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-
-
-
-
-
- Release |
- New Features |
- Issues Resolved |
-
-
- 2.11.1.0
- 22/04/2020 |
-
-
- -
- Map
- 'virtual' codon features shown on protein (or vice versa)
- for display in alignments, on structure views (including
- transfer to UCSF chimera), in feature reports and for
- export.
-
- -
- Feature attributes from VCF files can be
- exported and re-imported as GFF3 files
-
- -
- Capture VCF "fixed column" values
- POS, ID, QUAL, FILTER as Feature Attributes
-
- -
- More robust VCF numeric data field
- validation while parsing
-
- -
- Feature Settings dialog keeps same screen
- position if reopened
-
- -
- Feature Settings dialog title includes name
- of associated view
-
- -
- Font anti-aliasing in alignment views
- enabled by default
-
- -
- Very long feature descriptions truncated in
- tooltips and menus
-
- -
- Warn if Sort by Score or Density attempted
- with no feature types visible
-
- -
- Improved support for filtering feature attributes with large integer values
-
- Jalview Installer
-
- -
- Versions for install4j and getdown and installer template version reported
- in console (may be null when Jalview launched as executable jar or via conda)
-
- -
- Layout improvements for OSX .dmg Finder and higher quality background images
-
- -
- New installer/application launcher generated with install4j 8.0.4
-
- -
- Jalview File Associations shown for Unix Platforms
- -
- Improved defaults for maximum memory setting when running on large memory machines
- Release processes
-
- -
- New point release version scheme - 2.11.1.0
-
- -
- 'Jalview Test' installers/apps for easier access to test-release channel builds
-
- Build System
-
- -
- Clover updated to 4.4.1
-
- -
- Test code included in Clover coverage
- report
-
-
- Groovy Scripts
-
- -
- exportconsensus.groovy prints a FASTA file
- to stdout containing the consensus sequence for each
- alignment in a Jalview session
-
- -
- ComputePeptideVariants.groovy to translate
- genomic sequence_variant annotation from CDS as
- missense_variant or synonymous_variant on protein products.
-
-
- |
-
-
- -
- Hidden sequence markers still visible when
- 'Show hidden markers' option is not ticked
-
- -
- Hidden sequence markers not shown in EPS and
- PNG output when 'Automatically set ID width' is set in
- jalview preferences or properties file
-
- -
- Feature Editor dialog can be opened when
- 'Show Sequence Features' option is not ticked
-
- -
- Undo 'Null' operation shown after sort by
- buttons in Feature Settings dialog are clicked when no
- features are visible
-
- -
- ID margins for CDS and Protein views not
- equal when split frame is first opened
-
- -
- Sequence position numbers in status bar not
- correct after editing a sequence's start position
-
- -
- Alignment is misaligned in wrapped mode
- with annotation and exceptions thrown when only a few
- columns shown in wrapped mode
-
- -
- Sequence IDs missing in headless export of
- wrapped alignment figure with annotations
-
- -
- Sorting Structure Chooser table by Sequence
- ID fails with ClassCastException
-
- -
- Chimera session not restored from Jalview
- Project
-
- -
- Double-click on 'Show feature' checkbox in
- feature settings dialog also selects columns
-
- -
- SpinnerNumberModel causes
- IllegalArgumentException in some circumstances
-
- -
- Multiple feature settings dialogs can be
- opened for a view
-
- -
- Feature Settings dialog is orphaned if
- alignment window is closed
-
- -
- Credits missing some authors in Jalview
- help documentation for 2.11.0 release
-
- -
- Export of Pfam alignment as Stockholm
- includes Pfam ID as sequence's accession rather than its
- Uniprot Accession
-
- Java 11 Compatibility issues
-
- -
- OSX - Can't view some search results in
- PDB/Uniprot search panel
-
- Installer
-
- -
- Jalview should not create file associations
- for 3D structure files (.pdb, .mmcif. .cif)
-
- Repository and Source Release
-
- -
- removed obsolete .cvsignore files from
- repository
-
- -
- Clover report generation running out of
- memory
-
- New Known Issues
-
- -
- OSX - Current working directory not
- preserved when Jalview.app launched with parameters from
- command line
-
- -
- Sequence IDs aligned to wrong margin and
- clipped in headless figure export when Right Align option
- enabled
-
- -
- Jalview Installation type always reports
- 'Source' in console output
-
- -
- Test Suite: Certain Functional tests fail on jalview's
- bamboo server but run fine locally.
