Release History

Release
New Features
Issues Resolved
2.10.1
29/11/2016
General
  • Improved memory usage: sparse arrays used for all consensus calculations
  • Jmol updated to version 14.6.4 (released 3rd Oct 2016)
  • Updated Jalview's Certum code signing certificate for 2016-2017
Application
  • Sequence ID tool tip presents abridged set of database cross-references, sorted alphabetically
  • New replacement token for creating URLs just from database cross references. Users with custom links will receive a warning dialog asking them to update their preferences.
  • Cancel button and escape listener on dialog warning user about disconnecting Jalview from a Chimera session
  • Jalview's Chimera control window closes if the Chimera it is connected to is shut down
  • New keystroke (B) and Select highlighted columns menu item to mark columns containing highlighted regions (e.g. from structure selections or results of a Find operation)
  • Command line option for batch-generation of HTML pages rendering alignment data with the BioJS MSAviewer
General
  • Columns with more than one modal residue are not coloured or thresholded according to percent identity (first observed in Jalview 2.8.2)
  • Threonine incorrectly reported as not hydrophobic
  • Updates to documentation pages (above PID threshold, amino acid properties)
  • Lower case residues in sequences are not reported as mapped to residues in a structure file in the View Mapping report
  • Identical features with non-numeric scores could be added multiple times to a sequence
  • Disulphide bond features shown as two highlighted residues rather than a range in linked structure views, and treated correctly when selecting and computing trees from features
  • Custom URL links for database cross-references are matched to database name regardless of case
Application
  • Custom URL links for specific database names without regular expressions also offer links from Sequence ID
  • Removing a single configured link in the URL links pane in Connections preferences doesn't actually update Jalview configuration
  • CTRL-Click on a selected region to open the alignment area popup menu doesn't work on El-Capitan
  • Jalview doesn't offer to associate mmCIF files with similarly named sequences if dropped onto the alignment
  • Additional mappings are shown for PDB entries where more chains exist in the PDB accession than are reported in the SIFTS file
  • Certain structures do not get mapped to the structure view when displayed with Chimera
  • No chains shown in the Chimera view panel's View->Show Chains submenu
  • Export as HTML with embedded SVG doesn't work for wrapped alignment views
  • Rename UI components for running JPred predictions from 'JNet' to 'JPred'
  • Export as PNG or SVG is corrupted when annotation panel vertical scroll is not at first annotation row
  • Attempting to view structure for Hen lysozyme results in a PDB Client error dialog box
2.10.0b1
25/10/2016
Application
  • 3D Structure chooser opens with 'Cached structures' view if structures already loaded
  • Progress bar reports models as they are loaded to structure views
General
  • Colour by conservation always enabled and no tick shown in menu when BLOSUM or PID shading applied
  • FER1_ARATH and FER2_ARATH labels were switched in example sequences/projects/trees
Application
  • Jalview projects with views of local PDB structure files saved on Windows cannot be opened on OSX
  • Multiple structure views can be opened and superposed without timeout for structures with multiple models or multiple sequences in alignment
  • Cannot import or associated local PDB files without a PDB ID HEADER line
  • RMSD is not output in Jmol console when superposition is performed
  • Drag and drop of URL from Browser fails for Linux and OSX versions earlier than El Capitan
  • ENA client ignores invalid content from ENA server
  • Exceptions are not raised in console when ENA client attempts to fetch non-existent IDs via Fetch DB Refs UI option
  • Exceptions are not raised in console when a new view is created on the alignment
  • OSX right-click fixed for group selections: CMD-click to insert/remove gaps in groups and CTRL-click to open group pop-up menu
Build and deployment
  • URL link checker now copes with multi-line anchor tags
New Known Issues
  • Drag and drop from URL links in browsers do not work on Windows
2.10.0
06/10/2016
General
  • Updated Spanish translations.
  • Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.
