Release History

+ General +

More robust colours and shader model for alignments and groups
Custom shading schemes created via groovy scripts
linked scrolling of CDS/Protein views via Overview or sequence motif search operations
Efficiency improvements for interacting with alignment and overview windows
Hidden columns and sequences can be omitted in Overview
+ Posterior probability annotation from + Stockholm files imported as sequence associated annotation +
+ Sequence names don't include file + extension when importing structure files without embedded + names or PDB accessions +
Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent

+ Application +

+ + Experimental Features Checkbox in Desktop's Tools + menu to hide or show untested features in the application. +
Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera
Faster Chimera/Jalview communication by file-based command exchange
URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB
Updated JABAWS client to v2.2

+ Experimental features +

+ New entries in the Chimera menu + to transfer Chimera's structure attributes as Jalview + features, and vice-versa. +

+ Applet +

+ Test Suite +

Added PrivilegedAccessor to test suite

Prevent or clear modal dialogs raised during tests

+ +

+ General +

+ 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 mean't + 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). To restore pre-2.10.2 + behaviour
+ jalview.viewmodel.PCAModel.scoreGapAsAny=true // for + 2.10.1 mode
+ jalview.viewmodel.PCAModel.scoreGapAsAny=false // to + restore 2.10.2 mode +
Reopening Colour by annotation dialog doesn't reselect a specific sequence's associated annotation after it was used for colouring a view
Hidden regions in alignment views are not coloured in linked structure views
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
PCA calculation could hang when generating output report when working with highly redundant alignments
Cannot configure feature colours with lightGray or darkGray via features file
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
'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups
Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds
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
Very large alignments take a long time to load
Cannot load Newick trees from eggnog ortholog database

+ Application +

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
Structure viewer's View -> Colour By view selection menu changes colours of alignment views
Proxy server address and port always appear enabled in Preferences->Connections
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'
DAS registry not found exceptions removed from console output
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
+ Structures loaded via URL are saved in + Jalview Projects rather than fetched via URL again when + the project is loaded and the structure viewed +
Trackpad horizontal scroll gesture adjusts start position in wrap mode
Status bar doesn't show positions for ambiguous amino acids
Hide insertions in PopUp menu excludes gaps in selection, current sequence and only within selected columns

+ Applet +

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

+ 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

+ +

+ 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

+ +

+ 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

+ General +

+ reinstate CTRL-click for opening pop-up + menu on OSX +
+ Export features in Jalview format (again) + includes graduated colourschemes +
+ More responsive when + working with big alignments and lots of hidden columns +
+ Hidden column markers not always rendered + at right of alignment window +
+ Tidied up links in help file table of + contents +
+ Feature based tree calculation not shown + for DNA alignments +
+ Hidden columns ignored during feature + based tree calculation +
+ Alignment view stops updating when show + unconserved enabled for group on alignment +
+ Cannot insert gaps into sequence when + set as reference +
+ Alignment column in status incorrectly + shown as "Sequence position" when mousing over + annotation +
+ Incorrect column numbers in ruler when + hidden columns present +
+ Colour by RNA Helices not enabled when + user created annotation added to alignment +
+ RNA Structure consensus only computed for + '()' base pair annotation +
+ Enabling 'Ignore Gaps' results + in zero scores for all base pairs in RNA Structure + Consensus +
+ Extend selection with columns containing + feature not working +
+ Pfam format writer puts extra space at + beginning of sequence +
+ Incomplete sequence extracted from pdb + entry 3a6s +
+ Cannot create groups on an alignment from + from a tree when t-coffee scores are shown +
+ Cannot import and view PDB + structures with chains containing negative resnums (4q4h) +
+ ArithmeticExceptions raised when parsing + some structures +
+ 'Empty' alignment blocks added + to Clustal, PIR and PileUp output +
+ Reordering sequence features that are + not visible causes alignment window to repaint +
+ Threshold sliders don't work in + graduated colour and colour by annotation row for e-value + scores associated with features and annotation rows +
+ amino acid physicochemical conservation + calculation should be case independent +
+ Remove annotation also updates hidden + columns +
+ FER1_ARATH and FER2_ARATH mislabelled in + example file (uniref50.fa, feredoxin.fa, unaligned.fa, + exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar) +
+ Null pointer exceptions and redraw + problems when reference sequence defined and 'show + non-conserved' enabled +
+ Quality and Conservation are now shown on + load even when Consensus calculation is disabled +
+ Remove right on penultimate column of + alignment does nothing +

+ Application +

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

+ Applet +

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

+ 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