X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=92af37720f38fd1b721cc6ef4b2609b8d68f0a50;hb=b1e2aea95b3839a1a53f809c579666075cd3d348;hp=f35494d30d43c3f90304a6a557c6342beefdd72f;hpb=71a996fbcf51882725dd0e22a8fd986e1c5cd97a;p=jalview.git
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index f35494d..92af377 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -21,6 +21,29 @@
-->
Release History
+
@@ -47,92 +70,1250 @@
|
+ |
+
+
+
+ -
+ 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
+
+ - 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
+
+ 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 only aligns selected regions of each selected sequence
+ - 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
+
+ Applet
+
+ - Concurrent modification exception when closing alignment panel
+
+ BioJSON
+
+ -
+ BioJSON export does not preserve non-positional features
+
+
+ |
+
+
+ |
+
+ |
+
+ 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.
+
+
+ |
+ |
+
+ |
+
+ 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
+
+ -
+ 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
+
+
+
+ |
+
+
+
+ |
+ 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
+
+ |
+
+
+ |
+
|
General
- - Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.
- - Alignment ruler shows positions relative to reference sequence
- - Position/residue shown in status bar when mousing over sequence associated annotation
- - Default RNA SS symbol to 'matching bracket' for manual entry
- - RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column
- - Feature settings popup menu options for showing or hiding columns containing a feature
- - Edit selected group by double clicking on group and sequence associated annotation labels
- - Sequence name added to annotation label in select/hide columns by annotation and colour by annotation dialogs
-
+ -
+ Updated Spanish translations.
+
+ -
+ Jmol now primary parser
+ for importing structure data to Jalview. Enables mmCIF and
+ better PDB parsing.
+
+ -
+ Alignment ruler shows positions relative to
+ reference sequence
+
+ -
+ Position/residue shown in status bar when
+ mousing over sequence associated annotation
+
+ -
+ Default RNA SS symbol to 'matching bracket'
+ for manual entry
+
+ -
+ RNA Structure consensus indicates wc-only
+ '()', canonical '[]' and invalid '{}' base pair populations
+ for each column
+
+ -
+ Feature settings popup menu options for
+ showing or hiding columns containing a feature
+
+ -
+ Edit selected group by double clicking on
+ group and sequence associated annotation labels
+
+ -
+ Sequence name added to annotation label in
+ select/hide columns by annotation and colour by annotation
+ dialogs
+
+
Application
- - Automatically hide introns when opening a gene/transcript view
- - Uniprot Sequence fetcher Free Text Search dialog
- - UniProt - PDB protein structure mappings with the EMBL-EBI PDBe SIFTS database
- - Updated download sites used for Rfam and Pfam sources to xfam.org
- - Disabled Rfam(Full) in the sequence fetcher
- - Show residue labels in Chimera when mousing over sequences in Jalview
- - Support for reverse-complement coding regions in ENA and EMBL
- - Upgrade to EMBL XML 1.2 for record retrieval via ENA rest API
- - Support for ENA CDS records with reverse complement operator
- - Update to groovy-2.4.6-indy - for faster groovy script execution
- - New 'execute Groovy script' option in an alignment window's Calculate menu
- - Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode
- - Support for creating new alignment calculation workers from groovy scripts
- - Store/restore reference sequence in Jalview projects
- - Chain codes for a sequence's PDB associations are now saved/restored from project
- - Database selection dialog always shown before sequence fetcher is opened
- - Double click on an entry in Jalview's database chooser opens a sequence fetcher
- - Free-text search client for UniProt using the UniProt REST API
- - -nonews command line parameter to prevent the news reader opening
- - Displayed columns for PDBe and Uniprot querying stored in preferences
- - Pagination for displaying PDBe and Uniprot search results
- - Tooltips shown on database chooser
- - Reverse complement function in calculate menu for nucleotide sequences
+ -
+ Automatically hide introns when opening a
+ gene/transcript view
+
+ -
+ Uniprot Sequence fetcher Free Text Search
+ dialog
+
+ -
+ UniProt - PDB protein
+ structure mappings with the EMBL-EBI PDBe SIFTS database
+
+ -
+ Updated download sites used for Rfam and
+ Pfam sources to xfam.org
+
+ -
+ Disabled Rfam(Full) in the sequence fetcher
+
+ -
+ Show residue labels in Chimera when mousing
