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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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<head>
<title>Release History</title>
+<style>
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+ /* separate the items from eachother */
+ margin-left: -3px;
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+</style>
</head>
<body>
-<p><strong>Release History</strong></p>
-<table border="1">
- <tr>
- <td width="60" nowrap>
- <div align="center"><em><strong>Release</strong></em></div>
- </td>
- <td>
- <div align="center"><em><strong>New Features</strong></em></div>
- </td>
- <td>
- <div align="center"><em><strong>Issues Resolved</strong></em></div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
- <em>23/9/2010</em></div>
- </td>
- <td><em>Application</em>
- <ul>
- <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
- <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices (JABAWS)</li>
- <li>Web Services preference tab</li>
- <li>Analysis parameters dialog box and user defined preferences</li>
- <li>Improved speed and layout of Envision2 service menu</li>
- <li>Superpose structures using associated sequence alignment</li>
- <li>Export coordinates and projection as CSV from PCA viewer</li>
- </ul>
- <em>Applet</em>
- <ul>
- <li>enable javascript: execution by the applet via the link out
- mechanism</li>
- </ul>
- <em>Other</em>
- <ul>
- <li>Updated the Jmol Jalview interface to work with Jmol series
- 12</li>
- <li>The Jalview Desktop and JalviewLite applet now require Java
- 1.5</li>
- <li>Allow Jalview feature colour specification for GFF sequence
- annotation files</li>
- <li>New 'colour by label' keword in jalview feature file type
- colour specification</li>
- <li>New Jalview Desktop Groovy API method that allows a script
- to check if it being run in an interactive session or in a batch
- operation from the jalview command line</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>clustalx colourscheme colours Ds preferentially when both
- D+E are present in over 50% of the column</li>
- </ul>
-
- <em>Application</em>
- <ul>
- <li>typo in AlignmentFrame->View->Hide->all but
- selected Regions menu item</li>
- <li>sequence fetcher replaces ',' for ';' when the ',' is part
- of a valid accession ID</li>
- <li>fatal OOM if object retrieved by sequence fetcher runs out
- of memory</li>
- <li>unhandled Out of Memory Error when viewing pca analysis
- results</li>
- <li>InstallAnywhere builds fail to launch on OS X java 10.5
- update 4 (due to apple Java 1.6 update)</li>
- <li>Installanywhere Jalview silently fails to launch</li>
- </ul>
- <em>Applet</em>
- <ul>
- <li>Jalview.getFeatureGroups() raises an
- ArrayIndexOutOfBoundsException if no feature groups are defined.</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
- <em>14/6/2010</em></div>
- </td>
- <td></td>
- <td>
- <ul>
- <li>Alignment prettyprinter doesn't cope with long sequence IDs
- </li>
- <li>clustalx colourscheme colours Ds preferentially when both
- D+E are present in over 50% of the column</li>
- <li>nucleic acid structures retrieved from PDB do not import
- correctly</li>
- <li>More columns get selected than were clicked on when a number
- of columns are hidden</li>
- <li>annotation label popup menu not providing correct
- add/hide/show options when rows are hidden or none are present</li>
- <li>Stockholm format shown in list of readable formats, and
- parser copes better with alignments from RFAM.</li>
- <li>CSV output of consensus only includes the percentage of all
- symbols if sequence logo display is enabled</li>
-
- </ul>
- <em>Applet</em>
- <ul>
- <li>annotation panel disappears when annotation is
- hidden/removed</li>
- </ul>
- <em>Application</em>
- <ul>
- <li>Alignment view not redrawn properly when new alignment
- opened where annotation panel is visible but no annotations are
- present on alignment</li>
- <li>pasted region containing hidden columns is incorrectly
- displayed in new alignment window</li>
- <li>Jalview slow to complete operations when stdout is flooded
- (fix is to close the Jalview console)</li>
- <li>typo in AlignmentFrame->View->Hide->all but
- selected Rregions menu item.</li>
- <li>inconsistent group submenu and Format submenu entry 'Un' or
- 'Non'conserved</li>
- <li>Sequence feature settings are being shared by multiple
- distinct alignments</li>
- <li>group annotation not recreated when tree partition is
- changed</li>
- <li>double click on group annotation to select sequences does
- not propagate to associated trees</li>
- <li>Mac OSX specific issues:
- <ul>
- <li>exception raised when mouse clicked on desktop window
- background</li>
- <li>Desktop menu placed on menu bar and application name set
- correctly</li>
- <li>sequence feature settings not wide enough for the save
- feature colourscheme button</li>
- </ul>
- </li>
- </ul>
- </td>
- </tr>
- <tr>
-
- <td>
- <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
- <em>30/4/2010</em></div>
- </td>
- <td><em>New Capabilities</em>
- <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>
- <li>Linked viewing of nucleic acid sequences and structures</li>
- <li>Automatic Scrolling option in View menu to display the
- currently highlighted region of an alignment.</li>
- <li>Order an alignment by sequence length, or using the average
- score or total feature count for each sequence.</li>
- <li>Shading features by score or associated description</li>
- <li>Subdivide alignment and groups based on identity of selected
- subsequence (Make Groups from Selection).</li>
- <li>New hide/show options including Shift+Control+H to hide
- everything but the currently selected region.</li>
- <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
- </ul>
- <em>Application</em>
- <ul>
- <li>Fetch DB References capabilities and UI expanded to support
- retrieval from DAS sequence sources</li>
- <li>Local DAS Sequence sources can be added via the command line
- or via the Add local source dialog box.</li>
- <li>DAS Dbref and DbxRef feature types are parsed as database
- references and protein_name is parsed as description line (BioSapiens
- terms).</li>
- <li>Enable or disable non-positional feature and database
- references in sequence ID tooltip from View menu in application.</li>
- <!-- <li>New hidden columns and rows and representatives capabilities
- in annotations file (in progress - not yet fully implemented)</li> -->
- <li>Group-associated consensus, sequence logos and conservation
- plots</li>
- <li>Symbol distributions for each column can be exported and
- visualized as sequence logos</li>
- <li>Optionally scale multi-character column labels to fit within
- each column of annotation row<!-- todo for applet --></li>
- <li>Optional automatic sort of associated alignment view when a
- new tree is opened.</li>
- <li>Jalview Java Console</li>
- <li>Better placement of desktop window when moving 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><em>Vamsas Capabilities</em>
- <ul>
- <li>Improved VAMSAS synchronization (jalview archive used to
- preserve views, structures, and tree display settings)</li>
- <li>Import of vamsas documents from disk or URL via command
- line</li>
- <li>Sharing of selected regions between views and with other
- VAMSAS applications (Experimental feature!)</li>
- <li>Updated API to VAMSAS version 0.2</li>
- </ul>
- </li>
- </ul>
- <em>Applet</em>
- <ul>
- <li>Middle button resizes annotation row height</li>
- <li>New Parameters
- <ul>
- <li>sortByTree (true/false) - automatically sort the associated
- alignment view by the tree when a new tree is opened.</li>
- <li>showTreeBootstraps (true/false) - show or hide branch
- bootstraps (default is to show them if available)</li>
- <li>showTreeDistances (true/false) - show or hide branch
- lengths (default is to show them if available)</li>
- <li>showUnlinkedTreeNodes (true/false) - indicate if
- unassociated nodes should be highlighted in the tree view</li>
- <li>heightScale and widthScale (1.0 or more) - increase the
- height or width of a cell in the alignment grid relative to the
- current font size.</li>
- </ul>
- </li>
- <li>Non-positional features displayed in sequence ID tooltip</li>
- </ul>
- <em>Other</em>
- <ul>
- <li>Features format: graduated colour definitions and
- specification of feature scores</li>
- <li>Alignment Annotations format: new keywords for group
- associated annotation (GROUP_REF) and annotation row display
- properties (ROW_PROPERTIES)</li>
- <li>XML formats extended to support graduated feature
- colourschemes, group associated annotation, and profile visualization
- settings.</li>
- </td>
- <td>
- <ul>
- <li>Source field in GFF files parsed as feature source rather
- than description</li>
- <li>Non-positional features are now included in sequence feature
- and gff files (controlled via non-positional feature visibility in
- tooltip).</li>
- <li>URL links generated for all feature links (bugfix)</li>
- <li>Added URL embedding instructions to features file
- documentation.</li>
- <li>Codons containing ambiguous nucleotides translated as 'X' in
- peptide product</li>
- <li>Match case switch in find dialog box works for both sequence
- ID and sequence string and query strings do not have to be in upper
- case to match case-insensitively.</li>
- <li>AMSA files only contain first column of multi-character
- column annotation labels</li>
- <li>Jalview Annotation File generation/parsing consistent with
- documentation (e.g. Stockholm annotation can be exported and
- re-imported)</li>
- <li>PDB files without embedded PDB IDs given a friendly name</li>
- <li>Find incrementally searches ID string matches as well as
- subsequence matches, and correctly reports total number of both.</li>
- <li>Application:
- <ul>
- <li>Better handling of exceptions during sequence retrieval</li>
- <li>Dasobert generated non-positional feature URL link text
- excludes the start_end suffix</li>
- <li>DAS feature and source retrieval buttons disabled when
- fetch or registry operations in progress.</li>
- <li>PDB files retrieved from URLs are cached properly</li>
- <li>Sequence description lines properly shared via VAMSAS</li>
- <li>Sequence fetcher fetches multiple records for all data
- sources</li>
- <li>Ensured that command line das feature retrieval completes
- before alignment figures are generated.</li>
- <li>Reduced time taken when opening file browser for first
- time.</li>
- <li>isAligned check prior to calculating tree, PCA or
- submitting an MSA to JNet now excludes hidden sequences.</li>
- <li>User defined group colours properly recovered from Jalview
- projects.</li>
- </ul>
- </li>
- </ul>
- </td>
-
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.4.0.b2</strong><br>
- 28/10/2009</div>
- </td>
- <td>
- <ul>
- <li>Experimental support for google analytics usage tracking.</li>
- <li>Jalview privacy settings (user preferences and docs).</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
- <li>Exception when feature created from selection beyond length
- of sequence.</li>
- <li>Allow synthetic PDB files to be imported gracefully</li>
- <li>Sequence associated annotation rows associate with all
- sequences with a given id</li>
- <li>Find function matches case-insensitively for sequence ID
- string searches</li>
- <li>Non-standard characters do not cause pairwise alignment to
- fail with exception</li>
- </ul>
- <em>Application Issues</em>
- <ul>
- <li>Sequences are now validated against EMBL database</li>
- <li>Sequence fetcher fetches multiple records for all data
- sources</li>
- </ul>
- <em>InstallAnywhere Issues</em>
- <ul>
- <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
- installAnywhere mechanism)</li>
- <li>Command line launching of JARs from InstallAnywhere version
- (java class versioning error fixed)</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
-
- <div align="center"><strong>2.4</strong><br>
- 27/8/2008</div>
- </td>
- <td><em>User Interface</em>
- <ul>
- <li>Linked highlighting of codon and amino acid from translation
- and protein products</li>
- <li>Linked highlighting of structure associated with residue
- mapping to codon position</li>
- <li>Sequence Fetcher provides example accession numbers and
- 'clear' button</li>
- <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
- <li>Extract score function to parse whitespace separated numeric
- data in description line</li>
- <li>Column labels in alignment annotation can be centred.</li>
- <li>Tooltip for sequence associated annotation give name of
- sequence</li>
- </ul>
- <em>Web Services and URL fetching</em>
- <ul>
- <li>JPred3 web service</li>
- <li>Prototype sequence search client (no public services
- available yet)</li>
- <li>Fetch either seed alignment or full alignment from PFAM</li>
- <li>URL Links created for matching database cross references as
- well as sequence ID</li>
- <li>URL Links can be created using regular-expressions</li>
- </ul>
- <em>Sequence Database Connectivity</em>
- <ul>
- <li>Retrieval of cross-referenced sequences from other databases
- </li>
- <li>Generalised database reference retrieval and validation to
- all fetchable databases</li>
- <li>Fetch sequences from DAS sources supporting the sequence
- command</li>
- </ul>
- <em>Import and Export</em>
- <li>export annotation rows as CSV for spreadsheet import</li>
- <li>Jalview projects record alignment dataset associations, EMBL
- products, and cDNA sequence mappings</li>
- <li>Sequence Group colour can be specified in Annotation File</li>
- <li>Ad-hoc colouring of group in Annotation File using RGB
- triplet as name of colourscheme</li>
- </ul>
- <em>VAMSAS Client capabilities (Experimental)</em>
- <ul>
- <li>treenode binding for VAMSAS tree exchange</li>
- <li>local editing and update of sequences in VAMSAS alignments
- (experimental)</li>
- <li>Create new or select existing session to join</li>
- <li>load and save of vamsas documents</li>
- </ul>
- <em>Application command line</em>
- <ul>
- <li>-tree parameter to open trees (introduced for passing from
- applet)</li>
- <li>-fetchfrom command line argument to specify nicknames of DAS
- servers to query for alignment features</li>
- <li>-dasserver command line argument to add new servers that are
- also automatically queried for features</li>
- <li>-groovy command line argument executes a given groovy script
- after all input data has been loaded and parsed</li>
- </ul>
- <em>Applet-Application data exchange</em>
- <ul>
- <li>Trees passed as applet parameters can be passed to
- application (when using "View in full application")</li>
- </ul>
- <em>Applet Parameters</em>
- <ul>
- <li>feature group display control parameter</li>
- <li>debug parameter</li>
- <li>showbutton parameter</li>
- </ul>
- <em>Applet API methods</em>
- <ul>
- <li>newView public method</li>
- <li>Window (current view) specific get/set public methods</li>
- <li>Feature display control methods</li>
- <li>get list of currently selected sequences</li>
- </ul>
- <em>New Jalview distribution features</em>
- <ul>
- <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
- <li>RELEASE file gives build properties for the latest Jalview
- release.</li>
- <li>Java 1.1 Applet build made easier and donotobfuscate
- property controls execution of obfuscator</li>
- <li>Build target for generating source distribution</li>
- <li>Debug flag for javacc</li>
- <li>.jalview_properties file is documented (slightly) in
- jalview.bin.Cache</li>
- <li>Continuous Build Integration for stable and development
- version of Application, Applet and source distribution</li>
- </ul>
-
- </td>
- <td>
- <ul>
- <li>selected region output includes visible annotations (for
- certain formats)</li>
- <li>edit label/displaychar contains existing label/char for
- editing</li>
- <li>update PDBEntries when DBRefEntries change (vamsas)</li>
- <li>shorter peptide product names from EMBL records</li>
- <li>Newick string generator makes compact representations</li>
- <li>bootstrap values parsed correctly for tree files with
- comments</li>
- <li>pathological filechooser bug avoided by not allowing
- filenames containing a ':'</li>
- <li>Fixed exception when parsing GFF files containing global
- sequence features</li>
- <li>Alignment datasets are finalized only when number of
- references from alignment sequences goes to zero</li>
- <li>Close of tree branch colour box without colour selection
- causes cascading exceptions</li>
- <li>occasional negative imgwidth exceptions</li>
- <li>better reporting of non-fatal warnings to user when file
- parsing fails.</li>
