Release

New Features

Issues Resolved

2.10.3
10/10/2017

• Faster and more efficient management and rendering of sequence features
• More reliable Ensembl fetching with HTTP 429 rate limit request hander

• Protein annotation panel too high in CDS/Protein view

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.

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