+ over sequences in Jalview
+
+ -
+ Support for reverse-complement coding
+ regions in ENA and EMBL
+
+ -
+ Upgrade to EMBL XML 1.2
+ for record retrieval via ENA rest API
+
+ -
+ Support for ENA CDS records with reverse
+ complement operator
+
+ -
+ Update to groovy-2.4.6-indy - for faster
+ groovy script execution
+
+ -
+ New 'execute Groovy script' option in an
+ alignment window's Calculate menu
+
+ -
+ Allow groovy scripts that call
+ Jalview.getAlignFrames() to run in headless mode
+
+ -
+ Support for creating new alignment
+ calculation workers from groovy scripts
+
+ -
+ Store/restore reference sequence in
+ Jalview projects
+
+ -
+ Chain codes for a sequence's PDB
+ associations are now saved/restored from project
+
+ -
+ Database selection dialog always shown
+ before sequence fetcher is opened
+
+ -
+ Double click on an entry in Jalview's
+ database chooser opens a sequence fetcher
+
+ -
+ Free-text search client for UniProt using
+ the UniProt REST API
+
+ -
+ -nonews command line parameter to prevent
+ the news reader opening
+
+ -
+ Displayed columns for PDBe and Uniprot
+ querying stored in preferences
+
+ -
+ Pagination for displaying PDBe and Uniprot
+ search results
+
+ -
+ Tooltips shown on database chooser
+
+ -
+ Reverse complement function in calculate
+ menu for nucleotide sequences
+
+ -
+ Alignment sort by feature scores
+ and feature counts preserves alignment ordering (and
+ debugged for complex feature sets).
+
+ -
+ Chimera 1.11.1 minimum requirement for
+ viewing structures with Jalview 2.10
+
+ -
+ Retrieve
+ genome, transcript CCDS and gene ids via the Ensembl and
+ Ensembl Genomes REST API
+
+ -
+ Protein sequence variant annotation
+ computed for 'sequence_variant' annotation on CDS regions
+ (Ensembl)
+
+ -
+ ENA CDS 'show cross references' for Uniprot
+ sequences
+
+ -
+ Improved warning messages when DB
+ Ref Fetcher fails to match, or otherwise updates sequence
+ data from external database records.
+
+ -
+ Revised Jalview Project format for
+ efficient recovery of sequence coding and alignment
+ annotation relationships.
+
+ |
+
+
+ General
+
-
- Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets).
+ reinstate CTRL-click for opening pop-up
+ menu on OSX
-
-
+ Export features in Jalview format (again)
+ includes graduated colourschemes
-
-
+ More responsive when
+ working with big alignments and lots of hidden columns
-
-
+ Hidden column markers not always rendered
+ at right of alignment window
-
-
+ Tidied up links in help file table of
+ contents
+
+ -
+ Feature based tree calculation not shown
+ for DNA alignments
+
+ -
+ Hidden columns ignored during feature
+ based tree calculation
+
+ -
+ Alignment view stops updating when show
+ unconserved enabled for group on alignment
+
+ -
+ Cannot insert gaps into sequence when
+ set as reference
+
+ -
+ Alignment column in status incorrectly
+ shown as "Sequence position" when mousing over
+ annotation
+
+ -
+ Incorrect column numbers in ruler when
+ hidden columns present
+
+ -
+ Colour by RNA Helices not enabled when
+ user created annotation added to alignment
+
+ -
+ RNA Structure consensus only computed for
+ '()' base pair annotation
+
+ -
+ Enabling 'Ignore Gaps' results
+ in zero scores for all base pairs in RNA Structure
+ Consensus
+
+ -
+ Extend selection with columns containing
+ feature not working
+
+ -
+ Pfam format writer puts extra space at
+ beginning of sequence
+
+ -
+ Incomplete sequence extracted from pdb
+ entry 3a6s
+
+ -
+ Cannot create groups on an alignment from
+ from a tree when t-coffee scores are shown
+
+ -
+ Cannot import and view PDB
+ structures with chains containing negative resnums (4q4h)
+
+ -
+ ArithmeticExceptions raised when parsing
+ some structures
+
+ -
+ 'Empty' alignment blocks added
+ to Clustal, PIR and PileUp output
+
+ -
+ Reordering sequence features that are
+ not visible causes alignment window to repaint
-
-
- Applet
- |
-
-
- General
-
- - reinstate CTRL-click for opening pop-up menu on OSX
- - Export features in Jalview format (again) includes graduated colourschemes
- - More responsive when working with big alignments and lots of hidden columns
- - Hidden column markers not always rendered at right of alignment window
- - Tidied up links in help file table of contents
- - Feature based tree calculation not shown for DNA alignments
- - Hidden columns ignored during feature based tree calculation
- - Alignment view stops updating when show unconserved enabled for group on alignment
- - Cannot insert gaps into sequence when set as reference
- - Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation
- - Incorrect column numbers in ruler when hidden columns present
