Jalview Changelog

What's new in Jalview 2.11.3.0

Nov 25, 2023
  • The 2.11.3 Jalview release features a new and more powerful command line interface, support for in-depth exploration of predicted alignment error (PAE) matrices from AlphaFold in the context of multiple alignments, AlphaFold’s standard Blue-Orange-Red confidence colourscheme, and a substantial number of minor improvements and bug fixes.
  • Interactive exploration of AlphaFold Predicted Alignment Error Matrices:
  • Predicted alignment error (PAE) matrices are JSON files produced by AlphaFold and other 3D structure prediction tools, which reflect how well any two positions in a predicted structure are positioned correctly relative to each other. Jalview automatically imports PAE matrices when retrieving protein structures from the EBI-AlphaFold database. A PAE matrix file can also be provided when manually importing 3D structure data.
  • Once imported, PAE matrices are shown in annotation tracks as a heat map shaded pale to dark green, where darker shades indicate higher confidence in relative positioning. Right-clicking a PAE Matrix’s annotation label provides the option to cluster the columns of the matrix, producing a tree where regions of well arranged structure are grouped together, allowing columns containing those regions to be selected and manipulated further.
  • Jalview’s Next Generation Command Line Interface:
  • Jalview 2’s original command line interface (CLI) allowed alignments to be imported, annotated and overlaid with sequence features, coloured, associated with trees, and exported either as figures (EPS, PNG, SVG, HTML SVG or an interactive BioJS page) or with one of Jalview’s supported alignment export file formats. The new command line interface provides all this, as well as a range of additional functionality previously only available via the GUI:
  • 3D structures can be associated with sequences in alignments and shown in Jmol or external viewers
  • Secondary structure, Model Reliability and Temperature factor can be shown and used to colour alignments
  • PAE Matrices can be imported and shown as annotation
  • 3D structure data shown in Jmol can be exported as PNG
  • Scale factors and dimensions can be specified, allowing high resolution image exports
  • In addition to these new functionality, next generation CLI operations can be applied to a range of files and directories through the use of wild-cards. This allows faster and more efficient processing of large numbers of alignments. It also facilitates modularisation of operations through the use of ‘command-line argument files’.
  • All new CLI parameters are preceded by ‘–’, as opposed to an optional single ‘-’ which was used in Jalview’s old CLI. Old style arguments can still be used, so existing scripts will still work as before, but old-style operations cannot be mixed with new operations in the same CLI call. Use of old command line operations will also raise a warning, and we plan to completely remove support in Jalview’s next major release (2.12).

New in Jalview 2.11.2.7 (Jul 1, 2023)

  • New:
  • Jalview now reports usage statistics via Plausible.io
  • Issues Resolved:
  • PDB structures slow to view when Jalview Java console is open
  • chains in PDB or mmCIF files with negative RESNUMs not correctly parsed

New in Jalview 2.11.2.4 (Aug 9, 2022)

  • New Features:
  • New GECOS amino acid colourschemes flower, blossum, ocean and sunset
  • Migrated Uniprot Free Text Search to latest Uniprot search API
  • Improved Structure Chooser’s 3D-Beacons search button design and visual delay indicators
  • 3D beacons Fetch Uniprot References confirmation dialog is only shown when number of sequences exceeds a threshold
  • Warning when Jalview compiled for Java 1.8 is run in a Java 11+ JRE
  • Updated tldr; section of Jalview’s build documentation (doc/building.md)
  • Issues Resolved:
  • buggy PCA plot axes rendering can make them appear to be non-orthogonal
  • Enable ‘All groups’ option when conservation slider is opened and ‘Colour All Groups’ is enabled in Colours menu

New in Jalview 2.11.2.1 (Apr 5, 2022)

  • New Features:
  • Distribution Tarball includes git commit and branch details
  • Issues Resolved:
  • Keyboard mode (F2) stops working after using the "Create sequence feature" dialog >
  • 3D Structure chooser fails to select structures from 3D-beacons and pops up a 'null' dialog
  • PDB FTS query results in error dialog containing '414' [URL too long]
  • Sequence ID tooltip not shown during long running retrieval/crossref operations (affects at least 2.11.1 onwards)
  • Cannot build Jalview 2.11.2.0 via gradle from its source tarball
  • New Known Issues:
  • Keyboard mode (F2) stops working after using the "Text Colour" dialog
  • Colour by->all views doesn't allow colouring same structure from different views (since 2.11.2.0)
  • Pfam and Rfam alignment retrieval as gzipped stockholm doesn't work on JalviewJS build of 2.11.2
  • Java 11 Only: Jalview 2.11.2.0 OSX install not working due to VAqua requiring sun.awt.image.MultiResolutionImage
  • Sequence Details can take a long time to be displayed for heavily annotated sequences (all versions)

New in Jalview 2.11.2.0 (Mar 9, 2022)