- <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 vamsas</li>
- <li>Histidine should be midblue (not pink!) in Zappo</li>
- <li>error messages passed up and output when data read fails</li>
- <li>edit undo recovers previous dataset sequence when sequence
- is edited</li>
- <li>allow PDB files without pdb ID HEADER lines (like those
- generated by MODELLER) to be read in properly</li>
- <li>allow reading of JPred concise files as a normal filetype</li>
- <li>Stockholm annotation parsing and alignment properties import
- fixed for PFAM records</li>
- <li>Structure view windows have correct name in Desktop window
- list</li>
- <li>annotation consisting of sequence associated scores can be
- read and written correctly to annotation file</li>
- <li>Aligned cDNA translation to aligned peptide works correctly</li>
- <li>Fixed display of hidden sequence markers and non-italic font
- for representatives in Applet</li>
- <li>Applet Menus are always embedded in applet window on Macs.</li>
- <li>Newly shown features appear at top of stack (in Applet)</li>
- <li>Annotations added via parameter not drawn properly 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 July
- 2008</li>
- <li>Sequence feature to sequence ID match for Features file is
- case-insensitive</li>
- <li>Sequence features read from Features file appended to all
- sequences with matching IDs</li>
- <li>PDB structure coloured correctly for associated views
- containing a sub-sequence</li>
- <li>PDB files can be retrieved by applet from Jar files</li>
- <li>feature and annotation file applet parameters referring to
- different directories are retrieved correctly</li>
- <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
- <li>Fixed application hang whilst waiting for splash-screen
- version check to complete</li>
- <li>Applet properly URLencodes input parameter values when
- passing them to the launchApp service</li>
- <li>display name and local features preserved in results
- retrieved from web service</li>
- <li>Visual delay indication for sequence retrieval and sequence
- fetcher initialisation</li>
- <li>updated Application to use DAS 1.53e version of dasobert DAS
- client</li>
- <li>Re-instated Full AMSA support and .amsa file association</li>
- <li>Fixed parsing of JNet Concise annotation <em>sans</em>
- sequences</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.3</strong><br>
- 9/5/07</div>
- </td>
- <td>
- <ul>
- <li>Jmol 11.0.2 integration</li>
- <li>PDB views stored in Jalview XML files</li>
- <li>Slide sequences</li>
- <li>Edit sequence in place</li>
- <li>EMBL CDS features</li>
- <li>DAS Feature mapping</li>
- <li>Feature ordering</li>
- <li>Alignment Properties</li>
- <li>Annotation Scores</li>
- <li>Sort by scores</li>
- <li>Feature/annotation editing in applet</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Headless state operation in 2.2.1</li>
- <li>Incorrect and unstable DNA pairwise alignment</li>
- <li>Cut and paste of sequences with annotation</li>
- <li>Feature group display state in XML</li>
- <li>Feature ordering in XML</li>
- <li>blc file iteration selection using filename # suffix</li>
- <li>Stockholm alignment properties</li>
- <li>Stockhom alignment secondary structure annotation</li>
- <li>2.2.1 applet had no feature transparency</li>
- <li>Number pad keys can be used in cursor mode</li>
- <li>Structure Viewer mirror image resolved</li>
- </ul>
- </td>
-
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.2.1</strong><br>
- 12/2/07</div>
- </td>
- <td>
- <ul>
- <li>Non standard characters can be read and displayed
- <li>Annotations/Features can be imported/exported to the applet
- via textbox
- <li>Applet allows editing of sequence/annotation/group name
- & description
- <li>Preference setting to display sequence name in italics
- <li>Annotation file format extended to allow Sequence_groups to
- be defined
- <li>Default opening of alignment overview panel can be specified
- in preferences
- <li>PDB residue numbering annotation added to associated
- sequences
- </ul>
- </td>
- <td>
- <ul>
- <li>Applet crash under certain Linux OS with Java 1.6 installed
- <li>Annotation file export / import bugs fixed
- <li>PNG / EPS image output bugs fixed
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.2</strong><br>
- 27/11/06</div>
- </td>
- <td>
- <ul>
- <li>Multiple views on alignment
- <li>Sequence feature editing
- <li>"Reload" alignment
- <li>"Save" to current filename
- <li>Background dependent text colour
- <li>Right align sequence ids
- <li>User-defined lower case residue colours
- <li>Format Menu
- <li>Select Menu
- <li>Menu item accelerator keys
- <li>Control-V pastes to current alignment
- <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>
- </td>
- <td>
- <ul>
- <li>New memory efficient Undo/Redo System
- <li>Optimised symbol lookups and conservation/consensus
- calculations
- <li>Region Conservation/Consensus recalculated after edits
- <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>WsDbFetch query/result association resolved
- <li>Tree leaf to sequence mapping improved
- <li>Smooth fonts switch moved to FontChooser dialog box.
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.1.1</strong><br>
- 12/9/06</div>
- </td>
- <td>
- <ul>
- <li>Copy consensus sequence to clipboard</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Image output - rightmost residues are rendered if sequence
- id panel has been resized</li>
- <li>Image output - all offscreen group boundaries are rendered</li>
- <li>Annotation files with sequence references - all elements in
- file are relative to sequence position</li>
- <li>Mac Applet users can use Alt key for group editing</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.1</strong><br>
- 22/8/06</div>
- </td>
- <td>
- <ul>
- <li>MAFFT Multiple Alignment in default Web Service list</li>
- <li>DAS Feature fetching</li>
- <li>Hide sequences and columns</li>
- <li>Export Annotations and Features</li>
- <li>GFF file reading / writing</li>
- <li>Associate structures with sequences from local PDB files</li>
- <li>Add sequences to exisiting alignment</li>
- <li>Recently opened files / URL lists</li>
- <li>Applet can launch the full application</li>
- <li>Applet has transparency for features (Java 1.2 required)</li>
- <li>Applet has user defined colours parameter</li>
- <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Redundancy Panel reinstalled in the Applet</li>
- <li>Monospaced font - EPS / rescaling bug fixed</li>
- <li>Annotation files with sequence references bug fixed</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.08.1</strong><br>
- 2/5/06</div>
- </td>
- <td>
- <ul>
- <li>Change case of selected region from Popup menu</li>
- <li>Choose to match case when searching</li>
- <li>Middle mouse button and mouse movement can compress / expand
- the visible width and height of the alignment</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Annotation Panel displays complete JNet results</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.08b</strong><br>
- 18/4/06</div>
- </td>
- <td> </td>
- <td>
- <ul>
- <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
- <li>Righthand label on wrapped alignments shows correct value</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.08</strong><br>
- 10/4/06</div>
- </td>
- <td>
- <ul>
- <li>Editing can be locked to the selection area</li>
- <li>Keyboard editing</li>
- <li>Create sequence features from searches</li>
- <li>Precalculated annotations can be loaded onto alignments</li>
- <li>Features file allows grouping of features</li>
- <li>Annotation Colouring scheme added</li>
- <li>Smooth fonts off by default - Faster rendering</li>
- <li>Choose to toggle Autocalculate Consensus On/Off</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Drag & Drop fixed on Linux</li>
- <li>Jalview Archive file faster to load/save, sequence
- descriptions saved.</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.07</strong><br>
- 12/12/05</div>
- </td>
- <td>
- <ul>
- <li>PDB Structure Viewer enhanced</li>
- <li>Sequence Feature retrieval and display enhanced</li>
- <li>Choose to output sequence start-end after sequence name for
- file output</li>
- <li>Sequence Fetcher WSDBFetch@EBI</li>
- <li>Applet can read feature files, PDB files and can be used for
- HTML form input</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>HTML output writes groups and features</li>
- <li>Group editing is Control and mouse click</li>
- <li>File IO bugs</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.06</strong><br>
- 28/9/05</div>
- </td>
- <td>
- <ul>
- <li>View annotations in wrapped mode</li>
- <li>More options for PCA viewer</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>GUI bugs resolved</li>
- <li>Runs with -nodisplay from command line</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td height="63">
- <div align="center"><strong>2.05b</strong><br>
- 15/9/05</div>
- </td>
- <td>
- <ul>
- <li>Choose EPS export as lineart or text</li>
- <li>Jar files are executable</li>
- <li>Can read in Uracil - maps to unknown residue</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Known OutOfMemory errors give warning message</li>
- <li>Overview window calculated more efficiently</li>
- <li>Several GUI bugs resolved</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.05</strong><br>
- 30/8/05</div>
- </td>
- <td>
- <ul>
- <li>Edit and annotate in "Wrapped" view</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Several GUI bugs resolved</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.04</strong><br>
- 24/8/05</div>
- </td>
- <td>
- <ul>
- <li>Hold down mouse wheel & scroll to change font size</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Improved JPred client reliability</li>
- <li>Improved loading of Jalview files</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.03</strong><br>
- 18/8/05</div>
- </td>
- <td>
- <ul>
- <li>Set Proxy server name and port in preferences</li>
- <li>Multiple URL links from sequence ids</li>
- <li>User Defined Colours can have a scheme name and added to
- Colour Menu</li>
- <li>Choose to ignore gaps in consensus calculation</li>
- <li>Unix users can set default web browser</li>
- <li>Runs without GUI for batch processing</li>
- <li>Dynamically generated Web Service Menus</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>InstallAnywhere download for Sparc Solaris</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.02</strong><br>
- 18/7/05</div>
- </td>
- <td> </td>
- <td>
- <ul>
- <li>Copy & Paste order of sequences maintains alignment
- order.</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.01</strong><br>
- 12/7/05</div>
- </td>
- <td>
- <ul>
- <li>Use delete key for deleting selection.</li>
- <li>Use Mouse wheel to scroll sequences.</li>
- <li>Help file updated to describe how to add alignment
- annotations.</li>
- <li>Version and build date written to build properties file.</li>
- <li>InstallAnywhere installation will check for updates at
- launch of Jalview.</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Delete gaps bug fixed.</li>
- <li>FileChooser sorts columns.</li>
- <li>Can remove groups one by one.</li>
- <li>Filechooser icons installed.</li>
- <li>Finder ignores return character when searching. Return key
- will initiate a search.<br>
- </li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.0</strong><br>
- 20/6/05</div>
- </td>
- <td>
- <ul>
- <li>New codebase</li>
- </ul>
- </td>
- <td> </td>
- </tr>
-</table>
-<p> </p>
+ <p>
+ <strong>Release History</strong>
+ </p>
+ <table border="1">
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <em><strong>Release</strong></em>
+ </div>
+ </td>
+ <td>
+ <div align="center">
+ <em><strong>New Features</strong></em>
+ </div>
+ </td>
+ <td>
+ <div align="center">
+ <em><strong>Issues Resolved</strong></em>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.3">2.10.3</a><br />
+ <em>10/10/2017</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-2446 -->Faster and more efficient management and
+ rendering of sequence features
+ </li>
+ <li>
+ <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
+ 429 rate limit request hander
+ </li>
+ <li>
+ <!-- JAL-2773 -->Structure views don't get updated unless
+ their colours have changed
+ </li>
+ <li><!-- JAL-2495 -->All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)</li>
+ <li><!-- JAL-2790 -->'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
+ </li>
+
+ <li><!-- JAL-2617 -->Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references</li>
+ <li><!-- JAL-2685 -->Start/End limits are shown in Pairwise Alignment report</li>
+ </ul>
+ <ul><li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li></ul>
+ <em>Testing and Deployment</em>
+ <ul><li><!-- JAL-2727 -->Test to catch memory leaks in Jalview UI</li></ul>
+ </div>
+ </td>
+ <td><div align="left">
+ <em>General</em>
+ <ul>
+ <li><!-- JAL-2643 -->Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
+ <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
+ <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
+ <li><!-- JAL-2548 -->Export of features doesn't always respect group visibility</li>
+ </ul>
+ <em>Desktop</em>
+ <ul>
+ <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
+ <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
+ </li>
+ <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
+ </li>
+ <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
+ <li><!-- JAL-2529 -->Revised Ensembl REST API CDNA query</li>
+ <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
+ <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
+ <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
+ <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
+ <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
+ <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
+ <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
+ <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
+ <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
+ <li><!-- JAL-2667 -->Mouse wheel doesn't scroll vertically when in wrapped alignment mode</li>
+ <li><!-- JAL-2636 -->Scale mark not shown when close to right hand end of alignment</li>
+ <li><!-- JAL-2684 -->Pairwise alignment only aligns selected regions of each selected sequence</li>
+ <li><!-- JAL-2973 -->Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog</li>
+ <li><!-- JAL-2036 -->Show cross-references not enabled after restoring project until a new view is created</li>
+ </ul>
+ <strong><em>Applet</em></strong><br/>
+ <ul>
+ <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
+ </ul>
+ <strong><em>BioJSON</em></strong><br/>
+ <ul>
+ <li>
+ <!-- JAL-2546 -->BioJSON export does not preserve non-positional features
+ </li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
+ <em>2/10/2017</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em>New features in Jalview Desktop</em>
+ <ul>
+ <li>
+ <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
+ </li>
+ <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
+ </li>
+ </ul>
+ </div></td>
+ <td><div align="left">
+ </div></td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
+ <em>7/9/2017</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-2588 -->Show gaps in overview window by colouring
+ in grey (sequences used to be coloured grey, and gaps were
+ white)
+ </li>
+ <li>
+ <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
+ Preferences
+ </li>
+ <li>
+ <!-- JAL-2587 -->Overview updates immediately on increase
+ in size and progress bar shown as higher resolution
+ overview is recalculated
+ </li>
+
+ </ul>
+ </div></td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-2664 -->Overview window redraws every hidden
+ column region row by row
+ </li>
+ <li>
+ <!-- JAL-2681 -->duplicate protein sequences shown after
+ retrieving Ensembl crossrefs for sequences from Uniprot
+ </li>
+ <li>
+ <!-- JAL-2603 -->Overview window throws NPE if show boxes
+ format setting is unticked
+ </li>
+ <li>
+ <!-- JAL-2610 -->Groups are coloured wrongly in overview
+ if group has show boxes format setting unticked
+ </li>
+ <li>
+ <!-- JAL-2672,JAL-2665 -->Redraw problems when
+ autoscrolling whilst dragging current selection group to
+ include sequences and columns not currently displayed
+ </li>
+ <li>
+ <!-- JAL-2691 -->Not all chains are mapped when multimeric
+ assemblies are imported via CIF file
+ </li>
+ <li>
+ <!-- JAL-2704 -->Gap colour in custom colourscheme is not
+ displayed when threshold or conservation colouring is also
+ enabled.
