Release

New Features

Issues Resolved

2.10.5
6/09/2018

• Default memory for Jalview webstart and InstallAnywhere increased to 1G.
• Hidden sequence markers and representative sequence bolding included when exporting alignment as EPS, SVG, PNG or HTML. Display is configured via the Format menu, or for command-line use via a jalview properties file.
• Ensembl client updated to Version 7 REST API and sequence data now imported as JSON.
• Change in recommended way of starting Jalview via a Java command line: add jars in lib directory to CLASSPATH, rather than via the deprecated java.ext.dirs property.

Development

• Support added to execute test suite instrumented with Open Clover

• Corrupted display when switching to wrapped mode when sequence panel's vertical scrollbar is visible.
• Alignment is black in exported EPS file when sequences are selected in exported view.
• Groups with different coloured borders aren't rendered with correct colour.
• Jalview could hang when importing certain types of knotted RNA secondary structure.
• Sequence highlight and selection in trimmed VARNA 2D structure is incorrect for sequences that do not start at 1.
• '.' inserted into RNA secondary structure annotation when columns are inserted into an alignment, and when exporting as Stockholm flatfile.
• Jalview annotation rows containing upper and lower-case 'E' and 'H' do not automatically get treated as RNA secondary structure.

Java 10 Issues

• OSX - Can't save new files via the File or export menus by typing in a name into the Save dialog box.

2.10.4b1
7/06/2018

• Use HGVS nomenclature for variant annotation retrieved from Uniprot
• Windows File Shortcuts can be dragged onto the Jalview Desktop

• Cannot import features with multiple variant elements (blocks import of some Uniprot records)
• Clustal files with sequence positions in right-hand column parsed correctly
• Wrap view - export to SVG - IDs shown but not alignment area in exported graphic
• F2/Keyboard mode edits work when Overview window has input focus
• Annotation panel set too high when annotation added to view (Windows)
• Jalview Desktop is slow to start up when network connectivity is poor
• Drag URL from chrome, firefox, IE to Jalview desktop on Windows doesn't open file
  Dragging the currently open URL and links from a page viewed in Firefox or Chrome on Windows is now fully supported. If you are using Edge, only links in the page can be dragged, and with Internet Explorer, only the currently open URL in the browser can be dropped onto Jalview.

2.10.4
10/05/2018

• New Structure Chooser control for disabling automatic superposition of multiple structures and open structures in existing views
• Mouse cursor changes to indicate Sequence ID and annotation area margins can be click-dragged to adjust them.
• Jalview uses HTTPS for Uniprot, Xfam and Ensembl services
• Improved performance for large alignments and lots of hidden columns
• Improved performance when rendering lots of features (particularly when transparency is disabled)

• Structure and Overview aren't updated when Colour By Annotation threshold slider is adjusted
• Slow redraw when Overview panel shown overlapping alignment panel
• Overview doesn't show end of unpadded sequence as gaps
• Cross-reference handling improved: CDS not handled correctly if transcript has no UTR
• Secondary structure and temperature factor annotation not added to sequence when local PDB file associated with it by drag'n'drop or structure chooser
• Answering 'No' to PDB Autoassociate dialog doesn't import PDB files dropped on an alignment
• Linked scrolling via protein horizontal scroll bar doesn't work for some CDS/Protein views
• Trackpad scrolling is broken on OSX on Java 1.8u153 onwards and Java 1.9u4+.
• Tooltip shouldn't be displayed for empty columns in annotation row
• Preferences panel's ID Width control is not honored in batch mode
• Linked sequence highlighting doesn't work for structures added to existing Jmol view
• 'View Mappings' includes duplicate entries after importing project with multiple views
• Viewing or annotating Uniprot protein sequences via SIFTS from associated PDB entries with negative residue numbers or missing residues fails
• Exception when shading sequence with negative Temperature Factor values from annotated PDB files (e.g. as generated by CONSURF)
• Uniprot 'sequence variant' features tooltip doesn't include a text description of mutation
• Invert displayed features very slow when structure and/or overview windows are also shown
• Selecting columns from highlighted regions very slow for alignments with large numbers of sequences
• Copy Consensus fails for group consensus with 'StringIndexOutOfBounds'
• VAqua(4) provided as fallback Look and Feel for OSX platforms running Java 10
• Adding a structure to existing structure view appears to do nothing because the view is hidden behind the alignment view