  • New Features:
  • Support for viewing 3D structures with ChimeraX and Pymol in addition to Jmol and Chimera.
  • Discover 3D structure data for sequences with Uniprot references via 3D-Beacons
  • Rank and select available structures for Uniprot sequences according to number of residues in structure mapped to positions involved in the alignment
  • Structure annotation rows for all mapped chains in 3D structures are included in the 'Reference Annotation' for a sequence
  • Import Genbank and EMBL format flatfiles
  • ENA record's mol_type honoured so RNA molecules imported from ENA records are shown as RNA
  • Support for Canonical Uniprot IDs
  • New Preferences tab for adjusting Jalview's memory settings at launch
  • Sequence IDs split on '_' as well as other non-alphanumerics when discovering database references with 'Fetch DB Refs'
  • Suppressed harmless exceptions output to Console whilst discovering database references for a sequence
  • Updated Jalview bindings for Uniprot XML schema
  • Uniprot and PDBe autosearch option is disabled by default
  • Reverted to Jalview 'classic' drop-down menu for selecting which database to fetch from in sequence fetcher dialog.
  • Updated Ensembl REST Client compatibility to 15.2 and revised model organism names (rat, xenopus, dmelanogaster now rattus_norvegicus, xenopus_tropicalis, drosophila_melanogaster)
  • -nowebservicediscovery command line argument to prevent automatic discovery of analysis webservices on launch
  • Allow 'App' directories to be opened when locating Chimera, ChimeraX or Pymol binaries via filechooser opened by double clicking the Structure Preferences' path textbox
  • support for HTTP/S access via proxies that require authentication
  • New mechanism for opening URLs with system default browser (works on OSX and Linux as well as Windows)
  • Upgraded bundled version of Jmol to 14.31.53
  • GPL license info on splash screen and About text
  • Jalview Native App:
  • New command line launcher scripts (.sh, .ps1, .bat) usable on macOS, Linux/Unix, Windows and documentation in Help. Installer wizard has option to add this to PATH, or link to it in your PATH.
  • This is the recommended workaround for known issue about working directory preservation when running native application from command line.
  • Notarized MacOS installer for compliance with latest OSX releases (Monterey)
  • Uninstaller application for old (InstallAnywhere based) Jalview installations removed from the OSX disk image
  • Options to allow user to choose the (Swing) Look and Feel (LaF) used by Jalview
  • Metal LaF used to improved operation on Linux Ubuntu with HiDPI display in Java 11 (still known issues with HiDPI screens in java 8 and 11. see JAL-3137)
  • Getdown launcher inherits HTTP/S proxy configuration from jalview_properties
  • New Jalview Develop app - making it even easier to get at Jalview's development builds
  • New splashscreens for Jalview, Jalview Test and Jalview Develop applications.
  • Jalview logos shown for Jalview Java Console and other window widgets in taskbar and dock rather than anonymous 'Java' icons
  • JalviewJS:
  • PDB structures mapped to Uniprot Sequences with SIFTS
  • setprop commandline argument reinstated for JalviewJS only
  • Missing message bundle keys are only reported once per key (avoids excessive log output in js console)
  • Feature type is included in the title of the Feature Settings' Colour Chooser dialog
  • Build details reported in About window
  • Numerous minor GUI additions and improvements in sync with Java application.
  • Development:
  • First integrated JalviewJS and Jalview release
  • Updated README and doc/building.md
  • Improved JalviewJS/Jalview build process, added support for system package provided eclipse installs on linux
  • Install4j 9.0.x used for installer packaging
  • Improved use of installers for unattended installation with a customizedId of "JALVIEW" in install4j's Jalview Launcher
  • Improved compatibility of Jalview build with Java 17 (next LTS target)
  • Issues Resolved:
  • Slow structure commands can block Jalview execution
  • Structure window's viewer-specific menu disappears when only one structure is shown (and many sequences:one chain mappings are present)
  • Annotation file: PROPERTIES apply only to the first SEQUENCE_GROUP defined
  • Selections not propagated between Linked CDS - Protein alignments and their trees (known defect from 2.11.1.3)
  • Not all codon positions highlighted for overlapping exon splice sites (e.g due to RNA slippage)
  • X was not being recognised as the unknown base in DNA sequences
  • Removed RNAview checkbox and logic from Structure Preferences
  • Tooltip behaviour improved (slightly)
  • Can edit a feature so that start > end
  • Cancel from Amend Features doesn't reset a modified graduated colour
  • New View with automatic 'Show Overview' preference enabled results in Null Pointer Exceptions when clustal colouring is enabled
  • Can open multiple Preferences panels
  • Properly configure HTTPS proxy settings from Preferences
  • Standard out logging broken: messages only routing to stderr and appear as a raw template
  • Entering web service parameter values in numerical field doesn't update the value of the parameter until return is pressed.
  • Resolved known issue (from 2.11.1.1) concerning duplicate CDS sequences generated when protein products for certain ENA records are repeatedly shown via Calculate->Show Cross Refs
  • JalviewJS:
  • Consensus profile may include zero (rounded down) percentage values causing a divide by zero
  • JalviewJS doesn't honour arguments passed via Info.args when there are arguments on the URL
  • gradle closure-compiler not using UTF-8
  • Annotation file fails to load from URL in JalviewJS
  • Development:
  • Gradle
  • Fixed non-fatal gradle errors during build
  • Updated build.gradle for use with Gradle v.6.6+

New in Jalview 2.11.1.7 (Jan 19, 2022)

  • Issues Resolved:
  • Files open in Jalview cannot be updated by Jalview or other applications (Windows, other non Unix/BSD OSs).
  • Security:
  • Enable AIA download of HTTPS intermediate certificates.

New in Jalview 2.11.1.6 (Jan 6, 2022)

  • New Features:
  • Version bump library dependency: Log4j 2.16.0 to 2.17.0.

New in Jalview 2.11.1.5 (Dec 20, 2021)

  • Jalview 2.11.1.5 is a critical patch release that updates one of the open source components, log4j, that Jalview relies on. The update addresses the widely reported log4shell security vunerability. This release also addresses a bug in the occupancy calculation that occurs when working with alignments of more than 32,000 sequences.
  • New Features:
  • Update library dependency: Log4j 2.16.0 (was log4j 1.2.x).
  • Development:
  • Updated building instructions
  • Issues Resolved:
  • Occupancy calculation is incorrect for alignment columns with over -1+2^32 gaps (breaking filtering and display)
  • Caps on Hi-DPI scaling to prevent crazy scale factors being set with buggy window-managers (linux only)
  • Development Issues Resolved:
  • Fixed non-fatal gradle errors during build

New in Jalview 2.11.1.4 (Mar 10, 2021)

  • New Features:
  • New .jalview_properties token controlling launch of the news browser (like -nonews argument)
  • New .jalview_properties token controlling download of linkout URLs from www.jalview.org/services/identifiers
  • New .jalview_properties token controlling download of BIOJSHTML templates
  • New 'Discover Web Services' option to trigger a one off JABAWS discovery if autodiscovery was disabled
  • Issues Resolved:
  • Intermittent deadlock opening structure in Jmol
  • New Known defects:
  • Protein Cross-Refs for Gene Sequence not always restored from project (since 2.10.3)
  • Selections from tree built from CDS aren't propagated to Protein alignment (since 2.11.1.3)

New in Jalview 2.11.1.3 (Oct 30, 2020)

  • Issues Resolved:
  • Find doesn't always highlight all matching positions in a sequence (bug introduced in 2.11.1.2)
  • Alignments containing one or more protein sequences can be classed as nucleotide
  • CDS alignment doesn't match original CDS sequences after alignment of protein products (known defect first reported for 2.11.1.0)
  • No tooltip or popup menu for genomic features outwith CDS shown overlaid on protein
  • Overlapping CDS in ENA accessions are not correctly mapped by Jalview (e.g. affects viral CDS with ribosomal slippage, since 2.9.0)
  • Spliced transcript CDS sequences don't show CDS features
  • Selections in CDS sequence panel don't always select corresponding protein sequences
  • Make groups from selection for a column selection doesn't always ignore hidden columns
  • Installer:
  • Space character in Jalview install path on Windows prevents install4j launching getdown
  • Development:
  • Fixed typos and specified compatible gradle version numbers in doc/building.md

