+
+ |
+
+ 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
+ - 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
+
+
+ |
+
+
+ |
+
+ |
+
+
+ |
+
+
+
+ - Reinstated the display of default example file on
+ startup
+ - All pairs shown in Jalview window when viewing
+ result of pairwise alignment
+
+ |
+
+
+ |
+ General
+
+ - Updated Java code signing certificate donated by
+ Certum.PL.
+ - Features and annotation preserved when performing
+ pairwise alignment
+ - RNA pseudoknot annotation can be
+ imported/exported/displayed
+ - 'colour by annotation' can colour by RNA and
+ protein secondary structure
+ - Warn user if 'Find' regular expression is invalid (mentioned
+ post-hoc with 2.9 release)
+
+
+ Application
+
+ - Extract and display secondary structure for sequences
+ with 3D structures
+ - Support for parsing RNAML
+ - Annotations menu for layout
+
+ - sort sequence annotation rows by alignment
+ - place sequence annotation above/below alignment
+ annotation
+
+ - Output in Stockholm format
+ - Internationalisation: improved Spanish (es)
+ translation
+ - Structure viewer preferences tab
+ - Disorder and Secondary Structure annotation tracks
+ shared between alignments
+ - UCSF Chimera launch and linked highlighting from
+ Jalview
+ - Show/hide all sequence associated annotation rows for
+ all or current selection
+ - disorder and secondary structure predictions
+ available as dataset annotation
+ - Per-sequence rna helices colouring
+
+
+ - Sequence database accessions imported when fetching
+ alignments from Rfam
+ - update VARNA version to 3.91
+
+ - 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
+
- 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
+ - 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
-
- - 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
-
-
-
- |
-
-
+ 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
-
-
- |
- 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.
-
-
-
- |
+ - 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
- |
-
- |
- 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)
-
- |
-
-
-
+
+
+ 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
- 27/8/2008
-
- User Interface
-
- - Linked highlighting of codon and amino acid from translation
- and protein products
- - Linked highlighting of structure associated with residue
- mapping to codon position
- - Sequence Fetcher provides example accession numbers and
- 'clear' button
- - MemoryMonitor added as an option under Desktop's Tools menu
- - Extract score function to parse whitespace separated numeric
- data in description line
- - Column labels in alignment annotation can be centred.
- - Tooltip for sequence associated annotation give name of
- sequence
-
- Web Services and URL fetching
-
- - JPred3 web service
- - Prototype sequence search client (no public services
- available yet)
- - Fetch either seed alignment or full alignment from PFAM
- - URL Links created for matching database cross references as
- well as sequence ID
- - URL Links can be created using regular-expressions
-
- Sequence Database Connectivity
-
- - Retrieval of cross-referenced sequences from other databases
-
- - Generalised database reference retrieval and validation to
- all fetchable databases
- - Fetch sequences from DAS sources supporting the sequence
- command
-
- Import and Export
- export annotation rows as CSV for spreadsheet import
- Jalview projects record alignment dataset associations, EMBL
- products, and cDNA sequence mappings
- Sequence Group colour can be specified in Annotation File
- Ad-hoc colouring of group in Annotation File using RGB
- triplet as name of colourscheme
-
- VAMSAS Client capabilities (Experimental)
-
- - treenode binding for VAMSAS tree exchange
- - local editing and update of sequences in VAMSAS alignments
- (experimental)
- - Create new or select existing session to join
- - load and save of vamsas documents
-
- Application command line
-
- - -tree parameter to open trees (introduced for passing from
- applet)
- - -fetchfrom command line argument to specify nicknames of DAS
- servers to query for alignment features
- - -dasserver command line argument to add new servers that are
- also automatically queried for features
- - -groovy command line argument executes a given groovy script
- after all input data has been loaded and parsed
-
- Applet-Application data exchange
-
- - Trees passed as applet parameters can be passed to
- application (when using "View in full application")
-
- Applet Parameters
-
- - feature group display control parameter
- - debug parameter
- - showbutton parameter
-
- Applet API methods
-
- - newView public method
- - Window (current view) specific get/set public methods
- - Feature display control methods
- - get list of currently selected sequences
-
- New Jalview distribution features
-
- - InstallAnywhere Installer upgraded to IA 2008 VP1
- - RELEASE file gives build properties for the latest Jalview
- release.
