X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=6e30942bf01f8eb406aee136a8a3b2bb409b343b;hb=6764c7be2ae71536ef150f5753ab36e585d56e5c;hp=351b05553586025ec9f856b6ef2b1735a3b7bfac;hpb=cc0b6158d11333a9ee0b5cf57fbe890d5309e510;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 351b055..91ba69c 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -67,16 +67,858 @@ li:before {
+
+
+
+ 2.11.0
+ 14/05/2019 (final due date !)
+ |
+
+
+ -
+ Principal Components Analysis and
+ Viewer state is saved in Jalview Project
The 'Change
+ parameters' option has also been removed from the PCA
+ viewer.
+
+ -
+ More efficient creation of selections and
+ multiple groups when working with large alignments
+
+ -
+ Speedier import of annotation rows when
+ parsing stockholm files
+
+ -
+ Update of Ensembl Rest Client to API v9.0
+
+ -
+ Sequence features can be filtered and
+ shaded according to any associated attributes (e.g. variant
+ attributes from VCF file, or key-value pairs imported from
+ column 9 of GFF file)
+
+ -
+ More efficient sequence feature render
+ algorithm (Z-sort/transparency and filter aware)
+
+ -
+ Alignment Overview now by default shows
+ only visible region of alignment (this can be changed in
+ user preferences)
+
+ -
+
+
+ Deprecations
+
+ -
+ DAS sequence retrieval and annotation
+ capabilities removed from the Jalview Desktop
+
+
+ Release Processes
+
+ - Atlassian Bamboo continuous integration server for
+ unattended Test Suite execution
+ -
+ Memory test suite to detect leaks in common
+ operations
+
+ -
+ IntervalStoreJ (new updatable NCList
+ implementation) used for Sequence Feature collections
+
+ -
+ Castor library for XML marshalling and
+ unmarshalling has been replaced by JAXB for Jalview projects
+ and XML based data retrieval clients
+
+ -
+
+
+
+ |
+
+
+
+ -
+ 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 the overview updates 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.
+
+ -
+ Error message for trying to load in invalid
+ URLs doesn't tell users the invalid URL
+
+
+ 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)
+
+ -
+
+
+
+ New Known Defects
+
+ -
+ Nonpositional features lose feature group
+ on export as jalview features file
+
+ - Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project
+
+ |
+
+
+ |
+
+ |
+
+
+
+ -
+ Default memory for Jalview webstart and
+ InstallAnywhere increased to 1G.
+
+ -
+ Hidden sequence markers and representative
+ sequence bolding included when exporting alignment as EPS,
+ SVG, PNG or HTML. Display is configured via the
+ Format menu, or for command-line use via a jalview
+ properties file.
+
+ -
+ Ensembl client updated to Version 7 REST
+ API and sequence data now imported as JSON.
+
+ -
+ Change in recommended way of starting
+ Jalview via a Java command line: add jars in lib directory
+ to CLASSPATH, rather than via the deprecated java.ext.dirs
+ property.
+
+
+ Development
+
+ -
+ Support added to execute test suite
+ instrumented with Open
+ Clover
+
+
+ |
+
+
+
+ -
+ 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.
+
+
+ |
+
+
+ |
+
+ |
+
+
+
+ -
+ Use HGVS nomenclature for variant
+ annotation retrieved from Uniprot
+
+ -
+ Windows File Shortcuts can be dragged
+ onto the Jalview Desktop
+
+
+ |
+
+
+
+ -
+ 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 Structure Chooser control
+ for disabling automatic superposition of multiple
+ structures and open structures in existing views
+
+ -
+ Mouse cursor changes to indicate Sequence
+ ID and annotation area margins can be click-dragged to
+ adjust them.
