Issues Resolved

• Annotation tracks displayed on top of each other after ‘Add reference annotations’
• Secondary structure tree calculation in 2.11.4.0 breaks for example jalview project
• Blank tooltips shown for some annotation tracks
• When building Jalview releases, getdownArchive task fails looking for the archive background image

Issues Resolved

• jalview does not fetch from a URL containing a redirect
• HTTP errors are often interpreted to the user as a file format error - and FileNotFound errors are not propagated from Web or Local file import
• launcher.log from jalview runtime missing newlines and also lacks stdout/stderr reported in Jalview Console
• Possible “Zip Slip Vulnerability” in getdown
• jalview.bin.CommandsTest.headlessOrGuiImageOutputTest produces different images for –gui and –headless when using certain .jalview_properties
• Release installer DMG does not display the background image
• Getdown splash screen should disappear as soon as the Jalview Desktop is created/visible
• Race condition in Jalview quit handler that can cause a hang on very slow interactive systems
• Adjusting the saved as file format via the Alignment window Save As… dialog box doesn’t actually change the format used to save the alignment
• Annotation labels from protein disorder services include html tags from description

development and deployment

• Removed gradle build’s dependency on gradle-imagemagick plugin to allow building on windows (still need imagemagick installed on path for splashscreen commit watermark)
• Fixed inconsistencies in test suite on different platforms
• The rendering of the text “Window” for the Window menu item is different to the other menus when testing in Linux

New Known Issues

• PaSiMap not available in JalviewJS
• Jalview ignores ncrna genes when importing from genbank format files
• Sequence letter aspect ratio not set correctly when aspect ratio is very narrow after middle-mouse drag
• cannot store/restore group associated secondary structure consensus annotations
• spurious output image .extensions cause jalview CLI execution to fail with Null Pointer Exception (since 2.11.3.0)

Issues Resolved

• Secondary structure not available after dragging a 3D structure onto a sequence to associate it when ‘Process secondary structure’ flag is true in preferences
• Clustal colourscheme documentation not consistent with implementation
• Handles to adjust ID panel width or annotation panel height can be dragged out of the Alignment window
• Trackpad scrolling not proportional to gesture velocity
• Cannot output individual images of more than one structure view attached to one open alignment
• –jvmempc and –jvmemmax don’t work for jalview installed via conda or jar
• User’s default colour scheme is erroneously applied to alignments in Jalview projects opened via command line when no –colour argument supplied
• Headless alignment export with structure annotations doesn’t include secondary structure and temperature factor (Known defect since 2.11.3.0)
• Uniprot record retrieval not working in JalviewJS (affects all versions)
• bio.tools record version number updated
• Miscellaneous patches to fix hangs in 2.11.3 test suite
• Jalview archive build getdown doesn’t include wrapper scripts

New Known Issues

• Protein structure derived annotation tracks not available as reference annotation unless ‘add to alignment’ preference is enabled
• Enabling just “Add Secondary Structure” Structure preference when importing structure via CLI results in temperature factor being shown in alignment

Issues Resolved

• –structureimage exports an image without the fully rendered structure when run via CLI (known defect since 2.11.3.0)
• Missing last letter when copying consensus sequence from alignment after applying filter (known defect affecting 2.10.4 onwards)
• export all alignment annotation as CSV produces an empty file or cut’n’paste text box

Issues Resolved

• Getdown does not preserve executable permission of jalview.sh file when it gets updated
• Single position features from Uniprot are incorrectly parsed as non-positional features
• Double clicking in PAE annotation to select column groups doesn’t always select group under the mouse
• ChimeraX 1.3 and Chimera 1.16.2 are not automatically found