- - Java 1.1 Applet build made easier and donotobfuscate
- property controls execution of obfuscator
- - Build target for generating source distribution
- - Debug flag for javacc
- - .jalview_properties file is documented (slightly) in
- jalview.bin.Cache
- - Continuous Build Integration for stable and development
- version of Application, Applet and source distribution
-
+ |
+
+ |
+
+ 2.4.0.b2
28/10/2009
+
+ |
+
+
+ - Experimental support for google analytics usage
+ tracking.
+ - Jalview privacy settings (user preferences and docs).
+
+ |
+
+
+ - Race condition in applet preventing startup in
+ jre1.6.0u12+.
+ - Exception when feature created from selection beyond
+ length of sequence.
+ - Allow synthetic PDB files to be imported gracefully
+ - Sequence associated annotation rows associate with
+ all sequences with a given id
+ - Find function matches case-insensitively for sequence
+ ID string searches
+ - Non-standard characters do not cause pairwise
+ alignment to fail with exception
+ Application Issues
+
+ - Sequences are now validated against EMBL database
+ - Sequence fetcher fetches multiple records for all
+ data sources
+ InstallAnywhere Issues
+
+ - Dock icon works for Mac OS X java (Mac 1.6 update
+ issue with installAnywhere mechanism)
+ - Command line launching of JARs from InstallAnywhere
+ version (java class versioning error fixed)
+
+ |
+
+
+ |
- |
-
-
- - selected region output includes visible annotations (for
- certain formats)
- - edit label/displaychar contains existing label/char for
- editing
- - update PDBEntries when DBRefEntries change (vamsas)
- - shorter peptide product names from EMBL records
- - Newick string generator makes compact representations
- - bootstrap values parsed correctly for tree files with
- comments
- - pathological filechooser bug avoided by not allowing
- filenames containing a ':'
- - Fixed exception when parsing GFF files containing global
- sequence features
- - Alignment datasets are finalized only when number of
- references from alignment sequences goes to zero
- - Close of tree branch colour box without colour selection
- causes cascading exceptions
- - occasional negative imgwidth exceptions
- - better reporting of non-fatal warnings to user when file
- parsing fails.
- - Save works when Jalview project is default format
- - Save as dialog opened if current alignment format is not a
- valid output format
- - Uniprot canonical names introduced for both das and vamsas
- - Histidine should be midblue (not pink!) in Zappo
- - error messages passed up and output when data read fails
- - edit undo recovers previous dataset sequence when sequence
- is edited
- - allow PDB files without pdb ID HEADER lines (like those
- generated by MODELLER) to be read in properly
- - allow reading of JPred concise files as a normal filetype
- - Stockholm annotation parsing and alignment properties import
- fixed for PFAM records
- - Structure view windows have correct name in Desktop window
- list
- - annotation consisting of sequence associated scores can be
- read and written correctly to annotation file
- - Aligned cDNA translation to aligned peptide works correctly
- - Fixed display of hidden sequence markers and non-italic font
- for representatives in Applet
- - Applet Menus are always embedded in applet window on Macs.