New in Jalview 2.11.1.1 (Sep 17, 2020)

  • Jalview 2.11.1.1 is the first patch release in the 2.11.1 series. It includes fixes for critical bugs, and brings a some new features suggested by the Jalview community:
  • Shift+arrow keys navigate to next gap or residue in cursor mode (enable with F2)
  • Support import of VCF 4.3 by updating HTSJDK from 2.12 to 2.23
  • Improved recognition of GZipped files from local disk or retrieved via the web
  • EMBL and EMBL CDS database records retrieved from the European Nucleotide Archive's Data API as 'EMBL Flatfile' records
  • Improved Java Console and logging to help track down problems
  • Improved support for Hi-DPI (4K) screens when running on Linux (Requires Java 11+)
  • Critical bug fixes include:
  • Jalview runs correctly when launched with Turkish language settings
  • Peptide-to-CDS tracking broken when multiple EMBL gene products shown for a single contig (such as viral genomes)
  • Errors encountered when processing variants from VCF files yield "Error processing VCF: Format specifier '%s'" on the console
  • Count of features not shown can be wrong when there are both DNA and Protein features mapped to the position under the cursor
  • Sequence ID for reference sequence is clipped when Right align Sequence IDs enabled
  • Find doesn't report matches that span hidden gapped columns
  • Jalview ignores file format parameter specifying output format when exporting an alignment via the command line
  • Known Issues:
  • We've had reports from a small number of windows 10 users who see a warning dialog pop up when Jalview tries to save a new version of an existing file. If you are affected by this bug and this latest version of Jalview doesn't fix it, please let us know!
  • Drag and drop of alignment file onto alignment window when in a HiDPI scaled mode in Linux only works for the top left quadrant of the alignment window
  • Co-located features exported and re-imported are ordered differently when shown on alignment and in tooltips. (Also affects v2.11.1.0)
  • Linked CDS/Protein alignment of genes sharing the same ENA accession doesn't work as expected.

New in Jalview 2.11.1 (Apr 22, 2020)

  • New Features:
  • Map 'virtual' codon features shown on protein (or vice versa) for display in alignments, on structure views (including transfer to UCSF chimera), in feature reports and for export.
  • Feature attributes from VCF files can be exported and re-imported as GFF3 files
  • Capture VCF "fixed column" values POS, ID, QUAL, FILTER as Feature Attributes
  • More robust VCF numeric data field validation while parsing
  • Feature Settings dialog keeps same screen position if reopened
  • Feature Settings dialog title includes name of associated view
  • Font anti-aliasing in alignment views enabled by default
  • Very long feature descriptions truncated in tooltips and menus
  • Warn if Sort by Score or Density attempted with no feature types visible
  • Improved support for filtering feature attributes with large integer values
  • Jalview Installer:
  • Versions for install4j and getdown and installer template version reported in console (may be null when Jalview launched as executable jar or via conda)
  • Layout improvements for OSX .dmg Finder and higher quality background images
  • New installer/application launcher generated with install4j 8.0.4
  • Jalview File Associations shown for Unix Platforms
  • Improved defaults for maximum memory setting when running on large memory machines
  • Release processes:
  • New point release version scheme - 2.11.1.0
  • 'Jalview Test' installers/apps for easier access to test-release channel builds
  • Build System
  • Clover updated to 4.4.1
  • Test code included in Clover coverage report
  • Groovy Scripts:
  • Exportconsensus.groovy prints a FASTA file to stdout containing the consensus sequence for each alignment in a Jalview session
  • ComputePeptideVariants.groovy to translate genomic sequence_variant annotation from CDS as missense_variant or synonymous_variant on protein products.
  • Issues Resolved
  • Hidden sequence markers still visible when 'Show hidden markers' option is not ticked
  • Hidden sequence markers not shown in EPS and PNG output when 'Automatically set ID width' is set in jalview preferences or properties file
  • Feature Editor dialog can be opened when 'Show Sequence Features' option is not ticked
  • Undo 'Null' operation shown after sort by buttons in Feature Settings dialog are clicked when no features are visible
  • ID margins for CDS and Protein views not equal when split frame is first opened
  • Sequence position numbers in status bar not correct after editing a sequence's start position
  • Alignment is misaligned in wrapped mode with annotation and exceptions thrown when only a few columns shown in wrapped mode
  • Sequence IDs missing in headless export of wrapped alignment figure with annotations
  • Sorting Structure Chooser table by Sequence ID fails with ClassCastException
  • Chimera session not restored from Jalview Project
  • Double-click on 'Show feature' checkbox in feature settings dialog also selects columns
  • SpinnerNumberModel causes IllegalArgumentException in some circumstances
  • Multiple feature settings dialogs can be opened for a view
  • Feature Settings dialog is orphaned if alignment window is closed
  • Credits missing some authors in Jalview help documentation for 2.11.0 release
  • Export of Pfam alignment as Stockholm includes Pfam ID as sequence's accession rather than its Uniprot Accession
  • Java 11 Compatibility issues:
  • OSX - Can't view some search results in PDB/Uniprot search panel
  • Installer:
  • Alview should not create file associations for 3D structure files (.pdb, .mmcif. .cif)
  • Repository and Source Release:
  • Removed obsolete .cvsignore files from repository
  • Clover report generation running out of memory

New in Jalview 2.11.0 (Jul 5, 2019)