Issues Resolved

• Jmol view not always centred on structures when multiple structures are viewed
• Unsaved Alignment windows close without prompting to save, individually or at application quit.
• Can quit Jalview while ‘save project’ is in progress
• ‘Use original colours’ option of colour by annotation not honoured when restoring view from project
• PDB structures slow to view when Jalview Java Console is open (2.11.2.7 patch)
• Multiple overview windows can be opened for a particular alignment view when multiple views are present
• Overview windows opened automatically (due to preferences settings) lack title
• Show Crossrefs fails to retrieve CDS from ENA or Ensembl for sequences retrieved from Uniprot due to version numbers in cross-reference accession
• Uniprot parser fails to import sequences with features that have ‘unknown’ start or end
• Stockholm export does not include sequence descriptions
• Don’t add string label version of DSSP secondary structure codes in secondary structure annotation rows
• reference annotation not correctly transferred to alignment containing a sub-sequence when a selection is active
• Can press ‘Add’ or ‘New View’ multiple times when manually adding and viewing a 3D structure via structure chooser
• 3D beacons sources providing models scored with PLDDT and pTM not sorted against alphaFoldDB models
• Jalview project does not preserve font aspect ratio when Viewport is zoomed with mouse
• Lower line of the sequence group border does not align with vertical and background residue box
• Resizing overview quickly with solid-drags enabled causes exception
• Sequences copied to clipboard from within Jalview cannot be pasted via the desktop’s popup menu to a new alignment window
• Overview window is saved in project file, and state of ‘show hidden regions’ is preserved.
• JvCacheableInputBoxTest flaky on build server
• SLF4J produces an error to STDERR at Jalview startup due to missing class
• macOS Dock and KDE taskbar names Jalview icon “java” when running jalview via the getdown app launcher
• HeadlessException in console in headless mode (actually fixed in 2.11.{0,1,2))
• Groovy console does not open when Jalview launched from jalview’s Java 11 executable jar (available via conda) for recent versions of groovy
• Don’t offer View model page for sources that do not have model pages
• Java Console opening at startup with the exampleFile_v2_7.jvp opening (nearly always) causes Jalview to hang
• automatic positioning of ID width for imported project can fail for certain font size configured in User preferences (affects most versions of Jalview prior to 2.11.3.0)
• RNAML import missing terminal residue
• RNA secondary structure annotation final-ending-solo-brace arrow points the wrong way
• Jalview source distribution unnecessarily includes dist directory with built jalview jar and dependencies
• Jmol sessions involving large molecules may not be fully saved in Jalview project files (known defect in 2.11.2.x)

New Known Issues

• EBI-AlphaFold PLDDT colours cannot be overlaid on alignment via ‘Colour by annotation’ unless the alignment’s colourscheme has been set to ‘None’ via the Colours menu.
• Tree renderer doesn’t show bottom-most leaves of tree when Fit-To-Window is enabled.
• PAE partition not shown in the same place when tree is closed and reopened
• Cannot cancel structure view open action once it has been started via the structure chooser dialog
• Example project’s multiple views do not open in distinct locations when eXpand views is used to show them all separately
• ‘Reload’ for a jalview project results in all windows being duplicated (since 2.11.2.6, more severe in 2.11.3.0)
• Overview shown and then closed when importing legacy jalview projects without overview store/restore information
• Missing last letter when copying consensus sequence from alignment if first column is hidden
• Last sequence ID in alignment not shown and annotation labels are misaligned in HTML export
• Files opened via command line with a relative path are added as relative paths to Recent files list (since 2.0.x)
• Test coverage for ID width adjustment disabled pending fix for new annotation label geometry and width calculation
• scripts adding new fileformats or colourschemes do not work when run via command line
• Headless alignment export with structure annotations doesn’t include secondary structure and temperature factor
• Copy sequences from one alignment and Pasting as new window in another alignment doesn’t propagate title from original alignment’s window
• Annotation colouring dialog box doesn’t remember ‘use original colours’ settings when opened via the Colour menu
• When the Groovy console is open Jalview does not prompt to save before quitting
• Jalview works with but is not fully compatible with latest Ensembl REST API (15.6)

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

Issues Resolved

• ignore sequence version numbers in IDs when resolving Ensembl Cross-References from Uniprot
• Updated RFAM fetcher to use rfam.org
• Update 3D Beacons Client for 3D-Beacons API Version 2.0

Issues Resolved

• Pfam Full and Seed alignment retrieval switched to use http://www.ebi.ac.uk/interpro/api/
• URLs reporting Content-Type as application/gzip not being recognized as a gzipped stream
• Clustalx colour scheme renamed (back) to Clustal in the GUI
• Spanish translations added for gecos colour schemes introduced in 2.11.2.4
• Overview doesn’t colour nested features the same as in the alignment view