- - Colour by RNA Helices not enabled when user created annotation added to alignment
- - RNA Structure consensus only computed for '()' base pair annotation
- - Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus
- - Extend selection with columns containing feature not working
- - Pfam format writer puts extra space at beginning of sequence
- - Incomplete sequence extracted from pdb entry 3a6s
- - Cannot create groups on an alignment from from a tree when t-coffee scores are shown
- - Cannot import and view PDB structures with chains containing negative resnums (4q4h)
- - ArithmeticExceptions raised when parsing some structures
- - 'Empty' alignment blocks added to Clustal, PIR and PileUp output
- - Reordering sequence features that are not visible causes alignment window to repaint
-
Threshold sliders don't work in
graduated colour and colour by annotation row for e-value
@@ -147,95 +1328,203 @@
columns
-
- FER1_ARATH and FER2_ARATH mislabelled in example file (uniref50.fa, feredoxin.fa, unaligned.fa, exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
-
- -
- Null pointer exceptions and redraw problems when reference sequence defined and 'show non-conserved' enabled
+ FER1_ARATH and FER2_ARATH mislabelled in
+ example file (uniref50.fa, feredoxin.fa, unaligned.fa,
+ exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
-
-
+ Null pointer exceptions and redraw
+ problems when reference sequence defined and 'show
+ non-conserved' enabled
-
-
+ Quality and Conservation are now shown on
+ load even when Consensus calculation is disabled
-
-
+ Remove right on penultimate column of
+ alignment does nothing
Application
-
- - Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms
- - URLs and links can imported by drag'n'drop on OSX webstart
- - InstallAnywhere distribution fails when launching Chimera
- - Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)
- - Cannot save project when view has a reference sequence defined
- - Columns are suddenly selected in other alignments and views when revealing hidden columns
- - Hide columns not mirrored in complement view in a cDNA/Protein splitframe
- - Cannot save/restore representative sequence from project when only one sequence is represented
- - Disabled 'Best Uniprot Coverage' option in Structure Chooser
- - Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel
- - View mapping in structure view shows mappings between sequence and all chains in a PDB file
- - PDB and Uniprot FTS dialogs format columns correctly, don't display array data, sort columns according to type
- - Export complete shown after destination file chooser is cancelled during an image export
- - Error when querying PDB Service with sequence name containing special characters
- - Manual PDB structure querying should be case insensitive
- - Large tooltips with broken HTML formatting don't wrap
- - Figures exported from wrapped view are truncated so L looks like I in consensus annotation
- - Export features should only export the currently displayed features for the current selection or view
- - Enable 'Get Cross-References' in menu after fetching cross-references
- - Mouseover of a copy of a sequence is not followed in the structure viewer
- - Titles for individual alignments in splitframe not restored from project
- -
- missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default
-
- -
- amino acid physicochemical conservation is case dependent
-
- -
- RSS reader doesn't stay hidden after last article has been read (reopened issue due to internationalisation problems)
-
- - Only offer PDB structures in structure viewer based on sequence name, PDB and Uniprot cross-references
-
-
- No progress bar shown during export of alignment as HTML
+ URLs and links can't be imported by
+ drag'n'drop on OSX when launched via webstart (note - not
+ yet fixed for El Capitan)
+
+ -
+ Corrupt preferences for SVG, EPS & HTML
+ output when running on non-gb/us i18n platforms
+
+ -
+ Error thrown when exporting a view with
+ hidden sequences as flat-file alignment
+
+ -
+ InstallAnywhere distribution fails when
+ launching Chimera
+
+ -
+ Jalview very slow to launch via webstart
+ (also hotfix for 2.9.0b2)
-
- Improved warning messages when DB Ref Fetcher fails to match, or otherwise updates sequence data from external database records.
+ Cannot save project when view has a
+ reference sequence defined
-
- Structures not always superimposed after multiple structures are shown for one or more sequences.
+ Columns are suddenly selected in other
+ alignments and views when revealing hidden columns
-
- Reference sequence characters should not be replaced with '.' when 'Show unconserved' format option is enabled.
