X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=f29f708683f2c81f89be47e2cac823632e9c73dc;hb=21c2deb35c435e6097b0f05c83d21cfdf4929ba2;hp=dfb747f64c91a7e2208ec7eba763bed231265ba2;hpb=e505e1bf357a0df0b6075d36c70032f8341ddfe1;p=jalview.git

diff --git a/help/html/releases.html b/help/html/releases.html
index dfb747f..f29f708 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -47,57 +47,482 @@
     <tr>
       <td width="60" nowrap>
         <div align="center">
-          <strong><a name="Jalview.2.9.1">2.9.1</a><br /> <em>21/6/2016</em></strong>
+          <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>04/10/2016</em></strong>
         </div>
       </td>
       <td><em>General</em>
         <ul>
-            <li><!-- JAL---></li>
-            <li><!-- JAL-192 --->Alignment ruler shows positions relative to reference sequence</li>
+          <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-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 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-1369 --->Store/restore reference sequence in Jalview projects</li>
-             
+          <li>
+            <!-- JAL-2050-->Automatically hide introns when opening a
+            gene/transcript view
+          </li>
+          <li>
+            <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
+            dialog
+          </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 record retrieval via ENA rest API
+          </li>
+          <li>
+            <!-- JAL-2027 -->Support for ENA CDS records with reverse
+            complement operator
+          </li>
+          <li>
+            <!--  JAL-1812 -->Update to groovy-2.4.6-indy - for faster
+            groovy script execution
+          </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-1993 -->Database selection dialog always shown
+            before sequence fetcher is opened
+          </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>
+          <li>
+            <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
+            querying stored in preferences
+          </li>
+          <li>
+            <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
+            search results
+          </li>
+          <li>
+            <!-- JAL-1977-->Tooltips shown on database chooser
+          </li>
+          <li>
+            <!--  JAL-391 -->Reverse complement function in calculate
+            menu for nucleotide sequences
+          </li>
+          <li>
+            <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
+            and feature counts preserves alignment ordering (and
+            debugged for complex feature sets).
+          </li>
+          <li>
+            <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
+            viewing structures with Jalview 2.10
+          </li>
+          <li>
+            <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
+            genome, transcript CCDS and gene ids via the Ensembl and
+            Ensembl Genomes REST API
+          </li>
+          <li>
+            <!-- JAL-2049 -->Protein sequence variant annotation
+            computed for 'sequence_variant' annotation on CDS regions
+            (Ensembl)
+          </li>
+          <li>
+            <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
+            sequences
+          </li>
+          <li>
+            <!-- JAL- -->
+          </li>
+          <li>
+            <!-- JAL- -->
+          </li>
+
+
         </ul> <em>Applet</em>
         <ul>
-            <li><!-- JAL---></li>
+          <li>
+            <!-- JAL--->
+          </li>
         </ul></td>
       <td>
         <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-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-2172,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 -->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>
+            <li>
+              <!-- JAL-2238 -->Cannot create groups on an alignment from
+              from a tree when t-coffee scores are shown
+            </li>
+            <li>
+              <!-- JAL-1836,1967 -->Cannot import and view PDB
+              structures with chains containing negative resnums (4q4h)
+            </li>
+            <li>
+              <!--  JAL-1998 -->ArithmeticExceptions raised when parsing
+              some structures
+            </li>
+            <li>
+              <!--  JAL-1991, JAl-1952 -->'Empty' alignment blocks added
+              to Clustal, PIR and PileUp output
+            </li>
+            <li>
+              <!--  JAL-2008 -->Reordering sequence features that are
+              not visible causes alignment window to repaint
+            </li>
+            <li>
+              <!--  JAL-2006 -->Threshold sliders don't work in
+              graduated colour and colour by annotation row for e-value
+              scores associated with features and annotation rows
+            </li>
+            <li>
+              <!-- JAL-1797 -->amino acid physicochemical conservation
+              calculation should be case independent
+            </li>
+            <li>
+              <!-- JAL-2173 -->Remove annotation also updates hidden
+              columns
+            </li>
+            <li>
+              <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
+              example file (uniref50.fa, feredoxin.fa, unaligned.fa,
+              exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
+            </li>
+            <li>
+              <!-- JAL-2065 -->Null pointer exceptions and redraw
+              problems when reference sequence defined and 'show
+              non-conserved' enabled
+            </li>
+            <li>
+              <!-- JAL-1306 -->Quality and Conservation are now shown on
+              load even when Consensus calculation is disabled
+            </li>
+            <li>
+              <!--  -->
+            </li>
+            <li>
+              <!-- JAL- -->
+            </li>
+            <li>
+              <!-- JAL- -->
+            </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-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>