-
-
- |
-
-
-
- 2.11.0
- 04/07/2019
- |
-
-
- -
- Jalview Native Application and
- Installers built with install4j (licensed to the Jalview open
- source project) rather than InstallAnywhere
-
- -
- Jalview Launcher System to auto-configure memory
- settings, receive over the air updates and launch specific
- versions via (Three
- Rings' GetDown)
-
- -
- File type associations for
- formats supported by Jalview (including .jvp project files)
-
- -
- Jalview launch files (.jvl) to pass command line
- arguments and switch between different getdown channels
-
- -
- Backup files created when saving Jalview project
- or alignment files
-
-
- -
- Annotate nucleotide alignments from VCF data files
- - Version of HTSJDK shipped with Jalview updated to version 2.12.0
- -
- Alternative genetic code tables for
- 'Translate as cDNA'
- -
- Update of Ensembl Rest Client to API v10.0
- - Enhanced visualisation and analysis of Sequence Features
-
- -
- IntervalStoreJ (NCList
- implementation that allows updates) used for Sequence Feature collections
- -
- Sequence
- features can be filtered and shaded according to any
- associated attributes (e.g. variant attributes from VCF
- file, or key-value pairs imported from column 9 of GFF
- file)
-
- -
- Feature Attributes and shading schemes
- stored and restored from Jalview Projects
-
- -
- Use full Sequence Ontology (via BioJava) to
- recognise variant features
-
- -
- Show synonymous codon variants on peptide
- sequences (also coloured red by default)
-
- -
- Popup window to show full report for a selected sequence feature's
- details
-
- -
- More efficient sequence feature render
- algorithm (Z-sort/transparency and filter aware)
-
- -
- Improved tooltips in Feature Settings
- dialog
-
-
-
- -
- Symmetric score matrices for faster
- tree and PCA calculations
-
- - Principal Components Analysis Viewer
-
- -
- Principal Components Analysis results
- and Viewer state saved in Jalview Project
-
- - 'Change parameters' option removed from viewer's
- drop-down menus
- -
- Can use shift + arrow keys to rotate PCA image
- incrementally
-
- -
- PCA plot is depth cued
-
-
-
- -
- New 'Colour by Sequence ID' option
-
- - Speed and Efficiency
-
- -
- More efficient creation of selections and
- multiple groups when working with large alignments
-
- -
- Speedier import of annotation rows when parsing
- Stockholm files
-
-
- - User Interface
-
- -
- Finder panel remembers last position in each
- view
-
- -
- Alignment Overview now WYSIWIS (What you see is
- what is shown)
Only visible regions of alignment are shown by
- default (can be changed in user preferences)
-
- -
- File Chooser stays open after responding Cancel
- to the Overwrite Dialog
-
- -
- Better popup menu behaviour when all
- sequences are hidden
-
- -
- Status bar shows bounds when dragging a
- selection region, and gap count when inserting or deleting gaps
-
- -
- Status bar updates over sequence and annotation
- labels
-
- -
- Annotation tooltips and popup menus are shown
- when in wrapped mode
-
- -
- Can select columns by dragging left/right in a graph or histogram
- annotation
-
- -
- Help button on Uniprot and PDB search panels
-
- -
- Cursor changes over draggable box in Overview
- panel
-
- -
- Consistent ordering of links in sequence id
- popup menu
-
- -
- Red line indicating tree-cut position not shown if no subgroups are created
- -
- Removed ability to configure length of search history by right-clicking search box
-
-
-
- - Jalview Groovy Scripting Console updated to Groovy v2.5
- - Java 11 Support (not yet on general release)
-
- -
- OSX GUI integrations for App menu's 'About' entry and
- trapping CMD-Q
-
-
-
- Deprecations
-
- - DAS sequence retrieval and annotation
- capabilities removed from the Jalview Desktop
-