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

Issues Resolved

• Uniprot Free Text Search in Jalview 2.11.2.2 and earlier stopped working on 29th June 2022
• Validation fails when trying to configure custom JABAWS server
• Jalview doesn’t call PymolWIN.exe correctly - improved recognition of binaries on Windows
• Jumping from left to far right via rapid drag of scroll bar or clicking the overview window can cause Jalview to temporarily hang when working with alignments with more than 10 thousand columns
• Labels for tree branches smaller than 0.005 are shown as ‘0’ in the tree viewer
• Fixed typos in documentation
• defensive patches in code and improvements for failing tests

Issues Resolved

• Secondary structure annotation from Pfam not displayed correctly
• Null pointer exceptions when displaying annotation tooltips whilst in wrapped mode

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)

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+

Known Issues

• Display of RESNUM sequence features are not suppressed when structures associated with a sequence are viewed with an external viewer (Regression from 2.11.1 series)

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.

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

• Fixed non-fatal gradle errors during build

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)

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

Issues Resolved

• Fresh install of Jalview 2.11.1.1 reports “Encountered problems opening https://www.jalview.org/examples/exampleFile_2_7.jvp"

Issues Resolved

• Conservation and Quality tracks are shown but not calculated and no protein or DNA score models are available for tree/PCA calculation when launched with Turkish language locale
• Escape does not clear highlights on the alignment (Since Jalview 2.10.3)
• Alt+Left or Right arrow in cursor mode doesn’t slide selected sequences, just sequence under cursor
• Alt+Up/Down in cursor mode doesn’t move sequence under the cursor
• Peptide-to-CDS tracking broken when multiple EMBL gene products shown for a single contig
• 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 local and complementary features mapped to the position under the cursor
• Sequence ID for reference sequence is clipped when Right align Sequence IDs enabled
• Slider with negative range values not rendered correctly in VAqua4 (Since 2.10.4)
• Single quotes not displayed correctly in internationalised text for some messages and log output
• Find doesn’t report matches that span hidden gapped columns
• Resolved memory leaks in Tree and PCA panels, Alignment viewport and annotation renderer.
• Jalview ignores file format parameter specifying output format when exporting an alignment via the command line
• Windows 10: For a minority of users, if backups are not enabled, Jalview sometimes fails to overwrite an existing file and raises a warning dialog. (in 2.11.0, and 2.11.1.0, the workaround is to try to save the file again, and if that fails, delete the original file and save in place.)
• Dragging a PDB file onto an alignment with sequence features displayed causes displayed features to be hidden.
• Cannot process alignments from HTTPS urls via command line
• References to https://www.jalview.org in program and documentation

Launching Jalview

• Jalview application fails when launched the first time for a version that has different jars to the previous launched version.

Developing Jalview

• Fixed issue with cleaning up old coverage data, causing cloverReport gradle task to fail with an OutOfMemory error.
• Migrated the Jalview Version Checker to monitor the release channel

New Known defects

• CDS shown in result of submitting proteins in a CDS/Protein alignment to a web service is wrong when proteins share a common transcript sequence (e.g. genome of RNA viruses)
• Co-located features exported and re-imported are ordered differently when shown on alignment and in tooltips. (Also affects v2.11.1.0)
• 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
• Stale build data in jalview standalone jar builds (only affects 2.11.1.1 branch)
• Sequence ID colourscheme not re-applied when alignment view restored from project (since Jalview 2.11.0)
• Duplicate CDS sequences are generated when protein products for certain ENA records are repeatedly shown via Calculate->Show Cross Refs

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

• Jalview 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 Known Issues

• OSX - Current working directory not preserved when Jalview.app launched with parameters from command line
• Sequence IDs aligned to wrong margin and clipped in headless figure export when Right Align option enabled
• Jalview Installation type always reports ‘Source’ in console output
• Test Suite: Certain Functional tests fail on jalview’s bamboo server but run fine locally.

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

Issues Resolved

• Poorly scaled bar in quality annotation row shown in Feredoxin Structure alignment view of example alignment.
• Annotation obscures sequences if lots of annotation displayed.
• Group conservation/consensus not shown for newly created group when ‘Apply to all groups’ selected
• 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.
• .jvp should be used as default extension (not .jar) when saving a Jalview project file.
• Mac Users: closing a window correctly transfers focus to previous window on OSX

Java 10 Issues Resolved

• OSX - Can’t save new files via the File or export menus by typing in a name into the Save dialog box.
• Jalview now uses patched version of the VAqua5 ’look and feel’ which has improved compatibility with the latest version of OSX.

