|
|
- General
+
-
+ 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.
+
+
+ |
+
+
+ |
+
+ |
+
+ 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 +156,20 @@ 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
@@ -107,178 +177,207 @@ 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
+ Structure chooser automatically shows
+ Cached Structures rather than querying the PDBe if
+ structures are already available for sequences
-
- Updated JABAWS client to v2.2
+ Structures imported via URL are cached in
+ the Jalview project rather than downloaded again when the
+ project is reopened.
-
- Drag and drop load of AAIndex and NCBI
- format sequence substitution matrices
+ New entries in the Chimera menu
+ to transfer Chimera's structure attributes as Jalview
+ features, and vice-versa (Experimental
+ Feature)
+
+ Web Services
+
-
- Structure chooser automatically shows Cached Structures rather than querying the PDBe if structures are already available for sequences
+ Updated JABAWS client to v2.2
-
- Structures imported via URL are cached in
- the Jalview project rather than downloaded again when the
- project is reopened.
+ 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
-
- Experimental features
+
+ Scripting
-
- New entries in the Chimera menu
- to transfer Chimera's structure attributes as Jalview
- features, and vice-versa.
+ 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)
- Applet
+ Example files
-
-
+ Graduated feature colour style example
+ included in the example feature file
- Test Suite
+ Documentation
-
- Added PrivilegedAccessor to test suite
+ Release notes reformatted for readability
+ with the built-in Java help viewer
-
- Prevent or clear modal dialogs raised
- during tests
+ 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).
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.
+
-
- 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
+ PCA calculation could hang when
+ generating output report when working with highly
+ redundant alignments
-
- Fixed off-by-one bug that affected scaling
- of branch lengths for trees computed using Sequence
- Feature Similarity.
+ 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
@@ -295,38 +394,11 @@ 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
@@ -339,17 +411,12 @@ 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
@@ -357,10 +424,6 @@ 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
@@ -368,20 +431,18 @@ 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
+ Minimum size set for Jalview windows so
+ widgets don't permanently disappear
-
Cannot select or filter quantitative
@@ -389,13 +450,8 @@ 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
+ Exception thrown if trying to create a
+ sequence feature on gaps only
-
Features created with 'New feature'
@@ -407,47 +463,126 @@ li:before {
exporting tree calculated in Jalview
-
- Per-sequence RNA secondary structures added after a sequence was imported are not written to Stockholm File
+ Hiding sequences at bottom of alignment
+ and then revealing them reorders sequences on the
+ alignment
-
- WUSS notation for simple pseudoknots lost when importing RNA secondary structure via Stockholm
+ Group panel in sequence feature settings
+ doesn't update to reflect available set of groups after
+ interactively adding or modifying features
-
- Secondary structure arrows for [] and {} not shown in correct direction for simple pseudoknots
+ Sequence Database chooser unusable on
+ Linux
-
- 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
+ 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
-
- Sequence Database chooser unusable on Linux
+ 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
- Documentation
+ Data import/export
-
- Release notes reformatted for readibility
- with the built-in Java help viewer
+ 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
- - Find documentation updated with 'search sequence description' option
- Application
+ 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
-
- Sequence Database chooser doesn't show available databases panel on Linux
+ User Defined Colours not added to Colour
+ menu
- - EnsemblGenomes example failing after release of Ensembl v.88
- - User Defined Colours not added to Colour menu
-
Easier creation of colours for all 'Lower
case' residues (button in colourscheme editor debugged and
@@ -462,16 +597,17 @@ li:before {
new features are added to alignment
-
- Cancel in feature settings reverts changes to feature colours via the Amend features dialog
+ 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
+ Null pointer exception when attempting to
+ edit graduated feature colour via amend features dialog
+ box
-
- Proxy server address and port always
- appear enabled in Preferences->Connections
+ Structure viewer's View -> Colour By view
+ selection menu changes colours of alignment views
-
Spurious exceptions in console raised
@@ -491,24 +627,6 @@ 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
@@ -517,31 +635,18 @@ 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
-
- SIFTs mappings not created for some structures
+ 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
@@ -559,22 +664,6 @@ 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
-
@@ -591,7 +680,31 @@ 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.
+
|