  • New Features:
  • Jalview Native Application and Installers built with install4j (licensed to the Jalview open source project) rather than InstallAnywhere
  • Jalview Launcher System to auto-configure memory settings, receive over the air updates and launch specific versions via (Three Rings' GetDown)
  • File type associations for formats supported by Jalview (including .jvp project files)
  • Jalview launch files (.jvl) to pass command line arguments and switch between different getdown channels
  • Backup files created when saving Jalview project or alignment files
  • Annotate nucleotide alignments from VCF data files
  • Version of HTSJDK shipped with Jalview updated to version 2.12.0
  • Alternative genetic code tables for 'Translate as cDNA'
  • Update of Ensembl Rest Client to API v10.0
  • Enhanced visualisation and analysis of Sequence Features
  • IntervalStoreJ (NCList implementation that allows updates) used for Sequence Feature collections
  • Sequence features can be filtered and shaded according to any associated attributes (e.g. variant attributes from VCF file, or key-value pairs imported from column 9 of GFF file)
  • Feature Attributes and shading schemes stored and restored from Jalview Projects
  • Use full Sequence Ontology (via BioJava) to recognise variant features
  • Show synonymous codon variants on peptide sequences (also coloured red by default)
  • Popup window to show full report for a selected sequence feature's details
  • More efficient sequence feature render algorithm (Z-sort/transparency and filter aware)
  • Improved tooltips in Feature Settings dialog
  • Symmetric score matrices for faster tree and PCA calculations
  • Principal Components Analysis Viewer
  • Principal Components Analysis results and Viewer state saved in Jalview Project
  • 'Change parameters' option removed from viewer's drop-down menus
  • Can use shift + arrow keys to rotate PCA image incrementally
  • PCA plot is depth cued
  • New 'Colour by Sequence ID' option
  • Speed and Efficiency
  • More efficient creation of selections and multiple groups when working with large alignments
  • Speedier import of annotation rows when parsing Stockholm files
  • User Interface
  • Finder panel remembers last position in each view
  • Alignment Overview now WYSIWIS (What you see is what is shown)
  • Only visible regions of alignment are shown by default (can be changed in user preferences)
  • File Chooser stays open after responding Cancel to the Overwrite Dialog
  • Better popup menu behaviour when all sequences are hidden
  • Status bar shows bounds when dragging a selection region, and gap count when inserting or deleting gaps
  • Status bar updates over sequence and annotation labels
  • Annotation tooltips and popup menus are shown when in wrapped mode
  • Can select columns by dragging left/right in a graph or histogram annotation
  • Help button on Uniprot and PDB search panels
  • Cursor changes over draggable box in Overview panel
  • Consistent ordering of links in sequence id popup menu
  • Red line indicating tree-cut position not shown if no subgroups are created
  • Removed ability to configure length of search history by right-clicking search box
  • Jalview Groovy Scripting Console updated to Groovy v2.5
  • Java 11 Support (not yet on general release)
  • OSX GUI integrations for App menu's 'About' entry and trapping CMD-Q
  • Deprecations:
  • DAS sequence retrieval and annotation capabilities removed from the Jalview Desktop
  • Castor library for XML marshalling and unmarshalling has been replaced by JAXB for Jalview projects and XML based data retrieval clients
  • Disable VAMSAS menu in preparation for removal
  • Jalview Desktop no longer distributed via Java Web Start
  • Documentation
  • Added remarks about transparent rendering effects not supported in EPS figure export
  • Typos in documentation for Preferences dialog
  • Development and Release Processes:
  • Build system migrated from Ant to Gradle
  • Enhanced checks for missing and duplicated keys in Message bundles
  • Eclipse project configuration managed with gradle-eclipse
  • Atlassian Bamboo continuous integration for unattended Test Suite execution
  • Memory test suite to detect leaks in common operations
  • More unit test coverage, and minor issues resolved
  • Developer documentation migrated to markdown (with HTML rendering)
  • HelpLinksChecker runs on Windows
  • New URLs for publishing development versions of Jalview
  • Issues Resolved:
  • Timeouts when retrieving data from Ensembl
  • 'View [Structure] Mappings' and structure superposition in Jmol fail on Windows
  • Blank error dialog is displayed when discovering structures for sequences with lots of PDB structures
  • Text misaligned in EPS or SVG image export with monospaced font
  • Warning of 'Duplicate entry' when saving Jalview project involving multiple views
  • Overview for complementary view in a linked CDS/Protein alignment is not updated when Hide Columns by Annotation dialog hides columns
  • Selection highlighting in the complement of a CDS/Protein alignment stops working after making a selection in one view, then making another selection in the other view
  • Annotations tooltip changes beyond visible columns
  • Table Columns could be re-ordered in Feature Settings and Jalview Preferences panels
  • Jalview hangs when closing windows, or redrawing the overview with large alignments
  • Tree and PCA calculation fails for selected region if columns were selected by dragging right-to-left and the mouse moved to the left of the first column
  • Couldn't hide selected columns adjacent to a hidden column marker via scale popup menu
  • Error message for trying to load in invalid URLs doesn't tell users the invalid URL
  • Tooltips displayed for features filtered by score from view
  • Sequence Variants retrieved from Ensembl during show cross references or Fetch Database References are shown in red in original view
  • stop_gained variants not shown correctly on peptide sequence (computed variant shown as p.Res.null)
  • 'Graduated colour' option not offered for manually created features (where feature score is Float.NaN)
  • Blank extra columns drawn or printed when columns are hidden
  • Regular expression error for '(' in Select Columns by Annotation description
  • Scroll doesn't stop on mouse up after dragging out of Scale or Annotation Panel
  • Column selection incorrect after scrolling out of scale panel
  • Left/right drag in annotation can scroll alignment down
  • Error if mouse moved before clicking Reveal in scale panel
  • Column display is out by one after Page Down, Page Up in wrapped mode
  • Finder doesn't skip hidden regions
  • Finder searches in minimised alignments
  • 'Apply Colour to All Groups' not always selected on opening an alignment
  • 'Colour by Annotation' not marked selected in Colour menu
  • Per-group Clustal colour scheme changes when different groups in the alignment are selected
  • Internationalised colour scheme names not shown correctly in menu
  • Colour by Annotation can go black at min/max threshold limit
  • Value input for graduated feature colour threshold gets 'unrounded'
  • PCA image export doesn't respect background colour
  • PCA points don't dim when rotated about y axis
  • PCA Print dialog continues after Cancel
  • Cancel in Tree Font dialog resets alignment, not Tree font
  • Associate Tree with All Views not restored from project file
  • Scrolling of split frame is sluggish if Overview shown in complementary view
  • Codon consensus incorrectly scaled when shown without normalisation
  • Sequence Details report should open positioned at top of report
  • Help page can be opened twice
  • Fuzzy text in web service status menu on OSX Mojave
  • Editing:
  • Start and End should be updated when sequence data at beginning or end of alignment added/removed via 'Edit' sequence
  • Delete/Cut selection doesn't relocate sequence features correctly when start of sequence is removed (Known defect since 2.10)
  • Inserting gap sequence via the Edit Sequence dialog corrupts dataset sequence
  • Structure colours not updated when associated tree repartitions the alignment view (Regression in 2.10.5)
  • Datamodel:
  • Sequence.findIndex returns wrong value when sequence's End is greater than its length
  • Bugs fixed for Java 11 Support (not yet on general release)
  • Menus work properly in split-screen
  • New Known Defects:
  • Select columns containing feature by double clicking ignores bounds of an existing selected region
  • Codon consensus logo incorrectly scaled in gapped regions of protein alignment.
  • Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project
  • Alignment panel height can be too small after 'New View'
  • Display is incorrect after removing gapped columns within hidden columns
  • Rightmost selection is lost when mouse re-enters window after dragging left to select columns to left of visible region
  • Features coloured according to their description string and thresholded by score in earlier versions of Jalview are not shown as thresholded features in 2.11. To workaround please create a Score filter instead.
  • Cancel on Feature Settings dialog doesn't reset group visibility
  • F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
  • Closing tree windows with CMD/CTRL-W for alignments with multiple views can close views unexpectedly
  • Java 11 Specific defects:
  • Jalview Properties file is not sorted alphabetically when saved

New in Jalview 2.10.5 (Sep 6, 2018)

  • New Features:
  • 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
  • Issues Resolved:
  • 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.