Issues Resolved

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

New Known Defects

• Cancel option doesn’t reset Colour by Annotation

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)
• Uniprot ‘sequence variant’ features tooltip doesn’t include a text description of mutation
• Invert displayed features very slow when structure and/or overview windows are also shown
• Selecting columns from highlighted regions very slow for alignments with large numbers of sequences
• Copy Consensus fails for group consensus with ‘StringIndexOutOfBounds’
• VAqua(4) provided as fallback Look and Feel for OSX platforms running Java 10
• Adding a structure to existing structure view appears to do nothing because the view is hidden behind the alignment view

Applet

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

Batch Mode

• Fixed ID width preference is not respected

New Known Defects

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

Issues Resolved

Desktop

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

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 Known Issues

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

Known Java 9 Issues

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

Issues Resolved

• 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

Issues Resolved

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
• Feature settings for different views not recovered correctly from Jalview project file
• Feature colours in overview when first opened (automatically via preferences) are different to the main alignment panel

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.

Issues Resolved

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

Issues Resolved

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

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
• Remove right on penultimate column of alignment does nothing

Application

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

Applet

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

Issues Resolved

Application

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

Issues Resolved

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

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

Application Known issues

• Incomplete sequence extracted from PDB entry 3a6s
• Misleading message appears after trying to delete solid column.
• Jalview icon not shown in dock after InstallAnywhere version launches
• Fetching EMBL reference for an RNA sequence results fails with a sequence mismatch
• Corrupted or unreadable alignment display when scrolling alignment to right
• ArrayIndexOutOfBoundsException thrown when remove empty columns called on alignment with ragged gapped ends
• auto calculated alignment annotation rows do not get placed above or below non-autocalculated rows
• Jalview dekstop becomes sluggish at full screen in ultra-high resolution
• Cannot disable consensus calculation independently of quality and conservation
• Mouseover highlighting between cDNA and protein can become sluggish with more than one splitframe shown

Applet Known Issues

• Core PDB parsing code requires Jmol
• Sequence canvas panel goes white when alignment window is being resized

Issues Resolved

• Reinstated the display of default example file on startup
• All pairs shown in Jalview window when viewing result of pairwise alignment

Issues Resolved

Application

• 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 addition 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

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

Application Known issues

• corrupted or unreadable alignment display when scrolling alignment to right
• retrieval fails but progress bar continues for DAS retrieval with large number of ID
• flatfile output of visible region has incorrect sequence start/end
• rna structure consensus doesn't update when secondary structure tracks are rearranged
• invalid rna structure positional highlighting does not highlight position of invalid base pairs
• out of memory errors are not raised when saving Jalview project from alignment window file menu
• Switching to RNA Helices colouring doesn't propagate to structures
• colour by RNA Helices not enabled when user created annotation added to alignment
• Jalview icon not shown on dock in Mountain Lion/Webstart

Applet Known Issues

• JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
• Jalview and Jmol example not compatible with IE9
• Sort by annotation score doesn’t reverse order when selected

Issues Resolved

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

Other

• 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

Issues Resolved

• Slow scrolling when lots of annotation rows are displayed
• Lots of NPE (and slowness) after creating RNA secondary structure annotation line
• Sequence database accessions not imported when fetching alignments from Rfam
• Incorrect SHMR submission for sequences with identical IDs
• View all structures does not always superpose structures
• Option widgets in service parameters not updated to reflect user or preset settings
• Null pointer exceptions for some services without presets or adjustable parameters
• Discover PDB IDs entry in structure menu doesn’t discover PDB xRefs
• Exception encountered while trying to retrieve features with DAS
• Lowest value in annotation row isn’t coloured when colour by annotation (per sequence) is coloured
• Keyboard mode P jumps to start of gapped region when residue follows a gap
• Jalview appears to hang importing an alignment with Wrap as default or after enabling Wrap
• ‘Right click to add annotations’ message shown in wrap mode when no annotations present
• Disorder predictions fail with NPE if no automatic annotation already exists on alignment
• oninit javascript function should be called after initialisation completes
• Remove redundancy after disorder prediction corrupts alignment window display
• Example annotation file in documentation is invalid
• Grouped line graph annotation rows are not exported to annotation file
• Multi-harmony analysis cannot be run when only two groups created
• Cannot create multiple groups of line graphs with several ‘combine’ statements in annotation file
• Pressing return several times causes Number Format exceptions in keyboard mode
• Multi-harmony (SHMMR) method doesn’t submit correct partitions for input data
• Translation from DNA to Amino Acids fails
• Jalview fail to load newick tree with quoted label
• –headless flag isn’t understood
• ClassCastException when generating EPS in headless mode
• Adjusting sequence-associated shading threshold only changes one row’s threshold
• Preferences and Feature settings panel panel doesn’t open
• hide consensus histogram also hides conservation and quality histograms