+            <li>
+              <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
+              dialogs format columns correctly, don't display array
+              data, sort columns according to type
+            </li>
+            <li>
+              <!-- JAL-1975 -->Export complete shown after destination
+              file chooser is cancelled during an image export
+            </li>
+            <li>
+              <!-- JAL-2025 -->Error when querying PDB Service with
+              sequence name containing special characters
+            </li>
+            <li>
+              <!-- JAL-2024 -->Manual PDB structure querying should be
+              case insensitive
+            </li>
+            <li>
+              <!-- JAL-2104 -->Large tooltips with broken HTML
+              formatting don't wrap
+            </li>
+            <li>
+              <!-- JAL-1128 -->Figures exported from wrapped view are
+              truncated so L looks like I in consensus annotation
+            </li>
+            <li>
+              <!-- JAL-2003 -->Export features should only export the
+              currently displayed features for the current selection or
+              view
+            </li>
+            <li>
+              <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
+              after fetching cross-references
+            </li>
+            <li>
+              <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
+              followed in the structure viewer
+            </li>
+            <li>
+              <!-- JAL-2163 -->Titles for individual alignments in
+              splitframe not restored from project
+            </li>
+            <li>
+              <!-- JAL-2145 -->missing autocalculated annotation at
+              trailing end of protein alignment in transcript/product
+              splitview when pad-gaps not enabled by default
+            </li>
+            <li>
+              <!-- JAL-1797 -->amino acid physicochemical conservation
+              is case dependent
+            </li>
+            <li>
+              <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
+              article has been read (reopened issue due to
+              internationalisation problems)
+            </li>
+            <li>
+              <!-- JAL-1960 -->Only offer PDB structures in structure
+              viewer based on sequence name, PDB and Uniprot
+              cross-references
+            </li>
+
+            <li>
+              <!-- JAL-1976 -->No progress bar shown during export of
+              alignment as HTML
+            </li>
+            <li>
+              <!-- JAL-2213,JAL-1856 -->Improved warning messages when
+              DB Ref Fetcher fails to match, or otherwise updates
+              sequence data from external database records.
+            </li>
+            <li>
+              <!-- JAL-2213 -->Structures not always superimposed after
+              multiple structures are shown for one or more sequences.
+            </li>
+            <li>
+              <!-- JAL-1370 -->Reference sequence characters should not
+              be replaced with '.' when 'Show unconserved' format option
+              is enabled.
+            </li>
+            <li>
+              <!-- JAL-1823 -->Cannot specify chain code when entering
+              specific PDB id for sequence
+            </li>
+            <li>
+              <!-- JAL-1944 -->File->Export->.. as doesn't work when
+              'Export hidden sequences' is enabled, but 'export hidden
+              columns' is disabled.
+            </li>
+            <li>
+              <!--JAL-2026-->Best Quality option in structure chooser
+              selects lowest rather than highest resolution structures
+              for each sequence
+            </li>
+            <li>
+              <!-- JAL-1887 -->Incorrect start and end reported for PDB
+              to sequence mapping in 'View Mappings' report
+            </li>
+            <li>
+              <!-- JAL- -->
+            </li>
+            <li>
+              <!-- JAL- -->
+            </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><!--  --></li>
+            <li>
+              <!-- JAL-2151 -->Incorrect columns are selected when
+              hidden columns present before start of sequence
+            </li>
+            <li>
+              <!-- JAL-1986 -->Missing dependencies on applet pages
+              (JSON jars)
+            </li>
+            <li>
+              <!-- JAL-1947 -->Overview pixel size changes when
+              sequences are hidden in applet
+            </li>
+            <li>
+              <!-- JAL-1996 -->Updated instructions for applet
+              deployment on examples pages.
+            </li>
           </ul>
         </div>
       </td>
@@ -138,7 +563,7 @@
           <li>Updated Spanish translations of localized text for
             2.9</li>
         </ul> <em>Application</em>
-      <ul>
+        <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>
@@ -258,7 +683,7 @@
                 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
@@ -743,7 +1168,7 @@
             <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>
@@ -1098,8 +1523,8 @@
             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>
@@ -1374,6 +1799,7 @@
           <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>
@@ -1417,7 +1843,8 @@
             between different screens.</li>
           <li>New preference items for sequence ID tooltip and
             consensus annotation</li>
-          <li>Client to submit sequences and IDs to Envision2 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
@@ -1674,7 +2101,7 @@
           <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
@@ -1703,7 +2130,7 @@
             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>
@@ -1826,6 +2253,7 @@
           <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>
@@ -1841,18 +2269,20 @@
             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>