-
- 2.9 9/9/2015
+
+
+ Release
+
+ |
+
+
+ New Features
+
+ |
+
+
+ Issues Resolved
+
+ |
+ |
+
+
+
+ |
+ |
+
+
+
+ -
+ DAS sequence retrieval and annotation capabilities removed from the Jalview Desktop
+
+
+ |
+
+
+
+
+ |
+
+
+
+ -
+ Windows File Shortcuts can be dragged
+ onto the Jalview Desktop
+
+
+ |
+
+
+
+ -
+ Clustal files with sequence positions in
+ right-hand column parsed correctly
+
+ -
+ F2/Keyboard mode edits work when Overview
+ window has input focus
+
+ -
+ Wrap view - export to SVG - IDs shown but
+ not alignment area in exported graphic
+
+ -
+ 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.
+
+
+
+ |
+
+
+ |
+
+ 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
- - Linked visualisation and analysis of DNA and Protein
- alignments:
- - Translated cDNA alignments shown as split protein and
- DNA alignment views
- - Codon consensus annotation for linked protein and
- cDNA alignment views
- - Add cDNA or Protein product sequences to Protein or
- cDNA alignments
- - Reconstruct linked cDNA alignment from aligned
- protein sequences
-
+ -
+ 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
+
- - Update Jmol to v14.2n
+ 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
+
+ -
+ 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
+
+ -
+ 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
+ scores associated with features and annotation rows
+
+ -
+ amino acid physicochemical conservation
+ calculation should be case independent
+
+ -
+ Remove annotation also updates hidden
+ 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
+
+ -
+ Quality and Conservation are now shown on
+ load even when Consensus calculation is disabled
+
+ -
+ Remove right on penultimate column of
+ alignment does nothing
+
+
+ Application
+
+ -
+ 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)
+
+ -
+ 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, 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
+
- - BioJSON data exchange
+ -
+ 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
+
+ -
+ Updated instructions for applet
+ deployment on examples pages.
+
+
+
+ |
+
+
+
+
+ |
+ General
+
+ - Time stamps for signed Jalview application and applet
+ jars
+ |
+
+
+ Application
+
+ - Duplicate group consensus and conservation rows
+ shown when tree is partitioned
+ - Erratic behaviour when tree partitions made with
+ multiple cDNA/Protein split views
+
+
+ |
+
+
+
+
+ |
+ General
+
+ - Updated Spanish translations of localized text for
+ 2.9
+ Application
+
+
+ - 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
+
+ |
+
+
+ General
+
+ - Mapping of cDNA to protein in split frames
+ incorrect when sequence start > 1
+ - Broken images in filter column by annotation dialog
+ documentation
+ - Feature colours not parsed from features file
+ - Exceptions and incomplete link URLs recovered when
+ loading a features file containing HTML tags in feature
+ description
+
+ Application
+
+ - Annotations corrupted after BioJS export and
+ reimport
+ - Incorrect sequence limits after Fetch DB References
+ with 'trim retrieved sequences'
+ - Incorrect warning about deleting all data when
+ deleting selected columns
+ - Patch to build system for shipping properly signed
+ JNLP templates for webstart launch
+ - EMBL-PDBe fetcher/viewer dialogs do not offer
+ unreleased structures for download or viewing
+ - Tab/space/return keystroke operation of EMBL-PDBe
+ fetcher/viewer dialogs works correctly
+ - Disabled 'minimise' button on Jalview windows
+ running on OSX to workaround redraw hang bug
+ - Split cDNA/Protein view position and geometry not
+ recovered from jalview project
+ - Initial enabled/disabled state of annotation menu
+ sorter 'show autocalculated first/last' corresponds to
+ alignment view
+ - Restoring of Clustal, RNA Helices and T-Coffee
+ color schemes from BioJSON
+
+ Applet
+
+ - Reorder sequences mirrored in cDNA/Protein split
+ frame
+ - Applet with Jmol examples not loading correctly
+
+
+ |
+
+
+ |
+ General
+
+ - Linked visualisation and analysis of DNA and Protein
+ alignments:
+
+ - Translated cDNA alignments shown as split protein
+ and DNA alignment views
+ - Codon consensus annotation for linked protein and
+ cDNA alignment views
+ - Link cDNA or Protein product sequences by loading
+ them onto Protein or cDNA alignments
+ - Reconstruct linked cDNA alignment from aligned
+ protein sequences
+
+
+ - Jmol integration updated to Jmol v14.2.14
+ - Import and export of Jalview alignment views as BioJSON
- New alignment annotation file statements for
reference sequences and marking hidden columns
-
- - Alignments can be sorted by number of RNA helices
-
- - Assign a reference sequence to highlight
- variation and consensus analysis
-
+ - Reference sequence based alignment shading to
+ highlight variation
- Select or hide columns according to alignment
annotation
- - Find option for locating sequences by
- description
-
+ - Find option for locating sequences by description
- Conserved physicochemical properties shown in amino
acid conservation row
-
+ - Alignments can be sorted by number of RNA helices
Application
- - Optional embedding of BioJSON data when exporting
- alignment figures to HTML
- - New Export Settings dialog to control hidden region export in flat file
- generation
- - New cDNA/Protein analysis capabilities
- - Get Cross-References should open a Split Frame view
- with cDNA/Protein
- - Detect when nucleotide sequences and protein
- sequences are placed in the same alignment
- - Split cDNA/Protein views are saved in Jalview
- projects
- - support '*' in amino acid sequences to indicate stop
- codon
-
+ - New cDNA/Protein analysis capabilities
+
+ - Get Cross-References should open a Split Frame
+ view with cDNA/Protein
+ - Detect when nucleotide sequences and protein
+ sequences are placed in the same alignment
+ - Split cDNA/Protein views are saved in Jalview
+ projects
+
+
- Use REST API to talk to Chimera
- - Selected regions in Chimera are highlighted in linked Jalview windows
-
- - Calculate UPGMA and NJ trees using sequence feature
- similarity
+ - Selected regions in Chimera are highlighted in linked
+ Jalview windows
- VARNA RNA viewer updated to v3.93
- - VARNA views are saved in Jalview
- Projects
- - Pseudoknots displayed as Jalview RNA annotation can be shown in VARNA
-
- - changed 'View nucleotide structure' submenu to 'View VARNA 2D Structure'
- - change "View protein structure" menu option to "3D
- Structure ..."
+ - VARNA views are saved in Jalview Projects
+ - Pseudoknots displayed as Jalview RNA annotation can
+ be shown in VARNA
- Make groups for selection uses marked columns as well
as the active selected region
- - allow different similarity matrix calculations for
- tree building and PCA
+ - Calculate UPGMA and NJ trees using sequence feature
+ similarity
+ - New Export options
+
+ - New Export Settings dialog to control hidden
+ region export in flat file generation
- - Export alignment views for display with the BioJS MSAViewer
- - Scrollable SVG for HTML export
+ - Export alignment views for display with the BioJS MSAViewer
- - Novel data discovery and retrieval mechanism using
- PDBe Search API
- - Smarter technique for selecting PDB structures to
- view in Jalview
+ - Export scrollable SVG in HTML page
+ - Optional embedding of BioJSON data when exporting
+ alignment figures to HTML
+
+ - 3D structure retrieval and display
+
+ - Free text and structured queries with the PDBe
+ Search API
+ - PDBe Search API based discovery and selection of
+ PDB structures for a sequence set
+
+
- JPred4 employed for protein secondary structure
predictions
- Hide Insertions menu option to hide unaligned columns
for one or a group of sequences
- - Automatically hide insertions in alignments imported from the JPred4 web server
+ - Automatically hide insertions in alignments imported
+ from the JPred4 web server
+ - (Nearly) Native 'Quaqua' dialogs for browsing file
+ system on OSX
LGPL libraries courtesy of http://www.randelshofer.ch/quaqua/
+
+ - changed 'View nucleotide structure' submenu to 'View
+ VARNA 2D Structure'
+ - change "View protein structure" menu option to "3D
+ Structure ..."
+
Applet
- - Parameter to enable SplitFrame view
? check other
- parameters in applet ?
+ - New layout for applet example pages
+ - New parameters to enable SplitFrame view
+ (file2,enableSplitFrame, scaleProteinAsCdna)
- New example demonstrating linked viewing of cDNA and
Protein alignments
- - New layout for applet example pages
-
- Development and deployment
- Java 1.7 minimum requirement for Jalview 2.9
- Include installation type and git revision in build
- properties and console log output
- Github project and web URL for storing BioJsMSA
- Templates
- Jalview's unit tests now managed with TestNG |
- General
+ Development and deployment
+
+ - Java 1.7 minimum requirement for Jalview 2.9
+ - Include installation type and git revision in build
+ properties and console log output
+ - Jalview Github organisation, and new github site for
+ storing BioJsMSA Templates
+ - Jalview's unit tests now managed with TestNG
+ |
+
+ Application
+ --> Application
- Escape should close any open find dialogs
- - typo in select-by-features status report
+ - Typo in select-by-features status report
- Consensus RNA secondary secondary structure
predictions are not highlighted in amber
- - missing gap character means v2.7 example file appears
- unaligned REVIEW
+ - Missing gap character in v2.7 example file means
+ alignment appears unaligned when pad-gaps is not enabled
- First switch to RNA Helices colouring doesn't colour
associated structure views
- ID width preference option is greyed out when auto
@@ -181,12 +2186,12 @@
to a grey/invisible alignment window
- Exported Jpred annotation from a sequence region
imports to different position
- - Space at beginning of sequence feature mouseover
- tooltip on some platforms
+ - Space at beginning of sequence feature tooltips shown
+ on some platforms
- Chimera viewer 'View | Show Chain' menu is not
populated
- - 'New View' fails with a Null Pointer Exception if
- Chimera has been opened
+ - 'New View' fails with a Null Pointer Exception in
+ console if Chimera has been opened
- Mouseover to Chimera not working
- Miscellaneous ENA XML feature qualifiers not
retrieved
@@ -195,28 +2200,24 @@
either sequence shows on first structure
- 'Show annotations' options should not make
non-positional annotations visible
- - subsequence secondary structure annotation not shown
+
- Subsequence secondary structure annotation not shown
in right place after 'view flanking regions'
- File Save As type unset when current file format is
unknown
- - Native 'Quaqua' dialogs for saving and loading files
- on OSX
- Save as '.jar' option removed for saving Jalview
projects
- Colour by Sequence colouring in Chimera more
responsive
- - Can disable consensus calculation independently of
- quality and conservation
- Cannot 'add reference annotation' for a sequence in
several views on same alignment
- Cannot show linked products for EMBL / ENA records
- Jalview's tooltip wraps long texts containing no
spaces
Applet
- Jmol to JalviewLite mouseover/link not working
- JalviewLite can't import sequences with ID descriptions
- containing angle brackets
+ - Jmol to JalviewLite mouseover/link not working
+ - JalviewLite can't import sequences with ID
+ descriptions containing angle brackets
General
- Cannot export and reimport RNA secondary structure
@@ -242,7 +2243,8 @@
- Nucleotide ambiguity codes involving R not recognised
Deployment and Documentation
-
+ - Applet example pages appear different to the rest of
+ www.jalview.org
Application Known issues
- Incomplete sequence extracted from PDB entry 3a6s
@@ -260,338 +2262,341 @@
placed above or below non-autocalculated rows
- Jalview dekstop becomes sluggish at full screen in
ultra-high resolution
+ - Cannot disable consensus calculation independently of
+ quality and conservation
+ - Mouseover highlighting between cDNA and protein can
+ become sluggish with more than one splitframe shown
Applet Known Issues
- Core PDB parsing code requires Jmol
- Sequence canvas panel goes white when alignment
- window is being resized
-
-
-
|
+ window is being resized
+
+
+
-
-
- |
-
-
-
- |
-
-
- - Reinstated the display of default example file on startup
- - All pairs shown in Jalview window when viewing result of pairwise alignment
-
-
- |
-
-
- |
- General
-
- - Updated Java code signing certificate donated by Certum.PL.