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

Applet

• Sequence features are momentarily displayed before they are hidden using hidefeaturegroups applet parameter
• loading features via javascript API automatically enables feature display
• scrollToColumnIn javascript API method doesn’t work

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 coloured pink in sequence logo when alignment coloured 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 colour
• Grouped annotation graph label display is corrupted for lots of labels

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
• <= shown as = in tooltip
• Export features raises exception when no features exist
• Separator string used for serialising lists of IDs for javascript api is modified when separator string provided as parameter
• Null pointer exception when selecting tree leaves for alignment with no existing selection
• Relative URLs for datasources assumed to be relative to applet’s codebase
• Status bar not updated after finished searching and search wraps around to first result
• StructureSelectionManager instance shared between several Jalview applets causes race conditions and memory leaks
• Hover tooltip and mouseover of position on structure not sent from Jmol in applet
• Certain sequences of javascript method calls to applet API fatally hang browser

General

• View follows structure mouseover scrolls beyond position with wrapped view and hidden regions
• Find sequence position moves to wrong residue with/without hidden columns
• Sequence length given in alignment properties window is off by 1
• InvalidNumberFormat exceptions thrown when trying to import PDB like structure files
• Positional search results are only highlighted between user-supplied sequence start/end bounds
• End attribute of sequence is not validated
• Find dialog only finds first sequence containing a given sequence position
• Sequence numbering not preserved in MSF alignment output
• Jalview PDB file reader does not extract sequence from nucleotide chains correctly
• Structure colours not updated when tree partition changed in alignment
• Sequence associated secondary structure not correctly parsed in interleaved stockholm
• Colour by annotation dialog does not restore current state
• Hiding (nearly) all sequences doesn’t work properly
• Sequences containing lowercase letters are not properly associated with their pdb files

Documentation and Development

• schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright tool

Issues Resolved

• Modeller PIR IO broken - cannot correctly import a pir file emitted by Jalview
• Existing feature settings transferred to new alignment view created from cut’n’paste
• Improved test for mixed amino/nucleotide chains when parsing PDB files
• Consensus and conservation annotation rows occasionally become blank for all new windows
• Exception raised when right clicking above sequences in wrapped view mode

Application

• multiple multiply aligned structure views cause cpu usage to hit 100% and computer to hang
• Web Service parameter layout breaks for long user parameter names
• Jaba service discovery hangs desktop if Jaba server is down

Issues Resolved

• clustalx colourscheme colours Ds preferentially when both D+E are present in over 50% of the column

Application

• typo in AlignmentFrame->View->Hide->all but selected Regions menu item
• sequence fetcher replaces ‘,’ for ‘;’ when the ‘,’ is part of a valid accession ID
• fatal OOM if object retrieved by sequence fetcher runs out of memory
• unhandled Out of Memory Error when viewing pca analysis results
• InstallAnywhere builds fail to launch on OS X java 10.5 update 4 (due to apple Java 1.6 update)
• Installanywhere Jalview silently fails to launch

Applet

• Jalview.getFeatureGroups() raises an ArrayIndexOutOfBoundsException if no feature groups are defined.