  • Alignment ruler shows positions relative to reference sequence
  • Position/residue shown in status bar when mousing over sequence associated annotation
  • Default RNA SS symbol to 'matching bracket' for manual entry
  • RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column
  • Feature settings popup menu options for showing or hiding columns containing a feature
  • Edit selected group by double clicking on group and sequence associated annotation labels
  • Sequence name added to annotation label in select/hide columns by annotation and colour by annotation dialogs
Application
  • Automatically hide introns when opening a gene/transcript view
  • Uniprot Sequence fetcher Free Text Search dialog
  • UniProt - PDB protein structure mappings with the EMBL-EBI PDBe SIFTS database
  • Updated download sites used for Rfam and Pfam sources to xfam.org
  • Disabled Rfam(Full) in the sequence fetcher
  • Show residue labels in Chimera when mousing over sequences in Jalview
  • Support for reverse-complement coding regions in ENA and EMBL
  • Upgrade to EMBL XML 1.2 for record retrieval via ENA rest API
  • Support for ENA CDS records with reverse complement operator
  • Update to groovy-2.4.6-indy - for faster groovy script execution
  • New 'execute Groovy script' option in an alignment window's Calculate menu
  • Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode
  • Support for creating new alignment calculation workers from groovy scripts
  • Store/restore reference sequence in Jalview projects
  • Chain codes for a sequence's PDB associations are now saved/restored from project
  • Database selection dialog always shown before sequence fetcher is opened
  • Double click on an entry in Jalview's database chooser opens a sequence fetcher
  • Free-text search client for UniProt using the UniProt REST API
  • -nonews command line parameter to prevent the news reader opening
  • Displayed columns for PDBe and Uniprot querying stored in preferences
  • Pagination for displaying PDBe and Uniprot search results
  • Tooltips shown on database chooser
  • Reverse complement function in calculate menu for nucleotide sequences
  • Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets).
  • Chimera 1.11.1 minimum requirement for viewing structures with Jalview 2.10
  • Retrieve genome, transcript CCDS and gene ids via the Ensembl and Ensembl Genomes REST API
  • Protein sequence variant annotation computed for 'sequence_variant' annotation on CDS regions (Ensembl)
  • ENA CDS 'show cross references' for Uniprot sequences
  • Improved warning messages when DB Ref Fetcher fails to match, or otherwise updates sequence data from external database records.
  • Revised Jalview Project format for efficient recovery of sequence coding and alignment annotation relationships.
General
  • reinstate CTRL-click for opening pop-up menu on OSX
  • Export features in Jalview format (again) includes graduated colourschemes
  • More responsive when working with big alignments and lots of hidden columns
  • Hidden column markers not always rendered at right of alignment window
  • Tidied up links in help file table of contents
  • Feature based tree calculation not shown for DNA alignments
  • Hidden columns ignored during feature based tree calculation
  • Alignment view stops updating when show unconserved enabled for group on alignment
  • Cannot insert gaps into sequence when set as reference
  • Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation
  • Incorrect column numbers in ruler when hidden columns present
  • Colour by RNA Helices not enabled when user created annotation added to alignment
  • RNA Structure consensus only computed for '()' base pair annotation
  • Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus
  • Extend selection with columns containing feature not working
  • Pfam format writer puts extra space at beginning of sequence
  • Incomplete sequence extracted from pdb entry 3a6s
  • Cannot create groups on an alignment from from a tree when t-coffee scores are shown
  • Cannot import and view PDB structures with chains containing negative resnums (4q4h)
  • ArithmeticExceptions raised when parsing some structures
  • 'Empty' alignment blocks added to Clustal, PIR and PileUp output
  • Reordering sequence features that are not visible causes alignment window to repaint
  • Threshold sliders don't work in graduated colour and colour by annotation row for e-value scores associated with features and annotation rows
  • amino acid physicochemical conservation calculation should be case independent
  • Remove annotation also updates hidden columns
  • FER1_ARATH and FER2_ARATH mislabelled in example file (uniref50.fa, feredoxin.fa, unaligned.fa, exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
  • Null pointer exceptions and redraw problems when reference sequence defined and 'show non-conserved' enabled
  • Quality and Conservation are now shown on load even when Consensus calculation is disabled
  • Remove right on penultimate column of alignment does nothing
Application
  • URLs and links can't be imported by drag'n'drop on OSX when launched via webstart (note - not yet fixed for El Capitan)
  • Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms
  • Error thrown when exporting a view with hidden sequences as flat-file alignment
  • InstallAnywhere distribution fails when launching Chimera
  • Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)
  • Cannot save project when view has a reference sequence defined
  • Columns are suddenly selected in other alignments and views when revealing hidden columns
  • Hide columns not mirrored in complement view in a cDNA/Protein splitframe
  • Cannot save/restore representative sequence from project when only one sequence is represented
  • Disabled 'Best Uniprot Coverage' option in Structure Chooser
  • Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel
  • View mapping in structure view shows mappings between sequence and all chains in a PDB file
  • PDB and Uniprot FTS dialogs format columns correctly, don't display array data, sort columns according to type
  • Export complete shown after destination file chooser is cancelled during an image export
  • Error when querying PDB Service with sequence name containing special characters
  • Manual PDB structure querying should be case insensitive
  • Large tooltips with broken HTML formatting don't wrap
  • Figures exported from wrapped view are truncated so L looks like I in consensus annotation
  • Export features should only export the currently displayed features for the current selection or view
  • Enable 'Get Cross-References' in menu after fetching cross-references, and restoring from project
  • Mouseover of a copy of a sequence is not followed in the structure viewer
  • Titles for individual alignments in splitframe not restored from project
  • missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default
  • amino acid physicochemical conservation is case dependent
  • RSS reader doesn't stay hidden after last article has been read (reopened issue due to internationalisation problems)
  • Only offer PDB structures in structure viewer based on sequence name, PDB and UniProt cross-references
  • No progress bar shown during export of alignment as HTML
  • Structures not always superimposed after multiple structures are shown for one or more sequences.
  • Reference sequence characters should not be replaced with '.' when 'Show unconserved' format option is enabled.
  • Cannot specify chain code when entering specific PDB id for sequence
  • File->Export->.. as doesn't work when 'Export hidden sequences' is enabled, but 'export hidden columns' is disabled.
  • Best Quality option in structure chooser selects lowest rather than highest resolution structures for each sequence
  • Incorrect start and end reported for PDB to sequence mapping in 'View Mappings' report
  • Unable to read old Jalview projects that contain non-XML data added after Jalvew wrote project.
  • Newly created annotation row reorders after clicking on it to create new annotation for a column.
Applet
  • Incorrect columns are selected when hidden columns present before start of sequence
  • Missing dependencies on applet pages (JSON jars)
  • Overview pixel size changes when sequences are hidden in applet
  • Updated instructions for applet deployment on examples pages.
2.9.0b2
16/10/2015
General
  • Time stamps for signed Jalview application and applet jars
Application
  • Duplicate group consensus and conservation rows shown when tree is partitioned
  • Erratic behaviour when tree partitions made with multiple cDNA/Protein split views
2.9.0b1
8/10/2015
General
  • Updated Spanish translations of localized text for 2.9
Application
  • Signed OSX InstallAnywhere installer
  • Support for per-sequence based annotations in BioJSON
Applet
  • Split frame example added to applet examples page
Build and Deployment
  • New ant target for running Jalview's test suite
General
  • Mapping of cDNA to protein in split frames incorrect when sequence start > 1
  • Broken images in filter column by annotation dialog documentation
  • Feature colours not parsed from features file
  • Exceptions and incomplete link URLs recovered when loading a features file containing HTML tags in feature description
Application
  • Annotations corrupted after BioJS export and reimport
  • Incorrect sequence limits after Fetch DB References with 'trim retrieved sequences'
  • Incorrect warning about deleting all data when deleting selected columns
  • Patch to build system for shipping properly signed JNLP templates for webstart launch
  • EMBL-PDBe fetcher/viewer dialogs do not offer unreleased structures for download or viewing
  • Tab/space/return keystroke operation of EMBL-PDBe fetcher/viewer dialogs works correctly
  • Disabled 'minimise' button on Jalview windows running on OSX to workaround redraw hang bug
  • Split cDNA/Protein view position and geometry not recovered from jalview project
  • Initial enabled/disabled state of annotation menu sorter 'show autocalculated first/last' corresponds to alignment view
  • Restoring of Clustal, RNA Helices and T-Coffee color schemes from BioJSON
Applet
  • Reorder sequences mirrored in cDNA/Protein split frame
  • Applet with Jmol examples not loading correctly
2.9
10/9/2015
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
2.8.2
3/12/2014
General
  • Updated Java code signing certificate donated by Certum.PL.
