|
+ |
+
+
+
+ -
+ Faster and more efficient management and
+ rendering of sequence features
+
+ -
+ More reliable Ensembl fetching with HTTP
+ 429 rate limit request hander
+
+ -
+ Structure views don't get updated unless
+ their colours have changed
+
+ - All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)
+ - 'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
+
+
+ - Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references
+ - Start/End limits are shown in Pairwise Alignment report
+ - Sequence fetcher's Free text 'autosearch' feature can be disabled
+ - Retrieve IDs tab added for UniProt and PDB easier retrieval of sequences for lists of IDs
+ - Short names for sequences retrieved from Uniprot
+
+ Scripting
+
+ - Groovy interpreter updated to 2.4.12
+ - Example groovy script for generating a matrix of percent identity scores for current alignment.
+
+ Testing and Deployment
+
+ - Test to catch memory leaks in Jalview UI
+
|
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
+
+ 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
+
+ - 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
+
+
+ |
+
+
+ |
+
+ |
+
+
+
+ -
+ Show gaps in overview window by colouring
+ in grey (sequences used to be coloured grey, and gaps were
+ white)
+
+ -
+ Overview tab in Jalview Desktop
+ Preferences
+
+ -
+ Overview updates immediately on increase
+ in size and progress bar shown as higher resolution
+ overview is recalculated
+
+
+
+ |
+
+
+
+ -
+ Overview window redraws every hidden
+ column region row by row
+
+ -
+ duplicate protein sequences shown after
+ retrieving Ensembl crossrefs for sequences from Uniprot
+
+ -
+ Overview window throws NPE if show boxes
+ format setting is unticked
+
+ -
+ Groups are coloured wrongly in overview
+ if group has show boxes format setting unticked
+
+ -
+ Redraw problems when
+ autoscrolling whilst dragging current selection group to
+ include sequences and columns not currently displayed
+
+ -
+ Not all chains are mapped when multimeric
+ assemblies are imported via CIF file
+
+ -
+ Gap colour in custom colourscheme is not
+ displayed when threshold or conservation colouring is also
+ enabled.
+
+ -
+ JABAWS 2.2 services report wrong JABAWS
+ server version
+
+ -
+ Jalview continues to scroll after
+ dragging a selected region off the visible region of the
+ alignment
+
+ -
+ Cannot apply annotation based
+ colourscheme to all groups in a view
+
+ -
+ IDs don't line up with sequences
+ initially after font size change using the Font chooser or
+ middle-mouse zoom
+
+
+ |
+
+
+ |
+
+ |
+
+ 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)
@@ -84,22 +302,20 @@ li:before {
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
-
-
-
- Tree/PCA calculation menu items merged to
- a calculation dialog box
+ 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
@@ -107,85 +323,80 @@ li:before {
Custom shading schemes created via groovy
scripts
- -
- linked scrolling of CDS/Protein views
- via Overview or sequence motif search operations
-
+
+ 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
+
+ User Interface
+
-
- Graduated feature colour style example
- included in the example feature file
+ Experimental Features Checkbox in
+ Desktop's Tools menu to hide or show untested features in
+ the application.
-
- Occupancy annotation row shows number of
- ungapped positions in each column of the alignment.
+ Linked scrolling of CDS/Protein views
+ via Overview or sequence motif search operations
-
- File extension pruned from Sequence ID
- for sequences derived from structure files without
- embedded database accession
+ 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.
- -
- More robust per-sequence positional
- annotation input/output via stockholm flatfile
-
-
- Application
+ 3D Structure
-
- 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
+ Hidden regions in alignment views are not
+ coloured in linked structure views
-
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
-
- -
- Drag and drop load of AAIndex and NCBI
- format sequence substitution matrices
-
- -
Structure chooser automatically shows
Cached Structures rather than querying the PDBe if
structures are already available for sequences
@@ -195,93 +406,124 @@ li:before {
the Jalview project rather than downloaded again when the
project is reopened.