+ </li>
+ <li>
+ <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
+ server version
+ </li>
+ <li>
+ <!-- JAL-2673 -->Jalview continues to scroll after
+ dragging a selected region off the visible region of the
+ alignment
+ </li>
+ <li>
+ <!-- JAL-2724 -->Cannot apply annotation based
+ colourscheme to all groups in a view
+ </li>
+ <li>
+ <!-- JAL-2511 -->IDs don't line up with sequences
+ initially after font size change using the Font chooser or
+ middle-mouse zoom
+ </li>
+ </ul>
+ </div></td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <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)
+ </li>
+ <li>
+ <!-- JAL-2403 -->Revised implementation of sequence
+ similarity scores as used by Tree, PCA, Shading Consensus
+ and other calculations
+ </li>
+ <li>
+ <!-- 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>
+ <li>
+ <!-- JAL-384 -->Custom shading schemes created via groovy
+ scripts
+ </li>
+ </ul>
+ <em>Overview</em>
+ <ul>
+ <li>
+ <!-- JAL-2526 -->Efficiency improvements for interacting
+ with alignment and overview windows
+ </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>
+
+ <em>Data import/export</em>
+ <ul>
+ <li>
+ <!-- JAL-2535 -->Posterior probability annotation from
+ Stockholm files imported as sequence associated annotation
+ </li>
+ <li>
+ <!-- JAL-2507 -->More robust per-sequence positional
+ annotation input/output via stockholm flatfile
+ </li>
+ <li>
+ <!-- JAL-2533 -->Sequence names don't include file
+ extension when importing structure files without embedded
+ names or PDB accessions
+ </li>
+ <li>
+ <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
+ format sequence substitution matrices
+ </li>
+ </ul>
+ <em>User Interface</em>
+ <ul>
+ <li>
+ <!-- JAL-2447 --> Experimental Features Checkbox in
+ Desktop's Tools menu to hide or show untested features in
+ the application.
+ </li>
+ <li>
+ <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
+ via Overview or sequence motif search operations
+ </li>
+ <li>
+ <!-- JAL-2547 -->Amend sequence features dialog box can be
+ opened by double clicking gaps within sequence feature
+ extent
+ </li>
+ <li>
+ <!-- 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-2430 -->Hidden regions in alignment views are not
+ coloured in linked structure views
+ </li>
+ <li>
+ <!-- JAL-1596 -->Faster Chimera/Jalview communication by
+ file-based command exchange
+ </li>
+ <li>
+ <!-- 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
+ the Jalview project rather than downloaded again when the
+ project is reopened.
+ </li>
+ <li>
+ <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
+ to transfer Chimera's structure attributes as Jalview
+ features, and vice-versa (<strong>Experimental
+ Feature</strong>)
+ </li>
+ </ul>
+ <em>Web Services</em>
+ <ul>
+ <li>
+ <!-- JAL-2549 -->Updated JABAWS client to v2.2
+ </li>
+ <li>
+ <!-- JAL-2335 -->Filter non-standard amino acids and
+ nucleotides when submitting to AACon and other MSA
+ Analysis services
+ </li>
+ <li>
+ <!-- JAL-2316, -->URLs for viewing database
+ cross-references provided by identifiers.org and the
+ EMBL-EBI's MIRIAM DB
+ </li>
+ </ul>
+
+ <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>
+ </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 readability
+ 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>
+ <!-- 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>Calculations</em>
+ <ul>
+ <li>
+ <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
+ matrix - C->R should be '-3'<br />Old matrix restored
+ with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
+ </li>
+ <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
+ Jalview's treatment of gaps in PCA and substitution matrix
+ based Tree calculations.<br /> <br />In earlier versions
+ of Jalview, gaps matching gaps were penalised, and gaps
+ matching non-gaps penalised even more. In the PCA
+ calculation, gaps were actually treated as non-gaps - so
+ different costs were applied, which meant Jalview's PCAs
+ were different to those produced by SeqSpace.<br />Jalview
+ now treats gaps in the same way as SeqSpace (ie it scores
+ them as 0). <br /> <br />Enter the following in the
+ Groovy console to restore pre-2.10.2 behaviour:<br />
+ jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
+ // for 2.10.1 mode <br />
+ jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
+ // to restore 2.10.2 mode <br /> <br /> <em>Note:
+ these settings will affect all subsequent tree and PCA
+ calculations (not recommended)</em></li>
+ <li>
+ <!-- JAL-2424 -->Fixed off-by-one bug that affected
+ scaling of branch lengths for trees computed using
+ 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-2419 -->Current selection lost if popup menu
+ opened on a region of alignment without groups
+ </li>
+ <li>
+ <!-- JAL-2374 -->Popup menu not always shown for regions
+ of an alignment with overlapping groups
+ </li>
+ <li>
+ <!-- JAL-2310 -->Finder double counts if both a sequence's
+ name and description match
+ </li>
+ <li>
+ <!-- JAL-2370 -->Hiding column selection containing two
+ hidden regions results in incorrect hidden regions
+ </li>
+ <li>
+ <!-- JAL-2386 -->'Apply to all groups' setting when
+ changing colour does not apply Conservation slider value
+ to all groups
+ </li>
+ <li>
+ <!-- JAL-2373 -->Percentage identity and conservation menu
+ items do not show a tick or allow shading to be disabled
+ </li>
+ <li>
+ <!-- JAL-2385 -->Conservation shading or PID threshold
+ lost when base colourscheme changed if slider not visible
+ </li>
+ <li>
+ <!-- JAL-2547 -->Sequence features shown in tooltip for
+ gaps before start of features
+ </li>
+ <li>
+ <!-- JAL-2623 -->Graduated feature colour threshold not
+ restored to UI when feature colour is edited
+ </li>
+ <li>
+ <!-- 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
+ as graduate feature colour settings are modified via the
+ dialog box
+ </li>
+ <li>
+ <!-- JAL-2034 -->Overview window doesn't always update
+ when a group defined on the alignment is resized
+ </li>
+ <li>
+ <!-- JAL-2605 -->Mouseovers on left/right scale region in
+ wrapped view result in positional status updates
+ </li>
+
+ <li>
+ <!-- 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-2473 -->Minimum size set for Jalview windows so
+ widgets don't permanently disappear
+ </li>
+ <li>
+ <!-- JAL-2503 -->Cannot select or filter quantitative
+ annotation that are shown only as column labels (e.g.
+ T-Coffee column reliability scores)
+ </li>
+ <li>
+ <!-- JAL-2594 -->Exception thrown if trying to create a
+ sequence feature on gaps only
+ </li>
+ <li>
+ <!-- JAL-2504 -->Features created with 'New feature'
+ button from a Find inherit previously defined feature type
+ rather than the Find query string
+ </li>
+ <li>
+ <!-- JAL-2423 -->incorrect title in output window when
+ exporting tree calculated in Jalview
+ </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
+ </li>
+ <li>
+ <!-- JAL-2225 -->Sequence Database chooser unusable on
+ Linux
+ </li>
+ <li>
+ <!-- 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-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-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>Data import/export</em>
+ <ul>
+ <li>
+ <!-- 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>
+ <li>
+ <!-- JAL-2401 -->Easier creation of colours for all 'Lower
+ case' residues (button in colourscheme editor debugged and
+ new documentation and tooltips added)
+ </li>
+ <li>
+ <!-- JAL-2399-->Text colour threshold's 'Cancel' button
+ doesn't restore group-specific text colour thresholds
+ </li>
+ <li>
+ <!-- JAL-2243 -->Feature settings panel does not update as
+ new features are added to alignment
+ </li>
+ <li>
+ <!-- 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-2436 -->Structure viewer's View -> Colour By view
+ selection menu changes colours of alignment views
+ </li>
+ <li>
+ <!-- JAL-2426 -->Spurious exceptions in console raised
+ from alignment calculation workers after alignment has
+ been closed
+ </li>
+ <li>
+ <!-- JAL-1608 -->Typo in selection popup menu - Create
+ groups now 'Create Group'
+ </li>
+ <li>
+ <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
+ Create/Undefine group doesn't always work
+ </li>
+ <li>
+ <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
+ shown again after pressing 'Cancel'
+ </li>
+ <li>
+ <!-- JAL-1256 -->Trackpad horizontal scroll gesture
+ adjusts start position in wrap mode
+ </li>
+ <li>
+ <!-- JAL-2563 -->Status bar doesn't show positions for
+ ambiguous amino acids
+ </li>
+ <li>
+ <!-- JAL-2431 -->cDNA Consensus annotation not shown in
+ CDS/Protein view after CDS sequences added for aligned
+ proteins
+ </li>
+ <li>
+ <!-- JAL-2592 -->User defined colourschemes called 'User
+ Defined' don't appear in Colours menu
+ </li>
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li>
+ <!-- JAL-2468 -->Switching between Nucleotide and Protein
+ score models doesn't always result in an updated PCA plot
+ </li>
+ <li>
+ <!-- JAL-2442 -->Features not rendered as transparent on
+ overview or linked structure view
+ </li>
+ <li>
+ <!-- JAL-2372 -->Colour group by conservation doesn't
+ work (since 2.8)
+ </li>
+ <li>
+ <!-- JAL-2517 -->Hitting Cancel after applying
+ user-defined colourscheme doesn't restore original
+ 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>
+ <!-- JAL-2566 -->Protein/CDS view scrolling not always in
+ phase after a sequence motif find operation
+ </li>
+ <li>
+ <!-- JAL-2550 -->Importing annotation file with rows
+ containing just upper and lower case letters are
+ interpreted as WUSS RNA secondary structure symbols
+ </li>
+ <li>
+ <!-- JAL-2590 -->Cannot load and display Newick trees
+ reliably from eggnog Ortholog database
+ </li>
+ <li>
+ <!-- JAL-2468 -->Status bar shows 'Marked x columns
+ containing features of type Highlight' when 'B' is pressed
+ to mark columns containing highlighted regions.
+ </li>
+ <li>
+ <!-- JAL-2321 -->Dropping a PDB file onto a sequence
+ doesn't always add secondary structure annotation.
+ </li>
+ </ul>
+ </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>
+ </div>
+ </td>
+ <td><div align="left">
+ <em>General</em>
+ <ul>
+ <li>
+ <!-- JAL-98 -->Improved memory usage: sparse arrays used
+ for all consensus calculations
+ </li>
+ <li>
+ <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
+ 3rd Oct 2016)
+ </li>
+ <li>Updated Jalview's Certum code signing certificate
+ for 2016-2017</li>
+ </ul>
+ <em>Application</em>
+ <ul>
+ <li>
+ <!-- JAL-1723 -->Sequence ID tool tip presents abridged
+ set of database cross-references, sorted alphabetically
+ </li>
+ <li>
+ <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
+ from database cross references. Users with custom links
+ will receive a <a href="webServices/urllinks.html#warning">warning
+ dialog</a> asking them to update their preferences.