- - Newly shown features appear at top of stack (in Applet)
- - Annotations added via parameter not drawn properly due to
- null pointer exceptions
- - Secondary structure lines are drawn starting from first
- column of alignment
- - Uniprot XML import updated for new schema release in July
- 2008
- - Sequence feature to sequence ID match for Features file is
- case-insensitive
- - Sequence features read from Features file appended to all
- sequences with matching IDs
- - PDB structure coloured correctly for associated views
- containing a sub-sequence
- - PDB files can be retrieved by applet from Jar files
- - feature and annotation file applet parameters referring to
- different directories are retrieved correctly
-
- - Fixed application hang whilst waiting for splash-screen
- version check to complete
- - Applet properly URLencodes input parameter values when
- passing them to the launchApp service
- - display name and local features preserved in results
- retrieved from web service
- - Visual delay indication for sequence retrieval and sequence
- fetcher initialisation
- - updated Application to use DAS 1.53e version of dasobert DAS
- client
- - Re-instated Full AMSA support and .amsa file association
- - Fixed parsing of JNet Concise annotation sans
- sequences
-
- |
-
-
- |
- 2.3
- 9/5/07
- |
-
-
- - Jmol 11.0.2 integration
- - PDB views stored in Jalview XML files
- - Slide sequences
- - Edit sequence in place
- - EMBL CDS features
- - DAS Feature mapping
- - Feature ordering
- - Alignment Properties
- - Annotation Scores
- - Sort by scores
- - Feature/annotation editing in applet
-
- |
-
-
- - Headless state operation in 2.2.1
- - Incorrect and unstable DNA pairwise alignment
- - Cut and paste of sequences with annotation
- - Feature group display state in XML
- - Feature ordering in XML
- - blc file iteration selection using filename # suffix
- - Stockholm alignment properties
- - Stockhom alignment secondary structure annotation
- - 2.2.1 applet had no feature transparency
- - Number pad keys can be used in cursor mode
- - Structure Viewer mirror image resolved
-
- |
+
+ 2.4
27/8/2008
+
+
+ User Interface
+
+ - Linked highlighting of codon and amino acid from
+ translation and protein products
+ - Linked highlighting of structure associated with
+ residue mapping to codon position
+ - Sequence Fetcher provides example accession numbers
+ and 'clear' button
+ - MemoryMonitor added as an option under Desktop's
+ Tools menu
+ - Extract score function to parse whitespace separated
+ numeric data in description line
+ - Column labels in alignment annotation can be centred.
+ - Tooltip for sequence associated annotation give name
+ of sequence
+ Web Services and URL fetching
+
+ - JPred3 web service
+ - Prototype sequence search client (no public services
+ available yet)
+ - Fetch either seed alignment or full alignment from
+ PFAM
+ - URL Links created for matching database cross
+ references as well as sequence ID
+ - URL Links can be created using regular-expressions
+ Sequence Database Connectivity
+
+ - Retrieval of cross-referenced sequences from other
+ databases
+ - Generalised database reference retrieval and
+ validation to all fetchable databases
+ - Fetch sequences from DAS sources supporting the
+ sequence command
+ Import and Export
+ export annotation rows as CSV for spreadsheet import
+ Jalview projects record alignment dataset associations,
+ EMBL products, and cDNA sequence mappings
+ Sequence Group colour can be specified in Annotation
+ File
+ Ad-hoc colouring of group in Annotation File using RGB
+ triplet as name of colourscheme
+ VAMSAS Client capabilities (Experimental)
+
+ - treenode binding for VAMSAS tree exchange
+ - local editing and update of sequences in VAMSAS
+ alignments (experimental)
+ - Create new or select existing session to join
+ - load and save of vamsas documents
+ Application command line
+
+ - -tree parameter to open trees (introduced for passing
+ from applet)
+ - -fetchfrom command line argument to specify nicknames
+ of DAS servers to query for alignment features
+ - -dasserver command line argument to add new servers
+ that are also automatically queried for features
+ - -groovy command line argument executes a given groovy
+ script after all input data has been loaded and parsed
+ Applet-Application data exchange
+
+ - Trees passed as applet parameters can be passed to
+ application (when using "View in full
+ application")
+ Applet Parameters
+
+ - feature group display control parameter
+ - debug parameter
+ - showbutton parameter
+ Applet API methods
+
+ - newView public method
+ - Window (current view) specific get/set public methods
+ - Feature display control methods
+ - get list of currently selected sequences
+ New Jalview distribution features
+
+ - InstallAnywhere Installer upgraded to IA 2008 VP1
+ - RELEASE file gives build properties for the latest
+ Jalview release.