- - Features and annotation preserved when performing pairwise
- alignment
- - RNA pseudoknot annotation can be
- imported/exported/displayed
- - 'colour by annotation' can colour by RNA and
- protein secondary structure
- - Warn user if 'Find' regular expression is invalid (mentioned post-hoc with 2.9 release)
-
- Application
-
- - Extract and display secondary structure for sequences with
- 3D structures
- - Support for parsing RNAML
- - Annotations menu for layout
-
- - sort sequence annotation rows by alignment
- - place sequence annotation above/below alignment
- annotation
-
- - Output in Stockholm format
- - Internationalisation: improved Spanish (es) translation
- - Structure viewer preferences tab
- - Disorder and Secondary Structure annotation tracks shared
- between alignments
- - UCSF Chimera launch and linked highlighting from Jalview
- - Show/hide all sequence associated annotation rows for all
- or current selection
- - disorder and secondary structure predictions available as
- dataset annotation
- - Per-sequence rna helices colouring
-
-
- - Sequence database accessions imported when fetching
- alignments from Rfam
- - update VARNA version to 3.91
+ |
+ General
+
+ - Updated Java code signing certificate donated by
+ Certum.PL.
+ - Features and annotation preserved when performing
+ pairwise alignment
+ - RNA pseudoknot annotation can be
+ imported/exported/displayed
+ - 'colour by annotation' can colour by RNA and
+ protein secondary structure
+ - Warn user if 'Find' regular expression is invalid (mentioned
+ post-hoc with 2.9 release)
+
- - New groovy scripts for exporting aligned positions,
- conservation values, and calculating sum of pairs scores.
- - Command line argument to set default JABAWS server
- - include installation type in build properties and console
- log output
- - Updated Jalview project format to preserve dataset annotation
- |
-
- Application
-
- - Distinguish alignment and sequence associated RNA
- structure in structure->view->VARNA
- - Raise dialog box if user deletes all sequences in an
- alignment
- - Pressing F1 results in documentation opening twice
- - Sequence feature tooltip is wrapped
- - Double click on sequence associated annotation selects
- only first column
- - Redundancy removal doesn't result in unlinked leaves
- shown in tree
- - Undos after several redundancy removals don't undo
- properly
- - Hide sequence doesn't hide associated annotation
- - User defined colours dialog box too big to fit on screen
- and buttons not visible
- - author list isn't updated if already written to Jalview
- properties
- - Popup menu won't open after retrieving sequence from
- database
- - File open window for associate PDB doesn't open
- - Left-then-right click on a sequence id opens a browser
- search window
- - Cannot open sequence feature shading/sort popup menu in
- feature settings dialog
- - better tooltip placement for some areas of Jalview desktop
- - Allow addition of JABAWS Server which doesn't pass
- validation
- - Web services parameters dialog box is too large to fit on
- screen
- - Muscle nucleotide alignment preset obscured by tooltip
- - JABAWS preset submenus don't contain newly defined
- user preset
- - MSA web services warns user if they were launched with
- invalid input
- - Jalview cannot contact DAS Registy when running on Java 8
- -
-
- 'Superpose with' submenu not shown when new view created
-
+ Application
+
+ - Extract and display secondary structure for sequences
+ with 3D structures
+ - Support for parsing RNAML
+ - Annotations menu for layout
+
+ - sort sequence annotation rows by alignment
+ - place sequence annotation above/below alignment
+ annotation
+
+ - Output in Stockholm format
+ - Internationalisation: improved Spanish (es)
+ translation
+ - Structure viewer preferences tab
+ - Disorder and Secondary Structure annotation tracks
+ shared between alignments
+ - UCSF Chimera launch and linked highlighting from
+ Jalview
+ - Show/hide all sequence associated annotation rows for
+ all or current selection
+ - disorder and secondary structure predictions
+ available as dataset annotation
+ - Per-sequence rna helices colouring
- Deployment and Documentation
-
- - 2G and 1G options in launchApp have no effect on memory
- allocation
- - launchApp service doesn't automatically open
- www.jalview.org/examples/exampleFile.jar if no file is given
- -
-
- InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is
- available
-
- Application Known issues
-
- -
-
- corrupted or unreadable alignment display when scrolling alignment
- to right
-
- -
-
- retrieval fails but progress bar continues for DAS retrieval with
- large number of ID
-
- -
-
- flatfile output of visible region has incorrect sequence start/end
-
- -
-
- rna structure consensus doesn't update when secondary
- structure tracks are rearranged
-
- -
-
- invalid rna structure positional highlighting does not highlight
- position of invalid base pairs
-
- -
-
- out of memory errors are not raised when saving Jalview project
- from alignment window file menu
-
- -
-
- Switching to RNA Helices colouring doesn't propagate to
- structures
-
- -
-
- colour by RNA Helices not enabled when user created annotation
- added to alignment
-
- -
-
- Jalview icon not shown on dock in Mountain Lion/Webstart
-
- Applet Known Issues
-
- -
-
- JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
-
- -
-
- Jalview and Jmol example not compatible with IE9
-
- - Sort by annotation score doesn't reverse order when
- selected
-
- |
- |
-
- |
-
-
- General
-
- - Internationalisation of user interface (usually called
- i18n support) and translation for Spanish locale
- - Define/Undefine group on current selection with
- Ctrl-G/Shift Ctrl-G
- - Improved group creation/removal options in
- alignment/sequence Popup menu
- - Sensible precision for symbol distribution percentages
- shown in logo tooltip.
- - Annotation panel height set according to amount of
- annotation when alignment first opened
- Application
-
- - Interactive consensus RNA secondary structure prediction
- VIENNA RNAAliFold JABA 2.1 service
- - Select columns containing particular features from Feature
- Settings dialog
- - View all 'representative' PDB structures for selected
- sequences
- - Update Jalview project format:
-
- - New file extension for Jalview projects '.jvp'
- - Preserve sequence and annotation dataset (to store
- secondary structure annotation,etc)
- - Per group and alignment annotation and RNA helix
- colouring
-
-
- - New similarity measures for PCA and Tree calculation
- (PAM250)
- - Experimental support for retrieval and viewing of flanking
- regions for an alignment
-
- |
-
- Application
-
- - logo keeps spinning and status remains at queued or
- running after job is cancelled
- - cannot export features from alignments imported from
- Jalview/VAMSAS projects
- - Buggy slider for web service parameters that take float
- values
- - Newly created RNA secondary structure line doesn't have
- 'display all symbols' flag set
- - T-COFFEE alignment score shading scheme and other
- annotation shading not saved in Jalview project
- - Local file cannot be loaded in freshly downloaded Jalview
- - Jalview icon not shown on dock in Mountain Lion/Webstart
- - Load file from desktop file browser fails
- - Occasional NPE thrown when calculating large trees
- - Cannot reorder or slide sequences after dragging an
- alignment onto desktop
- - Colour by annotation dialog throws NPE after using
- 'extract scores' function
- - Loading/cut'n'pasting an empty file leads to a grey
- alignment window
- - Disorder thresholds rendered incorrectly after performing
- IUPred disorder prediction
- - Multiple group annotated consensus rows shown when
- changing 'normalise logo' display setting
- - Find shows blank dialog after 'finished searching' if
- nothing matches query
- - Null Pointer Exceptions raised when sorting by feature
- with lots of groups
-
- - Errors in Jmol console when structures in alignment don't
- overlap
-
- - Not all working JABAWS services are shown in Jalview's
- menu
- - JAVAWS version of Jalview fails to launch with 'invalid
- literal/length code'
- - Annotation/RNA Helix colourschemes cannot be applied to
- alignment with groups (actually fixed in 2.8.0b1)
- - RNA Helices and T-Coffee Scores available as default colourscheme
+ - Sequence database accessions imported when fetching
+ alignments from Rfam
+ - update VARNA version to 3.91
- Applet
-
- - Remove group option is shown even when selection is not a
- group
- - Apply to all groups ticked but colourscheme changes don't
- affect groups
- - Documented RNA Helices and T-Coffee Scores as valid colourscheme name
- - Annotation labels drawn on sequence IDs when Annotation panel is not displayed
- - Increased font size for dropdown menus on OSX and embedded windows
- Other
-
- - Consensus sequence for alignments/groups with a single
- sequence were not calculated
- - annotation files that contain only groups imported as
- annotation and junk sequences
- - Fasta files with sequences containing '*' incorrectly
- recognised as PFAM or BLC
- - conservation/PID slider apply all groups option doesn't
- affect background (2.8.0b1)
-
- - redundancy highlighting is erratic at 0% and 100%
- - Remove gapped columns fails for sequences with ragged
- trailing gaps
- - AMSA annotation row with leading spaces is not registered
- correctly on import
- - Jalview crashes when selecting PCA analysis for certain
- alignments
- - Opening the colour by annotation dialog for an existing
- annotation based 'use original colours' colourscheme loses
- original colours setting
-
- |
-
-
-
- |
+ New groovy scripts for exporting aligned positions,
+ conservation values, and calculating sum of pairs scores.
+ Command line argument to set default JABAWS server
+ include installation type in build properties and
+ console log output
+ Updated Jalview project format to preserve dataset
+ annotation
+
+ Application
- - Trusted certificates for JalviewLite applet and
- Jalview Desktop application
Certificate was donated by
- Certum to the Jalview
- open source project).