+ </li>
+ <li>
+ <!-- JAL-2287-->Cancel button and escape listener on
+ dialog warning user about disconnecting Jalview from a
+ Chimera session
+ </li>
+ <li>
+ <!-- JAL-2320-->Jalview's Chimera control window closes if
+ the Chimera it is connected to is shut down
+ </li>
+ <li>
+ <!-- JAL-1738-->New keystroke (B) and Select highlighted
+ columns menu item to mark columns containing highlighted
+ regions (e.g. from structure selections or results of a
+ Find operation)
+ </li>
+ <li>
+ <!-- JAL-2284-->Command line option for batch-generation
+ of HTML pages rendering alignment data with the BioJS
+ MSAviewer
+ </li>
+ </ul>
+ </div></td>
+ <td>
+ <div align="left">
+ <em>General</em>
+ <ul>
+ <li>
+ <!-- JAL-2286 -->Columns with more than one modal residue
+ are not coloured or thresholded according to percent
+ identity (first observed in Jalview 2.8.2)
+ </li>
+ <li>
+ <!-- JAL-2301 -->Threonine incorrectly reported as not
+ hydrophobic
+ </li>
+ <li>
+ <!-- JAL-2318 -->Updates to documentation pages (above PID
+ threshold, amino acid properties)
+ </li>
+ <li>
+ <!-- JAL-2292 -->Lower case residues in sequences are not
+ reported as mapped to residues in a structure file in the
+ View Mapping report
+ </li>
+ <li>
+ <!--JAL-2324 -->Identical features with non-numeric scores
+ could be added multiple times to a sequence
+ </li>
+ <li>
+ <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
+ bond features shown as two highlighted residues rather
+ than a range in linked structure views, and treated
+ correctly when selecting and computing trees from features
+ </li>
+ <li>
+ <!-- JAL-2281-->Custom URL links for database
+ cross-references are matched to database name regardless
+ of case
+ </li>
+
+ </ul>
+ <em>Application</em>
+ <ul>
+ <li>
+ <!-- JAL-2282-->Custom URL links for specific database
+ names without regular expressions also offer links from
+ Sequence ID
+ </li>
+ <li>
+ <!-- JAL-2315-->Removing a single configured link in the
+ URL links pane in Connections preferences doesn't actually
+ update Jalview configuration
+ </li>
+ <li>
+ <!-- JAL-2272-->CTRL-Click on a selected region to open
+ the alignment area popup menu doesn't work on El-Capitan
+ </li>
+ <li>
+ <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
+ files with similarly named sequences if dropped onto the
+ alignment
+ </li>
+ <li>
+ <!-- JAL-2312 -->Additional mappings are shown for PDB
+ entries where more chains exist in the PDB accession than
+ are reported in the SIFTS file
+ </li>
+ <li>
+ <!-- JAL-2317-->Certain structures do not get mapped to
+ the structure view when displayed with Chimera
+ </li>
+ <li>
+ <!-- JAL-2317-->No chains shown in the Chimera view
+ panel's View->Show Chains submenu
+ </li>
+ <li>
+ <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
+ work for wrapped alignment views
+ </li>
+ <li>
+ <!--JAL-2197 -->Rename UI components for running JPred
+ predictions from 'JNet' to 'JPred'
+ </li>
+ <li>
+ <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
+ corrupted when annotation panel vertical scroll is not at
+ first annotation row
+ </li>
+ <li>
+ <!--JAL-2332 -->Attempting to view structure for Hen
+ lysozyme results in a PDB Client error dialog box
+ </li>
+ <li>
+ <!-- JAL-2319 -->Structure View's mapping report switched
+ ranges for PDB and sequence for SIFTS
+ </li>
+ <!-- JAL-2319 -->
+ SIFTS 'Not_Observed' residues mapped to non-existant
+ coordindate data
+ </li>
+ </ul>
+ <!-- <em>New Known Issues</em>
+ <ul>
+ <li></li>
+ </ul> -->
+ </div>
+ </td>
+ </tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
+ <em>25/10/2016</em></strong>
+ </div>
+ </td>
+ <td><em>Application</em>
+ <ul>
+ <li>3D Structure chooser opens with 'Cached structures'
+ view if structures already loaded</li>
+ <li>Progress bar reports models as they are loaded to
+ structure views</li>
+ </ul></td>
+ <td>
+ <div align="left">
+ <em>General</em>
+ <ul>
+ <li>Colour by conservation always enabled and no tick
+ shown in menu when BLOSUM or PID shading applied</li>
+ <li>FER1_ARATH and FER2_ARATH labels were switched in
+ example sequences/projects/trees</li>
+ </ul>
+ <em>Application</em>
+ <ul>
+ <li>Jalview projects with views of local PDB structure
+ files saved on Windows cannot be opened on OSX</li>
+ <li>Multiple structure views can be opened and superposed
+ without timeout for structures with multiple models or
+ multiple sequences in alignment</li>
+ <li>Cannot import or associated local PDB files without a
+ PDB ID HEADER line</li>
+ <li>RMSD is not output in Jmol console when superposition
+ is performed</li>
+ <li>Drag and drop of URL from Browser fails for Linux and
+ OSX versions earlier than El Capitan</li>
+ <li>ENA client ignores invalid content from ENA server</li>
+ <li>Exceptions are not raised in console when ENA client
+ attempts to fetch non-existent IDs via Fetch DB Refs UI
+ option</li>
+ <li>Exceptions are not raised in console when a new view
+ is created on the alignment</li>
+ <li>OSX right-click fixed for group selections: CMD-click
+ to insert/remove gaps in groups and CTRL-click to open group
+ pop-up menu</li>
+ </ul>
+ <em>Build and deployment</em>
+ <ul>
+ <li>URL link checker now copes with multi-line anchor
+ tags</li>
+ </ul>
+ <em>New Known Issues</em>
+ <ul>
+ <li>Drag and drop from URL links in browsers do not work
+ on Windows</li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
+ </div>
+ </td>
+ <td><em>General</em>
+ <ul>
+ <li>
+ <!-- JAL-2124 -->Updated Spanish translations.
+ </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-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-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-2154 -->Revised Jalview Project format for
+ efficient recovery of sequence coding and alignment
+ annotation relationships.
+ </li>
+ </ul> <!-- <em>Applet</em>
+ <ul>
+ <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-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 "Sequence position" 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>
+ <!-- JAL-1932 -->Remove right on penultimate column of
+ alignment does nothing
+ </li>
+ </ul>
+ <em>Application</em>
+ <ul>
+ <li>
+ <!-- JAL-1552-->URLs and links can't be imported by
+ drag'n'drop on OSX when launched via webstart (note - not
+ yet fixed for El Capitan)
+ </li>
+ <li>
+ <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
+ output when running on non-gb/us i18n platforms
+ </li>
+ <li>
+ <!-- JAL-1944 -->Error thrown when exporting a view with
+ hidden sequences as flat-file alignment
+ </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, and restoring from
+ project
+ </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 -->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-2284 -->Unable to read old Jalview projects that
+ contain non-XML data added after Jalvew wrote project.
+ </li>
+ <li>
+ <!-- JAL-2118 -->Newly created annotation row reorders
+ after clicking on it to create new annotation for a
+ column.
+ </li>
+ <li>
+ <!-- JAL-1980 -->Null Pointer Exception raised when
+ pressing Add on an orphaned cut'n'paste window.
+ </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>
+ <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>
+ </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>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> <em>Build and Deployment</em>
+ <ul>
+ <li>
+ <!-- JAL-1888 -->New ant target for running Jalview's test
+ suite
+ </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>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>
+
+ </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>
+ <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>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
+ </div></td>
+ <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>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="features/bioJsonFormat.html">BioJSON</a></li>
+ <li>New alignment annotation file statements for
+ reference sequences and marking hidden columns</li>
+ <li>Reference sequence based alignment shading 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>
+ <li>Alignments can be sorted by number of RNA helices</li>
+ </ul> <em>Application</em>
+ <ul>
+ <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>
+
+ <li>VARNA RNA viewer updated to v3.93</li>
+ <li>VARNA views are saved in Jalview Projects</li>
+ <li>Pseudoknots displayed as Jalview RNA annotation can
+ be shown in VARNA</li>
+
+ <li>Make groups for selection uses marked columns as well
+ as the active selected region</li>
+
+ <li>Calculate UPGMA and NJ trees using sequence feature
+ similarity</li>
+ <li>New Export options
+ <ul>
+ <li>New Export Settings dialog to control hidden
+ region export in flat file generation</li>
+
+ <li>Export alignment views for display with the <a
+ 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
+ alignment figures to HTML</li>
+ </li>
+ <li>3D structure retrieval and display
+ <ul>
+ <li>Free text and structured queries with the PDBe
+ Search API</li>
+ <li>PDBe Search API based discovery and selection of
+ PDB structures for a sequence set</li>
+ </ul>
+ </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>
+ <li>changed 'View nucleotide structure' submenu to 'View
+ VARNA 2D Structure'</li>
+ <li>change "View protein structure" menu option to "3D
+ Structure ..."</li>
+
+ </ul> <em>Applet</em>
+ <ul>
+ <li>New layout for applet example pages</li>
+ <li>New parameters to enable SplitFrame view
+ (file2,enableSplitFrame, scaleProteinAsCdna)</li>
+ <li>New example demonstrating linked viewing of cDNA and
+ Protein alignments</li>
+ </ul> <em>Development and deployment</em>
+ <ul>
+ <li>Java 1.7 minimum requirement for Jalview 2.9</li>
+ <li>Include installation type and git revision in build
+ properties and console log output</li>
+ <li>Jalview Github organisation, and new github site for
+ storing BioJsMSA Templates</li>
+ <li>Jalview's unit tests now managed with TestNG</li>
+ </ul></td>
+ <td>
+ <!-- <em>General</em>
+ <ul>
+ </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>Consensus RNA secondary secondary structure
+ predictions are not highlighted in amber</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
+ width checkbox not enabled</li>
+ <li>Stopped a warning dialog from being shown when
+ creating user defined colours</li>
+ <li>'View Mapping' in structure viewer shows sequence
+ mappings for just that viewer's sequences</li>
+ <li>Workaround for superposing PDB files containing
+ multiple models in Chimera</li>
+ <li>Report sequence position in status bar when hovering
+ over Jmol structure</li>
+ <li>Cannot output gaps as '.' symbols with Selection ->
+ output to text box</li>
+ <li>Flat file exports of alignments with hidden columns
+ have incorrect sequence start/end</li>
+ <li>'Aligning' a second chain to a Chimera structure from
+ Jalview fails</li>
+ <li>Colour schemes applied to structure viewers don't
+ work for nucleotide</li>
+ <li>Loading/cut'n'pasting an empty or invalid file leads
+ 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 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 in
+ console if Chimera has been opened</li>
+ <li>Mouseover to Chimera not working</li>
+ <li>Miscellaneous ENA XML feature qualifiers not
+ retrieved</li>
+ <li>NPE in annotation renderer after 'Extract Scores'</li>
+ <li>If two structures in one Chimera window, mouseover of
+ 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
+ in right place after 'view flanking regions'</li>
+ <li>File Save As type unset when current file format is
+ unknown</li>
+ <li>Save as '.jar' option removed for saving Jalview
+ projects</li>
+ <li>Colour by Sequence colouring in Chimera more
+ responsive</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>
+ <li>Jalview's tooltip wraps long texts containing no
+ spaces</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Jmol to JalviewLite mouseover/link not working</li>
+ <li>JalviewLite can't import sequences with ID
+ descriptions containing angle brackets</li>
+ </ul> <em>General</em>
+ <ul>
+ <li>Cannot export and reimport RNA secondary structure
+ via jalview annotation file</li>
+ <li>Random helix colour palette for colour by annotation
+ with RNA secondary structure</li>
+ <li>Mouseover to cDNA from STOP residue in protein
+ translation doesn't work.</li>
+ <li>hints when using the select by annotation dialog box</li>
+ <li>Jmol alignment incorrect if PDB file has alternate CA
+ positions</li>
+ <li>FontChooser message dialog appears to hang after
+ choosing 1pt font</li>
+ <li>Peptide secondary structure incorrectly imported from
+ annotation file when annotation display text includes 'e' or
+ 'h'</li>
+ <li>Cannot set colour of new feature type whilst creating
+ new feature</li>
+ <li>cDNA translation alignment should not be sequence
+ order dependent</li>
+ <li>'Show unconserved' doesn't work for lower case
+ sequences</li>
+ <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>
+ <li>Misleading message appears after trying to delete
+ solid column.</li>
+ <li>Jalview icon not shown in dock after InstallAnywhere
+ version launches</li>
+ <li>Fetching EMBL reference for an RNA sequence results
+ fails with a sequence mismatch</li>
+ <li>Corrupted or unreadable alignment display when
+ scrolling alignment to right</li>
+ <li>ArrayIndexOutOfBoundsException thrown when remove
+ empty columns called on alignment with ragged gapped ends</li>
+ <li>auto calculated alignment annotation rows do not get
+ 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>
+ </tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
+ </div></td>
+ <td><em>General</em>
+ <ul>
+ <li>Updated Java code signing certificate donated by
+ Certum.PL.</li>
+ <li>Features and annotation preserved when performing
+ pairwise alignment</li>
+ <li>RNA pseudoknot annotation can be
+ imported/exported/displayed</li>
+ <li>'colour by annotation' can colour by RNA and
+ protein secondary structure</li>
+ <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
+ post-hoc with 2.9 release</em>)
+ </li>
+
+ </ul> <em>Application</em>
+ <ul>
+ <li>Extract and display secondary structure for sequences
+ with 3D structures</li>
+ <li>Support for parsing RNAML</li>
+ <li>Annotations menu for layout
+ <ul>
+ <li>sort sequence annotation rows by alignment</li>
