X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=25fc04bd396a1db701d3b2de658acb538b6cfe85;hb=181cd6607ecd631aa5972582ff1d99c5bea75b23;hp=ee1318d8b393e78a46d79ea8ac8e79f75a1ca18f;hpb=835ee7a85143a9e44d314976c4e56c424ff2e781;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index ee1318d..3eaf234 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -21,6 +21,29 @@
-->
Release History
+
@@ -42,37 +65,1524 @@
Issues Resolved
-
-
+
+
+
+
+
+ |
+ |
+
+
+
+ -
+ DAS sequence retrieval and annotation capabilities removed from the Jalview Desktop
+
+
+ |
+
+
+ |
+
+ |
+
+
+
+ -
+ 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)
+
+ -
+ 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
+
+ -
+ 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
+ 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.
+
+
+ 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 (Experimental
+ Feature)
+
+
+ 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
+
+ -
+ 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 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
+
+ -
+ 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
+
+
+ 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
+
+ -
+ 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
+
+ -
+ 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.
+
+
+ |
|
|
- Application
-
- - 3D Structure chooser opens with 'Cached structures' view if structures already loaded
- |
+
+ General
+
+ -
+ Improved memory usage: sparse arrays used
+ for all consensus calculations
+
+ -
+ Jmol updated to version 14.6.4 (released
+ 3rd Oct 2016)
+
+ - Updated Jalview's Certum code signing certificate
+ for 2016-2017
+
+ Application
+
+ -
+ Sequence ID tool tip presents abridged
+ set of database cross-references, sorted alphabetically
+
+ -
+ New replacement token for creating URLs just
+ from database cross references. Users with custom links
+ will receive a warning
+ dialog asking them to update their preferences.
+
+ -
+ Cancel button and escape listener on
+ dialog warning user about disconnecting Jalview from a
+ Chimera session
+
+ -
+ Jalview's Chimera control window closes if
+ the Chimera it is connected to is shut down
+
+ -
+ New keystroke (B) and Select highlighted
+ columns menu item to mark columns containing highlighted
+ regions (e.g. from structure selections or results of a
+ Find operation)
+
+ -
+ Command line option for batch-generation
+ of HTML pages rendering alignment data with the BioJS
+ MSAviewer
+
+
+ |
+ General
+
+ -
+ Columns with more than one modal residue
+ are not coloured or thresholded according to percent
+ identity (first observed in Jalview 2.8.2)
+
+ -
+ Threonine incorrectly reported as not
+ hydrophobic
+
+ -
+ Updates to documentation pages (above PID
+ threshold, amino acid properties)
+
+ -
+ Lower case residues in sequences are not
+ reported as mapped to residues in a structure file in the
+ View Mapping report
+
+ -
+ Identical features with non-numeric scores
+ could be added multiple times to a sequence
+
+ -
+ Disulphide
+ bond features shown as two highlighted residues rather
+ than a range in linked structure views, and treated
+ correctly when selecting and computing trees from features
+
+ -
+ Custom URL links for database
+ cross-references are matched to database name regardless
+ of case
+
+
+
Application
- - 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 when ENA client attempts to fetch non-existent IDs via Fetch DB Refs UI option
- - Exceptions are not raised when a new view is created on the alignment
+ -
+ Custom URL links for specific database
+ names without regular expressions also offer links from
+ Sequence ID
+
+ -
+ Removing a single configured link in the
+ URL links pane in Connections preferences doesn't actually
+ update Jalview configuration
+
+ -
+ CTRL-Click on a selected region to open
+ the alignment area popup menu doesn't work on El-Capitan
+
+ -
+ Jalview doesn't offer to associate mmCIF
+ files with similarly named sequences if dropped onto the
+ alignment
+
+ -
+ Additional mappings are shown for PDB
+ entries where more chains exist in the PDB accession than
+ are reported in the SIFTS file
+
+ -
+ Certain structures do not get mapped to
+ the structure view when displayed with Chimera
+
+ -
+ No chains shown in the Chimera view
+ panel's View->Show Chains submenu
+
+ -
+ Export as HTML with embedded SVG doesn't
+ work for wrapped alignment views
+
+ -
+ Rename UI components for running JPred
+ predictions from 'JNet' to 'JPred'
+
+ -
+ Export as PNG or SVG is
+ corrupted when annotation panel vertical scroll is not at
+ first annotation row
+
+ -
+ Attempting to view structure for Hen
+ lysozyme results in a PDB Client error dialog box
+
+ -
+ Structure View's mapping report switched
+ ranges for PDB and sequence for SIFTS
+
+
+ SIFTS 'Not_Observed' residues mapped to non-existant
+ coordindate data
+
- New Known Issues
- - Drag and drop from URL links in browsers do not work on Windows
- Build and deployment
- - URL link checker now copes with multi-line anchor tags
+
|
+
+
+ |
+ Application
+
+ - 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
+
+ |
+
@@ -82,8 +1592,8 @@
General
-
- Updated Spanish translations.
-
+ Updated Spanish translations.
+
-
Jmol now primary parser
for importing structure data to Jalview. Enables mmCIF and
@@ -372,6 +1882,10 @@
Quality and Conservation are now shown on
load even when Consensus calculation is disabled
+ -
+ Remove right on penultimate column of
+ alignment does nothing
+
Application
@@ -457,7 +1971,8 @@
-
Enable 'Get Cross-References' in menu
- after fetching cross-references, and restoring from project
+ after fetching cross-references, and restoring from
+ project
-
Mouseover of a copy of a sequence is not
@@ -518,6 +2033,19 @@
Incorrect start and end reported for PDB
to sequence mapping in 'View Mappings' report
+ -
+ Unable to read old Jalview projects that
+ contain non-XML data added after Jalvew wrote project.
+
+ -
+ Newly created annotation row reorders
+ after clicking on it to create new annotation for a
+ column.
+
+ -
+ Null Pointer Exception raised when
+ pressing Add on an orphaned cut'n'paste window.
+
@@ -586,6 +2114,12 @@
Applet
- Split frame example added to applet examples page
+ Build and Deployment
+
+ -
+ New ant target for running Jalview's test
+ suite
+
|
@@ -973,10 +2507,10 @@
Deployment and Documentation
+ General
+ --> Deployment and Documentation
- 2G and 1G options in launchApp have no effect on
memory allocation
@@ -1184,8 +2718,7 @@
Certum to the Jalview
open source project).
- - 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
@@ -1814,11 +3347,6 @@
- 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
@@ -1846,8 +3374,8 @@
- 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
@@ -2271,11 +3799,6 @@
- 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'
@@ -2290,11 +3813,6 @@
- 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
@@ -2306,11 +3824,6 @@
- WsDbFetch query/result association resolved
- Tree leaf to sequence mapping improved
- Smooth fonts switch moved to FontChooser dialog box.
-
-
-
-
-
|
|