+ - Distinguish alignment and sequence associated RNA
+ structure in structure->view->VARNA
+ - Raise dialog box if user deletes all sequences in an
+ alignment
+ - Pressing F1 results in documentation opening twice
+ - Sequence feature tooltip is wrapped
+ - Double click on sequence associated annotation
+ selects only first column
+ - Redundancy removal doesn't result in unlinked
+ leaves shown in tree
+ - Undos after several redundancy removals don't undo
+ properly
+ - Hide sequence doesn't hide associated annotation
+ - User defined colours dialog box too big to fit on
+ screen and buttons not visible
+ - author list isn't updated if already written to
+ Jalview properties
+ - Popup menu won't open after retrieving sequence
+ from database
+ - File open window for associate PDB doesn't open
+ - Left-then-right click on a sequence id opens a
+ browser search window
+ - Cannot open sequence feature shading/sort popup menu
+ in feature settings dialog
+ - better tooltip placement for some areas of Jalview
+ desktop
+ - Allow addition of JABAWS Server which doesn't
+ pass validation
+ - Web services parameters dialog box is too large to
+ fit on screen
+ - Muscle nucleotide alignment preset obscured by
+ tooltip
+ - JABAWS preset submenus don't contain newly
+ defined user preset
+ - MSA web services warns user if they were launched
+ with invalid input
+ - Jalview cannot contact DAS Registy when running on
+ Java 8
+ -
+
+ 'Superpose with' submenu not shown when new view
+ created
- - Jalview SRS links replaced by Uniprot and EBI-search
+
+
Deployment and Documentation
+
+ - 2G and 1G options in launchApp have no effect on
+ memory allocation
+ - launchApp service doesn't automatically open
+ www.jalview.org/examples/exampleFile.jar if no file is given
+ -
+
+ InstallAnywhere reports cannot find valid JVM when Java
+ 1.7_055 is available
- - Output in Stockholm format
- - Allow import of data from gzipped files
- - Export/import group and sequence associated line
- graph thresholds
- - Nucleotide substitution matrix that supports RNA and
- ambiguity codes
+ Application Known issues
+
+ -
+
+ corrupted or unreadable alignment display when scrolling
+ alignment to right
+
+ -
+
+ retrieval fails but progress bar continues for DAS retrieval
+ with large number of ID
+
+ -
+
+ flatfile output of visible region has incorrect sequence
+ start/end
+
+ -
+
+ rna structure consensus doesn't update when secondary
+ structure tracks are rearranged
+
+ -
+
+ invalid rna structure positional highlighting does not
+ highlight position of invalid base pairs
+
+ -
+
+ out of memory errors are not raised when saving Jalview
+ project from alignment window file menu
+
+ -
+
+ Switching to RNA Helices colouring doesn't propagate to
+ structures
+
+ -
+
+ colour by RNA Helices not enabled when user created
+ annotation added to alignment
+
+ -
+
+ Jalview icon not shown on dock in Mountain Lion/Webstart
+
+ Applet Known Issues
+
+ -
+
+ JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
+
+ -
+
+ Jalview and Jmol example not compatible with IE9
+
+
+ - Sort by annotation score doesn't reverse order
+ when selected
+
+ |
+
+
+ |
+
+
+ General
+
+ - Internationalisation of user interface (usually
+ called i18n support) and translation for Spanish locale
+ - Define/Undefine group on current selection with
+ Ctrl-G/Shift Ctrl-G
+ - Improved group creation/removal options in
+ alignment/sequence Popup menu
+ - Sensible precision for symbol distribution
+ percentages shown in logo tooltip.
+ - Annotation panel height set according to amount of
+ annotation when alignment first opened
+ Application
+
+ - Interactive consensus RNA secondary structure
+ prediction VIENNA RNAAliFold JABA 2.1 service
+ - Select columns containing particular features from
+ Feature Settings dialog
+ - View all 'representative' PDB structures for selected
+ sequences
+ - Update Jalview project format:
+
+ - New file extension for Jalview projects '.jvp'
+ - Preserve sequence and annotation dataset (to
+ store secondary structure annotation,etc)
+ - Per group and alignment annotation and RNA helix
+ colouring
+
+
+ - New similarity measures for PCA and Tree calculation
+ (PAM250)
+ - Experimental support for retrieval and viewing of
+ flanking regions for an alignment
+
+ |
+
+ Application
+
+ - logo keeps spinning and status remains at queued or
+ running after job is cancelled
+ - cannot export features from alignments imported from
+ Jalview/VAMSAS projects
+ - Buggy slider for web service parameters that take
+ float values
+ - Newly created RNA secondary structure line doesn't
+ have 'display all symbols' flag set
+ - T-COFFEE alignment score shading scheme and other
+ annotation shading not saved in Jalview project
+ - Local file cannot be loaded in freshly downloaded
+ Jalview
+ - Jalview icon not shown on dock in Mountain
+ Lion/Webstart
+ - Load file from desktop file browser fails
+ - Occasional NPE thrown when calculating large trees
+ - Cannot reorder or slide sequences after dragging an
+ alignment onto desktop
+ - Colour by annotation dialog throws NPE after using
+ 'extract scores' function
+ - Loading/cut'n'pasting an empty file leads to a grey
+ alignment window
+ - Disorder thresholds rendered incorrectly after
+ performing IUPred disorder prediction
+ - Multiple group annotated consensus rows shown when
+ changing 'normalise logo' display setting
+ - Find shows blank dialog after 'finished searching' if
+ nothing matches query
+ - Null Pointer Exceptions raised when sorting by
+ feature with lots of groups
+
+ - Errors in Jmol console when structures in alignment
+ don't overlap
+
+ - Not all working JABAWS services are shown in
+ Jalview's menu
+ - JAVAWS version of Jalview fails to launch with
+ 'invalid literal/length code'
+ - Annotation/RNA Helix colourschemes cannot be applied
+ to alignment with groups (actually fixed in 2.8.0b1)
+ - RNA Helices and T-Coffee Scores available as default
+ colourscheme
+
+ Applet
+
+ - Remove group option is shown even when selection is
+ not a group
+ - Apply to all groups ticked but colourscheme changes
+ don't affect groups
+ - Documented RNA Helices and T-Coffee Scores as valid
+ colourscheme name
+ - Annotation labels drawn on sequence IDs when
+ Annotation panel is not displayed
+ - Increased font size for dropdown menus on OSX and
+ embedded windows
+ Other
+
+ - Consensus sequence for alignments/groups with a
+ single sequence were not calculated
+ - annotation files that contain only groups imported as
+ annotation and junk sequences
+ - Fasta files with sequences containing '*' incorrectly
+ recognised as PFAM or BLC
+ - conservation/PID slider apply all groups option
+ doesn't affect background (2.8.0b1)
+
+ - redundancy highlighting is erratic at 0% and 100%
+ - Remove gapped columns fails for sequences with ragged
+ trailing gaps
+ - AMSA annotation row with leading spaces is not
+ registered correctly on import
+ - Jalview crashes when selecting PCA analysis for
+ certain alignments
+ - Opening the colour by annotation dialog for an
+ existing annotation based 'use original colours'
+ colourscheme loses original colours setting
+
+ |
+
+
+ |
+
+
+ - Trusted certificates for JalviewLite applet and
+ Jalview Desktop application
Certificate was donated by
+ Certum to the Jalview
+ open source project).
+
+ - 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
+ graph thresholds
+ - Nucleotide substitution matrix that supports RNA and
+ ambiguity codes
- Allow disorder predictions to be made on the current
selection (or visible selection) in the same way that JPred
works
@@ -664,1273 +2669,1339 @@
- ClassCastException when generating EPS in headless
mode
- Adjusting sequence-associated shading threshold only
- changes one row's threshold
+ changes one row's threshold
- Preferences and Feature settings panel panel
doesn't open
- - hide consensus histogram also hides conservation and
- quality histograms
-
+ hide consensus histogram also hides conservation and
+ quality histograms
+
|
-
- |
- Application
- - Support for JABAWS 2.0 Services (AACon alignment
- conservation, protein disorder and Clustal Omega)
- - JABAWS server status indicator in Web Services preferences
-
- - VARNA (http://varna.lri.fr) viewer for RNA structures in
- Jalview alignment window
- - Updated Jalview build and deploy framework for OSX mountain
- lion, windows 7, and 8
- - Nucleotide substitution matrix for PCA that supports RNA
- and ambiguity codes
+
+ |
+ Application
+
+ - Support for JABAWS 2.0 Services (AACon alignment
+ conservation, protein disorder and Clustal Omega)
+ - JABAWS server status indicator in Web Services
+ preferences
+ - VARNA (http://varna.lri.fr) viewer for RNA structures
+ in Jalview alignment window
+ - Updated Jalview build and deploy framework for OSX
+ mountain lion, windows 7, and 8
+ - Nucleotide substitution matrix for PCA that supports
+ RNA and ambiguity codes
- - Improved sequence database retrieval GUI
- - Support fetching and database reference look up against
- multiple DAS sources (Fetch all from in 'fetch db refs')
- - Jalview project improvements
-
- - Store and retrieve the 'belowAlignment' flag for
- annotation
- - calcId attribute to group annotation rows on the
- alignment
- - Store AACon calculation settings for a view in Jalview
- project
+ - Improved sequence database retrieval GUI
+ - Support fetching and database reference look up
+ against multiple DAS sources (Fetch all from in 'fetch db
+ refs')
+ - Jalview project improvements
+
+ - Store and retrieve the 'belowAlignment'
+ flag for annotation
+ - calcId attribute to group annotation rows on the
+ alignment
+ - Store AACon calculation settings for a view in
+ Jalview project
-
-
- - horizontal scrolling gesture support
- - Visual progress indicator when PCA calculation is running
- - Simpler JABA web services menus
- - visual indication that web service results are still being
- retrieved from server
- - Serialise the dialogs that are shown when Jalview starts up
- for first time
- - Jalview user agent string for interacting with HTTP
- services
- - DAS 1.6 and DAS 2.0 source support using new JDAS client
- library
- - Examples directory and Groovy library included in
- InstallAnywhere distribution
- Applet
-
- - RNA alignment and secondary structure annotation
- visualization applet example
- General
-
- - Normalise option for consensus sequence logo
- - Reset button in PCA window to return dimensions to
- defaults
- - Allow seqspace or Jalview variant of alignment PCA
- calculation
- - PCA with either nucleic acid and protein substitution
- matrices
-
- Allow windows containing HTML reports to be exported in
- HTML
- - Interactive display and editing of RNA secondary structure
- contacts
- - RNA Helix Alignment Colouring
- - RNA base pair logo consensus
- - Parse sequence associated secondary structure information
- in Stockholm files
- - HTML Export database accessions and annotation information
- presented in tooltip for sequences
- - Import secondary structure from LOCARNA clustalw style RNA
- alignment files
- - import and visualise T-COFFEE quality scores for an
- alignment
- - 'colour by annotation' per sequence option to
- shade each sequence according to its associated alignment
- annotation
- - New Jalview Logo
- Documentation and Development
-
- - documentation for score matrices used in Jalview
- - New Website!