Applet

• Copy consensus sequence option in applet should copy the group consensus when popup is opened on it

Batch Mode

• Fixed ID width preference is not respected

New Known Defects

• Exceptions occasionally raised when editing a large alignment and overview is displayed
• 'Overview updating' progress bar is shown repeatedly after a series of edits even when the overview is no longer reflecting updates
• 'SIFTS Mapping Error' when viewing structures for protein subsequence (if 'Trim Retrieved Sequences' enabled) or Ensembl isoforms (Workaround in 2.10.4 is to fail back to N&W mapping)

2.10.3b1
24/1/2018

• Updated Certum Codesigning Certificate (Valid till 30th November 2018)

Desktop

• Only one structure is loaded when several sequences and structures are selected for viewing/superposing
• Alignment doesn't appear to scroll vertically via trackpad and scrollwheel
• Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment
• Helix annotation has 'notches' when scrolled into view if columns are hidden
• Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns
• User preference for disabling inclusion of sequence limits when exporting as flat file has no effect
• Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes

2.10.3
17/11/2017

• Faster and more efficient management and rendering of sequence features
• More reliable Ensembl fetching with HTTP 429 rate limit request hander
• Structure views don't get updated unless their colours have changed
• All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)
• 'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
• Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references
• Start/End limits are shown in Pairwise Alignment report
• Sequence fetcher's Free text 'autosearch' feature can be disabled
• Retrieve IDs tab added for UniProt and PDB easier retrieval of sequences for lists of IDs
• Short names for sequences retrieved from Uniprot

Scripting

• Groovy interpreter updated to 2.4.12
• Example groovy script for generating a matrix of percent identity scores for current alignment.

Testing and Deployment

• Test to catch memory leaks in Jalview UI

General

• Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view
• Race condition when parsing sequence ID strings in parallel
• Overview windows are also closed when alignment window is closed
• Export of features doesn't always respect group visibility
• Jumping from column 1 to column 100,000 takes a long time in Cursor mode

Desktop

• Structures with whitespace chainCode cannot be viewed in Chimera
• Protein annotation panel too high in CDS/Protein view
• Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
• Slow EnsemblGenome ID lookup
• Revised Ensembl REST API CDNA query
• Hidden column marker in last column not rendered when switching back from Wrapped to normal view
• Annotation display corrupted when scrolling right in unwapped alignment view
• Existing features on subsequence incorrectly relocated when full sequence retrieved from database
• Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)
• Amend Features dialog doesn't allow features of same type and group to be selected for amending
• Jalview becomes sluggish in wide alignments when hidden columns are present
• Jalview freezes when loading and displaying several structures
• Black outlines left after resizing or moving a window
• Unable to minimise windows within the Jalview desktop on OSX
• Mouse wheel doesn't scroll vertically when in wrapped alignment mode
• Scale mark not shown when close to right hand end of alignment
• Pairwise alignment of selected regions of each selected sequence do not have correct start/end positions
• Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog
• Show cross-references not enabled after restoring project until a new view is created
• Warning popup about use of SEQUENCE_ID in URL links appears when only default EMBL-EBI link is configured (since 2.10.2b2)
• Overview redraws whole window when box position is adjusted
• Structure viewer doesn't map all chains in a multi-chain structure when viewing alignment involving more than one chain (since 2.10)
• Double residue highlights in cursor mode if new selection moves alignment window
• Alignment vanishes when using arrow key in cursor mode to pass hidden column marker
• Ensembl Genomes example ID changed to one that produces correctly annotated transcripts and products
• Toggling a feature group after first time doesn't update associated structure view