-
-
- Experimental features
-
-
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
- Test Suite
+
+ Scripting
-
- Added PrivilegedAccessor to test suite
+ FileFormatI interface for describing and
+ identifying file formats (instead of String constants)
-
- Prevent or clear modal dialogs raised
- during tests
+ FeatureCounter script refactored for
+ efficiency when counting all displayed features (not
+ backwards compatible with 2.10.1)
+
+
+ Example files
+
+ -
+ Graduated feature colour style example
+ included in the example feature file
+
+ Documentation
+
+ -
+ Release notes reformatted for readability
+ with the built-in Java help viewer
+
+ -
+ Find documentation updated with 'search
+ sequence description' option
+
+
+ Test Suite
+
-
External service integration tests for
Uniprot REST Free Text Search Client
-
- 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)
-
-
-
-
-
+ Added PrivilegedAccessor to test suite
+
+ -
+ Prevent or clear modal dialogs raised
+ during tests
+
|
- General
+ 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). 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
-
+ - 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
-
- 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
@@ -298,38 +540,11 @@ li:before {
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
@@ -342,17 +557,12 @@ li:before {
gaps before start of features
-
- Very large alignments take a long time to
- load
-
- -
Graduated feature colour threshold not
restored to UI when feature colour is edited
-
- Feature colour thresholds not respected
- when rendered on overview and structures when opacity at
- 100%
+ Vertical scrollbar jumps one page-width at
+ a time when scrolling vertically in wrapped mode.
-
Structure and alignment overview update
@@ -360,10 +570,6 @@ li:before {
dialog box
-
- Vertical scrollbar jumps one page-width at
- a time when scrolling vertically in wrapped mode.
-
- -
Overview window doesn't always update
when a group defined on the alignment is resized
@@ -371,19 +577,16 @@ li:before {
Mouseovers on left/right scale region in
wrapped view result in positional status updates
+
-
- Status bar shows position for ambiguous
- amino acid and nucleotide symbols
+ Status bar doesn't show position for
+ ambiguous amino acid and nucleotide symbols
-
Copy consensus sequence failed if
alignment included gapped columns
-
- User defined gap colour not shown in
- overview when features overlaid on alignment
-
- -
Minimum size set for Jalview windows so
widgets don't permanently disappear
@@ -393,19 +596,10 @@ li:before {
T-Coffee column reliability scores)
-
- Gap colours in user-defined colourschemes
- are not shown
-
- -
Exception thrown if trying to create a
sequence feature on gaps only
-
- Sort by features includes features to
- right of selected region when gaps present on right-hand
- boundary
-
- -
Features created with 'New feature'
button from a Find inherit previously defined feature type
rather than the Find query string
@@ -415,19 +609,6 @@ li:before {
exporting tree calculated in Jalview
-
- 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
-
- -
Hiding sequences at bottom of alignment
and then revealing them reorders sequences on the
alignment
@@ -442,37 +623,109 @@ li:before {
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
-
- Documentation
-
-
- Release notes reformatted for readibility
- with the built-in Java help viewer
+ Protein specific colours only offered in
+ colour and group colour menu for protein alignments
-
- Find documentation updated with 'search
- sequence description' option
+ 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
- Application
+ Data import/export
-
- Sequence Database chooser doesn't show
- available databases panel on Linux
+ 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
@@ -503,10 +756,6 @@ li:before {
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
@@ -524,24 +773,6 @@ li:before {
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 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
@@ -550,35 +781,18 @@ li:before {
ambiguous amino acids
-
- Hide insertions in PopUp menu excludes
- gaps in selection, current sequence and only within
- selected columns
-
- -
- Cannot retrieve protein products from
- Ensembl by Peptide ID
-
- -
cDNA Consensus annotation not shown in
CDS/Protein view after CDS sequences added for aligned
proteins
-
- 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).
+ 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
@@ -596,22 +810,6 @@ li:before {
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
-
- -
- Cannot load Newick trees from eggnog
- ortholog database
-
-
Test Suite
-
@@ -628,10 +826,33 @@ li:before {
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.
+
|