- |
- Application
-
- - PDB, Unprot and EMBL (ENA) databases retrieved via
- wsdbfetch REST service
- - Stop windows being moved outside desktop on OSX
- - Filetype associations not installed for webstart launch
- - Jalview does not always retrieve progress of a JABAWS job
- execution in full once it is complete
- - revise SHMR RSBS definition to ensure alignment is
- uploaded via ali_file parameter
- - Jalview 2.7 is incompatible with Jmol-12.2.2
- - View all structures superposed fails with exception
- - Jnet job queues forever if a very short sequence is
- submitted for prediction
- - Cut and paste menu not opened when mouse clicked on
- desktop window
- - Putting fractional value into integer text box in
- alignment parameter dialog causes Jalview to hang
- - Structure view highlighting doesn't work on windows 7
-
- - View all structures fails with exception shown in
- structure view
- - Characters in filename associated with PDBEntry not
- escaped in a platform independent way
- - Jalview desktop fails to launch with exception when using
- proxy
- - Tree calculation reports 'you must have 2 or more
- sequences selected' when selection is empty
- - Jalview desktop fails to launch with jar signature failure
- when java web start temporary file caching is disabled
- - DAS Sequence retrieval with range qualification results in
- sequence xref which includes range qualification
- - Errors during processing of command line arguments cause
- progress bar (JAL-898) to be removed
- - Replace comma for semi-colon option not disabled for DAS
- sources in sequence fetcher
- - Cannot close news reader when JABAWS server warning dialog
- is shown
- - Option widgets not updated to reflect user settings
- - Edited sequence not submitted to web service
- - Jalview 2.7 Webstart does not launch on mountain lion
- - InstallAnywhere installer doesn't unpack and run on
- OSX Mountain Lion
- - Annotation panel not given a scroll bar when sequences
- with alignment annotation are pasted into the alignment
- - Sequence associated annotation rows not associated when
- loaded from Jalview project
- - Browser launch fails with NPE on java 1.7
- - JABAWS alignment marked as finished when job was cancelled
- or job failed due to invalid input
- - NPE with v2.7 example when clicking on Tree associated
- with all views
- - Exceptions when copy/paste sequences with grouped
- annotation rows to new window
- Applet
-
- - Sequence features are momentarily displayed before they
- are hidden using hidefeaturegroups applet parameter
- - loading features via javascript API automatically enables
- feature display
- - scrollToColumnIn javascript API method doesn't work
- General
-
- - Redundancy removal fails for rna alignment
- - PCA calculation fails when sequence has been selected and
- then deselected
- - PCA window shows grey box when first opened on OSX
- - Letters coloured pink in sequence logo when alignment
- coloured with clustalx
- - Choosing fonts without letter symbols defined causes
- exceptions and redraw errors
- - Initial PCA plot view is not same as manually reconfigured
- view
- - Grouped annotation graph label has incorrect line colour
- - Grouped annotation graph label display is corrupted for
- lots of labels
-
- |
-
-
-
- |
- Application
-
- - Jalview Desktop News Reader
- - Tweaked default layout of web services menu
- - View/alignment association menu to enable user to easily
- specify which alignment a multi-structure view takes its
- colours/correspondences from
- - Allow properties file location to be specified as URL
- - Extend Jalview project to preserve associations between
- many alignment views and a single Jmol display
- - Store annotation row height in Jalview project file
- - Annotation row column label formatting attributes stored
- in project file
- - Annotation row order for auto-calculated annotation rows
- preserved in Jalview project file
- - Visual progress indication when Jalview state is saved
- using Desktop window menu
- - Visual indication that command line arguments are still
- being processed
- - Groovy script execution from URL
- - Colour by annotation default min and max colours in
- preferences
- - Automatically associate PDB files dragged onto an
- alignment with sequences that have high similarity and matching
- IDs
- - Update JGoogleAnalytics to latest release (0.3)
- - 'view structures' option to open many structures
- in same window
- - Sort associated views menu option for tree panel
- - Group all JABA and non-JABA services for a particular
- analysis function in its own submenu
- Applet
-
- - Userdefined and autogenerated annotation rows for groups
- - Adjustment of alignment annotation pane height
- - Annotation scrollbar for annotation panel
- - Drag to reorder annotation rows in annotation panel
- - 'automaticScrolling' parameter
- - Allow sequences with partial ID string matches to be
- annotated from GFF/Jalview features files
- - Sequence logo annotation row in applet
- - Absolute paths relative to host server in applet
- parameters are treated as such
- - New in the JalviewLite javascript API:
-
- - JalviewLite.js javascript library
- - Javascript callbacks for
+
+
+ - horizontal scrolling gesture support
+ - Visual progress indicator when PCA calculation is
+ running
+ - Simpler JABA web services menus
+ - visual indication that web service results are still
+ being retrieved from server
+ - Serialise the dialogs that are shown when Jalview
+ starts up for first time
+ - Jalview user agent string for interacting with HTTP
+ services
+ - DAS 1.6 and DAS 2.0 source support using new JDAS
+ client library
+ - Examples directory and Groovy library included in
+ InstallAnywhere distribution
+ Applet
+
+ - RNA alignment and secondary structure annotation
+ visualization applet example
+ General
+
+ - Normalise option for consensus sequence logo
+ - Reset button in PCA window to return dimensions to
+ defaults
+ - Allow seqspace or Jalview variant of alignment PCA
+ calculation
+ - PCA with either nucleic acid and protein substitution
+ matrices
+
- Allow windows containing HTML reports to be exported
+ in HTML
+ - Interactive display and editing of RNA secondary
+ structure contacts
+ - RNA Helix Alignment Colouring
+ - RNA base pair logo consensus
+ - Parse sequence associated secondary structure
+ information in Stockholm files
+ - HTML Export database accessions and annotation
+ information presented in tooltip for sequences
+ - Import secondary structure from LOCARNA clustalw
+ style RNA alignment files
+ - import and visualise T-COFFEE quality scores for an
+ alignment
+ - 'colour by annotation' per sequence option to
+ shade each sequence according to its associated alignment
+ annotation
+ - New Jalview Logo
+ Documentation and Development
+
+ - documentation for score matrices used in Jalview
+ - New Website!
+ |
+ Application
+
+ - PDB, Unprot and EMBL (ENA) databases retrieved via
+ wsdbfetch REST service
+ - Stop windows being moved outside desktop on OSX
+ - Filetype associations not installed for webstart
+ launch
+ - Jalview does not always retrieve progress of a JABAWS
+ job execution in full once it is complete
+ - revise SHMR RSBS definition to ensure alignment is
+ uploaded via ali_file parameter
+ - Jalview 2.7 is incompatible with Jmol-12.2.2
+ - View all structures superposed fails with exception
+ - Jnet job queues forever if a very short sequence is
+ submitted for prediction
+ - Cut and paste menu not opened when mouse clicked on
+ desktop window
+ - Putting fractional value into integer text box in
+ alignment parameter dialog causes Jalview to hang
+ - Structure view highlighting doesn't work on
+ windows 7
+ - View all structures fails with exception shown in
+ structure view
+ - Characters in filename associated with PDBEntry not
+ escaped in a platform independent way
+ - Jalview desktop fails to launch with exception when
+ using proxy
+ - Tree calculation reports 'you must have 2 or more
+ sequences selected' when selection is empty
+ - Jalview desktop fails to launch with jar signature
+ failure when java web start temporary file caching is
+ disabled
+ - DAS Sequence retrieval with range qualification
+ results in sequence xref which includes range qualification
+ - Errors during processing of command line arguments
+ cause progress bar (JAL-898) to be removed
+ - Replace comma for semi-colon option not disabled for
+ DAS sources in sequence fetcher
+ - Cannot close news reader when JABAWS server warning
+ dialog is shown
+ - Option widgets not updated to reflect user settings
+ - Edited sequence not submitted to web service
+ - Jalview 2.7 Webstart does not launch on mountain lion
+ - InstallAnywhere installer doesn't unpack and run
+ on OSX Mountain Lion
+ - Annotation panel not given a scroll bar when
+ sequences with alignment annotation are pasted into the
+ alignment
+ - Sequence associated annotation rows not associated
+ when loaded from Jalview project
+ - Browser launch fails with NPE on java 1.7
+ - JABAWS alignment marked as finished when job was
+ cancelled or job failed due to invalid input
+ - NPE with v2.7 example when clicking on Tree
+ associated with all views
+ - Exceptions when copy/paste sequences with grouped
+ annotation rows to new window
+ Applet
+
+ - Sequence features are momentarily displayed before
+ they are hidden using hidefeaturegroups applet parameter
+ - loading features via javascript API automatically
+ enables feature display
+ - scrollToColumnIn javascript API method doesn't
+ work
+ General
- - Applet initialisation
- - Sequence/alignment mouse-overs and selections
+ - Redundancy removal fails for rna alignment
+ - PCA calculation fails when sequence has been selected
+ and then deselected
+ - PCA window shows grey box when first opened on OSX
+ - Letters coloured pink in sequence logo when alignment
+ coloured with clustalx
+ - Choosing fonts without letter symbols defined causes
+ exceptions and redraw errors
+ - Initial PCA plot view is not same as manually
+ reconfigured view
+ - Grouped annotation graph label has incorrect line
+ colour
+ - Grouped annotation graph label display is corrupted
+ for lots of labels
-
- - scrollTo row and column alignment scrolling functions
- - Select sequence/alignment regions from javascript
- - javascript structure viewer harness to pass messages
- between Jmol and Jalview when running as distinct applets
- - sortBy method
- - Set of applet and application examples shipped with
- documentation
- - New example to demonstrate JalviewLite and Jmol
- javascript message exchange
-
- General
-
- - Enable Jmol displays to be associated with multiple
- multiple alignments
- - Option to automatically sort alignment with new tree
- - User configurable link to enable redirects to a
- www.Jalview.org mirror
- - Jmol colours option for Jmol displays
- - Configurable newline string when writing alignment and
- other flat files
- - Allow alignment annotation description lines to contain
- html tags
- Documentation and Development
-
- - Add groovy test harness for bulk load testing to examples
-
- - Groovy script to load and align a set of sequences using a
- web service before displaying the result in the Jalview desktop
- - Restructured javascript and applet api documentation
- - Ant target to publish example html files with applet
- archive
- - Netbeans project for building Jalview from source
- - ant task to create online javadoc for Jalview source
- |
- Application
-
- - User defined colourscheme throws exception when current
- built in colourscheme is saved as new scheme
- - AlignFrame->Save in application pops up save dialog for
- valid filename/format
- - Cannot view associated structure for Uniprot sequence
- - PDB file association breaks for Uniprot sequence P37173
- - Associate PDB from file dialog does not tell you which
- sequence is to be associated with the file
- - Find All raises null pointer exception when query only
- matches sequence IDs
- - Pre 2.6 Jalview project cannot be loaded into v2.6
- - Jalview project with Jmol views created with Jalview 2.4
- cannot be loaded
- - Filetype associations not installed for webstart launch
- - Two or more chains in a single PDB file associated with
- sequences in different alignments do not get coloured by their
- associated sequence
- - Visibility status of autocalculated annotation row not
- preserved when project is loaded
- - Annotation row height and visibility attributes not stored
- in Jalview project
- - Tree bootstraps are not preserved when saved as a Jalview
- project
- - Envision2 workflow tooltips are corrupted
- - Enabling show group conservation also enables colour by
- conservation
- - Duplicate group associated conservation or consensus
- created on new view
- - Annotation scrollbar not displayed after 'show all
- hidden annotation rows' option selected
- - Alignment quality not updated after alignment annotation
- row is hidden then shown
- - Preserve colouring of structures coloured by sequences in
- pre Jalview 2.7 projects
- - Web service job parameter dialog is not laid out properly
-
- - Web services menu not refreshed after 'reset
- services' button is pressed in preferences
- - Annotation off by one in Jalview v2_3 example project
- - Structures imported from file and saved in project get
- name like jalview_pdb1234.txt when reloaded
- - Jalview does not always retrieve progress of a JABAWS job
- execution in full once it is complete
- Applet
-
- - Alignment height set incorrectly when lots of annotation
- rows are displayed
- - Relative URLs in feature HTML text not resolved to
- codebase
- - View follows highlighting does not work for positions in
- sequences
- - <= shown as = in tooltip
- - Export features raises exception when no features exist
- - Separator string used for serialising lists of IDs for
- javascript api is modified when separator string provided as
- parameter
- - Null pointer exception when selecting tree leaves for
- alignment with no existing selection
- - Relative URLs for datasources assumed to be relative to
- applet's codebase
- - Status bar not updated after finished searching and search
- wraps around to first result
- - StructureSelectionManager instance shared between several
- Jalview applets causes race conditions and memory leaks
- - Hover tooltip and mouseover of position on structure not
- sent from Jmol in applet
- - Certain sequences of javascript method calls to applet API
- fatally hang browser
- General
-
- - View follows structure mouseover scrolls beyond position
- with wrapped view and hidden regions
- - Find sequence position moves to wrong residue with/without
- hidden columns
- - Sequence length given in alignment properties window is
- off by 1
- - InvalidNumberFormat exceptions thrown when trying to
- import PDB like structure files
- - Positional search results are only highlighted between
- user-supplied sequence start/end bounds
- - End attribute of sequence is not validated
- - Find dialog only finds first sequence containing a given
- sequence position
- - Sequence numbering not preserved in MSF alignment output
- - Jalview PDB file reader does not extract sequence from
- nucleotide chains correctly
- - Structure colours not updated when tree partition changed
- in alignment
- - Sequence associated secondary structure not correctly
- parsed in interleaved stockholm
- - Colour by annotation dialog does not restore current state
-
- - Hiding (nearly) all sequences doesn't work properly
- - Sequences containing lowercase letters are not properly
- associated with their pdb files
- Documentation and Development
-
- - schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
- tool
- |
-
-
-
- |
- Application
-
- - New warning dialog when the Jalview Desktop cannot contact
- web services
- - JABA service parameters for a preset are shown in service
- job window
- - JABA Service menu entries reworded
- |
-
-
- - Modeller PIR IO broken - cannot correctly import a pir
- file emitted by Jalview
- - Existing feature settings transferred to new alignment
- view created from cut'n'paste
- - Improved test for mixed amino/nucleotide chains when
- parsing PDB files
- - Consensus and conservation annotation rows occasionally
- become blank for all new windows
- - Exception raised when right clicking above sequences in
- wrapped view mode
- Application
-
- - multiple multiply aligned structure views cause cpu usage
- to hit 100% and computer to hang
- - Web Service parameter layout breaks for long user
- parameter names
- - Jaba service discovery hangs desktop if Jaba server is
- down
- |
-
-
-
-
- |
- Application
-
- - Support for Java bioinformatics
- analysis web services (JABAWS)
- - Web Services preference tab
- - Analysis parameters dialog box and user defined preferences
- - Improved speed and layout of Envision2 service menu
- - Superpose structures using associated sequence alignment
- - Export coordinates and projection as CSV from PCA viewer
-
- Applet
-
- - enable javascript: execution by the applet via the link out
- mechanism
-
- Other
-
- - Updated the Jmol Jalview interface to work with Jmol series
- 12
- - The Jalview Desktop and JalviewLite applet now require Java
- 1.5
- - Allow Jalview feature colour specification for GFF sequence
- annotation files
- - New 'colour by label' keword in Jalview feature file type
- colour specification
- - New Jalview Desktop Groovy API method that allows a script
- to check if it being run in an interactive session or in a batch
- operation from the Jalview command line
-
- |
-
-
- - clustalx colourscheme colours Ds preferentially when both
- D+E are present in over 50% of the column
-
-
- Application
-
- - typo in AlignmentFrame->View->Hide->all but
- selected Regions menu item
- - sequence fetcher replaces ',' for ';' when the ',' is part
- of a valid accession ID
- - fatal OOM if object retrieved by sequence fetcher runs out
- of memory
- - unhandled Out of Memory Error when viewing pca analysis
- results
- - InstallAnywhere builds fail to launch on OS X java 10.5
- update 4 (due to apple Java 1.6 update)
- - Installanywhere Jalview silently fails to launch
-
- Applet
-
- - Jalview.getFeatureGroups() raises an
- ArrayIndexOutOfBoundsException if no feature groups are defined.