New in Jalview 2.10.4 (May 10, 2018)

  • New Features
  • 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)
  • Issues Resolved
  • 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)
  • 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)

New in Jalview 2.10.3b1 (Jan 24, 2018)

  • 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

New in Jalview 2.10.3 (Nov 20, 2017)

  • NEW FEATURES:
  • 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
  • ISSUES RESOLVED:
  • 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 in Jalview 2.10.2b2 (Oct 27, 2017)

  • This is a patch release that fixes stability problems with Jalview's ability to retrieve Uniprot sequences and access other data hosted at the EMBL-EBI.
  • New Features:
  • Uniprot Sequence Fetcher now uses web API at uniprot.org
  • HTTPS used for all connections to ebi.ac.uk

New in Jalview 2.10.1 (Dec 8, 2016)

  • New Features:
  • 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 justfrom 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
  • Issues Resolved:
  • 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

New in Jalview 2.10 (Oct 10, 2016)

  • NEW FEATURES:
  • General:
  • Updated Spanish translations.
  • Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.
  • Alignment ruler shows positions relative to reference sequence
  • Position/residue shown in status bar when mousing over sequence associated annotation
  • Default RNA SS symbol to 'matching bracket' for manual entry
  • RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column
  • Feature settings popup menu options for showing or hiding columns containing a feature
  • Edit selected group by double clicking on group and sequence associated annotation labels
  • Sequence name added to annotation label in select/hide columns by annotation and colour by annotation dialogs
  • Application:
  • Automatically hide introns when opening a gene/transcript view
  • Uniprot Sequence fetcher Free Text Search dialog
  • UniProt - PDB protein structure mappings with the EMBL-EBI PDBe SIFTS database
  • Updated download sites used for Rfam and Pfam sources to xfam.org
  • Disabled Rfam(Full) in the sequence fetcher
  • Show residue labels in Chimera when mousing over sequences in Jalview
  • Support for reverse-complement coding regions in ENA and EMBL
  • Upgrade to EMBL XML 1.2 for record retrieval via ENA rest API
  • Support for ENA CDS records with reverse complement operator
  • Update to groovy-2.4.6-indy - for faster groovy script execution
  • New 'execute Groovy script' option in an alignment window's Calculate menu
  • Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode
  • Support for creating new alignment calculation workers from groovy scripts
  • Store/restore reference sequence in Jalview projects
  • Chain codes for a sequence's PDB associations are now saved/restored from project
  • Database selection dialog always shown before sequence fetcher is opened
  • Double click on an entry in Jalview's database chooser opens a sequence fetcher
  • Free-text search client for UniProt using the UniProt REST API
  • -nonews command line parameter to prevent the news reader opening
  • Displayed columns for PDBe and Uniprot querying stored in preferences
  • Pagination for displaying PDBe and Uniprot search results
  • Tooltips shown on database chooser
  • Reverse complement function in calculate menu for nucleotide sequences
  • Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets).
  • Chimera 1.11.1 minimum requirement for viewing structures with Jalview 2.10
  • Retrieve genome, transcript CCDS and gene ids via the Ensembl and Ensembl Genomes REST API
  • Protein sequence variant annotation computed for 'sequence_variant' annotation on CDS regions (Ensembl)
  • ENA CDS 'show cross references' for Uniprot sequences
  • Improved warning messages when DB Ref Fetcher fails to match, or otherwise updates sequence data from external database records.
  • Revised Jalview Project format for efficient recovery of sequence coding and alignment annotation relationships.
  • ISSUES RESOLVED:
  • 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
  • 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
  • RNA 3D structure not added via DSSR service
  • 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.
  • Duplicate group consensus and conservation rows shown when tree is partitioned
  • Erratic behaviour when tree partitions made with multiple cDNA/Protein split views

New in Jalview 2.9 (Sep 24, 2015)