Applet

• Concurrent modification exception when closing alignment panel

BioJSON

• BioJSON export does not preserve non-positional features

New Known Issues

• Delete/Cut selection doesn't relocate sequence features correctly (for many previous versions of Jalview)
• Cursor mode unexpectedly scrolls when using cursor in wrapped panel other than top
• Select columns containing feature ignores graduated colour threshold
• Edit sequence operation doesn't always preserve numbering and sequence features

Known Java 9 Issues

• Groovy Console very slow to open and is not responsive when entering characters (Webstart, Java 9.01, OSX 10.10)

2.10.2b2
2/10/2017

New features in Jalview Desktop

• Uniprot Sequence Fetcher now uses web API at uniprot.org
• HTTPS used for all connections to ebi.ac.uk

2.10.2b1
7/9/2017

• Show gaps in overview window by colouring in grey (sequences used to be coloured grey, and gaps were white)
• Overview tab in Jalview Desktop Preferences
• Overview updates immediately on increase in size and progress bar shown as higher resolution overview is recalculated

• Overview window redraws every hidden column region row by row
• duplicate protein sequences shown after retrieving Ensembl crossrefs for sequences from Uniprot
• Overview window throws NPE if show boxes format setting is unticked
• Groups are coloured wrongly in overview if group has show boxes format setting unticked
• Redraw problems when autoscrolling whilst dragging current selection group to include sequences and columns not currently displayed
• Not all chains are mapped when multimeric assemblies are imported via CIF file
• Gap colour in custom colourscheme is not displayed when threshold or conservation colouring is also enabled.
• JABAWS 2.2 services report wrong JABAWS server version
• Jalview continues to scroll after dragging a selected region off the visible region of the alignment
• Cannot apply annotation based colourscheme to all groups in a view
• IDs don't line up with sequences initially after font size change using the Font chooser or middle-mouse zoom

2.10.2
17/8/2017

Calculations

• Occupancy annotation row shows number of ungapped positions in each column of the alignment.
• Tree/PCA calculation menu items merged to a calculation dialog box
• Revised implementation of PCA for speed and memory efficiency (~30x faster)
• Revised implementation of sequence similarity scores as used by Tree, PCA, Shading Consensus and other calculations
• Score matrices are stored as resource files within the Jalview codebase
• Trees computed on Sequence Feature Similarity may have different topology due to increased precision

Rendering

• More robust colours and shader model for alignments and groups
• Custom shading schemes created via groovy scripts

Overview

• Efficiency improvements for interacting with alignment and overview windows
• Scrolling of wrapped alignment views via overview
• Hidden columns and sequences can be omitted in Overview
• Click-drag in visible area allows fine adjustment of visible position

Data import/export

• Posterior probability annotation from Stockholm files imported as sequence associated annotation
• More robust per-sequence positional annotation input/output via stockholm flatfile
• Sequence names don't include file extension when importing structure files without embedded names or PDB accessions
• Drag and drop load of AAIndex and NCBI format sequence substitution matrices

User Interface

• Experimental Features Checkbox in Desktop's Tools menu to hide or show untested features in the application.
• Linked scrolling of CDS/Protein views via Overview or sequence motif search operations
• Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent
• Status bar message shown when not enough aligned positions were available to create a 3D structure superposition.

3D Structure

• Hidden regions in alignment views are not coloured in linked structure views
• Faster Chimera/Jalview communication by file-based command exchange
• Structure chooser automatically shows Cached Structures rather than querying the PDBe if structures are already available for sequences
• Structures imported via URL are cached in the Jalview project rather than downloaded again when the project is reopened.
• New entries in the Chimera menu to transfer Chimera's structure attributes as Jalview features, and vice-versa (Experimental Feature)

Web Services

• Updated JABAWS client to v2.2
• Filter non-standard amino acids and nucleotides when submitting to AACon and other MSA Analysis services
• URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB

Scripting

• FileFormatI interface for describing and identifying file formats (instead of String constants)
• FeatureCounter script refactored for efficiency when counting all displayed features (not backwards compatible with 2.10.1)

Example files

• Graduated feature colour style example included in the example feature file

Documentation

• Release notes reformatted for readability with the built-in Java help viewer
• Find documentation updated with 'search sequence description' option

Test Suite

• External service integration tests for Uniprot REST Free Text Search Client
• Added PrivilegedAccessor to test suite
• Prevent or clear modal dialogs raised during tests

Calculations

• Fixed incorrect value in BLOSUM 62 score matrix - C->R should be '-3'
  Old matrix restored with this one-line groovy script:
  jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
• Fixed Jalview's treatment of gaps in PCA and substitution matrix based Tree calculations.
  