-
- |
-
-
-
-
- |
- |
-
-
- - Alignment prettyprinter doesn't cope with long sequence IDs
-
- - clustalx colourscheme colours Ds preferentially when both
- D+E are present in over 50% of the column
- - nucleic acid structures retrieved from PDB do not import
- correctly
- - More columns get selected than were clicked on when a number
- of columns are hidden
- - annotation label popup menu not providing correct
- add/hide/show options when rows are hidden or none are present
- - Stockholm format shown in list of readable formats, and
- parser copes better with alignments from RFAM.
- - CSV output of consensus only includes the percentage of all
- symbols if sequence logo display is enabled
-
-
- Applet
-
- - annotation panel disappears when annotation is
- hidden/removed
-
- Application
-
- - Alignment view not redrawn properly when new alignment
- opened where annotation panel is visible but no annotations are
- present on alignment
- - pasted region containing hidden columns is incorrectly
- displayed in new alignment window
- - Jalview slow to complete operations when stdout is flooded
- (fix is to close the Jalview console)
- - typo in AlignmentFrame->View->Hide->all but
- selected Rregions menu item.
- - inconsistent group submenu and Format submenu entry 'Un' or
- 'Non'conserved
- - Sequence feature settings are being shared by multiple
- distinct alignments
- - group annotation not recreated when tree partition is
- changed
- - double click on group annotation to select sequences does
- not propagate to associated trees
- - Mac OSX specific issues:
-
- - exception raised when mouse clicked on desktop window
- background
- - Desktop menu placed on menu bar and application name set
- correctly
- - sequence feature settings not wide enough for the save
- feature colourscheme button
-
-
-
- |
-
-
+
+
+
+
+ |
+ Application
+
+ - Jalview Desktop News Reader
+ - Tweaked default layout of web services menu
+ - View/alignment association menu to enable user to
+ easily specify which alignment a multi-structure view takes
+ its colours/correspondences from
+ - Allow properties file location to be specified as URL
+ - Extend Jalview project to preserve associations
+ between many alignment views and a single Jmol display
+ - Store annotation row height in Jalview project file
+ - Annotation row column label formatting attributes
+ stored in project file
+ - Annotation row order for auto-calculated annotation
+ rows preserved in Jalview project file
+ - Visual progress indication when Jalview state is
+ saved using Desktop window menu
+ - Visual indication that command line arguments are
+ still being processed
+ - Groovy script execution from URL
+ - Colour by annotation default min and max colours in
+ preferences
+ - Automatically associate PDB files dragged onto an
+ alignment with sequences that have high similarity and
+ matching IDs
+ - Update JGoogleAnalytics to latest release (0.3)
+ - 'view structures' option to open many
+ structures in same window
+ - Sort associated views menu option for tree panel
+ - Group all JABA and non-JABA services for a particular
+ analysis function in its own submenu
+ Applet
+
+ - Userdefined and autogenerated annotation rows for
+ groups
+ - Adjustment of alignment annotation pane height
+ - Annotation scrollbar for annotation panel
+ - Drag to reorder annotation rows in annotation panel
+ - 'automaticScrolling' parameter
+ - Allow sequences with partial ID string matches to be
+ annotated from GFF/Jalview features files
+ - Sequence logo annotation row in applet
+ - Absolute paths relative to host server in applet
+ parameters are treated as such
+ - New in the JalviewLite javascript API:
+
+ - JalviewLite.js javascript library
+ - Javascript callbacks for
+
+ - Applet initialisation
+ - Sequence/alignment mouse-overs and selections
+
+
+ - scrollTo row and column alignment scrolling
+ functions
+ - Select sequence/alignment regions from javascript
+ - javascript structure viewer harness to pass
+ messages between Jmol and Jalview when running as
+ distinct applets
+ - sortBy method
+ - Set of applet and application examples shipped
+ with documentation
+ - New example to demonstrate JalviewLite and Jmol
+ javascript message exchange
+
+ General
+
+ - Enable Jmol displays to be associated with multiple
+ multiple alignments
+ - Option to automatically sort alignment with new tree
+ - User configurable link to enable redirects to a
+ www.Jalview.org mirror
+ - Jmol colours option for Jmol displays
+ - Configurable newline string when writing alignment
+ and other flat files
+ - Allow alignment annotation description lines to
+ contain html tags
+ Documentation and Development
+
+ - Add groovy test harness for bulk load testing to
+ examples
+ - Groovy script to load and align a set of sequences
+ using a web service before displaying the result in the
+ Jalview desktop
+ - Restructured javascript and applet api documentation
+ - Ant target to publish example html files with applet
+ archive
+ - Netbeans project for building Jalview from source
+ - ant task to create online javadoc for Jalview source
+ |
+ Application
+
+ - User defined colourscheme throws exception when
+ current built in colourscheme is saved as new scheme
+ - AlignFrame->Save in application pops up save
+ dialog for valid filename/format
+ - Cannot view associated structure for UniProt sequence
+ - PDB file association breaks for UniProt sequence
+ P37173
+ - Associate PDB from file dialog does not tell you
+ which sequence is to be associated with the file
+ - Find All raises null pointer exception when query
+ only matches sequence IDs
+ - Pre 2.6 Jalview project cannot be loaded into v2.6
+ - Jalview project with Jmol views created with Jalview
+ 2.4 cannot be loaded
+ - Filetype associations not installed for webstart
+ launch
+ - Two or more chains in a single PDB file associated
+ with sequences in different alignments do not get coloured
+ by their associated sequence
+ - Visibility status of autocalculated annotation row
+ not preserved when project is loaded
+ - Annotation row height and visibility attributes not
+ stored in Jalview project
+ - Tree bootstraps are not preserved when saved as a
+ Jalview project
+ - Envision2 workflow tooltips are corrupted
+ - Enabling show group conservation also enables colour
+ by conservation
+ - Duplicate group associated conservation or consensus
+ created on new view
+ - Annotation scrollbar not displayed after 'show
+ all hidden annotation rows' option selected
+ - Alignment quality not updated after alignment
+ annotation row is hidden then shown
+ - Preserve colouring of structures coloured by
+ sequences in pre Jalview 2.7 projects
+ - Web service job parameter dialog is not laid out
+ properly
+ - Web services menu not refreshed after 'reset
+ services' button is pressed in preferences
+ - Annotation off by one in Jalview v2_3 example project
+ - Structures imported from file and saved in project
+ get name like jalview_pdb1234.txt when reloaded
+ - Jalview does not always retrieve progress of a JABAWS
+ job execution in full once it is complete
+ Applet
+
+ - Alignment height set incorrectly when lots of
+ annotation rows are displayed
+ - Relative URLs in feature HTML text not resolved to
+ codebase
+ - View follows highlighting does not work for positions
+ in sequences
+ - <= shown as = in tooltip
+ - Export features raises exception when no features
+ exist
+ - Separator string used for serialising lists of IDs
+ for javascript api is modified when separator string
+ provided as parameter
+ - Null pointer exception when selecting tree leaves for
+ alignment with no existing selection
+ - Relative URLs for datasources assumed to be relative
+ to applet's codebase
+ - Status bar not updated after finished searching and
+ search wraps around to first result
+ - StructureSelectionManager instance shared between
+ several Jalview applets causes race conditions and memory
+ leaks
+ - Hover tooltip and mouseover of position on structure
+ not sent from Jmol in applet
+ - Certain sequences of javascript method calls to
+ applet API fatally hang browser
+ General
+
+ - View follows structure mouseover scrolls beyond
+ position with wrapped view and hidden regions
+ - Find sequence position moves to wrong residue
+ with/without hidden columns
+ - Sequence length given in alignment properties window
+ is off by 1
+ - InvalidNumberFormat exceptions thrown when trying to
+ import PDB like structure files
+ - Positional search results are only highlighted
+ between user-supplied sequence start/end bounds
+ - End attribute of sequence is not validated
+ - Find dialog only finds first sequence containing a
+ given sequence position
+ - Sequence numbering not preserved in MSF alignment
+ output
+ - Jalview PDB file reader does not extract sequence
+ from nucleotide chains correctly
+ - Structure colours not updated when tree partition
+ changed in alignment
+ - Sequence associated secondary structure not correctly
+ parsed in interleaved stockholm
+ - Colour by annotation dialog does not restore current
+ state
+ - Hiding (nearly) all sequences doesn't work
+ properly
+ - Sequences containing lowercase letters are not
+ properly associated with their pdb files
+ Documentation and Development
+
+ - schemas/JalviewWsParamSet.xsd corrupted by
+ ApplyCopyright tool
+ |
+
+
+
+
+ |
+ Application
+
+ - New warning dialog when the Jalview Desktop cannot
+ contact web services
+ - JABA service parameters for a preset are shown in
+ service job window
+ - JABA Service menu entries reworded
+ |
+
+
+ - Modeller PIR IO broken - cannot correctly import a
+ pir file emitted by Jalview
+ - Existing feature settings transferred to new
+ alignment view created from cut'n'paste
+ - Improved test for mixed amino/nucleotide chains when
+ parsing PDB files
+ - Consensus and conservation annotation rows
+ occasionally become blank for all new windows
+ - Exception raised when right clicking above sequences
+ in wrapped view mode
+ Application
+
+ - multiple multiply aligned structure views cause cpu
+ usage to hit 100% and computer to hang
+ - Web Service parameter layout breaks for long user
+ parameter names
+ - Jaba service discovery hangs desktop if Jaba server
+ is down
+
+ |
+
+
+
+
+ |
+ Application
+
+ - Support for Java bioinformatics
+ analysis web services
+ (JABAWS)
+
+ - Web Services preference tab
+ - Analysis parameters dialog box and user defined
+ preferences
+ - Improved speed and layout of Envision2 service menu
+ - Superpose structures using associated sequence
+ alignment
+ - Export coordinates and projection as CSV from PCA
+ viewer
+ Applet
+
+ - enable javascript: execution by the applet via the
+ link out mechanism
+ Other
+
+ - Updated the Jmol Jalview interface to work with Jmol
+ series 12
+ - The Jalview Desktop and JalviewLite applet now
+ require Java 1.5
+ - Allow Jalview feature colour specification for GFF
+ sequence annotation files
+ - New 'colour by label' keword in Jalview feature file
+ type colour specification
+ - New Jalview Desktop Groovy API method that allows a
+ script to check if it being run in an interactive session or
+ in a batch operation from the Jalview command line
+ |
+
+
+ - clustalx colourscheme colours Ds preferentially when
+ both D+E are present in over 50% of the column
+ Application
+
+ - typo in AlignmentFrame->View->Hide->all but
+ selected Regions menu item
+ - sequence fetcher replaces ',' for ';' when the ',' is
+ part of a valid accession ID
+ - fatal OOM if object retrieved by sequence fetcher
+ runs out of memory
+ - unhandled Out of Memory Error when viewing pca
+ analysis results
+ - InstallAnywhere builds fail to launch on OS X java
+ 10.5 update 4 (due to apple Java 1.6 update)
+ - Installanywhere Jalview silently fails to launch
+ Applet
+
+ - Jalview.getFeatureGroups() raises an
+ ArrayIndexOutOfBoundsException if no feature groups are
+ defined.
