099 -->Incorrect column numbers in ruler when hidden columns present</li>
+            <li><!--  JAL-1577 -->Colour by RNA Helices not enabled when user created annotation added to alignment</li>
+            <li><!-- JAL-1841 -->RNA Structure consensus only computed for '()' base pair annotation</li>
+            <li><!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus</li>
+            <li><!-- JAL-2174-->Extend selection with columns containing feature not working</li>
+            <li><!-- JAL-2275 -->Pfam format writer puts extra space at beginning of sequence</li>            
+            <li><!-- JAL-1827 -->Incomplete sequence extracted from pdb entry 3a6s </li>
+            
+          </ul>
+          <em>Application</em>
+          <ul>
+            <li><!-- JAL-1944 not yet fixed Error thrown when exporting a view with hidden sequences as flat-file alignment--></li>
+            <li><!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms</li>
+            <li><!-- JAL-1552-->URLs and links can imported by drag'n'drop on OSX webstart</li>
+            <li><!-- JAL-2030-->InstallAnywhere distribution fails when launching Chimera</li>
+            <li><!-- JAL-2080-->Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)</li>
+            <li><!--  JAL-2085  -->Cannot save project when view has a reference sequence defined</li>
+            <li><!--  JAL-1011  -->Columns are suddenly selected in other alignments and views when revealing hidden columns</li>
+            <li><!--  JAL-1989  -->Hide columns not mirrored in complement view in a cDNA/Protein splitframe</li>
+            <li><!--  JAL-1369 -->Cannot save/restore representative sequence from project when only one sequence is represented</li>
+            <li><!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option in Structure Chooser</li>
+            <li><!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel</li>
+            <li><!-- JAL-1962 -->View mapping in structure view shows mappings between sequence and all chains in a PDB file</li>                        
+            <!--  may exclude, this is an external service stability issue  JAL-1941 /> RNA 3D structure not added via DSSR service</li> -->
+          </ul>
+          <em>Applet</em>
+          <ul>
+            <li><!-- JAL-2151 -->Incorrect columns are selected when hidden columns present before start of sequence</li>
+          </ul>
+        </div>
       </td>
+    </tr>
+    <tr>
+      <td width="60" nowrap>
+        <div align="center">
+          <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
+            <em>16/10/2015</em></strong>
+        </div>
+      </td>
+      <td><em>General</em>
+        <ul>
+          <li>Time stamps for signed Jalview application and applet
+            jars</li>
+        </ul></td>
       <td>
         <div align="left">
-        <em>General</em>
+          <em>Application</em>
+          <ul>
+            <li>Duplicate group consensus and conservation rows
+              shown when tree is partitioned</li>
+            <li>Erratic behaviour when tree partitions made with
+              multiple cDNA/Protein split views</li>
+          </ul>
+        </div>
+      </td>
+    </tr>
+    <tr>
+      <td width="60" nowrap>
+        <div align="center">
+          <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
+            <em>8/10/2015</em></strong>
+        </div>
+      </td>
+      <td><em>General</em>
+        <ul>
+          <li>Updated Spanish translations of localized text for
+            2.9</li>
+        </ul> <em>Application</em>
+      <ul>
+          <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
+          <li>Signed OSX InstallAnywhere installer<br></li>
+          <li>Support for per-sequence based annotations in BioJSON</li>
+        </ul> <em>Applet</em>
+        <ul>
+          <li>Split frame example added to applet examples page</li>
+        </ul></td>
+      <td>
+        <div align="left">
+          <em>General</em>
           <ul>
-            <li>Mapping of cDNA to protein in split frames incorrect when sequence start > 1</li>
-            <li>Broken images in filter column by annotation dialog documentation</li>
+            <li>Mapping of cDNA to protein in split frames
+              incorrect when sequence start > 1</li>
+            <li>Broken images in filter column by annotation dialog
+              documentation</li>
             <li>Feature colours not parsed from features file</li>
-            <li>Exceptions and incomplete link URLs recovered when loading a features file containing HTML tags in feature description</li>
-            
+            <li>Exceptions and incomplete link URLs recovered when
+              loading a features file containing HTML tags in feature
+              description</li>
+
           </ul>
-      <em>Application</em><ul>
-            <li>Annotations corrupted after BioJS export and reimport</li>
-            <li>Incorrect sequence limits after Fetch DB References with 'trim retrieved sequences'</li>
-            <li>Incorrect warning about deleting all data when deleting selected columns</li>
-            <li>Patch to build system for shipping properly signed JNLP templates for webstart launch</li>
-            <li>EMBL-PDBe fetcher/viewer dialogs do not offer unreleased structures for download or viewing</li>
-            <li>Tab/space/return keystroke operation of EMBL-PDBe fetcher/viewer dialogs works correctly</li>
-            <li>Disabled 'minimise' button on Jalview windows running on OSX to workaround redraw hang bug</li>
-            <li>Split cDNA/Protein view position and geometry not recovered from jalview project</li>
-            <li>Initial enabled/disabled state of annotation menu sorter 'show autocalculated first/last' corresponds to alignment view</li>
-            </ul>
-      <em>Applet</em><ul>
-            <li>Reorder sequences mirrored in cDNA/Protein split frame</li>
+          <em>Application</em>
+          <ul>
+            <li>Annotations corrupted after BioJS export and
+              reimport</li>
+            <li>Incorrect sequence limits after Fetch DB References
+              with 'trim retrieved sequences'</li>
+            <li>Incorrect warning about deleting all data when
+              deleting selected columns</li>
+            <li>Patch to build system for shipping properly signed
+              JNLP templates for webstart launch</li>
+            <li>EMBL-PDBe fetcher/viewer dialogs do not offer
+              unreleased structures for download or viewing</li>
+            <li>Tab/space/return keystroke operation of EMBL-PDBe
+              fetcher/viewer dialogs works correctly</li>
+            <li>Disabled 'minimise' button on Jalview windows
+              running on OSX to workaround redraw hang bug</li>
+            <li>Split cDNA/Protein view position and geometry not
+              recovered from jalview project</li>
+            <li>Initial enabled/disabled state of annotation menu
+              sorter 'show autocalculated first/last' corresponds to
+              alignment view</li>
+            <li>Restoring of Clustal, RNA Helices and T-Coffee
+              color schemes from BioJSON</li>
+          </ul>
+          <em>Applet</em>
+          <ul>
+            <li>Reorder sequences mirrored in cDNA/Protein split
+              frame</li>
             <li>Applet with Jmol examples not loading correctly</li>
-            </ul>
+          </ul>
         </div>
       </td>
     </tr>
@@ -156,7 +289,7 @@
                 region export in flat file generation</li>
 