+ - Java 1.1 Applet build made easier and donotobfuscate
+ property controls execution of obfuscator
+ - Build target for generating source distribution
+ - Debug flag for javacc
+ - .jalview_properties file is documented (slightly) in
+ jalview.bin.Cache
+ - Continuous Build Integration for stable and
+ development version of Application, Applet and source
+ distribution
+ |
+
+
+ - selected region output includes visible annotations
+ (for certain formats)
+ - edit label/displaychar contains existing label/char
+ for editing
+ - update PDBEntries when DBRefEntries change (vamsas)
+ - shorter peptide product names from EMBL records
+ - Newick string generator makes compact representations
+ - bootstrap values parsed correctly for tree files with
+ comments
+ - pathological filechooser bug avoided by not allowing
+ filenames containing a ':'
+ - Fixed exception when parsing GFF files containing
+ global sequence features
+ - Alignment datasets are finalized only when number of
+ references from alignment sequences goes to zero
+ - Close of tree branch colour box without colour
+ selection causes cascading exceptions
+ - occasional negative imgwidth exceptions
+ - better reporting of non-fatal warnings to user when
+ file parsing fails.
+ - Save works when Jalview project is default format
+ - Save as dialog opened if current alignment format is
+ not a valid output format
+ - Uniprot canonical names introduced for both das and
+ vamsas
+ - Histidine should be midblue (not pink!) in Zappo
+ - error messages passed up and output when data read
+ fails
+ - edit undo recovers previous dataset sequence when
+ sequence is edited
+ - allow PDB files without pdb ID HEADER lines (like
+ those generated by MODELLER) to be read in properly
+ - allow reading of JPred concise files as a normal
+ filetype
+ - Stockholm annotation parsing and alignment properties
+ import fixed for PFAM records
+ - Structure view windows have correct name in Desktop
+ window list
+ - annotation consisting of sequence associated scores
+ can be read and written correctly to annotation file
+ - Aligned cDNA translation to aligned peptide works
+ correctly
+ - Fixed display of hidden sequence markers and
+ non-italic font for representatives in Applet
+ - Applet Menus are always embedded in applet window on
+ Macs.
+ - Newly shown features appear at top of stack (in
+ Applet)
+ - Annotations added via parameter not drawn properly
+ due to null pointer exceptions
+ - Secondary structure lines are drawn starting from
+ first column of alignment
+ - Uniprot XML import updated for new schema release in
+ July 2008
+ - Sequence feature to sequence ID match for Features
+ file is case-insensitive
+ - Sequence features read from Features file appended to
+ all sequences with matching IDs
+ - PDB structure coloured correctly for associated views
+ containing a sub-sequence
+ - PDB files can be retrieved by applet from Jar files
+ - feature and annotation file applet parameters
+ referring to different directories are retrieved correctly
+
+ - Fixed application hang whilst waiting for
+ splash-screen version check to complete
+ - Applet properly URLencodes input parameter values
+ when passing them to the launchApp service
+ - display name and local features preserved in results
+ retrieved from web service
+ - Visual delay indication for sequence retrieval and
+ sequence fetcher initialisation
+ - updated Application to use DAS 1.53e version of
+ dasobert DAS client
+ - Re-instated Full AMSA support and .amsa file
+ association
+ - Fixed parsing of JNet Concise annotation sans
+ sequences
+
+
+ |
+
+
+ |
+
+ 2.3
9/5/07
+
+ |
+
+
+ - Jmol 11.0.2 integration
+ - PDB views stored in Jalview XML files
+ - Slide sequences
+ - Edit sequence in place
+ - EMBL CDS features
+ - DAS Feature mapping
+ - Feature ordering
+ - Alignment Properties
+ - Annotation Scores
+ - Sort by scores
+ - Feature/annotation editing in applet
+
+ |
+
+
+ - Headless state operation in 2.2.1
+ - Incorrect and unstable DNA pairwise alignment
+ - Cut and paste of sequences with annotation
+ - Feature group display state in XML
+ - Feature ordering in XML
+ - blc file iteration selection using filename # suffix
+ - Stockholm alignment properties