+
+ |
+
+
+
+
+ |
+ |
+
+
+ - Alignment prettyprinter doesn't cope with long
+ sequence IDs
+ - clustalx colourscheme colours Ds preferentially when
+ both D+E are present in over 50% of the column
+ - nucleic acid structures retrieved from PDB do not
+ import correctly
+ - More columns get selected than were clicked on when a
+ number of columns are hidden
+ - annotation label popup menu not providing correct
+ add/hide/show options when rows are hidden or none are
+ present
+ - Stockholm format shown in list of readable formats,
+ and parser copes better with alignments from RFAM.
+ - CSV output of consensus only includes the percentage
+ of all symbols if sequence logo display is enabled
-
-
- |
- New Capabilities
-
- - 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
- - Linked viewing of nucleic acid sequences and structures
- - Automatic Scrolling option in View menu to display the
- currently highlighted region of an alignment.
- - Order an alignment by sequence length, or using the average
- score or total feature count for each sequence.
- - Shading features by score or associated description
- - Subdivide alignment and groups based on identity of selected
- subsequence (Make Groups from Selection).
- - New hide/show options including Shift+Control+H to hide
- everything but the currently selected region.
-
-
- Application
-
- - Fetch DB References capabilities and UI expanded to support
- retrieval from DAS sequence sources
- - Local DAS Sequence sources can be added via the command line
- or via the Add local source dialog box.
- - DAS Dbref and DbxRef feature types are parsed as database
- references and protein_name is parsed as description line (BioSapiens
- terms).
- - 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 and
- visualized as sequence logos
- - Optionally scale multi-character column labels to fit within
- each column of annotation row
- - Optional automatic sort of associated alignment view when a
- new tree is opened.
- - Jalview Java Console
- - Better placement of desktop window when moving between
- different screens.
- - New preference items for sequence ID tooltip and consensus
- annotation
- - Client to submit sequences and IDs to Envision2 Workflows
- - Vamsas Capabilities
-
- - Improved VAMSAS synchronization (Jalview archive used to
- preserve views, structures, and tree display settings)
- - Import of vamsas documents from disk or URL via command
- line
- - Sharing of selected regions between views and with other
- VAMSAS applications (Experimental feature!)
- - Updated API to VAMSAS version 0.2
-
-
-
- Applet
-
- - Middle button resizes annotation row height
- - New Parameters
-
- - sortByTree (true/false) - automatically sort the associated
- alignment view by the tree when a new tree is opened.
- - showTreeBootstraps (true/false) - show or hide branch
- bootstraps (default is to show them if available)
- - showTreeDistances (true/false) - show or hide branch
- lengths (default is to show them if available)
- - showUnlinkedTreeNodes (true/false) - indicate if
- unassociated nodes should be highlighted in the tree view
- - heightScale and widthScale (1.0 or more) - increase the
- height or width of a cell in the alignment grid relative to the
- current font size.
-
-
- - Non-positional features displayed in sequence ID tooltip
-
- Other
-
- - Features format: graduated colour definitions and
- specification of feature scores
- - Alignment Annotations format: new keywords for group
- associated annotation (GROUP_REF) and annotation row display
- properties (ROW_PROPERTIES)
- - XML formats extended to support graduated feature
- colourschemes, group associated annotation, and profile visualization
- settings.
- |
-
-
- - Source field in GFF files parsed as feature source rather
- than description
- - Non-positional features are now included in sequence feature
- and gff files (controlled via non-positional feature visibility in
- tooltip).
- - URL links generated for all feature links (bugfix)
- - Added URL embedding instructions to features file
- documentation.
- - Codons containing ambiguous nucleotides translated as 'X' in
- peptide product
- - Match case switch in find dialog box works for both sequence
- ID and sequence string and query strings do not have to be in upper
- case to match case-insensitively.
- - AMSA files only contain first column of multi-character
- column annotation labels
- - Jalview Annotation File generation/parsing consistent with
- documentation (e.g. Stockholm annotation can be exported and
- re-imported)
- - PDB files without embedded PDB IDs given a friendly name
- - Find incrementally searches ID string matches as well as
- subsequence matches, and correctly reports total number of both.
- - Application:
-
- - Better handling of exceptions during sequence retrieval
- - Dasobert generated non-positional feature URL link text
- excludes the start_end suffix
- - DAS feature and source retrieval buttons disabled when
- fetch or registry operations in progress.
- - PDB files retrieved from URLs are cached properly
- - Sequence description lines properly shared via VAMSAS
- - Sequence fetcher fetches multiple records for all data
- sources
- - Ensured that command line das feature retrieval completes
- before alignment figures are generated.
- - Reduced time taken when opening file browser for first
- time.
- - isAligned check prior to calculating tree, PCA or
- submitting an MSA to JNet now excludes hidden sequences.
- - User defined group colours properly recovered from Jalview
- projects.
-
-
-
- |
+ Applet
+
+ - annotation panel disappears when annotation is
+ hidden/removed
+ Application
+
+ - Alignment view not redrawn properly when new
+ alignment opened where annotation panel is visible but no
+ annotations are present on alignment
+ - pasted region containing hidden columns is
+ incorrectly displayed in new alignment window
+ - Jalview slow to complete operations when stdout is
+ flooded (fix is to close the Jalview console)
+ - typo in AlignmentFrame->View->Hide->all but
+ selected Rregions menu item.
+ - inconsistent group submenu and Format submenu entry
+ 'Un' or 'Non'conserved
+ - Sequence feature settings are being shared by
+ multiple distinct alignments
+ - group annotation not recreated when tree partition is
+ changed
+ - double click on group annotation to select sequences
+ does not propagate to associated trees
+ - Mac OSX specific issues:
+
+ - exception raised when mouse clicked on desktop
+ window background
+ - Desktop menu placed on menu bar and application
+ name set correctly
+ - sequence feature settings not wide enough for the
+ save feature colourscheme button
+
+
+
+ |
+
+
-
-
-
- 2.4.0.b2
- 28/10/2009
- |
-
-
- - Experimental support for google analytics usage tracking.
- - Jalview privacy settings (user preferences and docs).
-
- |
-
-
- - Race condition in applet preventing startup in jre1.6.0u12+.
- - Exception when feature created from selection beyond length
- of sequence.
- - Allow synthetic PDB files to be imported gracefully
- - Sequence associated annotation rows associate with all
- sequences with a given id
- - Find function matches case-insensitively for sequence ID
- string searches
- - Non-standard characters do not cause pairwise alignment to
- fail with exception
-
- Application Issues
-
- - Sequences are now validated against EMBL database
- - Sequence fetcher fetches multiple records for all data
- sources
-
- InstallAnywhere Issues
-
- - Dock icon works for Mac OS X java (Mac 1.6 update issue with
- installAnywhere mechanism)
- - Command line launching of JARs from InstallAnywhere version
- (java class versioning error fixed)
-
- |
-
-
-
+ |
+
+ |
+ New Capabilities
+
+ - 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
+ - Linked viewing of nucleic acid sequences and
+ structures
+ - Automatic Scrolling option in View menu to display
+ the currently highlighted region of an alignment.
+ - Order an alignment by sequence length, or using the
+ average score or total feature count for each sequence.
+ - Shading features by score or associated description
+ - Subdivide alignment and groups based on identity of
+ selected subsequence (Make Groups from Selection).
+ - New hide/show options including Shift+Control+H to
+ hide everything but the currently selected region.
+
+ Application
+
+ - Fetch DB References capabilities and UI expanded to
+ support retrieval from DAS sequence sources
+ - Local DAS Sequence sources can be added via the
+ command line or via the Add local source dialog box.
+ - DAS Dbref and DbxRef feature types are parsed as
+ database references and protein_name is parsed as
+ description line (BioSapiens terms).
+ - 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
+ and visualized as sequence logos
+ - Optionally scale multi-character column labels to fit
+ within each column of annotation row
+
+ - Optional automatic sort of associated alignment view
+ when a new tree is opened.
+ - Jalview Java Console
+ - Better placement of desktop window when moving
+ between different screens.
+ - New preference items for sequence ID tooltip and
+ consensus annotation
+ - Client to submit sequences and IDs to Envision2
+ Workflows
+ - Vamsas Capabilities
+
+ - Improved VAMSAS synchronization (Jalview archive
+ used to preserve views, structures, and tree display
+ settings)
+ - Import of vamsas documents from disk or URL via
+ command line
+ - Sharing of selected regions between views and
+ with other VAMSAS applications (Experimental feature!)
+ - Updated API to VAMSAS version 0.2
+
+ Applet
+
+ - Middle button resizes annotation row height
+ - New Parameters
+
+ - sortByTree (true/false) - automatically sort the
+ associated alignment view by the tree when a new tree is
+ opened.
+ - showTreeBootstraps (true/false) - show or hide
+ branch bootstraps (default is to show them if available)
+ - showTreeDistances (true/false) - show or hide
+ branch lengths (default is to show them if available)
+ - showUnlinkedTreeNodes (true/false) - indicate if
+ unassociated nodes should be highlighted in the tree
+ view
+ - heightScale and widthScale (1.0 or more) -
+ increase the height or width of a cell in the alignment
+ grid relative to the current font size.