  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.
  Jalview now treats gaps in the same way as SeqSpace (ie it scores them as 0).
  
  Enter the following in the Groovy console to restore pre-2.10.2 behaviour:
  jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true // for 2.10.1 mode
  jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false // to restore 2.10.2 mode
  
  Note: these settings will affect all subsequent tree and PCA calculations (not recommended)
• Fixed off-by-one bug that affected scaling of branch lengths for trees computed using Sequence Feature Similarity.
• PCA calculation could hang when generating output report when working with highly redundant alignments
• Sort by features includes features to right of selected region when gaps present on right-hand boundary

User Interface

• Reopening Colour by annotation dialog doesn't reselect a specific sequence's associated annotation after it was used for colouring a view
• Current selection lost if popup menu opened on a region of alignment without groups
• Popup menu not always shown for regions of an alignment with overlapping groups
• Finder double counts if both a sequence's name and description match
• Hiding column selection containing two hidden regions results in incorrect hidden regions
• 'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups
• Percentage identity and conservation menu items do not show a tick or allow shading to be disabled
• Conservation shading or PID threshold lost when base colourscheme changed if slider not visible
• Sequence features shown in tooltip for gaps before start of features
• Graduated feature colour threshold not restored to UI when feature colour is edited
• Vertical scrollbar jumps one page-width at a time when scrolling vertically in wrapped mode.
• Structure and alignment overview update as graduate feature colour settings are modified via the dialog box
• Overview window doesn't always update when a group defined on the alignment is resized
• Mouseovers on left/right scale region in wrapped view result in positional status updates
• Status bar doesn't show position for ambiguous amino acid and nucleotide symbols
• Copy consensus sequence failed if alignment included gapped columns
• Minimum size set for Jalview windows so widgets don't permanently disappear
• Cannot select or filter quantitative annotation that are shown only as column labels (e.g. T-Coffee column reliability scores)
• Exception thrown if trying to create a sequence feature on gaps only
• Features created with 'New feature' button from a Find inherit previously defined feature type rather than the Find query string
• incorrect title in output window when exporting tree calculated in Jalview
• Hiding sequences at bottom of alignment and then revealing them reorders sequences on the alignment
• Group panel in sequence feature settings doesn't update to reflect available set of groups after interactively adding or modifying features
• Sequence Database chooser unusable on Linux
• Hide insertions in PopUp->Selection menu only excluded gaps in current sequence and ignored selection.

Rendering

• Overview window visible region moves erratically when hidden rows or columns are present
• Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring
• Protein specific colours only offered in colour and group colour menu for protein alignments
• Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds
• Feature colour thresholds not respected when rendered on overview and structures when opacity at 100%
• User defined gap colour not shown in overview when features overlaid on alignment

Data import/export

• Very large alignments take a long time to load
• Per-sequence RNA secondary structures added after a sequence was imported are not written to Stockholm File
• WUSS notation for simple pseudoknots lost when importing RNA secondary structure via Stockholm
• Secondary structure arrows for [] and {} not shown in correct direction for simple pseudoknots
• Cannot configure feature colours with lightGray or darkGray via features file (but can specify lightgray)
• Above PID colour threshold not recovered when alignment view imported from project
• No mappings generated between structure and sequences extracted from structure files imported via URL and viewed in Jmol
• Structures loaded via URL are saved in Jalview Projects rather than fetched via URL again when the project is loaded and the structure viewed

Web Services

• EnsemblGenomes example failing after release of Ensembl v.88
• Proxy server address and port always appear enabled in Preferences->Connections
• DAS registry not found exceptions removed from console output
• Cannot retrieve protein products from Ensembl by Peptide ID
• 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).