+ - Stockhom alignment secondary structure annotation
+ - 2.2.1 applet had no feature transparency
+ - Number pad keys can be used in cursor mode
+ - Structure Viewer mirror image resolved
+
+ |
-
-
- |
- 2.2.1
- 12/2/07
- |
-
-
- - Non standard characters can be read and displayed
-
- Annotations/Features can be imported/exported to the applet
- via textbox
-
- Applet allows editing of sequence/annotation/group name
- & description
-
- Preference setting to display sequence name in italics
-
- Annotation file format extended to allow Sequence_groups to
- be defined
-
- Default opening of alignment overview panel can be specified
- in preferences
-
- PDB residue numbering annotation added to associated
- sequences
-
- |
-
-
- - Applet crash under certain Linux OS with Java 1.6 installed
-
- Annotation file export / import bugs fixed
-
- PNG / EPS image output bugs fixed
-
- |
-
-
- |
- 2.2
- 27/11/06
- |
-
-
- - Multiple views on alignment
-
- Sequence feature editing
-
- "Reload" alignment
-
- "Save" to current filename
-
- Background dependent text colour
-
- Right align sequence ids
-
- User-defined lower case residue colours
-
- Format Menu
-
- Select Menu
-
- Menu item accelerator keys
-
- Control-V pastes to current alignment
-
- Cancel button for DAS Feature Fetching
-
- PCA and PDB Viewers zoom via mouse roller
-
- User-defined sub-tree colours and sub-tree selection
-
- 'New Window' button on the 'Output to Text box'
-
- |
-
-
- - New memory efficient Undo/Redo System
-
- Optimised symbol lookups and conservation/consensus
- calculations
-
- Region Conservation/Consensus recalculated after edits
-
- Fixed Remove Empty Columns Bug (empty columns at end of
- alignment)
-
- Slowed DAS Feature Fetching for increased robustness.
-
- Made angle brackets in ASCII feature descriptions display
- correctly
-
- Re-instated Zoom function for PCA
-
- Sequence descriptions conserved in web service analysis
- results
-
- Uniprot ID discoverer uses any word separated by ∣
-
- WsDbFetch query/result association resolved
-
- Tree leaf to sequence mapping improved
-
- Smooth fonts switch moved to FontChooser dialog box.
-
- |
-
-
- |
- 2.1.1
- 12/9/06
- |
-
-
- - Copy consensus sequence to clipboard
-
- |
-
-
- - Image output - rightmost residues are rendered if sequence
- id panel has been resized
- - Image output - all offscreen group boundaries are rendered
- - Annotation files with sequence references - all elements in
- file are relative to sequence position
- - Mac Applet users can use Alt key for group editing
-
- |
-
-
- |
- 2.1
- 22/8/06
- |
-
-
- - MAFFT Multiple Alignment in default Web Service list
- - DAS Feature fetching
- - Hide sequences and columns
- - Export Annotations and Features
- - GFF file reading / writing
- - Associate structures with sequences from local PDB files
- - Add sequences to exisiting alignment
- - Recently opened files / URL lists
- - Applet can launch the full application
- - Applet has transparency for features (Java 1.2 required)
- - Applet has user defined colours parameter
- - Applet can load sequences from parameter "sequencex"
-
- |
-
-
- - Redundancy Panel reinstalled in the Applet
- - Monospaced font - EPS / rescaling bug fixed
- - Annotation files with sequence references bug fixed
-
- |
-
-
- |
- 2.08.1
- 2/5/06
- |
-
-
- - Change case of selected region from Popup menu
- - Choose to match case when searching
- - Middle mouse button and mouse movement can compress / expand
- the visible width and height of the alignment
-
- |
-
-
- - Annotation Panel displays complete JNet results
-
- |
-
-
- |
- 2.08b
- 18/4/06
- |
- |
-
-
- - Java 1.5 bug - InternalMessageDialog fix for threads
- - Righthand label on wrapped alignments shows correct value
-
- |
-
-
- |
- 2.08
- 10/4/06
- |
-
-
- - Editing can be locked to the selection area
- - Keyboard editing
- - Create sequence features from searches
- - Precalculated annotations can be loaded onto alignments
- - Features file allows grouping of features
- - Annotation Colouring scheme added
- - Smooth fonts off by default - Faster rendering
- - Choose to toggle Autocalculate Consensus On/Off
-
- |
-
-
- - Drag & Drop fixed on Linux
- - Jalview Archive file faster to load/save, sequence
- descriptions saved.