Issues Resolved

• Alignment prettyprinter doesn’t cope with long sequence IDs
• clustalx colourscheme colours Ds preferentially when both D+E are present in over 50% of the column
• nucleic acid structures retrieved from PDB do not import correctly
• More columns get selected than were clicked on when a number of columns are hidden
• annotation label popup menu not providing correct add/hide/show options when rows are hidden or none are present
• Stockholm format shown in list of readable formats, and parser copes better with alignments from RFAM.
• CSV output of consensus only includes the percentage of all symbols if sequence logo display is enabled

Applet

• annotation panel disappears when annotation is hidden/removed

Application

• Alignment view not redrawn properly when new alignment opened where annotation panel is visible but no annotations are present on alignment
• pasted region containing hidden columns is incorrectly displayed in new alignment window
• Jalview slow to complete operations when stdout is flooded (fix is to close the Jalview console)
• typo in AlignmentFrame->View->Hide->all but selected Rregions menu item.
• inconsistent group submenu and Format submenu entry ‘Un’ or ‘Non’conserved
• Sequence feature settings are being shared by multiple distinct alignments
• group annotation not recreated when tree partition is changed
• double click on group annotation to select sequences does not propagate to associated trees
• Mac OSX specific issues:
  • exception raised when mouse clicked on desktop window background
  • Desktop menu placed on menu bar and application name set correctly
  • sequence feature settings not wide enough for the save feature colourscheme button

Issues Resolved

• Source field in GFF files parsed as feature source rather than description
• Non-positional features are now included in sequence feature and gff files (controlled via non-positional feature visibility in tooltip).
• URL links generated for all feature links (bugfix)
• Added URL embedding instructions to features file documentation.
• Codons containing ambiguous nucleotides translated as ‘X’ in peptide product
• Match case switch in find dialog box works for both sequence ID and sequence string and query strings do not have to be in upper case to match case-insensitively.
• AMSA files only contain first column of multi-character column annotation labels
• Jalview Annotation File generation/parsing consistent with documentation (e.g. Stockholm annotation can be exported and re-imported)
• PDB files without embedded PDB IDs given a friendly name
• Find incrementally searches ID string matches as well as subsequence matches, and correctly reports total number of both.
• Application:
  • Better handling of exceptions during sequence retrieval
  • Dasobert generated non-positional feature URL link text excludes the start_end suffix
  • DAS feature and source retrieval buttons disabled when fetch or registry operations in progress.
  • PDB files retrieved from URLs are cached properly
  • Sequence description lines properly shared via VAMSAS
  • Sequence fetcher fetches multiple records for all data sources
  • Ensured that command line das feature retrieval completes before alignment figures are generated.
  • Reduced time taken when opening file browser for first time.
  • isAligned check prior to calculating tree, PCA or submitting an MSA to JNet now excludes hidden sequences.
  • User defined group colours properly recovered from Jalview projects.

Issues Resolved

• Race condition in applet preventing startup in jre1.6.0u12+.
• Exception when feature created from selection beyond length of sequence.
• Allow synthetic PDB files to be imported gracefully
• Sequence associated annotation rows associate with all sequences with a given id
• Find function matches case-insensitively for sequence ID string searches
• Non-standard characters do not cause pairwise alignment to fail with exception

Application Issues

• Sequences are now validated against EMBL database
• Sequence fetcher fetches multiple records for all data sources

InstallAnywhere Issues

• Dock icon works for Mac OS X java (Mac 1.6 update issue with installAnywhere mechanism)
• Command line launching of JARs from InstallAnywhere version (java class versioning error fixed)