               <li>Export alignment views for display with the <a
-                href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
+                href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
 
               <li>Export scrollable SVG in HTML page</li>
               <li>Optional embedding of BioJSON data when exporting
@@ -632,7 +765,7 @@
     <tr>
       <td><div align="center">
           <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
-          <em>30/1/2014</em></strong>
+            <em>30/1/2014</em></strong>
         </div></td>
       <td>
         <ul>
@@ -641,7 +774,7 @@
             <a href="https://www.certum.eu">Certum</a> to the Jalview
             open source project).
           </li>
-          <li>Jalview SRS links replaced by Uniprot and EBI-search
+          <li>Jalview SRS links replaced by UniProt and EBI-search
           </li>
           <li>Output in Stockholm format</li>
           <li>Allow import of data from gzipped files</li>
@@ -996,8 +1129,8 @@
             current built in colourscheme is saved as new scheme</li>
           <li>AlignFrame-&gt;Save in application pops up save
             dialog for valid filename/format</li>
-          <li>Cannot view associated structure for Uniprot sequence</li>
-          <li>PDB file association breaks for Uniprot sequence
+          <li>Cannot view associated structure for UniProt sequence</li>
+          <li>PDB file association breaks for UniProt sequence
             P37173</li>
           <li>Associate PDB from file dialog does not tell you
             which sequence is to be associated with the file</li>
@@ -1271,6 +1404,7 @@
         <ul>
           <li>URL links generated from description line for
             regular-expression based URL links (applet and application)
+
           
           <li>Non-positional feature URL links are shown in link
             menu</li>
@@ -1314,10 +1448,7 @@
             between different screens.</li>
           <li>New preference items for sequence ID tooltip and
             consensus annotation</li>
-          <li>Client to submit sequences and IDs to <a
-            href="webServices/index.html#envision2">Envision2</a>
-            Workflows
-          </li>
+          <li>Client to submit sequences and IDs to Envision2 Workflows</li>
           <li><em>Vamsas Capabilities</em>
             <ul>
               <li>Improved VAMSAS synchronization (Jalview archive
@@ -1574,7 +1705,7 @@
           <li>Save works when Jalview project is default format</li>
           <li>Save as dialog opened if current alignment format is
             not a valid output format</li>
-          <li>Uniprot canonical names introduced for both das and
+          <li>UniProt canonical names introduced for both das and
             vamsas</li>
           <li>Histidine should be midblue (not pink!) in Zappo</li>
           <li>error messages passed up and output when data read
@@ -1603,7 +1734,7 @@
             due to null pointer exceptions</li>
           <li>Secondary structure lines are drawn starting from
             first column of alignment</li>
-          <li>Uniprot XML import updated for new schema release in
+          <li>UniProt XML import updated for new schema release in
             July 2008</li>
           <li>Sequence feature to sequence ID match for Features
             file is case-insensitive</li>
@@ -1725,6 +1856,7 @@
           <li>Cancel button for DAS Feature Fetching
           <li>PCA and PDB Viewers zoom via mouse roller
           <li>User-defined sub-tree colours and sub-tree selection
+
           
           <li>'New Window' button on the 'Output to Text box'
         </ul>
@@ -1739,17 +1871,19 @@
           <li>Fixed Remove Empty Columns Bug (empty columns at end
             of alignment)
           <li>Slowed DAS Feature Fetching for increased robustness.
+
           
           <li>Made angle brackets in ASCII feature descriptions
             display correctly
           <li>Re-instated Zoom function for PCA
           <li>Sequence descriptions conserved in web service
             analysis results
-          <li>Uniprot ID discoverer uses any word separated by
+          <li>UniProt ID discoverer uses any word separated by
             &#8739;
           <li>WsDbFetch query/result association resolved
           <li>Tree leaf to sequence mapping improved
           <li>Smooth fonts switch moved to FontChooser dialog box.
+
           
         </ul>
       </td>