  • Features and annotation preserved when performing pairwise alignment
  • RNA pseudoknot annotation can be imported/exported/displayed
  • 'colour by annotation' can colour by RNA and protein secondary structure
  • Warn user if 'Find' regular expression is invalid (mentioned post-hoc with 2.9 release)
Application
  • Extract and display secondary structure for sequences with 3D structures
  • Support for parsing RNAML
  • Annotations menu for layout
    • sort sequence annotation rows by alignment
    • place sequence annotation above/below alignment annotation
  • Output in Stockholm format
  • Internationalisation: improved Spanish (es) translation
  • Structure viewer preferences tab
  • Disorder and Secondary Structure annotation tracks shared between alignments
  • UCSF Chimera launch and linked highlighting from Jalview
  • Show/hide all sequence associated annotation rows for all or current selection
  • disorder and secondary structure predictions available as dataset annotation
  • Per-sequence rna helices colouring
  • Sequence database accessions imported when fetching alignments from Rfam
  • update VARNA version to 3.91
  • New groovy scripts for exporting aligned positions, conservation values, and calculating sum of pairs scores.
  • Command line argument to set default JABAWS server
  • include installation type in build properties and console log output
  • Updated Jalview project format to preserve dataset annotation
Application
  • Distinguish alignment and sequence associated RNA structure in structure->view->VARNA
  • Raise dialog box if user deletes all sequences in an alignment
  • Pressing F1 results in documentation opening twice
  • Sequence feature tooltip is wrapped
  • Double click on sequence associated annotation selects only first column
  • Redundancy removal doesn't result in unlinked leaves shown in tree
  • Undos after several redundancy removals don't undo properly
  • Hide sequence doesn't hide associated annotation
  • User defined colours dialog box too big to fit on screen and buttons not visible
  • author list isn't updated if already written to Jalview properties
  • Popup menu won't open after retrieving sequence from database
  • File open window for associate PDB doesn't open
  • Left-then-right click on a sequence id opens a browser search window
  • Cannot open sequence feature shading/sort popup menu in feature settings dialog
  • better tooltip placement for some areas of Jalview desktop
  • Allow addition of JABAWS Server which doesn't pass validation
  • Web services parameters dialog box is too large to fit on screen
  • Muscle nucleotide alignment preset obscured by tooltip
  • JABAWS preset submenus don't contain newly defined user preset
  • MSA web services warns user if they were launched with invalid input
  • Jalview cannot contact DAS Registy when running on Java 8
  • 'Superpose with' submenu not shown when new view created
Deployment and Documentation
  • 2G and 1G options in launchApp have no effect on memory allocation
  • launchApp service doesn't automatically open www.jalview.org/examples/exampleFile.jar if no file is given
  • InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is available
Application Known issues
  • corrupted or unreadable alignment display when scrolling alignment to right
  • retrieval fails but progress bar continues for DAS retrieval with large number of ID
  • flatfile output of visible region has incorrect sequence start/end
  • rna structure consensus doesn't update when secondary structure tracks are rearranged
  • invalid rna structure positional highlighting does not highlight position of invalid base pairs
  • out of memory errors are not raised when saving Jalview project from alignment window file menu
  • Switching to RNA Helices colouring doesn't propagate to structures
  • colour by RNA Helices not enabled when user created annotation added to alignment
  • Jalview icon not shown on dock in Mountain Lion/Webstart
Applet Known Issues
  • JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
  • Jalview and Jmol example not compatible with IE9
  • Sort by annotation score doesn't reverse order when selected
2.8.1
4/6/2014
General
  • Internationalisation of user interface (usually called i18n support) and translation for Spanish locale
  • Define/Undefine group on current selection with Ctrl-G/Shift Ctrl-G
  • Improved group creation/removal options in alignment/sequence Popup menu
  • Sensible precision for symbol distribution percentages shown in logo tooltip.