+ Hide columns not mirrored in complement
+ view in a cDNA/Protein splitframe
-
- Cannot specify chain code when entering specific PDB id for sequence
+ Cannot save/restore representative
+ sequence from project when only one sequence is
+ represented
-
- File->Export->.. as doesn't work when 'Export hidden sequences' is enabled, but 'export hidden columns' is disabled.
+ Disabled 'Best Uniprot Coverage' option
+ in Structure Chooser
- - Best Quality option in structure chooser selects lowest rather than highest resolution structures for each sequence
-
- Incorrect start and end reported for PDB to sequence mapping in 'View Mappings' report
+ Modifying 'Ignore Gaps' on consensus or
+ structure consensus didn't refresh annotation panel
-
-
+ View mapping in structure view shows
+ mappings between sequence and all chains in a PDB file
-
-
+ PDB and Uniprot FTS
+ dialogs format columns correctly, don't display array
+ data, sort columns according to type
+
+ -
+ Export complete shown after destination
+ file chooser is cancelled during an image export
+
+ -
+ Error when querying PDB Service with
+ sequence name containing special characters
+
+ -
+ Manual PDB structure querying should be
+ case insensitive
+
+ -
+ Large tooltips with broken HTML
+ formatting don't wrap
+
+ -
+ Figures exported from wrapped view are
+ truncated so L looks like I in consensus annotation
+
+ -
+ Export features should only export the
+ currently displayed features for the current selection or
+ view
+
+ -
+ Enable 'Get Cross-References' in menu
+ after fetching cross-references, and restoring from
+ project
+
+ -
+ Mouseover of a copy of a sequence is not
+ followed in the structure viewer
+
+ -
+ Titles for individual alignments in
+ splitframe not restored from project
+
+ -
+ missing autocalculated annotation at
+ trailing end of protein alignment in transcript/product
+ splitview when pad-gaps not enabled by default
+
+ -
+ amino acid physicochemical conservation
+ is case dependent
+
+ -
+ RSS reader doesn't stay hidden after last
+ article has been read (reopened issue due to
+ internationalisation problems)
+
+ -
+ Only offer PDB structures in structure
+ viewer based on sequence name, PDB and UniProt
+ cross-references
-
+ -
+ No progress bar shown during export of
+ alignment as HTML
+
+ -
+ Structures not always superimposed after
+ multiple structures are shown for one or more sequences.
+
+ -
+ Reference sequence characters should not
+ be replaced with '.' when 'Show unconserved' format option
+ is enabled.
+
+ -
+ Cannot specify chain code when entering
+ specific PDB id for sequence
+
+ -
+ File->Export->.. as doesn't work when
+ 'Export hidden sequences' is enabled, but 'export hidden
+ columns' is disabled.
+
+ -
+ Best Quality option in structure chooser
+ selects lowest rather than highest resolution structures
+ for each sequence
+
+ -
+ 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.
+
+
Applet
- - Incorrect columns are selected when hidden columns present before start of sequence
- - Missing dependencies on applet pages (JSON jars)
-
- Overview pixel size changes when sequences are hidden in applet
+ Incorrect columns are selected when
+ hidden columns present before start of sequence
+
+ -
+ Missing dependencies on applet pages
+ (JSON jars)
+
+ -
+ Overview pixel size changes when
+ sequences are hidden in applet
- - Updated instructions for applet deployment on examples pages.
+
-
+ Updated instructions for applet
+ deployment on examples pages.
+
- Signed OSX InstallAnywhere installer
- Support for per-sequence based annotations in BioJSON
Applet
- Split frame example added to applet examples page
+ Build and Deployment
+
+ -
+ New ant target for running Jalview's test
+ suite
+
|
@@ -671,10 +1966,10 @@
Deployment and Documentation
+ General
+ --> Deployment and Documentation
- 2G and 1G options in launchApp have no effect on
memory allocation
@@ -882,8 +2177,7 @@
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
@@ -1512,7 +2806,6 @@
- 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
@@ -1540,8 +2833,8 @@
- 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
@@ -1556,7 +2849,8 @@
between different screens.
- New preference items for sequence ID tooltip and
consensus annotation
- - Client to submit sequences and IDs to Envision2 Workflows
+ - Client to submit sequences and IDs to Envision2
+ Workflows
- Vamsas Capabilities
- Improved VAMSAS synchronization (Jalview archive
@@ -1964,7 +3258,6 @@
- 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'
@@ -1979,7 +3272,6 @@
- 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
@@ -1991,7 +3283,6 @@
- WsDbFetch query/result association resolved
- Tree leaf to sequence mapping improved
- Smooth fonts switch moved to FontChooser dialog box.
-
|