Application UI

• User Defined Colours not added to Colour menu
• Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added)
• Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds
• Feature settings panel does not update as new features are added to alignment
• Cancel in feature settings reverts changes to feature colours via the Amend features dialog
• Null pointer exception when attempting to edit graduated feature colour via amend features dialog box
• Structure viewer's View -> Colour By view selection menu changes colours of alignment views
• Spurious exceptions in console raised from alignment calculation workers after alignment has been closed
• Typo in selection popup menu - Create groups now 'Create Group'
• CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work
• Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'
• Trackpad horizontal scroll gesture adjusts start position in wrap mode
• Status bar doesn't show positions for ambiguous amino acids
• cDNA Consensus annotation not shown in CDS/Protein view after CDS sequences added for aligned proteins
• User defined colourschemes called 'User Defined' don't appear in Colours menu

Applet

• Switching between Nucleotide and Protein score models doesn't always result in an updated PCA plot
• Features not rendered as transparent on overview or linked structure view
• Colour group by conservation doesn't work (since 2.8)
• Hitting Cancel after applying user-defined colourscheme doesn't restore original colourscheme

Test Suite

• Unit test failure: jalview.ws.jabaws.RNAStructExportImport setup fails
• Unit test failure: jalview.ws.sifts.SiftsClientTest due to compatibility problems with deep array comparison equality asserts in successive versions of TestNG
• Relocated StructureChooserTest and ParameterUtilsTest Unit tests to Network suite

New Known Issues

• Protein/CDS view scrolling not always in phase after a sequence motif find operation
• Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS RNA secondary structure symbols
• Cannot load and display Newick trees reliably from eggnog Ortholog database
• Status bar shows 'Marked x columns containing features of type Highlight' when 'B' is pressed to mark columns containing highlighted regions.
• Dropping a PDB file onto a sequence doesn't always add secondary structure annotation.

2.10.1
29/11/2016

General

• Improved memory usage: sparse arrays used for all consensus calculations
• Jmol updated to version 14.6.4 (released 3rd Oct 2016)
• Updated Jalview's Certum code signing certificate for 2016-2017

Application

• Sequence ID tool tip presents abridged set of database cross-references, sorted alphabetically
• New replacement token for creating URLs just from database cross references. Users with custom links will receive a warning dialog asking them to update their preferences.
• Cancel button and escape listener on dialog warning user about disconnecting Jalview from a Chimera session
• Jalview's Chimera control window closes if the Chimera it is connected to is shut down
• 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)
• Command line option for batch-generation of HTML pages rendering alignment data with the BioJS MSAviewer

General

• Columns with more than one modal residue are not coloured or thresholded according to percent identity (first observed in Jalview 2.8.2)
• Threonine incorrectly reported as not hydrophobic
• Updates to documentation pages (above PID threshold, amino acid properties)
• Lower case residues in sequences are not reported as mapped to residues in a structure file in the View Mapping report
• Identical features with non-numeric scores could be added multiple times to a sequence
• 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
• Custom URL links for database cross-references are matched to database name regardless of case

Application

• Custom URL links for specific database names without regular expressions also offer links from Sequence ID
• Removing a single configured link in the URL links pane in Connections preferences doesn't actually update Jalview configuration
• CTRL-Click on a selected region to open the alignment area popup menu doesn't work on El-Capitan
• Jalview doesn't offer to associate mmCIF files with similarly named sequences if dropped onto the alignment
• Additional mappings are shown for PDB entries where more chains exist in the PDB accession than are reported in the SIFTS file
• Certain structures do not get mapped to the structure view when displayed with Chimera
• No chains shown in the Chimera view panel's View->Show Chains submenu
• Export as HTML with embedded SVG doesn't work for wrapped alignment views
• Rename UI components for running JPred predictions from 'JNet' to 'JPred'
• Export as PNG or SVG is corrupted when annotation panel vertical scroll is not at first annotation row
• Attempting to view structure for Hen lysozyme results in a PDB Client error dialog box
• Structure View's mapping report switched ranges for PDB and sequence for SIFTS
SIFTS 'Not_Observed' residues mapped to non-existant coordindate data

2.10.0b1
25/10/2016

General

• Colour by conservation always enabled and no tick shown in menu when BLOSUM or PID shading applied
• FER1_ARATH and FER2_ARATH labels were switched in example sequences/projects/trees

Application

• Jalview projects with views of local PDB structure files saved on Windows cannot be opened on OSX
• Multiple structure views can be opened and superposed without timeout for structures with multiple models or multiple sequences in alignment
• Cannot import or associated local PDB files without a PDB ID HEADER line
• RMSD is not output in Jmol console when superposition is performed
• Drag and drop of URL from Browser fails for Linux and OSX versions earlier than El Capitan
• ENA client ignores invalid content from ENA server
• Exceptions are not raised in console when ENA client attempts to fetch non-existent IDs via Fetch DB Refs UI option
• Exceptions are not raised in console when a new view is created on the alignment
• OSX right-click fixed for group selections: CMD-click to insert/remove gaps in groups and CTRL-click to open group pop-up menu

Build and deployment

• URL link checker now copes with multi-line anchor tags

New Known Issues

• Drag and drop from URL links in browsers do not work on Windows

2.10.0
06/10/2016

General

• reinstate CTRL-click for opening pop-up menu on OSX
• Export features in Jalview format (again) includes graduated colourschemes
• More responsive when working with big alignments and lots of hidden columns
• Hidden column markers not always rendered at right of alignment window
• Tidied up links in help file table of contents
• Feature based tree calculation not shown for DNA alignments
• Hidden columns ignored during feature based tree calculation
• Alignment view stops updating when show unconserved enabled for group on alignment
• Cannot insert gaps into sequence when set as reference
• Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation
• Incorrect column numbers in ruler when hidden columns present
• Colour by RNA Helices not enabled when user created annotation added to alignment
• RNA Structure consensus only computed for '()' base pair annotation
• Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus
• Extend selection with columns containing feature not working
• Pfam format writer puts extra space at beginning of sequence
• Incomplete sequence extracted from pdb entry 3a6s
• Cannot create groups on an alignment from from a tree when t-coffee scores are shown
• Cannot import and view PDB structures with chains containing negative resnums (4q4h)
• ArithmeticExceptions raised when parsing some structures
• 'Empty' alignment blocks added to Clustal, PIR and PileUp output
• Reordering sequence features that are not visible causes alignment window to repaint
• Threshold sliders don't work in graduated colour and colour by annotation row for e-value scores associated with features and annotation rows
• amino acid physicochemical conservation calculation should be case independent
• Remove annotation also updates hidden columns
• 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)
• Null pointer exceptions and redraw problems when reference sequence defined and 'show non-conserved' enabled
• Quality and Conservation are now shown on load even when Consensus calculation is disabled
• Remove right on penultimate column of alignment does nothing