- - Castor library for XML marshalling and
- unmarshalling has been replaced by JAXB for Jalview projects
- and XML based data retrieval clients
- - Disable VAMSAS menu in preparation for removal
- - Jalview Desktop no longer distributed via Java Web Start
- Documentation
-
- - Added remarks about transparent rendering effects
- not supported in EPS figure export
-
- - Typos in documentation for Preferences dialog
- Development and Release Processes
-
- -
- Build system migrated from Ant to Gradle
-
- -
- Enhanced checks for missing and duplicated keys in Message bundles
- -
- Eclipse project configuration managed with
- gradle-eclipse
-
- -
- Atlassian
- Bamboo continuous integration for unattended Test Suite
- execution
-
- -
- Memory test suite to detect leaks in common
- operations
-
- -
- More unit test coverage, and minor
- issues resolved
-
- -
- Developer documentation migrated to
- markdown (with HTML rendering)
-
- -
- HelpLinksChecker runs on Windows
-
- -
- New URLs for publishing development
- versions of Jalview
-
-
- |
-
-
- -
- Timeouts when retrieving data from Ensembl
-
- -
- 'View [Structure] Mappings' and structure
- superposition in Jmol fail on Windows
-
- -
- Blank error dialog is displayed when discovering
- structures for sequences with lots of PDB structures
-
- -
- Text misaligned in EPS or SVG image export with
- monospaced font
-
- -
- Warning of 'Duplicate entry' when saving Jalview
- project involving multiple views
-
- -
- Overview for complementary view in a linked
- CDS/Protein alignment is not updated when Hide Columns by
- Annotation dialog hides columns
-
- -
- Selection highlighting in the complement of a
- CDS/Protein alignment stops working after making a selection in
- one view, then making another selection in the other view
-
- -
- Annotations tooltip changes beyond visible
- columns
-
- -
- Table Columns could be re-ordered in Feature
- Settings and Jalview Preferences panels
-
- -
- Jalview hangs when closing windows, or redrawing the
- overview with large alignments
-
- -
- Tree and PCA calculation fails for selected
- region if columns were selected by dragging right-to-left and the
- mouse moved to the left of the first column
-
- -
- Couldn't hide selected columns adjacent to a
- hidden column marker via scale popup menu
-
- -
- Error message for trying to load in invalid URLs
- doesn't tell users the invalid URL
-
- -
- Tooltips displayed for features filtered by
- score from view
-
- -
- Sequence Variants retrieved from Ensembl during
- show cross references or Fetch Database References are shown in
- red in original view
-
- -
- stop_gained variants not shown correctly on
- peptide sequence (computed variant shown as p.Res.null)
-
- -
- 'Graduated colour' option not offered for
- manually created features (where feature score is Float.NaN)
-
- -
- Blank extra columns drawn or printed
- when columns are hidden
-
- -
- Regular expression error for '(' in Select
- Columns by Annotation description
-
- -
- Scroll doesn't stop on mouse up after dragging
- out of Scale or Annotation Panel
-
- -
- Column selection incorrect after scrolling out of
- scale panel
-
- -
- Left/right drag in annotation can scroll
- alignment down
-
- -
- Error if mouse moved before clicking Reveal in
- scale panel
-
- -
- Column display is out by one after Page Down,
- Page Up in wrapped mode
-
- -
- Finder doesn't skip hidden regions
-
- -
- Finder searches in minimised alignments
-
- -
- 'Apply Colour to All Groups' not always selected
- on opening an alignment
-
- -
- 'Colour by Annotation' not marked selected in
- Colour menu
-
- -
- Per-group Clustal colour scheme changes when
- different groups in the alignment are selected
-
- -
- Internationalised colour scheme names not shown
- correctly in menu
-
- -
