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
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

+ Applet
+

Concurrent modification exception when closing alignment panel

+ BioJSON
+

+ BioJSON export does not preserve non-positional 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) +

+ New Known Issues +

+ Calculations +

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

+ Rendering +

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

+ Overview +

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

+ + Data import/export +

Posterior probability annotation from Stockholm files imported as sequence associated annotation
+ More robust per-sequence positional + annotation input/output via stockholm flatfile +
Sequence names don't include file extension when importing structure files without embedded names or PDB accessions
Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent
+ Drag and drop load of AAIndex and NCBI + format sequence substitution matrices +

- Application + User Interface

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

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

- Applet + Web Services

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

+ + Scripting +

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

+ Example files +

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

+ Documentation +

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

Test Suite -

Added PrivilegedAccessor to test suite

Prevent or clear modal dialogs raised during tests

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

+ Calculations

Fixed incorrect value in BLOSUM 62 score - matrix - C->R should be '3'
Old matrix restored with - this one-line groovy script:
jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3 -
- Fixed Jalview's treatment of gaps in PCA - and substitution matrix based Tree calculations.
In - earlier versions of Jalview, gaps matching gaps were - penalised, and gaps matching non-gaps penalised even more. - In the PCA calculation, gaps were actually treated as - non-gaps - so different costs were applied, which 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

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 +

- Application + User Interface

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

+ Rendering +

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

+ Data import/export +

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

+ 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

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
+ 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
+ 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. +

- -

+ General

3D Structure chooser opens with 'Cached structures' - view if structures already loaded
Progress bar reports models as they are loaded to - structure views

- -

- 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

- +

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

@@ -1328,10 +1992,10 @@ li:before { Deployment and Documentation +

+ General +

+ --> Deployment and Documentation

2G and 1G options in launchApp have no effect on memory allocation

Certum

Jalview SRS links replaced by UniProt and EBI-search -
Jalview SRS links replaced by UniProt and EBI-search
Output in Stockholm format
Allow import of data from gzipped files
Export/import group and sequence associated line @@ -2169,11 +2832,6 @@ li:before {
- URL links generated from description line for regular-expression based URL links (applet and application) - - - - -
- Non-positional feature URL links are shown in link menu
- Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.
- Group-associated consensus, sequence logos and conservation plots
- Symbol distributions for each column can be exported @@ -2626,11 +3284,6 @@ li:before {
- Cancel button for DAS Feature Fetching
- PCA and PDB Viewers zoom via mouse roller
- User-defined sub-tree colours and sub-tree selection - - - - -
- 'New Window' button on the 'Output to Text box'
@@ -2645,11 +3298,6 @@ li:before {
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 @@ -2661,11 +3309,6 @@ li:before {
WsDbFetch query/result association resolved
Tree leaf to sequence mapping improved
Smooth fonts switch moved to FontChooser dialog box. - - - - -