+
+
+ - Non-positional features displayed in sequence ID
+ tooltip
+ Other
+
+ - Features format: graduated colour definitions and
+ specification of feature scores
+ - Alignment Annotations format: new keywords for group
+ associated annotation (GROUP_REF) and annotation row display
+ properties (ROW_PROPERTIES)
+ - XML formats extended to support graduated feature
+ colourschemes, group associated annotation, and profile
+ visualization settings.
|
+
+
+ - Source field in GFF files parsed as feature source
+ rather than description
+ - Non-positional features are now included in sequence
+ feature and gff files (controlled via non-positional feature
+ visibility in tooltip).
+ - URL links generated for all feature links (bugfix)
+ - Added URL embedding instructions to features file
+ documentation.
+ - Codons containing ambiguous nucleotides translated as
+ 'X' in peptide product
+ - Match case switch in find dialog box works for both
+ sequence ID and sequence string and query strings do not
+ have to be in upper case to match case-insensitively.
+ - AMSA files only contain first column of
+ multi-character column annotation labels
+ - Jalview Annotation File generation/parsing consistent
+ with documentation (e.g. Stockholm annotation can be
+ exported and re-imported)
+ - PDB files without embedded PDB IDs given a friendly
+ name
+ - Find incrementally searches ID string matches as well
+ as subsequence matches, and correctly reports total number
+ of both.
+ - Application:
+
+ - Better handling of exceptions during sequence
+ retrieval
+ - Dasobert generated non-positional feature URL
+ link text excludes the start_end suffix
+ - DAS feature and source retrieval buttons disabled
+ when fetch or registry operations in progress.
+ - PDB files retrieved from URLs are cached properly
+ - Sequence description lines properly shared via
+ VAMSAS
+ - Sequence fetcher fetches multiple records for all
+ data sources
+ - Ensured that command line das feature retrieval
+ completes before alignment figures are generated.
+ - Reduced time taken when opening file browser for
+ first time.
+ - isAligned check prior to calculating tree, PCA or
+ submitting an MSA to JNet now excludes hidden sequences.
+ - User defined group colours properly recovered
+ from Jalview projects.
+
+
+
+ |
- 2.4
- 27/8/2008
-
- User Interface
-
- - Linked highlighting of codon and amino acid from translation
- and protein products
- - Linked highlighting of structure associated with residue
- mapping to codon position
- - Sequence Fetcher provides example accession numbers and
- 'clear' button
- - MemoryMonitor added as an option under Desktop's Tools menu
- - Extract score function to parse whitespace separated numeric
- data in description line
- - Column labels in alignment annotation can be centred.
- - Tooltip for sequence associated annotation give name of
- sequence
-
- Web Services and URL fetching
-
- - JPred3 web service
- - Prototype sequence search client (no public services
- available yet)
- - Fetch either seed alignment or full alignment from PFAM
- - URL Links created for matching database cross references as
- well as sequence ID
- - URL Links can be created using regular-expressions
-
- Sequence Database Connectivity
-
- - Retrieval of cross-referenced sequences from other databases
-
- - Generalised database reference retrieval and validation to
- all fetchable databases
- - Fetch sequences from DAS sources supporting the sequence
- command
-
- Import and Export
- - export annotation rows as CSV for spreadsheet import
- - Jalview projects record alignment dataset associations, EMBL
- products, and cDNA sequence mappings
- - Sequence Group colour can be specified in Annotation File
- - Ad-hoc colouring of group in Annotation File using RGB
- triplet as name of colourscheme
-
- VAMSAS Client capabilities (Experimental)
-
- - treenode binding for VAMSAS tree exchange
- - local editing and update of sequences in VAMSAS alignments
- (experimental)
- - Create new or select existing session to join
- - load and save of vamsas documents
-
- Application command line
-
- - -tree parameter to open trees (introduced for passing from
- applet)
- - -fetchfrom command line argument to specify nicknames of DAS
- servers to query for alignment features
- - -dasserver command line argument to add new servers that are
- also automatically queried for features
- - -groovy command line argument executes a given groovy script
- after all input data has been loaded and parsed
-
- Applet-Application data exchange
-
- - Trees passed as applet parameters can be passed to
- application (when using "View in full application")
-
- Applet Parameters
-
- - feature group display control parameter
- - debug parameter
- - showbutton parameter
-
- Applet API methods
-
- - newView public method
- - Window (current view) specific get/set public methods
- - Feature display control methods
- - get list of currently selected sequences
-
- New Jalview distribution features
-
- - InstallAnywhere Installer upgraded to IA 2008 VP1
- - RELEASE file gives build properties for the latest Jalview
- release.
- - Java 1.1 Applet build made easier and donotobfuscate
- property controls execution of obfuscator
- - Build target for generating source distribution
- - Debug flag for javacc
- - .jalview_properties file is documented (slightly) in
- jalview.bin.Cache
- - Continuous Build Integration for stable and development
- version of Application, Applet and source distribution
-
+ |
+
+
+
+ 2.4.0.b2 28/10/2009
+
+ |
+
+
+ - Experimental support for google analytics usage
+ tracking.
+ - Jalview privacy settings (user preferences and docs).
+
+ |
+
+
+ - Race condition in applet preventing startup in
+ jre1.6.0u12+.
+ - Exception when feature created from selection beyond
+ length of sequence.
+ - Allow synthetic PDB files to be imported gracefully
+ - Sequence associated annotation rows associate with
+ all sequences with a given id
+ - Find function matches case-insensitively for sequence
+ ID string searches
+ - Non-standard characters do not cause pairwise
+ alignment to fail with exception
+ Application Issues
+
+ - Sequences are now validated against EMBL database
+ - Sequence fetcher fetches multiple records for all
+ data sources
+ InstallAnywhere Issues
+
+ - Dock icon works for Mac OS X java (Mac 1.6 update
+ issue with installAnywhere mechanism)
+ - Command line launching of JARs from InstallAnywhere
+ version (java class versioning error fixed)
+
+ |
+
+
+
- |
-
-
- - selected region output includes visible annotations (for
- certain formats)
- - edit label/displaychar contains existing label/char for
- editing
- - update PDBEntries when DBRefEntries change (vamsas)
- - shorter peptide product names from EMBL records
- - Newick string generator makes compact representations
- - bootstrap values parsed correctly for tree files with
- comments
- - pathological filechooser bug avoided by not allowing
- filenames containing a ':'
- - Fixed exception when parsing GFF files containing global
- sequence features
- - Alignment datasets are finalized only when number of
- references from alignment sequences goes to zero
- - Close of tree branch colour box without colour selection
- causes cascading exceptions
- - occasional negative imgwidth exceptions
- - better reporting of non-fatal warnings to user when file
- parsing fails.
- - Save works when Jalview project is default format
- - Save as dialog opened if current alignment format is not a
- valid output format
- - Uniprot canonical names introduced for both das and vamsas
- - Histidine should be midblue (not pink!) in Zappo
- - error messages passed up and output when data read fails
- - edit undo recovers previous dataset sequence when sequence
- is edited
- - allow PDB files without pdb ID HEADER lines (like those
- generated by MODELLER) to be read in properly
- - allow reading of JPred concise files as a normal filetype
- - Stockholm annotation parsing and alignment properties import
- fixed for PFAM records
- - Structure view windows have correct name in Desktop window
- list
- - annotation consisting of sequence associated scores can be
- read and written correctly to annotation file
- - Aligned cDNA translation to aligned peptide works correctly
- - Fixed display of hidden sequence markers and non-italic font
- for representatives in Applet
- - Applet Menus are always embedded in applet window on Macs.
- - Newly shown features appear at top of stack (in Applet)
- - Annotations added via parameter not drawn properly due to
- null pointer exceptions
- - Secondary structure lines are drawn starting from first
- column of alignment
- - Uniprot XML import updated for new schema release in July
- 2008
- - Sequence feature to sequence ID match for Features file is
- case-insensitive
- - Sequence features read from Features file appended to all
- sequences with matching IDs
- - PDB structure coloured correctly for associated views
- containing a sub-sequence
- - PDB files can be retrieved by applet from Jar files
- - feature and annotation file applet parameters referring to
- different directories are retrieved correctly
-
- - Fixed application hang whilst waiting for splash-screen
- version check to complete
- - Applet properly URLencodes input parameter values when
- passing them to the launchApp service
- - display name and local features preserved in results
- retrieved from web service
- - Visual delay indication for sequence retrieval and sequence
- fetcher initialisation
- - updated Application to use DAS 1.53e version of dasobert DAS
- client
- - Re-instated Full AMSA support and .amsa file association
- - Fixed parsing of JNet Concise annotation sans
- sequences
-
- |
-
-
-
- 2.3
- 9/5/07
- |
-
-
- - Jmol 11.0.2 integration
- - PDB views stored in Jalview XML files
- - Slide sequences
- - Edit sequence in place
- - EMBL CDS features
- - DAS Feature mapping
- - Feature ordering
- - Alignment Properties
- - Annotation Scores
- - Sort by scores
- - Feature/annotation editing in applet
-
- |
-
-
- - Headless state operation in 2.2.1
- - Incorrect and unstable DNA pairwise alignment
- - Cut and paste of sequences with annotation
- - Feature group display state in XML
- - Feature ordering in XML
- - blc file iteration selection using filename # suffix
- - Stockholm alignment properties
- - Stockhom alignment secondary structure annotation
- - 2.2.1 applet had no feature transparency
- - Number pad keys can be used in cursor mode
- - Structure Viewer mirror image resolved
-
- |
+
+ 2.4 27/8/2008
+
+
+ User Interface
+
+ - Linked highlighting of codon and amino acid from
+ translation and protein products
+ - Linked highlighting of structure associated with
+ residue mapping to codon position
+ - Sequence Fetcher provides example accession numbers
+ and 'clear' button
+ - MemoryMonitor added as an option under Desktop's
+ Tools menu
+ - Extract score function to parse whitespace separated
+ numeric data in description line
+ - Column labels in alignment annotation can be centred.
+ - Tooltip for sequence associated annotation give name
+ of sequence
+ Web Services and URL fetching
+
+ - JPred3 web service
+ - Prototype sequence search client (no public services
+ available yet)
+ - Fetch either seed alignment or full alignment from
+ PFAM
+ - URL Links created for matching database cross
+ references as well as sequence ID
+ - URL Links can be created using regular-expressions
+ Sequence Database Connectivity
+
+ - Retrieval of cross-referenced sequences from other
+ databases
+ - Generalised database reference retrieval and
+ validation to all fetchable databases
+ - Fetch sequences from DAS sources supporting the
+ sequence command
+ Import and Export
+ - export annotation rows as CSV for spreadsheet import
+ - Jalview projects record alignment dataset associations,
+ EMBL products, and cDNA sequence mappings
+ - Sequence Group colour can be specified in Annotation
+ File
+ - Ad-hoc colouring of group in Annotation File using RGB
+ triplet as name of colourscheme
+ VAMSAS Client capabilities (Experimental)
+
+ - treenode binding for VAMSAS tree exchange
+ - local editing and update of sequences in VAMSAS
+ alignments (experimental)
+ - Create new or select existing session to join
+ - load and save of vamsas documents
+ Application command line
+
+ - -tree parameter to open trees (introduced for passing
+ from applet)
+ - -fetchfrom command line argument to specify nicknames
+ of DAS servers to query for alignment features
+ - -dasserver command line argument to add new servers
+ that are also automatically queried for features
+ - -groovy command line argument executes a given groovy
+ script after all input data has been loaded and parsed
+ Applet-Application data exchange
+
+ - Trees passed as applet parameters can be passed to
+ application (when using "View in full
+ application")
+ Applet Parameters
+
+ - feature group display control parameter
+ - debug parameter
+ - showbutton parameter
+ Applet API methods
+
+ - newView public method
+ - Window (current view) specific get/set public methods
+ - Feature display control methods
+ - get list of currently selected sequences
+ New Jalview distribution features
+
+ - InstallAnywhere Installer upgraded to IA 2008 VP1
+ - RELEASE file gives build properties for the latest
+ Jalview release.