  • Annotation panel height set according to amount of annotation when alignment first opened
Application
  • Interactive consensus RNA secondary structure prediction VIENNA RNAAliFold JABA 2.1 service
  • Select columns containing particular features from Feature Settings dialog
  • View all 'representative' PDB structures for selected sequences
  • Update Jalview project format:
    • New file extension for Jalview projects '.jvp'
    • Preserve sequence and annotation dataset (to store secondary structure annotation,etc)
    • Per group and alignment annotation and RNA helix colouring
  • New similarity measures for PCA and Tree calculation (PAM250)
  • Experimental support for retrieval and viewing of flanking regions for an alignment
Application
  • logo keeps spinning and status remains at queued or running after job is cancelled
  • cannot export features from alignments imported from Jalview/VAMSAS projects
  • Buggy slider for web service parameters that take float values
  • Newly created RNA secondary structure line doesn't have 'display all symbols' flag set
  • T-COFFEE alignment score shading scheme and other annotation shading not saved in Jalview project
  • Local file cannot be loaded in freshly downloaded Jalview
  • Jalview icon not shown on dock in Mountain Lion/Webstart
  • Load file from desktop file browser fails
  • Occasional NPE thrown when calculating large trees
  • Cannot reorder or slide sequences after dragging an alignment onto desktop
  • Colour by annotation dialog throws NPE after using 'extract scores' function
  • Loading/cut'n'pasting an empty file leads to a grey alignment window
  • Disorder thresholds rendered incorrectly after performing IUPred disorder prediction
  • Multiple group annotated consensus rows shown when changing 'normalise logo' display setting
  • Find shows blank dialog after 'finished searching' if nothing matches query
  • Null Pointer Exceptions raised when sorting by feature with lots of groups
  • Errors in Jmol console when structures in alignment don't overlap
  • Not all working JABAWS services are shown in Jalview's menu
  • JAVAWS version of Jalview fails to launch with 'invalid literal/length code'
  • Annotation/RNA Helix colourschemes cannot be applied to alignment with groups (actually fixed in 2.8.0b1)
  • RNA Helices and T-Coffee Scores available as default colourscheme
Applet
  • Remove group option is shown even when selection is not a group
  • Apply to all groups ticked but colourscheme changes don't affect groups
  • Documented RNA Helices and T-Coffee Scores as valid colourscheme name
  • Annotation labels drawn on sequence IDs when Annotation panel is not displayed
  • Increased font size for dropdown menus on OSX and embedded windows
Other
  • Consensus sequence for alignments/groups with a single sequence were not calculated
  • annotation files that contain only groups imported as annotation and junk sequences
  • Fasta files with sequences containing '*' incorrectly recognised as PFAM or BLC
  • conservation/PID slider apply all groups option doesn't affect background (2.8.0b1)
  • redundancy highlighting is erratic at 0% and 100%
  • Remove gapped columns fails for sequences with ragged trailing gaps
  • AMSA annotation row with leading spaces is not registered correctly on import
  • Jalview crashes when selecting PCA analysis for certain alignments
  • Opening the colour by annotation dialog for an existing annotation based 'use original colours' colourscheme loses original colours setting
2.8.0b1
30/1/2014
  • 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
2.8
12/11/2012
Application
  • Support for JABAWS 2.0 Services (AACon alignment conservation, protein disorder and Clustal Omega)
  • JABAWS server status indicator in Web Services preferences
  • VARNA (http://varna.lri.fr) viewer for RNA structures in Jalview alignment window
  • Updated Jalview build and deploy framework for OSX mountain lion, windows 7, and 8
  • Nucleotide substitution matrix for PCA that supports RNA and ambiguity codes
  • Improved sequence database retrieval GUI
  • Support fetching and database reference look up against multiple DAS sources (Fetch all from in 'fetch db refs')
  • Jalview project improvements
    • Store and retrieve the 'belowAlignment' flag for annotation
    • calcId attribute to group annotation rows on the alignment
    • Store AACon calculation settings for a view in Jalview project
  • horizontal scrolling gesture support
  • Visual progress indicator when PCA calculation is running
  • Simpler JABA web services menus
  • visual indication that web service results are still being retrieved from server
  • Serialise the dialogs that are shown when Jalview starts up for first time
  • Jalview user agent string for interacting with HTTP services
  • DAS 1.6 and DAS 2.0 source support using new JDAS client library
  • Examples directory and Groovy library included in InstallAnywhere distribution
Applet
  • RNA alignment and secondary structure annotation visualization applet example
General
  • Normalise option for consensus sequence logo
  • Reset button in PCA window to return dimensions to defaults
  • Allow seqspace or Jalview variant of alignment PCA calculation
  • PCA with either nucleic acid and protein substitution matrices
  • Allow windows containing HTML reports to be exported in HTML
  • Interactive display and editing of RNA secondary structure contacts
  • RNA Helix Alignment Colouring
  • RNA base pair logo consensus
  • Parse sequence associated secondary structure information in Stockholm files
  • HTML Export database accessions and annotation information presented in tooltip for sequences
  • Import secondary structure from LOCARNA clustalw style RNA alignment files
  • import and visualise T-COFFEE quality scores for an alignment
  • 'colour by annotation' per sequence option to shade each sequence according to its associated alignment annotation
  • New Jalview Logo
Documentation and Development
  • documentation for score matrices used in Jalview
  • New Website!