- Colour by Annotation can go black at min/max
- threshold limit
-
- -
- Value input for graduated feature colour
- threshold gets 'unrounded'
-
- -
- PCA image export doesn't respect background
- colour
-
- -
- PCA points don't dim when rotated about y axis
-
- -
- PCA Print dialog continues after Cancel
-
- -
- Cancel in Tree Font dialog resets alignment, not
- Tree font
-
- -
- Associate Tree with All Views not restored from
- project file
-
- -
- Scrolling of split frame is sluggish if Overview
- shown in complementary view
-
- -
- Codon consensus incorrectly scaled when shown
- without normalisation
-
- -
- Sequence Details report should open positioned at top
- of report
-
- -
- Help page can be opened twice
-
- -
- Fuzzy text in web service status menu on OSX Mojave
-
- Editing
-
- -
- Start and End should be updated when sequence
- data at beginning or end of alignment added/removed via 'Edit'
- sequence
-
- -
- Delete/Cut selection doesn't
- relocate sequence features correctly when start of sequence is
- removed (Known defect since 2.10)
-
- -
- Inserting gap sequence via the Edit Sequence
- dialog corrupts dataset sequence
-
- -
- Structure colours not updated when associated tree
- repartitions the alignment view (Regression in 2.10.5)
-
- Datamodel
-
- -
- Sequence.findIndex returns wrong value when
- sequence's End is greater than its length
-
- Bugs fixed for Java 11 Support (not yet on
- general release)
-
- -
- Menus work properly in split-screen
-
- New Known Defects
-
- -
- Select columns containing feature by double clicking ignores bounds of an existing selected region
-
- -
- Codon consensus logo incorrectly scaled in gapped
- regions of protein alignment.
-
- -
- Input Data menu entry is greyed out when PCA View
- is restored from a Jalview 2.11 project
-
- -
- Alignment panel height can be too small after
- 'New View'
-
- -
- Display is incorrect after removing gapped
- columns within hidden columns
-
- -
- Rightmost selection is lost when mouse re-enters
- window after dragging left to select columns to left of visible
- region
-
- -
- Features coloured according to their description
- string and thresholded by score in earlier versions of Jalview are
- not shown as thresholded features in 2.11. To workaround please
- create a Score filter instead.
-
- -
- Cancel on Feature Settings dialog doesn't reset group visibility
- -
- F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
-
- -
- Closing tree windows with CMD/CTRL-W for
- alignments with multiple views can close views unexpectedly
-
-
- Java 11 Specific defects
-
- -
- Jalview Properties file is not sorted
- alphabetically when saved
-
-
- |
-
-
-
-
- |
-
-
-
- -
- Default memory for Jalview webstart and
- InstallAnywhere increased to 1G.
-
- -
- Hidden sequence markers and representative
- sequence bolding included when exporting alignment as EPS,
- SVG, PNG or HTML. Display is configured via the
- Format menu, or for command-line use via a Jalview
- properties file.
-
- -
- Ensembl client updated to Version 7 REST
- API and sequence data now imported as JSON.
-
- -
- Change in recommended way of starting
- Jalview via a Java command line: add jars in lib directory
- to CLASSPATH, rather than via the deprecated java.ext.dirs
- property.
-
-
- Development
-
- -
- Support added to execute test suite
- instrumented with Open
- Clover
-
-
- |
-
-
-
- -
- Poorly scaled bar in quality annotation
- row shown in Feredoxin Structure alignment view of example
- alignment.
-
- -
- Annotation obscures sequences if lots of
- annotation displayed.
-
- -
- Group conservation/consensus not shown
- for newly created group when 'Apply to all groups'
- selected
-
- -
- Corrupted display when switching to
- wrapped mode when sequence panel's vertical scrollbar is
- visible.
-
- -
- Alignment is black in exported EPS file
- when sequences are selected in exported view.
-
- -
- Groups with different coloured borders
- aren't rendered with correct colour.
-
- -
- Jalview could hang when importing certain
- types of knotted RNA secondary structure.
-
- -
- Sequence highlight and selection in
- trimmed VARNA 2D structure is incorrect for sequences that
- do not start at 1.
-
- -
- '.' inserted into RNA secondary structure
- annotation when columns are inserted into an alignment,
- and when exporting as Stockholm flatfile.
-
- -
- Jalview annotation rows containing upper
- and lower-case 'E' and 'H' do not automatically get
- treated as RNA secondary structure.
-
- -
- .jvp should be used as default extension
- (not .jar) when saving a Jalview project file.
-
- -
- Mac Users: closing a window correctly
- transfers focus to previous window on OSX
-
-
- Java 10 Issues Resolved
-
- -
- OSX - Can't save new files via the File
- or export menus by typing in a name into the Save dialog
- box.
-
- -
- Jalview now uses patched version
- of the VAqua5
- 'look and feel' which has improved compatibility with the
- latest version of OSX.
-
-
-
- |
-
-
-
-
- |
-
-
-
- -
- Use HGVS nomenclature for variant
- annotation retrieved from Uniprot
-
- -
- Windows File Shortcuts can be dragged
- onto the Jalview Desktop
-
-
- |
-
-
-
- -
- Cannot import features with multiple
- variant elements (blocks import of some Uniprot records)
-
- -
- Clustal files with sequence positions in
- right-hand column parsed correctly
-
- -
- Wrap view - export to SVG - IDs shown but
- not alignment area in exported graphic
-
- -
- F2/Keyboard mode edits work when Overview
- window has input focus
-
- -
- Annotation panel set too high when
- annotation added to view (Windows)
-
- -
- Jalview Desktop is slow to start up when
- network connectivity is poor
-
- -
- Drag URL from chrome, firefox, IE to
- Jalview desktop on Windows doesn't open file
Dragging
- the currently open URL and links from a page viewed in
- Firefox or Chrome on Windows is now fully supported. If
- you are using Edge, only links in the page can be
- dragged, and with Internet Explorer, only the currently
- open URL in the browser can be dropped onto Jalview.
-
-
- New Known Defects
-
- - Cancel option doesn't reset Colour by Annotation
-
- |
-
-
-
-
- |
-
-
-
- -
- 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)
-
- -
- Experimental features in 2.10.2 for
- exchange of Jalview features and Chimera attributes made
- generally available
-
-
-
- |
-
-
- -
- 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)
-
- -
- Export Annotations from File Menu with CSV
- option gives blank output
-
-
-
- |
-
-
-
-
- |
-
- - 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
-
- -
- Feature settings for different views not
- recovered correctly from Jalview project file
-
- -
- Feature colours in overview when first opened
- (automatically via preferences) are different to the main
- alignment panel
-
-
- 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
-
- -
- Updated Spanish translations.
-
- -
- Jmol now primary parser
- for importing structure data to Jalview. Enables mmCIF and
- better PDB parsing.