+ - Java 1.1 Applet build made easier and donotobfuscate
+ property controls execution of obfuscator
+ - Build target for generating source distribution
+ - Debug flag for javacc
+ - .jalview_properties file is documented (slightly) in
+ jalview.bin.Cache
+ - Continuous Build Integration for stable and
+ development version of Application, Applet and source
+ distribution
+ |
+
+
+ - selected region output includes visible annotations
+ (for certain formats)
+ - edit label/displaychar contains existing label/char
+ for editing
+ - update PDBEntries when DBRefEntries change (vamsas)
+ - shorter peptide product names from EMBL records
+ - Newick string generator makes compact representations
+ - bootstrap values parsed correctly for tree files with
+ comments
+ - pathological filechooser bug avoided by not allowing
+ filenames containing a ':'
+ - Fixed exception when parsing GFF files containing
+ global sequence features
+ - Alignment datasets are finalized only when number of
+ references from alignment sequences goes to zero
+ - Close of tree branch colour box without colour
+ selection causes cascading exceptions
+ - occasional negative imgwidth exceptions
+ - better reporting of non-fatal warnings to user when
+ file parsing fails.
+ - Save works when Jalview project is default format
+ - Save as dialog opened if current alignment format is
+ not a valid output format
+ - UniProt canonical names introduced for both das and
+ vamsas
+ - Histidine should be midblue (not pink!) in Zappo
+ - error messages passed up and output when data read
+ fails
+ - edit undo recovers previous dataset sequence when
+ sequence is edited
+ - allow PDB files without pdb ID HEADER lines (like
+ those generated by MODELLER) to be read in properly
+ - allow reading of JPred concise files as a normal
+ filetype
+ - Stockholm annotation parsing and alignment properties
+ import fixed for PFAM records
+ - Structure view windows have correct name in Desktop
+ window list
+ - annotation consisting of sequence associated scores
+ can be read and written correctly to annotation file
+ - Aligned cDNA translation to aligned peptide works
+ correctly
+ - Fixed display of hidden sequence markers and
+ non-italic font for representatives in Applet
+ - Applet Menus are always embedded in applet window on
+ Macs.
+ - Newly shown features appear at top of stack (in
+ Applet)
+ - Annotations added via parameter not drawn properly
+ due to null pointer exceptions
+ - Secondary structure lines are drawn starting from
+ first column of alignment
+ - UniProt XML import updated for new schema release in
+ July 2008
+ - Sequence feature to sequence ID match for Features
+ file is case-insensitive
+ - Sequence features read from Features file appended to
+ all sequences with matching IDs
+ - PDB structure coloured correctly for associated views
+ containing a sub-sequence
+ - PDB files can be retrieved by applet from Jar files
+ - feature and annotation file applet parameters
+ referring to different directories are retrieved correctly
+
+ - Fixed application hang whilst waiting for
+ splash-screen version check to complete
+ - Applet properly URLencodes input parameter values
+ when passing them to the launchApp service
+ - display name and local features preserved in results
+ retrieved from web service
+ - Visual delay indication for sequence retrieval and
+ sequence fetcher initialisation
+ - updated Application to use DAS 1.53e version of
+ dasobert DAS client
+ - Re-instated Full AMSA support and .amsa file
+ association
+ - Fixed parsing of JNet Concise annotation sans
+ sequences
+
+
+ |
+
+
+
+
+ 2.3 9/5/07
+
+ |
+
+
+ - Jmol 11.0.2 integration
+ - PDB views stored in Jalview XML files
+ - Slide sequences
+ - Edit sequence in place
+ - EMBL CDS features
+ - DAS Feature mapping
+ - Feature ordering
+ - Alignment Properties
+ - Annotation Scores
+ - Sort by scores
+ - Feature/annotation editing in applet
+
+ |
+
+
+ - Headless state operation in 2.2.1
+ - Incorrect and unstable DNA pairwise alignment
+ - Cut and paste of sequences with annotation
+ - Feature group display state in XML
+ - Feature ordering in XML
+ - blc file iteration selection using filename # suffix
+ - Stockholm alignment properties
+ - Stockhom alignment secondary structure annotation
+ - 2.2.1 applet had no feature transparency
+ - Number pad keys can be used in cursor mode
+ - Structure Viewer mirror image resolved
+
+ |
-
-
-
- 2.2.1
- 12/2/07
- |
-
-
- - Non standard characters can be read and displayed
-
- Annotations/Features can be imported/exported to the applet
- via textbox
-
- Applet allows editing of sequence/annotation/group name
- & description
-
- Preference setting to display sequence name in italics
-
- Annotation file format extended to allow Sequence_groups to
- be defined
-
- Default opening of alignment overview panel can be specified
- in preferences
-
- PDB residue numbering annotation added to associated
- sequences
-
- |
-
-
- - Applet crash under certain Linux OS with Java 1.6 installed
-
- Annotation file export / import bugs fixed
-
- PNG / EPS image output bugs fixed
-
- |
-
-
-
- 2.2
- 27/11/06
- |
-
-
- - Multiple views on alignment
-
- Sequence feature editing
-
- "Reload" alignment
-
- "Save" to current filename
-
- Background dependent text colour
-
- Right align sequence ids
-
- User-defined lower case residue colours
-
- Format Menu
-
- Select Menu
-
- Menu item accelerator keys
-
- Control-V pastes to current alignment
-
- 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'
-
- |
-
-
- - New memory efficient Undo/Redo System
-
- Optimised symbol lookups and conservation/consensus
- calculations
-
- Region Conservation/Consensus recalculated after edits
-
- 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
-
- Re-instated Zoom function for PCA
-
- Sequence descriptions conserved in web service analysis
- results
-
- Uniprot ID discoverer uses any word separated by ∣
-
- WsDbFetch query/result association resolved
-
- Tree leaf to sequence mapping improved
-
- Smooth fonts switch moved to FontChooser dialog box.
-
- |
-
-
-
- 2.1.1
- 12/9/06
- |
-
-
- - Copy consensus sequence to clipboard
-
- |
-
-
- - Image output - rightmost residues are rendered if sequence
- id panel has been resized
- - Image output - all offscreen group boundaries are rendered
- - Annotation files with sequence references - all elements in
- file are relative to sequence position
- - Mac Applet users can use Alt key for group editing
-
- |
-
-
-
- 2.1
- 22/8/06
- |
-
-
- - MAFFT Multiple Alignment in default Web Service list
- - DAS Feature fetching
- - Hide sequences and columns
- - Export Annotations and Features
- - GFF file reading / writing
- - Associate structures with sequences from local PDB files
- - Add sequences to exisiting alignment
- - Recently opened files / URL lists
- - Applet can launch the full application
- - Applet has transparency for features (Java 1.2 required)
- - Applet has user defined colours parameter
- - Applet can load sequences from parameter "sequencex"
-
- |
-
-
- - Redundancy Panel reinstalled in the Applet
- - Monospaced font - EPS / rescaling bug fixed
- - Annotation files with sequence references bug fixed
-
- |
-
-
-
- 2.08.1
- 2/5/06
- |
-
-
- - Change case of selected region from Popup menu
- - Choose to match case when searching
- - Middle mouse button and mouse movement can compress / expand
- the visible width and height of the alignment
-
- |
-
-
- - Annotation Panel displays complete JNet results
-
- |
-
-
-
- 2.08b
- 18/4/06
- |
- |
-
-
- - Java 1.5 bug - InternalMessageDialog fix for threads
- - Righthand label on wrapped alignments shows correct value
-
- |
-
-
-
- 2.08
- 10/4/06
- |
-
-
- - Editing can be locked to the selection area
- - Keyboard editing
- - Create sequence features from searches
- - Precalculated annotations can be loaded onto alignments
- - Features file allows grouping of features
- - Annotation Colouring scheme added
- - Smooth fonts off by default - Faster rendering
- - Choose to toggle Autocalculate Consensus On/Off
-
- |
-
-
- - Drag & Drop fixed on Linux
- - Jalview Archive file faster to load/save, sequence
- descriptions saved.
-
- |
-
-
-
- 2.07
- 12/12/05
- |
-
-
- - PDB Structure Viewer enhanced
- - Sequence Feature retrieval and display enhanced
- - Choose to output sequence start-end after sequence name for
- file output
- - Sequence Fetcher WSDBFetch@EBI
- - Applet can read feature files, PDB files and can be used for
- HTML form input
-
- |
-
-
- - HTML output writes groups and features
- - Group editing is Control and mouse click
- - File IO bugs
-
- |
-
-
-
- 2.06
- 28/9/05
- |
-
-
- - View annotations in wrapped mode
- - More options for PCA viewer
-
- |
-
-
- - GUI bugs resolved
- - Runs with -nodisplay from command line
-
- |
-
-
-
- 2.05b
- 15/9/05
- |
-
-
- - Choose EPS export as lineart or text
- - Jar files are executable
- - Can read in Uracil - maps to unknown residue
-
- |
-
-
- - Known OutOfMemory errors give warning message
- - Overview window calculated more efficiently
- - Several GUI bugs resolved
-
- |
-
-
-
- 2.05
- 30/8/05
- |
-
-
- - Edit and annotate in "Wrapped" view
-
- |
-
-
- - Several GUI bugs resolved
-
- |
-
-
-
- 2.04
- 24/8/05
- |
-
-
- - Hold down mouse wheel & scroll to change font size
-
- |
-
-
- - Improved JPred client reliability
- - Improved loading of Jalview files
-
- |
-
-
-
- 2.03
- 18/8/05
- |
-
-
- - Set Proxy server name and port in preferences
- - Multiple URL links from sequence ids
- - User Defined Colours can have a scheme name and added to
- Colour Menu
- - Choose to ignore gaps in consensus calculation
- - Unix users can set default web browser
- - Runs without GUI for batch processing
- - Dynamically generated Web Service Menus
-
- |
-
-
- - InstallAnywhere download for Sparc Solaris
-
- |
-
-
-
- 2.02
- 18/7/05
- |
- |
-
-
- - Copy & Paste order of sequences maintains alignment
- order.
-
- |
-
-
-
- 2.01
- 12/7/05
- |
-
-
- - Use delete key for deleting selection.
- - Use Mouse wheel to scroll sequences.
- - Help file updated to describe how to add alignment
- annotations.
- - Version and build date written to build properties file.
- - InstallAnywhere installation will check for updates at
- launch of Jalview.
-
- |
-
-
- - Delete gaps bug fixed.
- - FileChooser sorts columns.
- - Can remove groups one by one.
- - Filechooser icons installed.
- - Finder ignores return character when searching. Return key
- will initiate a search.
-
-
- |
-
-
-
- 2.0
- 20/6/05
- |
-
-
- |
- |
-
-
|
-