+
+ -
+ Jalview uses HTTPS for Uniprot, Xfam and
+ Ensembl services
+
+ -
+ Improved performance for large alignments
+ and lots of hidden columns
+
+ -
+ Improved performance when rendering lots
+ of features (particularly when transparency is disabled)
+
+
+ |
+
+
+ -
+ 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)
+
+
+ |
+
+
+ |
+
+ |
+
+ - Updated Certum Codesigning Certificate
+ (Valid till 30th November 2018)
|
+
+ 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
+
+ |
+
|
|
+
+
+ -
+ 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
+
+ -
+ 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)
+
+
+ |
+
+
+ |
+
+ |
+
+ New features in Jalview Desktop
+
+ -
+ Uniprot Sequence Fetcher now uses web API at uniprot.org
+
+ - HTTPS used for all connections to ebi.ac.uk
+
+
+ |
+
+ |
+
+
+ |
+
+ |
+
+
+
+ -
+ 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 +926,20 @@ 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
@@ -107,26 +947,57 @@ 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
-
- Sequence names don't include file
- extension when importing structure files without embedded
- names or PDB accessions
+ 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
+
+ -
+ Drag and drop load of AAIndex and NCBI
+ format sequence substitution matrices
+
+
+ User Interface
+
+ -
+ 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
@@ -134,151 +1005,149 @@ li:before {
extent
-
- Graduated feature colour style example
- included in the example feature file
+ Status bar message shown when not enough
+ aligned positions were available to create a 3D structure
+ superposition.
+
+ 3D Structure
+
-
- Occupancy annotation row shows number of
- ungapped positions in each column of the alignment.
+ Hidden regions in alignment views are not
+ coloured in linked structure views
-
- File extension pruned from Sequence ID
- for sequences derived from structure files without
- embedded database accession
+ Faster Chimera/Jalview communication by
+ file-based command exchange
-
- Status bar message shown when not enough
- aligned positions were available to create a 3D structure
- superposition.
+ Structure chooser automatically shows
+ Cached Structures rather than querying the PDBe if
+ structures are already available for sequences
-
- More robust per-sequence positional annotation input/output via stockholm flatfile
+ Structures imported via URL are cached in
+ the Jalview project rather than downloaded again when the
+ project is reopened.
-
-
- Application
-
-
- Experimental Features Checkbox in
- Desktop's Tools menu to hide or show untested features in
- the application.
+ New entries in the Chimera menu
+ to transfer Chimera's structure attributes as Jalview
+ features, and vice-versa (Experimental
+ Feature)
+
+ Web Services
+
-
- Warning in alignment status bar when
- there are not enough columns to superimpose structures in
- Chimera
+ Updated JABAWS client to v2.2
-
- Faster Chimera/Jalview communication by
- file-based command exchange
+ 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
+
-
- 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
+ FileFormatI interface for describing and
+ identifying file formats (instead of String constants)
-
- Structures imported via URL are cached in
- the Jalview project rather than downloaded again when the
- project is reopened.
+ FeatureCounter script refactored for
+ efficiency when counting all displayed features (not
+ backwards compatible with 2.10.1)
-
- Experimental features
+ Example files
-
- New entries in the Chimera menu
- to transfer Chimera's structure attributes as Jalview
- features, and vice-versa.
+ Graduated feature colour style example
+ included in the example feature file
- Applet
+ 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
+
+ -
Added PrivilegedAccessor to test suite
-
Prevent or clear modal dialogs raised
during tests
- -
- 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)
-
- -
-
-
-
-
-
|
- 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 +1164,11 @@ 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 +1181,12 @@ 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 +1194,6 @@ 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 +1201,18 @@ 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 +1220,8 @@ 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 +1233,126 @@ 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
+
+ -
+ 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
-
- WUSS notation for simple pseudoknots lost when importing RNA secondary structure via Stockholm
+ Hide insertions in PopUp->Selection menu
+ only excluded gaps in current sequence and ignored
+ selection.
+
+ Rendering
+
-
- Secondary structure arrows for [] and {} not shown in correct direction for simple pseudoknots
+ Overview window visible region moves
+ erratically when hidden rows or columns are present
-
- 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
+ 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 +1367,17 @@ 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 +1397,6 @@ 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 +1405,18 @@ 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 +1434,6 @@ 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 +1450,31 @@ 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.
+
|
@@ -1271,6 +2154,10 @@ li:before {
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.
+