-
- -
- Alignment ruler shows positions relative to
- reference sequence
-
- -
- Position/residue shown in status bar when
- mousing over sequence associated annotation
-
- -
- Default RNA SS symbol to 'matching bracket'
- for manual entry
-
- -
- RNA Structure consensus indicates wc-only
- '()', canonical '[]' and invalid '{}' base pair populations
- for each column
-
- -
- Feature settings popup menu options for
- showing or hiding columns containing a feature
-
- -
- Edit selected group by double clicking on
- group and sequence associated annotation labels
-
- -
- Sequence name added to annotation label in
- select/hide columns by annotation and colour by annotation
- dialogs
-
-
- Application
-
- -
- Automatically hide introns when opening a
- gene/transcript view
-
- -
- Uniprot Sequence fetcher Free Text Search
- dialog
-
- -
- UniProt - PDB protein
- structure mappings with the EMBL-EBI PDBe SIFTS database
-
- -
- Updated download sites used for Rfam and
- Pfam sources to xfam.org
-
- -
- Disabled Rfam(Full) in the sequence fetcher
-
- -
- Show residue labels in Chimera when mousing
- over sequences in Jalview
-
- -
- Support for reverse-complement coding
- regions in ENA and EMBL
-
- -
- Upgrade to EMBL XML 1.2
- for record retrieval via ENA rest API
-
- -
- Support for ENA CDS records with reverse
- complement operator
-
- -
- Update to groovy-2.4.6-indy - for faster
- groovy script execution
-
- -
- New 'execute Groovy script' option in an
- alignment window's Calculate menu
-
- -
- Allow groovy scripts that call
- Jalview.getAlignFrames() to run in headless mode
-
- -
- Support for creating new alignment
- calculation workers from groovy scripts
-
- -
- Store/restore reference sequence in
- Jalview projects
-
- -
- Chain codes for a sequence's PDB
- associations are now saved/restored from project
-
- -
- Database selection dialog always shown
- before sequence fetcher is opened
-
- -
- Double click on an entry in Jalview's
- database chooser opens a sequence fetcher
-
- -
- Free-text search client for UniProt using
- the UniProt REST API
-
- -
- -nonews command line parameter to prevent
- the news reader opening
-
- -
- Displayed columns for PDBe and Uniprot
- querying stored in preferences
-
- -
- Pagination for displaying PDBe and Uniprot
- search results
-
- -
- Tooltips shown on database chooser
-
- -
- Reverse complement function in calculate
- menu for nucleotide sequences
-
- -
- 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
-
-
- -
- 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
- - Reference sequence based alignment shading to
- highlight variation
- - Select or hide columns according to alignment
- annotation
- - 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
-
- - 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
-
- - 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
-
- - Make groups for selection uses marked columns as well
- as the active selected region
-
- - 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
-
- - 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
- - (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
-
- - 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
- 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
-
- - Escape should close any open find dialogs
- - Typo in select-by-features status report
- - Consensus RNA secondary secondary structure
- predictions are not highlighted in amber
- - 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
- width checkbox not enabled
- - Stopped a warning dialog from being shown when
- creating user defined colours
- - 'View Mapping' in structure viewer shows sequence
- mappings for just that viewer's sequences
- - Workaround for superposing PDB files containing
- multiple models in Chimera
- - Report sequence position in status bar when hovering
- over Jmol structure
- - Cannot output gaps as '.' symbols with Selection ->
- output to text box
- - Flat file exports of alignments with hidden columns
- have incorrect sequence start/end
- - 'Aligning' a second chain to a Chimera structure from
- Jalview fails
- - Colour schemes applied to structure viewers don't
- work for nucleotide
- - Loading/cut'n'pasting an empty or invalid file leads
- to a grey/invisible alignment window
- - Exported Jpred annotation from a sequence region
- imports to different position
- - 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 in
- console if Chimera has been opened
- - Mouseover to Chimera not working
- - Miscellaneous ENA XML feature qualifiers not
- retrieved
- - NPE in annotation renderer after 'Extract Scores'
- - If two structures in one Chimera window, mouseover of
- either sequence shows on first structure
- - 'Show annotations' options should not make
- non-positional annotations visible
- - Subsequence secondary structure annotation not shown
- in right place after 'view flanking regions'
- - File Save As type unset when current file format is
- unknown
- - Save as '.jar' option removed for saving Jalview
- projects
- - Colour by Sequence colouring in Chimera more
- responsive
- - 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
- General
-
- - Cannot export and reimport RNA secondary structure
- via jalview annotation file
- - Random helix colour palette for colour by annotation
- with RNA secondary structure
- - Mouseover to cDNA from STOP residue in protein
- translation doesn't work.