Issues Resolved

• selected region output includes visible annotations (for certain formats)
• edit label/displaychar contains existing label/char for editing
• update PDBEntries when DBRefEntries change (vamsas)
• shorter peptide product names from EMBL records
• Newick string generator makes compact representations
• bootstrap values parsed correctly for tree files with comments
• pathological filechooser bug avoided by not allowing filenames containing a ‘:’
• Fixed exception when parsing GFF files containing global sequence features
• Alignment datasets are finalized only when number of references from alignment sequences goes to zero
• Close of tree branch colour box without colour selection causes cascading exceptions
• occasional negative imgwidth exceptions
• better reporting of non-fatal warnings to user when file parsing fails.
• Save works when Jalview project is default format
• Save as dialog opened if current alignment format is not a valid output format
• UniProt canonical names introduced for both das and vamsas
• Histidine should be midblue (not pink!) in Zappo
• error messages passed up and output when data read fails
• edit undo recovers previous dataset sequence when sequence is edited
• allow PDB files without pdb ID HEADER lines (like those generated by MODELLER) to be read in properly
• allow reading of JPred concise files as a normal filetype
• Stockholm annotation parsing and alignment properties import fixed for PFAM records
• Structure view windows have correct name in Desktop window list
• annotation consisting of sequence associated scores can be read and written correctly to annotation file
• Aligned cDNA translation to aligned peptide works correctly
• Fixed display of hidden sequence markers and non-italic font for representatives in Applet
• Applet Menus are always embedded in applet window on Macs.
• Newly shown features appear at top of stack (in Applet)
• Annotations added via parameter not drawn properly due to null pointer exceptions
• Secondary structure lines are drawn starting from first column of alignment
• UniProt XML import updated for new schema release in July 2008
• Sequence feature to sequence ID match for Features file is case-insensitive
• Sequence features read from Features file appended to all sequences with matching IDs
• PDB structure coloured correctly for associated views containing a sub-sequence
• PDB files can be retrieved by applet from Jar files
• feature and annotation file applet parameters referring to different directories are retrieved correctly
• Fixed application hang whilst waiting for splash-screen version check to complete
• Applet properly URLencodes input parameter values when passing them to the launchApp service
• display name and local features preserved in results retrieved from web service
• Visual delay indication for sequence retrieval and sequence fetcher initialisation
• updated Application to use DAS 1.53e version of dasobert DAS client
• Re-instated Full AMSA support and .amsa file association
• Fixed parsing of JNet Concise annotation sans sequences

Issues Resolved

• Headless state operation in 2.2.1
• Incorrect and unstable DNA pairwise alignment
• Cut and paste of sequences with annotation
• Feature group display state in XML
• Feature ordering in XML
• blc file iteration selection using filename # suffix
• Stockholm alignment properties
• Stockhom alignment secondary structure annotation
• 2.2.1 applet had no feature transparency
• Number pad keys can be used in cursor mode
• Structure Viewer mirror image resolved

Issues Resolved

• Applet crash under certain Linux OS with Java 1.6 installed
• Annotation file export / import bugs fixed
• PNG / EPS image output bugs fixed

Issues Resolved

• New memory efficient Undo/Redo System
• Optimised symbol lookups and conservation/consensus calculations
• Region Conservation/Consensus recalculated after edits
• Fixed Remove Empty Columns Bug (empty columns at end of alignment)
• Slowed DAS Feature Fetching for increased robustness.
• Made angle brackets in ASCII feature descriptions display correctly
• Re-instated Zoom function for PCA
• Sequence descriptions conserved in web service analysis results
• UniProt ID discoverer uses any word separated by ∣
• WsDbFetch query/result association resolved
• Tree leaf to sequence mapping improved
• Smooth fonts switch moved to FontChooser dialog box.

Issues Resolved

• Image output - rightmost residues are rendered if sequence id panel has been resized
• Image output - all offscreen group boundaries are rendered
• Annotation files with sequence references - all elements in file are relative to sequence position
• Mac Applet users can use Alt key for group editing

Issues Resolved

• Redundancy Panel reinstalled in the Applet
• Monospaced font - EPS / rescaling bug fixed
• Annotation files with sequence references bug fixed

Issues Resolved

• Annotation Panel displays complete JNet results

Issues Resolved

• Java 1.5 bug - InternalMessageDialog fix for threads
• Righthand label on wrapped alignments shows correct value

Issues Resolved

• Drag & Drop fixed on Linux
• Jalview Archive file faster to load/save, sequence descriptions saved.

Issues Resolved

• HTML output writes groups and features
• Group editing is Control and mouse click
• File IO bugs

Issues Resolved

• GUI bugs resolved
• Runs with -nodisplay from command line

Issues Resolved

• Known OutOfMemory errors give warning message
• Overview window calculated more efficiently
• Several GUI bugs resolved

Issues Resolved

• Several GUI bugs resolved

Issues Resolved

• Improved JPred client reliability
• Improved loading of Jalview files

Issues Resolved

• InstallAnywhere download for Sparc Solaris

Issues Resolved

• Copy & Paste order of sequences maintains alignment order.

Issues Resolved

• Delete gaps bug fixed.
• FileChooser sorts columns.
• Can remove groups one by one.
• Filechooser icons installed.
• Finder ignores return character when searching. Return key will initiate a search.