+ <li>place sequence annotation above/below alignment
+ annotation</li>
+ </ul>
+ <li>Output in Stockholm format</li>
+ <li>Internationalisation: improved Spanish (es)
+ translation</li>
+ <li>Structure viewer preferences tab</li>
+ <li>Disorder and Secondary Structure annotation tracks
+ shared between alignments</li>
+ <li>UCSF Chimera launch and linked highlighting from
+ Jalview</li>
+ <li>Show/hide all sequence associated annotation rows for
+ all or current selection</li>
+ <li>disorder and secondary structure predictions
+ available as dataset annotation</li>
+ <li>Per-sequence rna helices colouring</li>
+
+
+ <li>Sequence database accessions imported when fetching
+ alignments from Rfam</li>
+ <li>update VARNA version to 3.91</li>
+
+ <li>New groovy scripts for exporting aligned positions,
+ conservation values, and calculating sum of pairs scores.</li>
+ <li>Command line argument to set default JABAWS server</li>
+ <li>include installation type in build properties and
+ console log output</li>
+ <li>Updated Jalview project format to preserve dataset
+ annotation</li>
+ </ul></td>
+ <td>
+ <!-- issues resolved --> <em>Application</em>
+ <ul>
+ <li>Distinguish alignment and sequence associated RNA
+ structure in structure->view->VARNA</li>
+ <li>Raise dialog box if user deletes all sequences in an
+ alignment</li>
+ <li>Pressing F1 results in documentation opening twice</li>
+ <li>Sequence feature tooltip is wrapped</li>
+ <li>Double click on sequence associated annotation
+ selects only first column</li>
+ <li>Redundancy removal doesn't result in unlinked
+ leaves shown in tree</li>
+ <li>Undos after several redundancy removals don't undo
+ properly</li>
+ <li>Hide sequence doesn't hide associated annotation</li>
+ <li>User defined colours dialog box too big to fit on
+ screen and buttons not visible</li>
+ <li>author list isn't updated if already written to
+ Jalview properties</li>
+ <li>Popup menu won't open after retrieving sequence
+ from database</li>
+ <li>File open window for associate PDB doesn't open</li>
+ <li>Left-then-right click on a sequence id opens a
+ browser search window</li>
+ <li>Cannot open sequence feature shading/sort popup menu
+ in feature settings dialog</li>
+ <li>better tooltip placement for some areas of Jalview
+ desktop</li>
+ <li>Allow addition of JABAWS Server which doesn't
+ pass validation</li>
+ <li>Web services parameters dialog box is too large to
+ fit on screen</li>
+ <li>Muscle nucleotide alignment preset obscured by
+ tooltip</li>
+ <li>JABAWS preset submenus don't contain newly
+ defined user preset</li>
+ <li>MSA web services warns user if they were launched
+ with invalid input</li>
+ <li>Jalview cannot contact DAS Registy when running on
+ Java 8</li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
+ 'Superpose with' submenu not shown when new view
+ created
+ </li>
+
+ </ul> <!-- <em>Applet</em>
+ <ul>
+ </ul> <em>General</em>
+ <ul>
+ </ul>--> <em>Deployment and Documentation</em>
+ <ul>
+ <li>2G and 1G options in launchApp have no effect on
+ memory allocation</li>
+ <li>launchApp service doesn't automatically open
+ www.jalview.org/examples/exampleFile.jar if no file is given</li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
+ InstallAnywhere reports cannot find valid JVM when Java
+ 1.7_055 is available
+ </li>
+ </ul> <em>Application Known issues</em>
+ <ul>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
+ corrupted or unreadable alignment display when scrolling
+ alignment to right
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
+ retrieval fails but progress bar continues for DAS retrieval
+ with large number of ID
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
+ flatfile output of visible region has incorrect sequence
+ start/end
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
+ rna structure consensus doesn't update when secondary
+ structure tracks are rearranged
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
+ invalid rna structure positional highlighting does not
+ highlight position of invalid base pairs
+ </li>
+ <li>
+ <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
+ out of memory errors are not raised when saving Jalview
+ project from alignment window file menu
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
+ Switching to RNA Helices colouring doesn't propagate to
+ structures
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
+ colour by RNA Helices not enabled when user created
+ annotation added to alignment
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
+ Jalview icon not shown on dock in Mountain Lion/Webstart
+ </li>
+ </ul> <em>Applet Known Issues</em>
+ <ul>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
+ JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
+ </li>
+ <li>
+ <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
+ Jalview and Jmol example not compatible with IE9
+ </li>
+
+ <li>Sort by annotation score doesn't reverse order
+ when selected</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
+ </div></td>
+ <td>
+ <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
+ <em>General</em>
+ <ul>
+ <li>Internationalisation of user interface (usually
+ called i18n support) and translation for Spanish locale</li>
+ <li>Define/Undefine group on current selection with
+ Ctrl-G/Shift Ctrl-G</li>
+ <li>Improved group creation/removal options in
+ alignment/sequence Popup menu</li>
+ <li>Sensible precision for symbol distribution
+ percentages shown in logo tooltip.</li>
+ <li>Annotation panel height set according to amount of
+ annotation when alignment first opened</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li>Interactive consensus RNA secondary structure
+ prediction VIENNA RNAAliFold JABA 2.1 service</li>
+ <li>Select columns containing particular features from
+ Feature Settings dialog</li>
+ <li>View all 'representative' PDB structures for selected
+ sequences</li>
+ <li>Update Jalview project format:
+ <ul>
+ <li>New file extension for Jalview projects '.jvp'</li>
+ <li>Preserve sequence and annotation dataset (to
+ store secondary structure annotation,etc)</li>
+ <li>Per group and alignment annotation and RNA helix
+ colouring</li>
+ </ul>
+ </li>
+ <li>New similarity measures for PCA and Tree calculation
+ (PAM250)</li>
+ <li>Experimental support for retrieval and viewing of
+ flanking regions for an alignment</li>
+ </ul>
+ </td>
+ <td>
+ <!-- issues resolved --> <em>Application</em>
+ <ul>
+ <li>logo keeps spinning and status remains at queued or
+ running after job is cancelled</li>
+ <li>cannot export features from alignments imported from
+ Jalview/VAMSAS projects</li>
+ <li>Buggy slider for web service parameters that take
+ float values</li>
+ <li>Newly created RNA secondary structure line doesn't
+ have 'display all symbols' flag set</li>
+ <li>T-COFFEE alignment score shading scheme and other
+ annotation shading not saved in Jalview project</li>
+ <li>Local file cannot be loaded in freshly downloaded
+ Jalview</li>
+ <li>Jalview icon not shown on dock in Mountain
+ Lion/Webstart</li>
+ <li>Load file from desktop file browser fails</li>
+ <li>Occasional NPE thrown when calculating large trees</li>
+ <li>Cannot reorder or slide sequences after dragging an
+ alignment onto desktop</li>
+ <li>Colour by annotation dialog throws NPE after using
+ 'extract scores' function</li>
+ <li>Loading/cut'n'pasting an empty file leads to a grey
+ alignment window</li>
+ <li>Disorder thresholds rendered incorrectly after
+ performing IUPred disorder prediction</li>
+ <li>Multiple group annotated consensus rows shown when
+ changing 'normalise logo' display setting</li>
+ <li>Find shows blank dialog after 'finished searching' if
+ nothing matches query</li>
+ <li>Null Pointer Exceptions raised when sorting by
+ feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
+ </li>
+ <li>Errors in Jmol console when structures in alignment
+ don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
+ </li>
+ <li>Not all working JABAWS services are shown in
+ Jalview's menu</li>
+ <li>JAVAWS version of Jalview fails to launch with
+ 'invalid literal/length code'</li>
+ <li>Annotation/RNA Helix colourschemes cannot be applied
+ to alignment with groups (actually fixed in 2.8.0b1)</li>
+ <li>RNA Helices and T-Coffee Scores available as default
+ colourscheme</li>
+
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Remove group option is shown even when selection is
+ not a group</li>
+ <li>Apply to all groups ticked but colourscheme changes
+ don't affect groups</li>
+ <li>Documented RNA Helices and T-Coffee Scores as valid
+ colourscheme name</li>
+ <li>Annotation labels drawn on sequence IDs when
+ Annotation panel is not displayed</li>
+ <li>Increased font size for dropdown menus on OSX and
+ embedded windows</li>
+ </ul> <em>Other</em>
+ <ul>
+ <li>Consensus sequence for alignments/groups with a
+ single sequence were not calculated</li>
+ <li>annotation files that contain only groups imported as
+ annotation and junk sequences</li>
+ <li>Fasta files with sequences containing '*' incorrectly
+ recognised as PFAM or BLC</li>
+ <li>conservation/PID slider apply all groups option
+ doesn't affect background (2.8.0b1)
+ <li></li>
+ <li>redundancy highlighting is erratic at 0% and 100%</li>
+ <li>Remove gapped columns fails for sequences with ragged
+ trailing gaps</li>
+ <li>AMSA annotation row with leading spaces is not
+ registered correctly on import</li>
+ <li>Jalview crashes when selecting PCA analysis for
+ certain alignments</li>
+ <li>Opening the colour by annotation dialog for an
+ existing annotation based 'use original colours'
+ colourscheme loses original colours setting</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
+ <em>30/1/2014</em></strong>
+ </div></td>
+ <td>
+ <ul>
+ <li>Trusted certificates for JalviewLite applet and
+ Jalview Desktop application<br />Certificate was donated by
+ <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>
+ <li>Output in Stockholm format</li>
+ <li>Allow import of data from gzipped files</li>
+ <li>Export/import group and sequence associated line
+ graph thresholds</li>
+ <li>Nucleotide substitution matrix that supports RNA and
+ ambiguity codes</li>
+ <li>Allow disorder predictions to be made on the current
+ selection (or visible selection) in the same way that JPred
+ works</li>
+ <li>Groovy scripting for headless Jalview operation</li>
+ </ul> <em>Other improvements</em>
+ <ul>
+ <li>Upgrade desktop installer to InstallAnywhere 2013</li>
+ <li>COMBINE statement uses current SEQUENCE_REF and
+ GROUP_REF scope to group annotation rows</li>
+ <li>Support '' style escaping of quotes in Newick
+ files</li>
+ <li>Group options for JABAWS service by command line name</li>
+ <li>Empty tooltip shown for JABA service options with a
+ link but no description</li>
+ <li>Select primary source when selecting authority in
+ database fetcher GUI</li>
+ <li>Add .mfa to FASTA file extensions recognised by
+ Jalview</li>
+ <li>Annotation label tooltip text wrap</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Slow scrolling when lots of annotation rows are
+ displayed</li>
+ <li>Lots of NPE (and slowness) after creating RNA
+ secondary structure annotation line</li>
+ <li>Sequence database accessions not imported when
+ fetching alignments from Rfam</li>
+ <li>Incorrect SHMR submission for sequences with
+ identical IDs</li>
+ <li>View all structures does not always superpose
+ structures</li>
+ <li>Option widgets in service parameters not updated to
+ reflect user or preset settings</li>
+ <li>Null pointer exceptions for some services without
+ presets or adjustable parameters</li>
+ <li>Discover PDB IDs entry in structure menu doesn't
+ discover PDB xRefs</li>
+ <li>Exception encountered while trying to retrieve
+ features with DAS</li>
+ <li>Lowest value in annotation row isn't coloured
+ when colour by annotation (per sequence) is coloured</li>
+ <li>Keyboard mode P jumps to start of gapped region when
+ residue follows a gap</li>
+ <li>Jalview appears to hang importing an alignment with
+ Wrap as default or after enabling Wrap</li>
+ <li>'Right click to add annotations' message
+ shown in wrap mode when no annotations present</li>
+ <li>Disorder predictions fail with NPE if no automatic
+ annotation already exists on alignment</li>
+ <li>oninit javascript function should be called after
+ initialisation completes</li>
+ <li>Remove redundancy after disorder prediction corrupts
+ alignment window display</li>
+ <li>Example annotation file in documentation is invalid</li>
+ <li>Grouped line graph annotation rows are not exported
+ to annotation file</li>
+ <li>Multi-harmony analysis cannot be run when only two
+ groups created</li>
+ <li>Cannot create multiple groups of line graphs with
+ several 'combine' statements in annotation file</li>
+ <li>Pressing return several times causes Number Format
+ exceptions in keyboard mode</li>
+ <li>Multi-harmony (SHMMR) method doesn't submit
+ correct partitions for input data</li>
+ <li>Translation from DNA to Amino Acids fails</li>
+ <li>Jalview fail to load newick tree with quoted label</li>
+ <li>--headless flag isn't understood</li>
+ <li>ClassCastException when generating EPS in headless
+ mode</li>
+ <li>Adjusting sequence-associated shading threshold only
+ changes one row's threshold</li>
+ <li>Preferences and Feature settings panel panel
+ doesn't open</li>
+ <li>hide consensus histogram also hides conservation and
+ quality histograms</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
+ </div></td>
+ <td><em>Application</em>
+ <ul>
+ <li>Support for JABAWS 2.0 Services (AACon alignment
+ conservation, protein disorder and Clustal Omega)</li>
+ <li>JABAWS server status indicator in Web Services
+ preferences</li>
+ <li>VARNA (http://varna.lri.fr) viewer for RNA structures
+ in Jalview alignment window</li>
+ <li>Updated Jalview build and deploy framework for OSX
+ mountain lion, windows 7, and 8</li>
+ <li>Nucleotide substitution matrix for PCA that supports
+ RNA and ambiguity codes</li>
+
+ <li>Improved sequence database retrieval GUI</li>
+ <li>Support fetching and database reference look up
+ against multiple DAS sources (Fetch all from in 'fetch db
+ refs')</li>
+ <li>Jalview project improvements
+ <ul>