Application
  • PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch REST service
  • Stop windows being moved outside desktop on OSX
  • Filetype associations not installed for webstart launch
  • Jalview does not always retrieve progress of a JABAWS job execution in full once it is complete
  • revise SHMR RSBS definition to ensure alignment is uploaded via ali_file parameter
  • Jalview 2.7 is incompatible with Jmol-12.2.2
  • View all structures superposed fails with exception
  • Jnet job queues forever if a very short sequence is submitted for prediction
  • Cut and paste menu not opened when mouse clicked on desktop window
  • Putting fractional value into integer text box in alignment parameter dialog causes Jalview to hang
  • Structure view highlighting doesn't work on windows 7
  • View all structures fails with exception shown in structure view
  • Characters in filename associated with PDBEntry not escaped in a platform independent way
  • Jalview desktop fails to launch with exception when using proxy
  • Tree calculation reports 'you must have 2 or more sequences selected' when selection is empty
  • Jalview desktop fails to launch with jar signature failure when java web start temporary file caching is disabled
  • DAS Sequence retrieval with range qualification results in sequence xref which includes range qualification
  • Errors during processing of command line arguments cause progress bar (JAL-898) to be removed
  • Replace comma for semi-colon option not disabled for DAS sources in sequence fetcher
  • Cannot close news reader when JABAWS server warning dialog is shown
  • Option widgets not updated to reflect user settings
  • Edited sequence not submitted to web service
  • Jalview 2.7 Webstart does not launch on mountain lion
  • InstallAnywhere installer doesn't unpack and run on OSX Mountain Lion
  • Annotation panel not given a scroll bar when sequences with alignment annotation are pasted into the alignment
  • Sequence associated annotation rows not associated when loaded from Jalview project
  • Browser launch fails with NPE on java 1.7
  • JABAWS alignment marked as finished when job was cancelled or job failed due to invalid input
  • NPE with v2.7 example when clicking on Tree associated with all views
  • Exceptions when copy/paste sequences with grouped annotation rows to new window
Applet
  • Sequence features are momentarily displayed before they are hidden using hidefeaturegroups applet parameter
  • loading features via javascript API automatically enables feature display
  • scrollToColumnIn javascript API method doesn't work
General
  • Redundancy removal fails for rna alignment
  • PCA calculation fails when sequence has been selected and then deselected
  • PCA window shows grey box when first opened on OSX
  • Letters coloured pink in sequence logo when alignment coloured with clustalx
  • Choosing fonts without letter symbols defined causes exceptions and redraw errors
  • Initial PCA plot view is not same as manually reconfigured view
  • Grouped annotation graph label has incorrect line colour
  • Grouped annotation graph label display is corrupted for lots of labels
2.7
27/09/2011
Application
  • Jalview Desktop News Reader
  • Tweaked default layout of web services menu
  • View/alignment association menu to enable user to easily specify which alignment a multi-structure view takes its colours/correspondences from
  • Allow properties file location to be specified as URL
  • Extend Jalview project to preserve associations between many alignment views and a single Jmol display
  • Store annotation row height in Jalview project file
  • