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Jalview Changelog

What's new in Jalview 2.9.0b2

Oct 18, 2015
  • New Features:
  • Time stamps for signed Jalview application and applet jars
  • Issues Resolved:
  • Duplicate group consensus and conservation rows shown when tree is partitioned
  • Erratic behaviour when tree partitions made with multiple cDNA/Protein split views

New in Jalview 2.9 (Sep 24, 2015)

  • New Features:
  • 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 opens 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
  • Issues Resolved:
  • 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

New in Jalview 2.8.2 (Dec 4, 2014)

  • New Features:
  • 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
  • New in the Jalview Desktop:
  • Extract and display secondary structure for sequences with 3D structures
  • Support for parsing RNAML
  • Annotations menu for layout: sort sequence annotation rows by alignment and 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
  • Issues resolved:
  • 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 additon 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
  • Changes in 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 - upgraded to InstallAnywhere 2014

New in Jalview 2.8.1 (Jun 5, 2014)

  • New Features:
  • Internationalisation of user interface (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
  • Bugs resolved:
  • 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
  • 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

New in Jalview 2.8 (Aug 14, 2013)

  • NEW FEATURES:
  • 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!
  • ISSUES RESOLVED
  • 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