+ <li>Store and retrieve the 'belowAlignment'
+ flag for annotation</li>
+ <li>calcId attribute to group annotation rows on the
+ alignment</li>
+ <li>Store AACon calculation settings for a view in
+ Jalview project</li>
+
+ </ul>
+ </li>
+ <li>horizontal scrolling gesture support</li>
+ <li>Visual progress indicator when PCA calculation is
+ running</li>
+ <li>Simpler JABA web services menus</li>
+ <li>visual indication that web service results are still
+ being retrieved from server</li>
+ <li>Serialise the dialogs that are shown when Jalview
+ starts up for first time</li>
+ <li>Jalview user agent string for interacting with HTTP
+ services</li>
+ <li>DAS 1.6 and DAS 2.0 source support using new JDAS
+ client library</li>
+ <li>Examples directory and Groovy library included in
+ InstallAnywhere distribution</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>RNA alignment and secondary structure annotation
+ visualization applet example</li>
+ </ul> <em>General</em>
+ <ul>
+ <li>Normalise option for consensus sequence logo</li>
+ <li>Reset button in PCA window to return dimensions to
+ defaults</li>
+ <li>Allow seqspace or Jalview variant of alignment PCA
+ calculation</li>
+ <li>PCA with either nucleic acid and protein substitution
+ matrices
+ <li>Allow windows containing HTML reports to be exported
+ in HTML</li>
+ <li>Interactive display and editing of RNA secondary
+ structure contacts</li>
+ <li>RNA Helix Alignment Colouring</li>
+ <li>RNA base pair logo consensus</li>
+ <li>Parse sequence associated secondary structure
+ information in Stockholm files</li>
+ <li>HTML Export database accessions and annotation
+ information presented in tooltip for sequences</li>
+ <li>Import secondary structure from LOCARNA clustalw
+ style RNA alignment files</li>
+ <li>import and visualise T-COFFEE quality scores for an
+ alignment</li>
+ <li>'colour by annotation' per sequence option to
+ shade each sequence according to its associated alignment
+ annotation</li>
+ <li>New Jalview Logo</li>
+ </ul> <em>Documentation and Development</em>
+ <ul>
+ <li>documentation for score matrices used in Jalview</li>
+ <li>New Website!</li>
+ </ul></td>
+ <td><em>Application</em>
+ <ul>
+ <li>PDB, Unprot and EMBL (ENA) databases retrieved via
+ wsdbfetch REST service</li>
+ <li>Stop windows being moved outside desktop on OSX</li>
+ <li>Filetype associations not installed for webstart
+ launch</li>
+ <li>Jalview does not always retrieve progress of a JABAWS
+ job execution in full once it is complete</li>
+ <li>revise SHMR RSBS definition to ensure alignment is
+ uploaded via ali_file parameter</li>
+ <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
+ <li>View all structures superposed fails with exception</li>
+ <li>Jnet job queues forever if a very short sequence is
+ submitted for prediction</li>
+ <li>Cut and paste menu not opened when mouse clicked on
+ desktop window</li>
+ <li>Putting fractional value into integer text box in
+ alignment parameter dialog causes Jalview to hang</li>
+ <li>Structure view highlighting doesn't work on
+ windows 7</li>
+ <li>View all structures fails with exception shown in
+ structure view</li>
+ <li>Characters in filename associated with PDBEntry not
+ escaped in a platform independent way</li>
+ <li>Jalview desktop fails to launch with exception when
+ using proxy</li>
+ <li>Tree calculation reports 'you must have 2 or more
+ sequences selected' when selection is empty</li>
+ <li>Jalview desktop fails to launch with jar signature
+ failure when java web start temporary file caching is
+ disabled</li>
+ <li>DAS Sequence retrieval with range qualification
+ results in sequence xref which includes range qualification</li>
+ <li>Errors during processing of command line arguments
+ cause progress bar (JAL-898) to be removed</li>
+ <li>Replace comma for semi-colon option not disabled for
+ DAS sources in sequence fetcher</li>
+ <li>Cannot close news reader when JABAWS server warning
+ dialog is shown</li>
+ <li>Option widgets not updated to reflect user settings</li>
+ <li>Edited sequence not submitted to web service</li>
+ <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
+ <li>InstallAnywhere installer doesn't unpack and run
+ on OSX Mountain Lion</li>
+ <li>Annotation panel not given a scroll bar when
+ sequences with alignment annotation are pasted into the
+ alignment</li>
+ <li>Sequence associated annotation rows not associated
+ when loaded from Jalview project</li>
+ <li>Browser launch fails with NPE on java 1.7</li>
+ <li>JABAWS alignment marked as finished when job was
+ cancelled or job failed due to invalid input</li>
+ <li>NPE with v2.7 example when clicking on Tree
+ associated with all views</li>
+ <li>Exceptions when copy/paste sequences with grouped
+ annotation rows to new window</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Sequence features are momentarily displayed before
+ they are hidden using hidefeaturegroups applet parameter</li>
+ <li>loading features via javascript API automatically
+ enables feature display</li>
+ <li>scrollToColumnIn javascript API method doesn't
+ work</li>
+ </ul> <em>General</em>
+ <ul>
+ <li>Redundancy removal fails for rna alignment</li>
+ <li>PCA calculation fails when sequence has been selected
+ and then deselected</li>
+ <li>PCA window shows grey box when first opened on OSX</li>
+ <li>Letters coloured pink in sequence logo when alignment
+ coloured with clustalx</li>
+ <li>Choosing fonts without letter symbols defined causes
+ exceptions and redraw errors</li>
+ <li>Initial PCA plot view is not same as manually
+ reconfigured view</li>
+ <li>Grouped annotation graph label has incorrect line
+ colour</li>
+ <li>Grouped annotation graph label display is corrupted
+ for lots of labels</li>
+ </ul>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
+ </div>
+ </td>
+ <td><em>Application</em>
+ <ul>
+ <li>Jalview Desktop News Reader</li>
+ <li>Tweaked default layout of web services menu</li>
+ <li>View/alignment association menu to enable user to
+ easily specify which alignment a multi-structure view takes
+ its colours/correspondences from</li>
+ <li>Allow properties file location to be specified as URL</li>
+ <li>Extend Jalview project to preserve associations
+ between many alignment views and a single Jmol display</li>
+ <li>Store annotation row height in Jalview project file</li>
+ <li>Annotation row column label formatting attributes
+ stored in project file</li>
+ <li>Annotation row order for auto-calculated annotation
+ rows preserved in Jalview project file</li>
+ <li>Visual progress indication when Jalview state is
+ saved using Desktop window menu</li>
+ <li>Visual indication that command line arguments are
+ still being processed</li>
+ <li>Groovy script execution from URL</li>
+ <li>Colour by annotation default min and max colours in
+ preferences</li>
+ <li>Automatically associate PDB files dragged onto an
+ alignment with sequences that have high similarity and
+ matching IDs</li>
+ <li>Update JGoogleAnalytics to latest release (0.3)</li>
+ <li>'view structures' option to open many
+ structures in same window</li>
+ <li>Sort associated views menu option for tree panel</li>
+ <li>Group all JABA and non-JABA services for a particular
+ analysis function in its own submenu</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Userdefined and autogenerated annotation rows for
+ groups</li>
+ <li>Adjustment of alignment annotation pane height</li>
+ <li>Annotation scrollbar for annotation panel</li>
+ <li>Drag to reorder annotation rows in annotation panel</li>
+ <li>'automaticScrolling' parameter</li>
+ <li>Allow sequences with partial ID string matches to be
+ annotated from GFF/Jalview features files</li>
+ <li>Sequence logo annotation row in applet</li>
+ <li>Absolute paths relative to host server in applet
+ parameters are treated as such</li>
+ <li>New in the JalviewLite javascript API:
+ <ul>
+ <li>JalviewLite.js javascript library</li>
+ <li>Javascript callbacks for
+ <ul>
+ <li>Applet initialisation</li>
+ <li>Sequence/alignment mouse-overs and selections</li>
+ </ul>
+ </li>
+ <li>scrollTo row and column alignment scrolling
+ functions</li>
+ <li>Select sequence/alignment regions from javascript</li>
+ <li>javascript structure viewer harness to pass
+ messages between Jmol and Jalview when running as
+ distinct applets</li>
+ <li>sortBy method</li>
+ <li>Set of applet and application examples shipped
+ with documentation</li>
+ <li>New example to demonstrate JalviewLite and Jmol
+ javascript message exchange</li>
+ </ul>
+ </ul> <em>General</em>
+ <ul>
+ <li>Enable Jmol displays to be associated with multiple
+ multiple alignments</li>
+ <li>Option to automatically sort alignment with new tree</li>
+ <li>User configurable link to enable redirects to a
+ www.Jalview.org mirror</li>
+ <li>Jmol colours option for Jmol displays</li>
+ <li>Configurable newline string when writing alignment
+ and other flat files</li>
+ <li>Allow alignment annotation description lines to
+ contain html tags</li>
+ </ul> <em>Documentation and Development</em>
+ <ul>
+ <li>Add groovy test harness for bulk load testing to
+ examples</li>
+ <li>Groovy script to load and align a set of sequences
+ using a web service before displaying the result in the
+ Jalview desktop</li>
+ <li>Restructured javascript and applet api documentation</li>
+ <li>Ant target to publish example html files with applet
+ archive</li>
+ <li>Netbeans project for building Jalview from source</li>
+ <li>ant task to create online javadoc for Jalview source</li>
+ </ul></td>
+ <td><em>Application</em>
+ <ul>
+ <li>User defined colourscheme throws exception when
+ current built in colourscheme is saved as new scheme</li>
+ <li>AlignFrame->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
+ P37173</li>
+ <li>Associate PDB from file dialog does not tell you
+ which sequence is to be associated with the file</li>
+ <li>Find All raises null pointer exception when query
+ only matches sequence IDs</li>
+ <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
+ <li>Jalview project with Jmol views created with Jalview
+ 2.4 cannot be loaded</li>
+ <li>Filetype associations not installed for webstart
+ launch</li>
+ <li>Two or more chains in a single PDB file associated
+ with sequences in different alignments do not get coloured
+ by their associated sequence</li>
+ <li>Visibility status of autocalculated annotation row
+ not preserved when project is loaded</li>
+ <li>Annotation row height and visibility attributes not
+ stored in Jalview project</li>
+ <li>Tree bootstraps are not preserved when saved as a
+ Jalview project</li>
+ <li>Envision2 workflow tooltips are corrupted</li>
+ <li>Enabling show group conservation also enables colour
+ by conservation</li>
+ <li>Duplicate group associated conservation or consensus
+ created on new view</li>
+ <li>Annotation scrollbar not displayed after 'show
+ all hidden annotation rows' option selected</li>
+ <li>Alignment quality not updated after alignment
+ annotation row is hidden then shown</li>
+ <li>Preserve colouring of structures coloured by
+ sequences in pre Jalview 2.7 projects</li>
+ <li>Web service job parameter dialog is not laid out
+ properly</li>
+ <li>Web services menu not refreshed after 'reset
+ services' button is pressed in preferences</li>
+ <li>Annotation off by one in Jalview v2_3 example project</li>
+ <li>Structures imported from file and saved in project
+ get name like jalview_pdb1234.txt when reloaded</li>
+ <li>Jalview does not always retrieve progress of a JABAWS
+ job execution in full once it is complete</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Alignment height set incorrectly when lots of
+ annotation rows are displayed</li>
+ <li>Relative URLs in feature HTML text not resolved to
+ codebase</li>
+ <li>View follows highlighting does not work for positions
+ in sequences</li>
+ <li><= shown as = in tooltip</li>
+ <li>Export features raises exception when no features
+ exist</li>
+ <li>Separator string used for serialising lists of IDs
+ for javascript api is modified when separator string
+ provided as parameter</li>
+ <li>Null pointer exception when selecting tree leaves for
+ alignment with no existing selection</li>
+ <li>Relative URLs for datasources assumed to be relative
+ to applet's codebase</li>
+ <li>Status bar not updated after finished searching and
+ search wraps around to first result</li>
+ <li>StructureSelectionManager instance shared between
+ several Jalview applets causes race conditions and memory
+ leaks</li>
+ <li>Hover tooltip and mouseover of position on structure
+ not sent from Jmol in applet</li>
+ <li>Certain sequences of javascript method calls to
+ applet API fatally hang browser</li>
+ </ul> <em>General</em>
+ <ul>
+ <li>View follows structure mouseover scrolls beyond
+ position with wrapped view and hidden regions</li>
+ <li>Find sequence position moves to wrong residue
+ with/without hidden columns</li>
+ <li>Sequence length given in alignment properties window
+ is off by 1</li>
+ <li>InvalidNumberFormat exceptions thrown when trying to
+ import PDB like structure files</li>
+ <li>Positional search results are only highlighted
+ between user-supplied sequence start/end bounds</li>
+ <li>End attribute of sequence is not validated</li>
+ <li>Find dialog only finds first sequence containing a
+ given sequence position</li>
+ <li>Sequence numbering not preserved in MSF alignment
+ output</li>
+ <li>Jalview PDB file reader does not extract sequence
+ from nucleotide chains correctly</li>
+ <li>Structure colours not updated when tree partition
+ changed in alignment</li>
+ <li>Sequence associated secondary structure not correctly
+ parsed in interleaved stockholm</li>
+ <li>Colour by annotation dialog does not restore current
+ state</li>
+ <li>Hiding (nearly) all sequences doesn't work
+ properly</li>
+ <li>Sequences containing lowercase letters are not
+ properly associated with their pdb files</li>
+ </ul> <em>Documentation and Development</em>
+ <ul>
+ <li>schemas/JalviewWsParamSet.xsd corrupted by
+ ApplyCopyright tool</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
+ </div>
+ </td>
+ <td><em>Application</em>
+ <ul>
+ <li>New warning dialog when the Jalview Desktop cannot
+ contact web services</li>
+ <li>JABA service parameters for a preset are shown in
