-
- |
- Release
- |
+
+ |
+
+ Release
+
+ |
+
+
+ New Features
+
+ |
+
+
+ Issues Resolved
+
+ |
+
+
+ |
+
+ |
+
+
+
+ |
+
+
+ - Reinstated the display of default example file on startup
+ - All pairs shown in Jalview window when viewing result of pairwise alignment
+
+ |
+
+
+ |
+ General
+
+ - Updated Java code signing certificate donated by Certum.PL.
+ - Features and annotation preserved when performing pairwise
+ alignment
+ - RNA pseudoknot annotation can be
+ imported/exported/displayed
+ - 'colour by annotation' can colour by RNA and
+ protein secondary structure
+ 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
+ |
+
+
|
- New Features
+
+ |
+ 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
+
|
- Issues Resolved
+
+ - 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.
+
|
-
|
- 2.4.1
- Not Yet Released
+
|
+ |
- - 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.
- - Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.
-
- - URL links generated from description line for regular-expression based URL links (applet and application)
-
- - Non-positional features displayed in sequence ID tooltip on applet
-
- - Non-positional feature URL links are shown in link menu (applet and application)
-
- - Automatic Scrolling option in View menu to display the currently highlighted region of an alignment.
-
- - Improved VAMSAS synchronization (jalview archive used to preserve views, structures, and tree display settings)
-
- - Sharing of selected regions between views and with other VAMSAS applications (Experimental feature!)
-
- - New hidden columns and rows and representatives capabilities in annotations file (in progress - not yet fully implemented)
- - Order an alignment in order of average feature score or total feature count
+ - 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.
|
- - Better handling of exceptions during sequence retrieval
- - URL links generated for all feature links (bugfix)
- - Dasobert generated non-positional feature URL link text excludes the start_end suffix (application)
- - Added URL embedding instructions to features file documentation.
- - Codons containing ambiguous nucleotides translated as 'X' in peptide product
- - Sequence description lines properly shared via VAMSAS
- - 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.
- - Sequence fetcher fetches multiple records for all data sources
+ - 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
+
+ |
+ 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
+ |
+
+
+ - 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)
+ - 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
-
+ 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
+ - 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
+ - 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
-
+ - 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)
+ - 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 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
-
+ - 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
+
- 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
+ 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
+ - 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
@@ -175,9 +1232,10 @@
- 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
+ - Continuous Build Integration for stable and development
+ version of Application, Applet and source distribution
-
+
|
@@ -202,7 +1260,8 @@
- 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
+ - 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
@@ -211,13 +1270,13 @@
- 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
+ - 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
-
+ - 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.
@@ -226,25 +1285,36 @@
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
+ - 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
+ - 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
+ - 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
+ - Fixed parsing of JNet Concise annotation sans
+ sequences
|
|
- |
+ |
2.3
9/5/07
|
|