  • NEW FEATURES:
  • General:
  • Jmol integration updated to Jmol v14.2.14
  • Import and export of Jalview alignment views as BioJSON
  • New alignment annotation file statements for reference sequences and marking hidden columns
  • Reference sequence based alignment shading to highlight variation
  • Select or hide columns according to alignment annotation
  • Find option for locating sequences by description
  • Conserved physicochemical properties shown in amino acid conservation row
  • Alignments can be sorted by number of RNA helices
  • Linked visualisation and analysis of DNA and Protein alignments:
  • Translated cDNA alignments shown as split protein and DNA alignment views
  • Codon consensus annotation for linked protein and cDNA alignment views
  • Link cDNA or Protein product sequences by loading them onto Protein or cDNA alignments
  • Reconstruct linked cDNA alignment from aligned protein sequences
  • Application:
  • Use REST API to talk to Chimera
  • Selected regions in Chimera are highlighted in linked Jalview windows
  • VARNA RNA viewer updated to v3.93
  • VARNA views are saved in Jalview Projects
  • Pseudoknots displayed as Jalview RNA annotation can be shown in VARNA
  • Make groups for selection uses marked columns as well as the active selected region
  • Calculate UPGMA and NJ trees using sequence feature similarity
  • JPred4 employed for protein secondary structure predictions
  • Hide Insertions menu option to hide unaligned columns for one or a group of sequences
  • Automatically hide insertions in alignments imported from the JPred4 web server
  • Nearly) Native 'Quaqua' dialogs for browsing file system on OSX
  • LGPL libraries courtesy of http://www.randelshofer.ch/quaqua/
  • changed 'View nucleotide structure' submenu to 'View VARNA 2D Structure'
  • change "View protein structure" menu option to "3D Structure ..."
  • New cDNA/Protein analysis capabilities:
  • Get Cross-References opens a Split Frame view with cDNA/Protein
  • Detect when nucleotide sequences and protein sequences are placed in the same alignment
  • Split cDNA/Protein views are saved in Jalview projects
  • New Export options:
  • New Export Settings dialog to control hidden region export in flat file generation
  • Export alignment views for display with the BioJS MSAViewer
  • Export scrollable SVG in HTML page
  • Optional embedding of BioJSON data when exporting alignment figures to HTML
  • 3D structure retrieval and display:
  • Free text and structured queries with the PDBe Search API
  • PDBe Search API based discovery and selection of PDB structures for a sequence set
  • Applet:
  • New layout for applet example pages
  • New parameters to enable SplitFrame view (file2,enableSplitFrame, scaleProteinAsCdna)
  • New example demonstrating linked viewing of cDNA and Protein alignments
  • Development and deployment:
  • Java 1.7 minimum requirement for Jalview 2.9
  • Include installation type and git revision in build properties and console log output
  • Jalview Github organisation, and new github site for storing BioJsMSA Templates
  • Jalview's unit tests now managed with TestNG
  • ISSUES RESOLVED:
  • Application:
  • Escape should close any open find dialogs
  • Typo in select-by-features status report
  • Consensus RNA secondary secondary structure predictions are not highlighted in amber
  • Missing gap character in v2.7 example file means alignment appears unaligned when pad-gaps is not enabled
  • First switch to RNA Helices colouring doesn't colour associated structure views
  • ID width preference option is greyed out when auto width checkbox not enabled
  • Stopped a warning dialog from being shown when creating user defined colours
  • View Mapping' in structure viewer shows sequence mappings for just that viewer's sequences
  • Workaround for superposing PDB files containing multiple models in Chimera
  • Report sequence position in status bar when hovering over Jmol structure
  • Cannot output gaps as '.' symbols with Selection -> output to text box
  • Flat file exports of alignments with hidden columns have incorrect sequence start/end
  • Aligning' a second chain to a Chimera structure from Jalview fails
  • Colour schemes applied to structure viewers don't work for nucleotide
  • Loading/cut'n'pasting an empty or invalid file leads to a grey/invisible alignment window
  • Exported Jpred annotation from a sequence region imports to different position
  • Space at beginning of sequence feature tooltips shown on some platforms
  • Chimera viewer 'View | Show Chain' menu is not populated
  • New View' fails with a Null Pointer Exception in console if Chimera has been opened
  • Mouseover to Chimera not working
  • Miscellaneous ENA XML feature qualifiers not retrieved
  • NPE in annotation renderer after 'Extract Scores'
  • If two structures in one Chimera window, mouseover of either sequence shows on first structure
  • Show annotations' options should not make non-positional annotations visible
  • Subsequence secondary structure annotation not shown in right place after 'view flanking regions'
  • File Save As type unset when current file format is unknown
  • Save as '.jar' option removed for saving Jalview projects
  • Colour by Sequence colouring in Chimera more responsive
  • Cannot 'add reference annotation' for a sequence in several views on same alignment
  • Cannot show linked products for EMBL / ENA records
  • Jalview's tooltip wraps long texts containing no spaces
  • Applet:
  • Jmol to JalviewLite mouseover/link not working
  • JalviewLite can't import sequences with ID descriptions containing angle brackets
  • General:
  • Cannot export and reimport RNA secondary structure via jalview annotation file
  • Random helix colour palette for colour by annotation with RNA secondary structure
  • Mouseover to cDNA from STOP residue in protein translation doesn't work.
  • hints when using the select by annotation dialog box
  • Jmol alignment incorrect if PDB file has alternate CA positions
  • FontChooser message dialog appears to hang after choosing 1pt font
  • Peptide secondary structure incorrectly imported from annotation file when annotation display text includes 'e' or 'h'
  • Cannot set colour of new feature type whilst creating new feature
  • cDNA translation alignment should not be sequence order dependent
  • Show unconserved' doesn't work for lower case sequences
  • Nucleotide ambiguity codes involving R not recognised
  • Deployment and Documentation:
  • Applet example pages appear different to the rest of www.jalview.org

New in Jalview 2.8.2 (Dec 4, 2014)

  • New Features:
  • Updated Java code signing certificate donated by Certum.PL.
  • Features and annotation preserved when performing pairwise alignment
  • RNA pseudoknot annotation can be imported/exported/displayed
  • colour by annotation' can colour by RNA and protein secondary structure
  • New in the Jalview Desktop:
  • Extract and display secondary structure for sequences with 3D structures
  • Support for parsing RNAML
  • Annotations menu for layout
  • sort sequence annotation rows by alignment
  • place sequence annotation above/below alignment annotation
  • Output in Stockholm format
  • Internationalisation: improved Spanish (es) translation
  • Structure viewer preferences tab
  • Disorder and Secondary Structure annotation tracks shared between alignments
  • UCSF Chimera launch and linked highlighting from Jalview
  • Show/hide all sequence associated annotation rows for all or current selection
  • disorder and secondary structure predictions available as dataset annotation
  • Per-sequence rna helices colouring
  • Sequence database accessions imported when fetching alignments from Rfam
  • update VARNA version to 3.91
  • New groovy scripts for exporting aligned positions, conservation values, and calculating sum of pairs scores.
  • Command line argument to set default JABAWS server
  • include installation type in build properties and console log output
  • Updated Jalview project format to preserve dataset annotation
  • Issues resolved:
  • Distinguish alignment and sequence associated RNA structure in structure->view->VARNA
  • Raise dialog box if user deletes all sequences in an alignment
  • Pressing F1 results in documentation opening twice
  • Sequence feature tooltip is wrapped
  • Double click on sequence associated annotation selects only first column
  • Redundancy removal doesn't result in unlinked leaves shown in tree
  • Undos after several redundancy removals don't undo properly
  • Hide sequence doesn't hide associated annotation
  • User defined colours dialog box too big to fit on screen and buttons not visible
  • author list isn't updated if already written to jalview properties
  • Popup menu won't open after retrieving sequence from database
  • File open window for associate PDB doesn't open
  • Left-then-right click on a sequence id opens a browser search window
  • Cannot open sequence feature shading/sort popup menu in feature settings dialog
  • better tooltip placement for some areas of Jalview desktop
  • Allow additon of JABAWS Server which doesn't pass validation
  • Web services parameters dialog box is too large to fit on screen
  • Muscle nucleotide alignment preset obscured by tooltip
  • JABAWS preset submenus don't contain newly defined user preset
  • MSA web services warns user if they were launched with invalid input
  • Jalview cannot contact DAS Registy when running on Java 8
  • Superpose with' submenu not shown when new view created
  • Changes in Deployment and Documentation:
  • 2G and 1G options in launchApp have no effect on memory allocation
  • launchApp service doesn't automatically open www.jalview.org/examples/exampleFile.jar if no file is given
  • InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is available - upgraded to InstallAnywhere 2014