-
- |
-
-
- |
- 2.07
- 12/12/05
- |
-
-
- - PDB Structure Viewer enhanced
- - Sequence Feature retrieval and display enhanced
- - Choose to output sequence start-end after sequence name for
- file output
- - Sequence Fetcher WSDBFetch@EBI
- - Applet can read feature files, PDB files and can be used for
- HTML form input
-
- |
-
-
- - HTML output writes groups and features
- - Group editing is Control and mouse click
- - File IO bugs
-
- |
-
-
- |
- 2.06
- 28/9/05
- |
-
-
- - View annotations in wrapped mode
- - More options for PCA viewer
-
- |
-
-
- - GUI bugs resolved
- - Runs with -nodisplay from command line
-
- |
-
-
- |
- 2.05b
- 15/9/05
- |
-
-
- - Choose EPS export as lineart or text
- - Jar files are executable
- - Can read in Uracil - maps to unknown residue
-
- |
-
-
- - Known OutOfMemory errors give warning message
- - Overview window calculated more efficiently
- - Several GUI bugs resolved
-
- |
-
-
- |
- 2.05
- 30/8/05
- |
-
-
- - Edit and annotate in "Wrapped" view
-
- |
-
-
- - Several GUI bugs resolved
-
- |
-
-
- |
- 2.04
- 24/8/05
- |
-
-
- - Hold down mouse wheel & scroll to change font size
-
- |
-
-
- - Improved JPred client reliability
- - Improved loading of Jalview files
-
- |
-
-
- |
- 2.03
- 18/8/05
- |
-
-
- - Set Proxy server name and port in preferences
- - Multiple URL links from sequence ids
- - User Defined Colours can have a scheme name and added to
- Colour Menu
- - Choose to ignore gaps in consensus calculation
- - Unix users can set default web browser
- - Runs without GUI for batch processing
- - Dynamically generated Web Service Menus
-
- |
-
-
- - InstallAnywhere download for Sparc Solaris
-
- |
-
-
- |
- 2.02
- 18/7/05
- |
- |
-
-
- - Copy & Paste order of sequences maintains alignment
- order.
-
- |
-
-
- |
- 2.01
- 12/7/05
- |
-
-
- - Use delete key for deleting selection.
- - Use Mouse wheel to scroll sequences.
- - Help file updated to describe how to add alignment
- annotations.
- - Version and build date written to build properties file.
- - InstallAnywhere installation will check for updates at
- launch of Jalview.
-
- |
-
-
- - Delete gaps bug fixed.
- - FileChooser sorts columns.
- - Can remove groups one by one.
- - Filechooser icons installed.
- - Finder ignores return character when searching. Return key
- will initiate a search.
-
-
- |
-
-
- |
- 2.0
- 20/6/05
- |
-
-
- |
- |
-
-
-