- - hints when using the select by annotation dialog box
- - Jmol alignment incorrect if PDB file has alternate CA
- positions
- - FontChooser message dialog appears to hang after
- choosing 1pt font
- - Peptide secondary structure incorrectly imported from
- annotation file when annotation display text includes 'e' or
- 'h'
- - Cannot set colour of new feature type whilst creating
- new feature
- - cDNA translation alignment should not be sequence
- order dependent
- - 'Show unconserved' doesn't work for lower case
- sequences
- - 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
- - Misleading message appears after trying to delete
- solid column.
- - Jalview icon not shown in dock after InstallAnywhere
- version launches
- - Fetching EMBL reference for an RNA sequence results
- fails with a sequence mismatch
- - Corrupted or unreadable alignment display when
- scrolling alignment to right
- - ArrayIndexOutOfBoundsException thrown when remove
- empty columns called on alignment with ragged gapped ends
- - auto calculated alignment annotation rows do not get
- 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
-
-
- |
-
-
- |
- 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
-
- - 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
-
-
- 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
-
- 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
- - Groovy scripting for headless Jalview operation
- Other improvements
-
- - Upgrade desktop installer to InstallAnywhere 2013
- - COMBINE statement uses current SEQUENCE_REF and
- GROUP_REF scope to group annotation rows
- - Support '' style escaping of quotes in Newick
- files
- - Group options for JABAWS service by command line name
- - Empty tooltip shown for JABA service options with a
- link but no description
- - Select primary source when selecting authority in
- database fetcher GUI
- - Add .mfa to FASTA file extensions recognised by
- Jalview
- - Annotation label tooltip text wrap
-
- |
-
-
- - Slow scrolling when lots of annotation rows are
- displayed
- - Lots of NPE (and slowness) after creating RNA
- secondary structure annotation line
- - Sequence database accessions not imported when
- fetching alignments from Rfam
- - Incorrect SHMR submission for sequences with
- identical IDs
- - View all structures does not always superpose
- structures
- - Option widgets in service parameters not updated to
- reflect user or preset settings
- - Null pointer exceptions for some services without
- presets or adjustable parameters
- - Discover PDB IDs entry in structure menu doesn't
- discover PDB xRefs
- - Exception encountered while trying to retrieve
- features with DAS
- - Lowest value in annotation row isn't coloured
- when colour by annotation (per sequence) is coloured
- - Keyboard mode P jumps to start of gapped region when
- residue follows a gap
- - Jalview appears to hang importing an alignment with
- Wrap as default or after enabling Wrap
- - 'Right click to add annotations' message
- shown in wrap mode when no annotations present
- - Disorder predictions fail with NPE if no automatic
- annotation already exists on alignment
- - oninit javascript function should be called after
- initialisation completes
- - Remove redundancy after disorder prediction corrupts
- alignment window display
- - Example annotation file in documentation is invalid
- - Grouped line graph annotation rows are not exported
- to annotation file
- - Multi-harmony analysis cannot be run when only two
- groups created
- - Cannot create multiple groups of line graphs with
- several 'combine' statements in annotation file
- - Pressing return several times causes Number Format
- exceptions in keyboard mode
- - Multi-harmony (SHMMR) method doesn't submit
- correct partitions for input data
- - Translation from DNA to Amino Acids fails
- - Jalview fail to load newick tree with quoted label
- - --headless flag isn't understood
- - ClassCastException when generating EPS in headless
- mode
- - Adjusting sequence-associated shading threshold only
- changes one row's threshold
- - Preferences and Feature settings panel panel
- doesn't open
- - 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
-
- - 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
-
- - 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
-
- 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
-
-
-
- |
-
-
-
-
-
- |
- 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.
-
-
-
- |
-
-
-
-
-
- 2.4.0.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)
-
- |
-
-
-
-
-
- 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
-
- |
-
-
- |
- |
-
-
-