New in Jalview 2.8.1 (Jun 5, 2014)

  • New Features:
  • Internationalisation of user interface (i18n support) and translation for Spanish locale
  • Define/Undefine group on current selection with Ctrl-G/Shift Ctrl-G
  • Improved group creation/removal options in alignment/sequence Popup menu
  • Sensible precision for symbol distribution percentages shown in logo tooltip.
  • Annotation panel height set according to amount of annotation when alignment first opened
  • Application:
  • Interactive consensus RNA secondary structure prediction VIENNA RNAAliFold JABA 2.1 service
  • Select columns containing particular features from Feature Settings dialog
  • View all 'representative' PDB structures for selected sequences
  • Update Jalview project format:
  • New file extension for Jalview projects '.jvp'
  • Preserve sequence and annotation dataset (to store secondary structure annotation,etc)
  • Per group and alignment annotation and RNA helix colouring
  • New similarity measures for PCA and Tree calculation (PAM250)
  • Experimental support for retrieval and viewing of flanking regions for an alignment
  • Bugs resolved:
  • Consensus sequence for alignments/groups with a single sequence were not calculated
  • annotation files that contain only groups imported as annotation and junk sequences
  • Fasta files with sequences containing '*' incorrectly recognised as PFAM or BLC
  • conservation/PID slider apply all groups option doesn't affect background (2.8.0b1)
  • redundancy highlighting is erratic at 0% and 100%
  • Remove gapped columns fails for sequences with ragged trailing gaps
  • AMSA annotation row with leading spaces is not registered correctly on import
  • Jalview crashes when selecting PCA analysis for certain alignments
  • Opening the colour by annotation dialog for an existing annotation based 'use original colours' colourscheme loses original colours setting
  • Application:
  • logo keeps spinning and status remains at queued or running after job is cancelled
  • cannot export features from alignments imported from Jalview/VAMSAS projects
  • Buggy slider for web service parameters that take float values
  • Newly created RNA secondary structure line doesn't have 'display all symbols' flag set
  • T-COFFEE alignment score shading scheme and other annotation shading not saved in jalview project
  • Local file cannot be loaded in freshly downloaded Jalview
  • Jalview icon not shown on dock in Mountain Lion/Webstart
  • Load file from desktop file browser fails
  • Occasional NPE thrown when calculating large trees
  • Cannot reorder or slide sequences after dragging an alignment onto desktop
  • Colour by annotation dialog throws NPE after using 'extract scores' function
  • Loading/cut'n'pasting an empty file leads to a grey alignment window
  • Disorder thresholds rendered incorrectly after performing IUPred disorder prediction
  • Multiple group annotated consensus rows shown when changing 'normalise logo' display setting
  • Find shows blank dialog after 'finished searching' if nothing matches query
  • Null Pointer Exceptions raised when sorting by feature with lots of groups
  • Errors in Jmol console when structures in alignment don't overlap
  • Not all working JABAWS services are shown in Jalview's menu
  • JAVAWS version of jalview fails to launch with 'invalid literal/length code'
  • Annotation/RNA Helix colourschemes cannot be applied to alignment with groups (actually fixed in 2.8.0b1)
  • RNA Helices and T-Coffee Scores available as default colourscheme
  • Applet:
  • Remove group option is shown even when selection is not a group
  • Apply to all groups ticked but colourscheme changes don't affect groups
  • Documented RNA Helices and T-Coffee Scores as valid colourscheme name
  • Annotation labels drawn on sequence IDs when Annotation panel is not displayed
  • Increased font size for dropdown menus on OSX and embedded windows

New in Jalview 2.8 (Oct 17, 2013)

  • NEW FEATURES:
  • Application:
  • Support for JABAWS 2.0 Services (AACon alignment conservation, protein disorder and Clustal Omega)
  • JABAWS server status indicator in Web Services preferences
  • VARNA (http://varna.lri.fr) viewer for RNA structures in Jalview alignment window
  • Updated jalview build and deploy framework for OSX mountain lion, windows 7, and 8
  • Nucleotide substitution matrix for PCA that supports RNA and ambiguity codes
  • Improved sequence database retrieval GUI
  • Support fetching and database reference look up against multiple DAS sources (Fetch all from in 'fetch db refs')
  • Jalview project improvements
  • Store and retrieve the 'belowAlignment' flag for annotation
  • calcId attribute to group annotation rows on the alignment
  • Store AACon calculation settings for a view in Jalview project
  • horizontal scrolling gesture support
  • Visual progress indicator when PCA calculation is running
  • Simpler JABA web services menus
  • visual indication that web service results are still being retrieved from server
  • Serialise the dialogs that are shown when jalview starts up for first time
  • Jalview user agent string for interacting with HTTP services
  • DAS 1.6 and DAS 2.0 source support using new JDAS client library
  • Examples directory and Groovy library included in InstallAnywhere distribution
  • General:
  • Normalize option for consensus sequence logo
  • Reset button in PCA window to return dimensions to defaults
  • Allow seqspace or Jalview variant of alignment PCA calculation
  • PCA with either nucleic acid and protein substitution matrices
  • Allow windows containing HTML reports to be exported in HTML
  • Interactive display and editing of RNA secondary structure contacts
  • RNA Helix Alignment Colouring
  • RNA base pair logo consensus
  • Parse sequence associated secondary structure information in Stockholm files
  • HTML Export database accessions and annotation information presented in tooltip for sequences
  • Import secondary structure from LOCARNA clustalw style RNA alignment files
  • import and visualise T-COFFEE quality scores for an alignment
  • colour by annotation' per sequence option to shade each sequence according to its associated alignment annotation
  • New Jalview Logo
  • Documentation and Development:
  • documentation for score matrices used in Jalview
  • New Website!
  • ISSUES RESOLVED:
  • Application:
  • PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch REST service
  • Stop windows being moved outside desktop on OSX
  • Filetype associations not installed for webstart launch
  • Jalview does not always retrieve progress of a JABAWS job execution in full once it is complete
  • revise SHMR RSBS definition to ensure alignment is uploaded via ali_file parameter
  • Jalview 2.7 is incompatible with Jmol-12.2.2
  • View all structures superposed fails with exception
  • Jnet job queues forever if a very short sequence is submitted for prediction
  • Cut and paste menu not opened when mouse clicked on desktop window
  • Putting fractional value into integer text box in alignment parameter dialog causes jalview to hang
  • Structure view highlighting doesn't work on windows 7
  • View all structures fails with exception shown in structure view
  • Characters in filename associated with PDBEntry not escaped in a platform independent way
  • Jalview desktop fails to launch with exception when using proxy
  • Tree calculation reports 'you must have 2 or more sequences selected' when selection is empty
  • Jalview desktop fails to launch with jar signature failure when java web start temporary file caching is disabled
  • DAS Sequence retrieval with range qualification results in sequence xref which includes range qualification
  • Errors during processing of command line arguments cause progress bar (JAL-898) to be removed
  • Replace comma for semi-colon option not disabled for DAS sources in sequence fetcher
  • Cannot close news reader when JABAWS server warning dialog is shown
  • Option widgets not updated to reflect user settings
  • Edited sequence not submitted to web service
  • Jalview 2.7 Webstart does not launch on mountain lion
  • InstallAnywhere installer doesn't unpack and run on OSX Mountain Lion
  • Annotation panel not given a scroll bar when sequences with alignment annotation are pasted into the alignment
  • Sequence associated annotation rows not associated when loaded from jalview project
  • Browser launch fails with NPE on java 1.7
  • JABAWS alignment marked as finished when job was cancelled or job failed due to invalid input
  • NPE with v2.7 example when clicking on Tree associated with all views
  • Exceptions when copy/paste sequences with grouped annotation rows to new window
  • General:
  • Redundancy removal fails for rna alignment
  • PCA calculation fails when sequence has been selected and then deselected
  • PCA window shows grey box when first opened on OSX
  • Letters colored pink in sequence logo when alignment colored with clustalx
  • Choosing fonts without letter symbols defined causes exceptions and redraw errors
  • Initial PCA plot view is not same as manually reconfigured view
  • Grouped annotation graph label has incorrect line color
  • Grouped annotation graph label display is corrupted for lots of labels