+ service job window</li>
+ <li>JABA Service menu entries reworded</li>
+ </ul></td>
+ <td>
+ <ul>
+ <li>Modeller PIR IO broken - cannot correctly import a
+ pir file emitted by Jalview</li>
+ <li>Existing feature settings transferred to new
+ alignment view created from cut'n'paste</li>
+ <li>Improved test for mixed amino/nucleotide chains when
+ parsing PDB files</li>
+ <li>Consensus and conservation annotation rows
+ occasionally become blank for all new windows</li>
+ <li>Exception raised when right clicking above sequences
+ in wrapped view mode</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li>multiple multiply aligned structure views cause cpu
+ usage to hit 100% and computer to hang</li>
+ <li>Web Service parameter layout breaks for long user
+ parameter names</li>
+ <li>Jaba service discovery hangs desktop if Jaba server
+ is down</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
+ </div>
+ </td>
+ <td><em>Application</em>
+ <ul>
+ <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
+ <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
+ (JABAWS)
+ </li>
+ <li>Web Services preference tab</li>
+ <li>Analysis parameters dialog box and user defined
+ preferences</li>
+ <li>Improved speed and layout of Envision2 service menu</li>
+ <li>Superpose structures using associated sequence
+ alignment</li>
+ <li>Export coordinates and projection as CSV from PCA
+ viewer</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>enable javascript: execution by the applet via the
+ link out mechanism</li>
+ </ul> <em>Other</em>
+ <ul>
+ <li>Updated the Jmol Jalview interface to work with Jmol
+ series 12</li>
+ <li>The Jalview Desktop and JalviewLite applet now
+ require Java 1.5</li>
+ <li>Allow Jalview feature colour specification for GFF
+ sequence annotation files</li>
+ <li>New 'colour by label' keword in Jalview feature file
+ type colour specification</li>
+ <li>New Jalview Desktop Groovy API method that allows a
+ script to check if it being run in an interactive session or
+ in a batch operation from the Jalview command line</li>
+ </ul></td>
+ <td>
+ <ul>
+ <li>clustalx colourscheme colours Ds preferentially when
+ both D+E are present in over 50% of the column</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li>typo in AlignmentFrame->View->Hide->all but
+ selected Regions menu item</li>
+ <li>sequence fetcher replaces ',' for ';' when the ',' is
+ part of a valid accession ID</li>
+ <li>fatal OOM if object retrieved by sequence fetcher
+ runs out of memory</li>
+ <li>unhandled Out of Memory Error when viewing pca
+ analysis results</li>
+ <li>InstallAnywhere builds fail to launch on OS X java
+ 10.5 update 4 (due to apple Java 1.6 update)</li>
+ <li>Installanywhere Jalview silently fails to launch</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Jalview.getFeatureGroups() raises an
+ ArrayIndexOutOfBoundsException if no feature groups are
+ defined.</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
+ </div>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li>Alignment prettyprinter doesn't cope with long
+ sequence IDs</li>
+ <li>clustalx colourscheme colours Ds preferentially when
+ both D+E are present in over 50% of the column</li>
+ <li>nucleic acid structures retrieved from PDB do not
+ import correctly</li>
+ <li>More columns get selected than were clicked on when a
+ number of columns are hidden</li>
+ <li>annotation label popup menu not providing correct
+ add/hide/show options when rows are hidden or none are
+ present</li>
+ <li>Stockholm format shown in list of readable formats,
+ and parser copes better with alignments from RFAM.</li>
+ <li>CSV output of consensus only includes the percentage
+ of all symbols if sequence logo display is enabled</li>
+
+ </ul> <em>Applet</em>
+ <ul>
+ <li>annotation panel disappears when annotation is
+ hidden/removed</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li>Alignment view not redrawn properly when new
+ alignment opened where annotation panel is visible but no
+ annotations are present on alignment</li>
+ <li>pasted region containing hidden columns is
+ incorrectly displayed in new alignment window</li>
+ <li>Jalview slow to complete operations when stdout is
+ flooded (fix is to close the Jalview console)</li>
+ <li>typo in AlignmentFrame->View->Hide->all but
+ selected Rregions menu item.</li>
+ <li>inconsistent group submenu and Format submenu entry
+ 'Un' or 'Non'conserved</li>
+ <li>Sequence feature settings are being shared by
+ multiple distinct alignments</li>
+ <li>group annotation not recreated when tree partition is
+ changed</li>
+ <li>double click on group annotation to select sequences
+ does not propagate to associated trees</li>
+ <li>Mac OSX specific issues:
+ <ul>
+ <li>exception raised when mouse clicked on desktop
+ window background</li>
+ <li>Desktop menu placed on menu bar and application
+ name set correctly</li>
+ <li>sequence feature settings not wide enough for the
+ save feature colourscheme button</li>
+ </ul>
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
+ </div>
+ </td>
+ <td><em>New Capabilities</em>
+ <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>
+ <li>Linked viewing of nucleic acid sequences and
+ structures</li>
+ <li>Automatic Scrolling option in View menu to display
+ the currently highlighted region of an alignment.</li>
+ <li>Order an alignment by sequence length, or using the
+ average score or total feature count for each sequence.</li>
+ <li>Shading features by score or associated description</li>
+ <li>Subdivide alignment and groups based on identity of
+ selected subsequence (Make Groups from Selection).</li>
+ <li>New hide/show options including Shift+Control+H to
+ hide everything but the currently selected region.</li>
+ <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
+ </ul> <em>Application</em>
+ <ul>
+ <li>Fetch DB References capabilities and UI expanded to
+ support retrieval from DAS sequence sources</li>
+ <li>Local DAS Sequence sources can be added via the
+ command line or via the Add local source dialog box.</li>
+ <li>DAS Dbref and DbxRef feature types are parsed as
+ database references and protein_name is parsed as
+ description line (BioSapiens terms).</li>
+ <li>Enable or disable non-positional feature and database
+ references in sequence ID tooltip from View menu in
+ application.</li>
+ <!-- <li>New hidden columns and rows and representatives capabilities
+ in annotations file (in progress - not yet fully implemented)</li> -->
+ <li>Group-associated consensus, sequence logos and
+ conservation plots</li>
+ <li>Symbol distributions for each column can be exported
+ and visualized as sequence logos</li>
+ <li>Optionally scale multi-character column labels to fit
+ within each column of annotation row<!-- todo for applet -->
+ </li>
+ <li>Optional automatic sort of associated alignment view
+ when a new tree is opened.</li>
+ <li>Jalview Java Console</li>
+ <li>Better placement of desktop window when moving
+ 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><em>Vamsas Capabilities</em>
+ <ul>
+ <li>Improved VAMSAS synchronization (Jalview archive
+ used to preserve views, structures, and tree display
+ settings)</li>
+ <li>Import of vamsas documents from disk or URL via
+ command line</li>
+ <li>Sharing of selected regions between views and
+ with other VAMSAS applications (Experimental feature!)</li>
+ <li>Updated API to VAMSAS version 0.2</li>
+ </ul></li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Middle button resizes annotation row height</li>
+ <li>New Parameters
+ <ul>
+ <li>sortByTree (true/false) - automatically sort the
+ associated alignment view by the tree when a new tree is
+ opened.</li>
+ <li>showTreeBootstraps (true/false) - show or hide
+ branch bootstraps (default is to show them if available)</li>
+ <li>showTreeDistances (true/false) - show or hide
+ branch lengths (default is to show them if available)</li>
+ <li>showUnlinkedTreeNodes (true/false) - indicate if
+ unassociated nodes should be highlighted in the tree
+ view</li>
+ <li>heightScale and widthScale (1.0 or more) -
+ increase the height or width of a cell in the alignment
+ grid relative to the current font size.</li>
+ </ul>
+ </li>
+ <li>Non-positional features displayed in sequence ID
+ tooltip</li>
+ </ul> <em>Other</em>
+ <ul>
+ <li>Features format: graduated colour definitions and
+ specification of feature scores</li>
+ <li>Alignment Annotations format: new keywords for group
+ associated annotation (GROUP_REF) and annotation row display
+ properties (ROW_PROPERTIES)</li>
+ <li>XML formats extended to support graduated feature
+ colourschemes, group associated annotation, and profile
+ visualization settings.</li></td>
+ <td>
+ <ul>
+ <li>Source field in GFF files parsed as feature source
+ rather than description</li>
+ <li>Non-positional features are now included in sequence
+ feature and gff files (controlled via non-positional feature
+ visibility in tooltip).</li>
+ <li>URL links generated for all feature links (bugfix)</li>
+ <li>Added URL embedding instructions to features file
+ documentation.</li>
+ <li>Codons containing ambiguous nucleotides translated as
+ 'X' in peptide product</li>
+ <li>Match case switch in find dialog box works for both
+ sequence ID and sequence string and query strings do not
+ have to be in upper case to match case-insensitively.</li>
+ <li>AMSA files only contain first column of
+ multi-character column annotation labels</li>
+ <li>Jalview Annotation File generation/parsing consistent
+ with documentation (e.g. Stockholm annotation can be
+ exported and re-imported)</li>
+ <li>PDB files without embedded PDB IDs given a friendly
+ name</li>
+ <li>Find incrementally searches ID string matches as well
+ as subsequence matches, and correctly reports total number
+ of both.</li>
+ <li>Application:
+ <ul>
+ <li>Better handling of exceptions during sequence
+ retrieval</li>
+ <li>Dasobert generated non-positional feature URL
+ link text excludes the start_end suffix</li>
+ <li>DAS feature and source retrieval buttons disabled
+ when fetch or registry operations in progress.</li>
+ <li>PDB files retrieved from URLs are cached properly</li>
+ <li>Sequence description lines properly shared via
+ VAMSAS</li>
+ <li>Sequence fetcher fetches multiple records for all
+ data sources</li>
+ <li>Ensured that command line das feature retrieval
+ completes before alignment figures are generated.</li>
+ <li>Reduced time taken when opening file browser for
+ first time.</li>
+ <li>isAligned check prior to calculating tree, PCA or
+ submitting an MSA to JNet now excludes hidden sequences.</li>
+ <li>User defined group colours properly recovered
+ from Jalview projects.</li>
+ </ul>
+ </li>
+ </ul>
+ </td>
+
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.4.0.b2</strong><br> 28/10/2009
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Experimental support for google analytics usage
+ tracking.</li>
+ <li>Jalview privacy settings (user preferences and docs).</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Race condition in applet preventing startup in
+ jre1.6.0u12+.</li>
+ <li>Exception when feature created from selection beyond
+ length of sequence.</li>
+ <li>Allow synthetic PDB files to be imported gracefully</li>
+ <li>Sequence associated annotation rows associate with
+ all sequences with a given id</li>
+ <li>Find function matches case-insensitively for sequence
+ ID string searches</li>
+ <li>Non-standard characters do not cause pairwise
+ alignment to fail with exception</li>
+ </ul> <em>Application Issues</em>
+ <ul>
+ <li>Sequences are now validated against EMBL database</li>
+ <li>Sequence fetcher fetches multiple records for all
+ data sources</li>
+ </ul> <em>InstallAnywhere Issues</em>
+ <ul>
+ <li>Dock icon works for Mac OS X java (Mac 1.6 update
+ issue with installAnywhere mechanism)</li>
+ <li>Command line launching of JARs from InstallAnywhere
+ version (java class versioning error fixed)</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+
+ <div align="center">
+ <strong>2.4</strong><br> 27/8/2008
+ </div>
+ </td>
+ <td><em>User Interface</em>
+ <ul>
+ <li>Linked highlighting of codon and amino acid from
+ translation and protein products</li>
+ <li>Linked highlighting of structure associated with
+ residue mapping to codon position</li>
+ <li>Sequence Fetcher provides example accession numbers
+ and 'clear' button</li>
+ <li>MemoryMonitor added as an option under Desktop's
+ Tools menu</li>
+ <li>Extract score function to parse whitespace separated
+ numeric data in description line</li>
+ <li>Column labels in alignment annotation can be centred.</li>
+ <li>Tooltip for sequence associated annotation give name
+ of sequence</li>
+ </ul> <em>Web Services and URL fetching</em>
+ <ul>
+ <li>JPred3 web service</li>
+ <li>Prototype sequence search client (no public services
+ available yet)</li>
+ <li>Fetch either seed alignment or full alignment from
+ PFAM</li>
+ <li>URL Links created for matching database cross
+ references as well as sequence ID</li>
+ <li>URL Links can be created using regular-expressions</li>
+ </ul> <em>Sequence Database Connectivity</em>
+ <ul>
+ <li>Retrieval of cross-referenced sequences from other
+ databases</li>
+ <li>Generalised database reference retrieval and
+ validation to all fetchable databases</li>
+ <li>Fetch sequences from DAS sources supporting the
+ sequence command</li>
+ </ul> <em>Import and Export</em>
+ <li>export annotation rows as CSV for spreadsheet import</li>
+ <li>Jalview projects record alignment dataset associations,
+ EMBL products, and cDNA sequence mappings</li>
+ <li>Sequence Group colour can be specified in Annotation
+ File</li>
+ <li>Ad-hoc colouring of group in Annotation File using RGB
+ triplet as name of colourscheme</li>
+ </ul> <em>VAMSAS Client capabilities (Experimental)</em>
+ <ul>
+ <li>treenode binding for VAMSAS tree exchange</li>
+ <li>local editing and update of sequences in VAMSAS
+ alignments (experimental)</li>
+ <li>Create new or select existing session to join</li>
+ <li>load and save of vamsas documents</li>
+ </ul> <em>Application command line</em>
+ <ul>
+ <li>-tree parameter to open trees (introduced for passing
+ from applet)</li>
+ <li>-fetchfrom command line argument to specify nicknames
