-
- |
- Release
- |
-
- New Features
- |
-
- Issues Resolved
- |
-
+ |
+
+ Release
+
+ |
+
+
+ New Features
+
+ |
+
+
+ Issues Resolved
+
+ |
+
+
+ |
+ 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
+ - Assign an alignment reference sequence 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
+
+ - Optional embedding of BioJSON data when exporting
+ alignment figures to HTML
+ - New Export Settings dialog to control hidden region
+ export in flat file generation
+ - New cDNA/Protein analysis capabilities
+
+ - Get Cross-References should open a Split Frame
+ view with cDNA/Protein
+ - Detect when nucleotide sequences and protein
+ sequences are placed in the same alignment
+ - Split cDNA/Protein views are saved in Jalview
+ projects
+
+
+
+ - Use REST API to talk to Chimera
+ - Selected regions in Chimera are highlighted in linked Jalview windows
+
+ - Calculate UPGMA and NJ trees using sequence feature
+ similarity
+
+ - VARNA RNA viewer updated to v3.93
+ - VARNA views are saved in Jalview
+ Projects
+ - Pseudoknots displayed as Jalview RNA annotation can be shown in VARNA
+
+ - changed 'View nucleotide structure' submenu to 'View VARNA 2D Structure'
+ - change "View protein structure" menu option to "3D Structure ..."
+
+ - Make groups for selection uses marked columns as well
+ as the active selected region
+
+ - allow different similarity matrix calculations for
+ tree building and PCA
+
+ - Export alignment views for display with the BioJS MSAViewer
+
+ - Export scrollable SVG in HTML page
+
+ - Interactive free text and structured queries with the
+ PDBe Search API for PDB data retrieval
+ - PDBe Search API based discovery and selection of PDB structures to
+ view 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/
+
+ Applet
+
+ - New parameters to enable SplitFrame view (file2, scaleProteinAsCdna)
+ - New example demonstrating linked viewing of cDNA and
+ Protein alignments
+ - New layout for applet example pages
+
+ Development and deployment
+ Java 1.7 minimum requirement for Jalview 2.9
+ Include installation type and git revision in build
+ properties and console log output
+ Github project and web URL for storing BioJsMSA
+ Templates
+ Jalview's unit tests now managed with TestNG |
+
+
+ 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
+
-
+
+ |
+
+
+ |
+
+ |
+ |
+
+
+ - Reinstated the display of default example file on startup
+ - All pairs shown in Jalview window when viewing result of pairwise alignment
+
+ |
+
+
+ |
- Application
+ | General
- - 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:
+
- 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
- - 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
+ - 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
- - 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
+ 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
- - Add groovy test harness for bulk load testing to examples
+
-
+
+ corrupted or unreadable alignment display when scrolling alignment
+ to right
- - 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
+
+
+ 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
- - 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
+
-
+
+ JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
- - 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
+
+
+ Jalview and Jmol example not compatible with IE9
+
+
+ Sort by annotation score doesn't reverse order when
+ selected
+
+ |
+
+
+ |
+
+
+ General
- - 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
+
- 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
- - <= 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
+ 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
- - 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
+
- 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
- - Hiding (nearly) all sequences doesn't work properly
- - Sequences containing lowercase letters are not properly
- associated with their pdb files
- Documentation and Development
+ 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
- - schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
- tool
- |
+ 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
+ |
+
+
2.6.1
@@ -244,7 +1043,7 @@
- Modeller PIR IO broken - cannot correctly import a pir
- file emitted by jalview
+ 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
@@ -291,11 +1090,11 @@
1.5
- Allow Jalview feature colour specification for GFF sequence
annotation files
- - New 'colour by label' keword in jalview feature file type
+
- 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
+ operation from the Jalview command line
|
@@ -439,7 +1238,7 @@
href="webServices/index.html#envision2">Envision2 Workflows
Vamsas Capabilities
- - Improved VAMSAS synchronization (jalview archive used to
+
- 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
| |