New in Jalview 2.7 (Dec 1, 2011)

  • New Features:
  • Application:
  • Jalview Desktop News Reader
  • Tweaked default layout of web services menu
  • View/alignment association menu to enable user to easily specify which alignment a multi-structure view takes its colours/correspondences from
  • Allow properties file location to be specified as URL
  • Extend jalview project to preserve associations between many alignment views and a single Jmol display
  • Store annotation row height in jalview project file
  • Annotation row column label formatting attributes stored in project file
  • Annotation row order for auto-calculated annotation rows preserved in jalview project file
  • Visual progress indication when Jalview state is saved using Desktop window menu
  • Visual indication that command line arguments are still being processed
  • Groovy script execution from URL
  • Colour by annotation default min and max colours in preferences
  • Automatically associate PDB files dragged onto an alignment with sequences that have high similarity and matching IDs
  • Update JGoogleAnalytics to latest release (0.3)
  • 'view structures' option to open many structures in same window
  • Sort associated views menu option for tree panel
  • Group all JABA and non-JABA services for a particular analysis function in its own submenu
  • Applet:
  • Userdefined and autogenerated annotation rows for groups
  • Adjustment of alignment annotation pane height
  • Annotation scrollbar for annotation panel
  • Drag to reorder annotation rows in annotation panel
  • 'automaticScrolling' parameter
  • Allow sequences with partial ID string matches to be annotated from GFF/jalview features files
  • Sequence logo annotation row in applet
  • Absolute paths relative to host server in applet parameters are treated as such
  • New in the JalviewLite javascript API:
  • JalviewLite.js javascript library
  • Javascript callbacks for
  • Applet initialisation
  • Sequence/alignment mouse-overs and selections
  • scrollTo row and column alignment scrolling functions
  • Select sequence/alignment regions from javascript
  • javascript structure viewer harness to pass messages between Jmol and Jalview when running as distinct applets
  • sortBy method
  • Set of applet and application examples shipped with documentation
  • New example to demonstrate jalviewLite and Jmol javascript message exchange
  • General:
  • Enable Jmol displays to be associated with multiple multiple alignments
  • Option to automatically sort alignment with new tree
  • User configurable link to enable redirects to a www.jalview.org mirror
  • Jmol colours option for Jmol displays
  • Configurable newline string when writing alignment and other flat files
  • Allow alignment annotation description lines to contain html tags
  • Documentation and Development
  • Add groovy test harness for bulk load testing to examples
  • Groovy script to load and align a set of sequences using a web service before displaying the result in the Jalview desktop
  • Restructured javascript and applet api documentation
  • Ant target to publish example html files with applet archive
  • Netbeans project for building jalview from source
  • ant task to create online javadoc for jalview source
  • Issues Resolved:
  • Application:
  • User defined colourscheme throws exception when current built in colourscheme is saved as new scheme
  • AlignFrame->Save in application pops up save dialog for valid filename/format
  • Cannot view associated structure for Uniprot sequence
  • PDB file association breaks for Uniprot sequence P37173
  • Associate PDB from file dialog does not tell you which sequence is to be associated with the file
  • Find All raises null pointer exception when query only matches sequence IDs
  • Pre 2.6 Jalview project cannot be loaded into v2.6
  • Jalview project with Jmol views created with Jalview 2.4 cannot be loaded
  • Filetype associations not installed for webstart launch
  • Two or more chains in a single PDB file associated with sequences in different alignments do not get coloured by their associated sequence
  • Visibility status of autocalculated annotation row not preserved when project is loaded
  • Annotation row height and visibility attributes not stored in jalview project
  • Tree bootstraps are not preserved when saved as a jalview project
  • Envision2 workflow tooltips are corrupted
  • Enabling show group conservation also enables colour by conservation
  • Duplicate group associated conservation or consensus created on new view
  • Annotation scrollbar not displayed after 'show all hidden annotation rows' option selected
  • Alignment quality not updated after alignment annotation row is hidden then shown
  • Preserve colouring of structures coloured by sequences in pre jalview 2.7 projects
  • Web service job parameter dialog is not laid out properly
  • Web services menu not refreshed after 'reset services' button is pressed in preferences
  • Annotation off by one in jalview v2_3 example project
  • Structures imported from file and saved in project get name like jalview_pdb1234.txt when reloaded
  • Jalview does not always retrieve progress of a JABAWS job execution in full once it is complete
  • Applet:
  • Alignment height set incorrectly when lots of annotation rows are displayed
  • Relative URLs in feature HTML text not resolved to codebase
  • View follows highlighting does not work for positions in sequences