+ of DAS servers to query for alignment features</li>
+ <li>-dasserver command line argument to add new servers
+ that are also automatically queried for features</li>
+ <li>-groovy command line argument executes a given groovy
+ script after all input data has been loaded and parsed</li>
+ </ul> <em>Applet-Application data exchange</em>
+ <ul>
+ <li>Trees passed as applet parameters can be passed to
+ application (when using "View in full
+ application")</li>
+ </ul> <em>Applet Parameters</em>
+ <ul>
+ <li>feature group display control parameter</li>
+ <li>debug parameter</li>
+ <li>showbutton parameter</li>
+ </ul> <em>Applet API methods</em>
+ <ul>
+ <li>newView public method</li>
+ <li>Window (current view) specific get/set public methods</li>
+ <li>Feature display control methods</li>
+ <li>get list of currently selected sequences</li>
+ </ul> <em>New Jalview distribution features</em>
+ <ul>
+ <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
+ <li>RELEASE file gives build properties for the latest
+ Jalview release.</li>
+ <li>Java 1.1 Applet build made easier and donotobfuscate
+ property controls execution of obfuscator</li>
+ <li>Build target for generating source distribution</li>
+ <li>Debug flag for javacc</li>
+ <li>.jalview_properties file is documented (slightly) in
+ jalview.bin.Cache</li>
+ <li>Continuous Build Integration for stable and
+ development version of Application, Applet and source
+ distribution</li>
+ </ul></td>
+ <td>
+ <ul>
+ <li>selected region output includes visible annotations
+ (for certain formats)</li>
+ <li>edit label/displaychar contains existing label/char
+ for editing</li>
+ <li>update PDBEntries when DBRefEntries change (vamsas)</li>
+ <li>shorter peptide product names from EMBL records</li>
+ <li>Newick string generator makes compact representations</li>
+ <li>bootstrap values parsed correctly for tree files with
+ comments</li>
+ <li>pathological filechooser bug avoided by not allowing
+ filenames containing a ':'</li>
+ <li>Fixed exception when parsing GFF files containing
+ global sequence features</li>
+ <li>Alignment datasets are finalized only when number of
+ references from alignment sequences goes to zero</li>
+ <li>Close of tree branch colour box without colour
+ selection causes cascading exceptions</li>
+ <li>occasional negative imgwidth exceptions</li>
+ <li>better reporting of non-fatal warnings to user when
+ file parsing fails.</li>
+ <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
+ vamsas</li>
+ <li>Histidine should be midblue (not pink!) in Zappo</li>
+ <li>error messages passed up and output when data read
+ fails</li>
+ <li>edit undo recovers previous dataset sequence when
+ sequence is edited</li>
+ <li>allow PDB files without pdb ID HEADER lines (like
+ those generated by MODELLER) to be read in properly</li>
+ <li>allow reading of JPred concise files as a normal
+ filetype</li>
+ <li>Stockholm annotation parsing and alignment properties
+ import fixed for PFAM records</li>
+ <li>Structure view windows have correct name in Desktop
+ window list</li>
+ <li>annotation consisting of sequence associated scores
+ can be read and written correctly to annotation file</li>
+ <li>Aligned cDNA translation to aligned peptide works
+ correctly</li>
+ <li>Fixed display of hidden sequence markers and
+ non-italic font for representatives in Applet</li>
+ <li>Applet Menus are always embedded in applet window on
+ Macs.</li>
+ <li>Newly shown features appear at top of stack (in
+ Applet)</li>
+ <li>Annotations added via parameter not drawn properly
+ 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
+ July 2008</li>
+ <li>Sequence feature to sequence ID match for Features
+ file is case-insensitive</li>
+ <li>Sequence features read from Features file appended to
+ all sequences with matching IDs</li>
+ <li>PDB structure coloured correctly for associated views
+ containing a sub-sequence</li>
+ <li>PDB files can be retrieved by applet from Jar files</li>
+ <li>feature and annotation file applet parameters
+ referring to different directories are retrieved correctly</li>
+ <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
+ <li>Fixed application hang whilst waiting for
+ splash-screen version check to complete</li>
+ <li>Applet properly URLencodes input parameter values
+ when passing them to the launchApp service</li>
+ <li>display name and local features preserved in results
+ retrieved from web service</li>
+ <li>Visual delay indication for sequence retrieval and
+ sequence fetcher initialisation</li>
+ <li>updated Application to use DAS 1.53e version of
+ dasobert DAS client</li>
+ <li>Re-instated Full AMSA support and .amsa file
+ association</li>
+ <li>Fixed parsing of JNet Concise annotation <em>sans</em>
+ sequences
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.3</strong><br> 9/5/07
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Jmol 11.0.2 integration</li>
+ <li>PDB views stored in Jalview XML files</li>
+ <li>Slide sequences</li>
+ <li>Edit sequence in place</li>
+ <li>EMBL CDS features</li>
+ <li>DAS Feature mapping</li>
+ <li>Feature ordering</li>
+ <li>Alignment Properties</li>
+ <li>Annotation Scores</li>
+ <li>Sort by scores</li>
+ <li>Feature/annotation editing in applet</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Headless state operation in 2.2.1</li>
+ <li>Incorrect and unstable DNA pairwise alignment</li>
+ <li>Cut and paste of sequences with annotation</li>
+ <li>Feature group display state in XML</li>
+ <li>Feature ordering in XML</li>
+ <li>blc file iteration selection using filename # suffix</li>
+ <li>Stockholm alignment properties</li>
+ <li>Stockhom alignment secondary structure annotation</li>
+ <li>2.2.1 applet had no feature transparency</li>
+ <li>Number pad keys can be used in cursor mode</li>
+ <li>Structure Viewer mirror image resolved</li>
+ </ul>
+ </td>
+
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.2.1</strong><br> 12/2/07
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Non standard characters can be read and displayed
+ <li>Annotations/Features can be imported/exported to the
+ applet via textbox
+ <li>Applet allows editing of sequence/annotation/group
+ name & description
+ <li>Preference setting to display sequence name in
+ italics
+ <li>Annotation file format extended to allow
+ Sequence_groups to be defined
+ <li>Default opening of alignment overview panel can be
+ specified in preferences
+ <li>PDB residue numbering annotation added to associated
+ sequences
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Applet crash under certain Linux OS with Java 1.6
+ installed
+ <li>Annotation file export / import bugs fixed
+ <li>PNG / EPS image output bugs fixed
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.2</strong><br> 27/11/06
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Multiple views on alignment
+ <li>Sequence feature editing
+ <li>"Reload" alignment
+ <li>"Save" to current filename
+ <li>Background dependent text colour
+ <li>Right align sequence ids
+ <li>User-defined lower case residue colours
+ <li>Format Menu
+ <li>Select Menu
+ <li>Menu item accelerator keys
+ <li>Control-V pastes to current alignment
+ <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>
+ </td>
+ <td>
+ <ul>
+ <li>New memory efficient Undo/Redo System
+ <li>Optimised symbol lookups and conservation/consensus
+ calculations
+ <li>Region Conservation/Consensus recalculated after
+ edits
+ <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>WsDbFetch query/result association resolved
+ <li>Tree leaf to sequence mapping improved
+ <li>Smooth fonts switch moved to FontChooser dialog box.
+
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.1.1</strong><br> 12/9/06
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Copy consensus sequence to clipboard</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Image output - rightmost residues are rendered if
+ sequence id panel has been resized</li>
+ <li>Image output - all offscreen group boundaries are
+ rendered</li>
+ <li>Annotation files with sequence references - all
+ elements in file are relative to sequence position</li>
+ <li>Mac Applet users can use Alt key for group editing</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.1</strong><br> 22/8/06
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>MAFFT Multiple Alignment in default Web Service list</li>
+ <li>DAS Feature fetching</li>
+ <li>Hide sequences and columns</li>
+ <li>Export Annotations and Features</li>
+ <li>GFF file reading / writing</li>
+ <li>Associate structures with sequences from local PDB
+ files</li>
+ <li>Add sequences to exisiting alignment</li>
+ <li>Recently opened files / URL lists</li>
+ <li>Applet can launch the full application</li>
+ <li>Applet has transparency for features (Java 1.2
+ required)</li>
+ <li>Applet has user defined colours parameter</li>
+ <li>Applet can load sequences from parameter
+ "sequence<em>x</em>"
+ </li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Redundancy Panel reinstalled in the Applet</li>
+ <li>Monospaced font - EPS / rescaling bug fixed</li>
+ <li>Annotation files with sequence references bug fixed</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.08.1</strong><br> 2/5/06
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Change case of selected region from Popup menu</li>
+ <li>Choose to match case when searching</li>
+ <li>Middle mouse button and mouse movement can compress /
+ expand the visible width and height of the alignment</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Annotation Panel displays complete JNet results</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.08b</strong><br> 18/4/06
+ </div>
+ </td>
+ <td> </td>
+ <td>
+ <ul>
+ <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
+ <li>Righthand label on wrapped alignments shows correct
+ value</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.08</strong><br> 10/4/06
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Editing can be locked to the selection area</li>
+ <li>Keyboard editing</li>
+ <li>Create sequence features from searches</li>
+ <li>Precalculated annotations can be loaded onto
+ alignments</li>
+ <li>Features file allows grouping of features</li>
+ <li>Annotation Colouring scheme added</li>
+ <li>Smooth fonts off by default - Faster rendering</li>
+ <li>Choose to toggle Autocalculate Consensus On/Off</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Drag & Drop fixed on Linux</li>
+ <li>Jalview Archive file faster to load/save, sequence
+ descriptions saved.</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.07</strong><br> 12/12/05
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>PDB Structure Viewer enhanced</li>
+ <li>Sequence Feature retrieval and display enhanced</li>
+ <li>Choose to output sequence start-end after sequence
+ name for file output</li>
+ <li>Sequence Fetcher WSDBFetch@EBI</li>
+ <li>Applet can read feature files, PDB files and can be
+ used for HTML form input</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>HTML output writes groups and features</li>
+ <li>Group editing is Control and mouse click</li>
+ <li>File IO bugs</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.06</strong><br> 28/9/05
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>View annotations in wrapped mode</li>
+ <li>More options for PCA viewer</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>GUI bugs resolved</li>
+ <li>Runs with -nodisplay from command line</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td height="63">
+ <div align="center">
+ <strong>2.05b</strong><br> 15/9/05
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Choose EPS export as lineart or text</li>
+ <li>Jar files are executable</li>
+ <li>Can read in Uracil - maps to unknown residue</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Known OutOfMemory errors give warning message</li>
+ <li>Overview window calculated more efficiently</li>
+ <li>Several GUI bugs resolved</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.05</strong><br> 30/8/05
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Edit and annotate in "Wrapped" view</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Several GUI bugs resolved</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.04</strong><br> 24/8/05
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Hold down mouse wheel & scroll to change font
+ size</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Improved JPred client reliability</li>
+ <li>Improved loading of Jalview files</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.03</strong><br> 18/8/05
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Set Proxy server name and port in preferences</li>
+ <li>Multiple URL links from sequence ids</li>
+ <li>User Defined Colours can have a scheme name and added
+ to Colour Menu</li>
+ <li>Choose to ignore gaps in consensus calculation</li>
+ <li>Unix users can set default web browser</li>
+ <li>Runs without GUI for batch processing</li>
+ <li>Dynamically generated Web Service Menus</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>InstallAnywhere download for Sparc Solaris</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.02</strong><br> 18/7/05
+ </div>
+ </td>
+ <td> </td>
+ <td>
+ <ul>
+ <li>Copy & Paste order of sequences maintains
+ alignment order.</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.01</strong><br> 12/7/05
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Use delete key for deleting selection.</li>
+ <li>Use Mouse wheel to scroll sequences.</li>
+ <li>Help file updated to describe how to add alignment
+ annotations.</li>
+ <li>Version and build date written to build properties
+ file.</li>
+ <li>InstallAnywhere installation will check for updates
+ at launch of Jalview.</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Delete gaps bug fixed.</li>
+ <li>FileChooser sorts columns.</li>
+ <li>Can remove groups one by one.</li>
+ <li>Filechooser icons installed.</li>
+ <li>Finder ignores return character when searching.
+ Return key will initiate a search.<br>
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.0</strong><br> 20/6/05
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>New codebase</li>
+ </ul>
+ </td>
+ <td> </td>
+ </tr>
+ </table>
+ <p> </p>
</body>
</html>