Application

• URLs and links can't be imported by drag'n'drop on OSX when launched via webstart (note - not yet fixed for El Capitan)
• Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms
• Error thrown when exporting a view with hidden sequences as flat-file alignment
• InstallAnywhere distribution fails when launching Chimera
• Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)
• Cannot save project when view has a reference sequence defined
• Columns are suddenly selected in other alignments and views when revealing hidden columns
• Hide columns not mirrored in complement view in a cDNA/Protein splitframe
• Cannot save/restore representative sequence from project when only one sequence is represented
• Disabled 'Best Uniprot Coverage' option in Structure Chooser
• Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel
• View mapping in structure view shows mappings between sequence and all chains in a PDB file
• PDB and Uniprot FTS dialogs format columns correctly, don't display array data, sort columns according to type
• Export complete shown after destination file chooser is cancelled during an image export
• Error when querying PDB Service with sequence name containing special characters
• Manual PDB structure querying should be case insensitive
• Large tooltips with broken HTML formatting don't wrap
• Figures exported from wrapped view are truncated so L looks like I in consensus annotation
• Export features should only export the currently displayed features for the current selection or view
• Enable 'Get Cross-References' in menu after fetching cross-references, and restoring from project
• Mouseover of a copy of a sequence is not followed in the structure viewer
• Titles for individual alignments in splitframe not restored from project
• missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default
• amino acid physicochemical conservation is case dependent
• RSS reader doesn't stay hidden after last article has been read (reopened issue due to internationalisation problems)
• Only offer PDB structures in structure viewer based on sequence name, PDB and UniProt cross-references
• No progress bar shown during export of alignment as HTML
• Structures not always superimposed after multiple structures are shown for one or more sequences.
• Reference sequence characters should not be replaced with '.' when 'Show unconserved' format option is enabled.
• Cannot specify chain code when entering specific PDB id for sequence
• File->Export->.. as doesn't work when 'Export hidden sequences' is enabled, but 'export hidden columns' is disabled.
• Best Quality option in structure chooser selects lowest rather than highest resolution structures for each sequence
• Incorrect start and end reported for PDB to sequence mapping in 'View Mappings' report
• Unable to read old Jalview projects that contain non-XML data added after Jalvew wrote project.
• Newly created annotation row reorders after clicking on it to create new annotation for a column.
• Null Pointer Exception raised when pressing Add on an orphaned cut'n'paste window.

Applet

• Incorrect columns are selected when hidden columns present before start of sequence
• Missing dependencies on applet pages (JSON jars)
• Overview pixel size changes when sequences are hidden in applet
• Updated instructions for applet deployment on examples pages.

2.9.0b2
16/10/2015

Application

• Duplicate group consensus and conservation rows shown when tree is partitioned
• Erratic behaviour when tree partitions made with multiple cDNA/Protein split views

2.9.0b1
8/10/2015

General

• Mapping of cDNA to protein in split frames incorrect when sequence start > 1
• Broken images in filter column by annotation dialog documentation
• Feature colours not parsed from features file
• Exceptions and incomplete link URLs recovered when loading a features file containing HTML tags in feature description

Application

• Annotations corrupted after BioJS export and reimport
• Incorrect sequence limits after Fetch DB References with 'trim retrieved sequences'
• Incorrect warning about deleting all data when deleting selected columns
• Patch to build system for shipping properly signed JNLP templates for webstart launch
• EMBL-PDBe fetcher/viewer dialogs do not offer unreleased structures for download or viewing
• Tab/space/return keystroke operation of EMBL-PDBe fetcher/viewer dialogs works correctly
• Disabled 'minimise' button on Jalview windows running on OSX to workaround redraw hang bug
• Split cDNA/Protein view position and geometry not recovered from jalview project
• Initial enabled/disabled state of annotation menu sorter 'show autocalculated first/last' corresponds to alignment view
• Restoring of Clustal, RNA Helices and T-Coffee color schemes from BioJSON

Applet

• Reorder sequences mirrored in cDNA/Protein split frame
• Applet with Jmol examples not loading correctly

2.9
10/9/2015

2.8.2
3/12/2014

2.8.1
4/6/2014

2.8.0b1
30/1/2014

2.8
12/11/2012

2.7
27/09/2011

2.6.1
15/11/2010

2.6
26/9/2010

2.5.1
14/6/2010

2.5
30/4/2010

2.4.0.b2
28/10/2009

2.4
27/8/2008

2.3
9/5/07

2.2.1
12/2/07

2.2
27/11/06

2.1.1
12/9/06

2.1
22/8/06

2.08.1
2/5/06

2.08b
18/4/06

2.08
10/4/06

2.07
12/12/05

2.06
28/9/05

2.05b
15/9/05

2.05
30/8/05

2.04
24/8/05

2.03
18/8/05

2.02
18/7/05

2.01
12/7/05

2.0
20/6/05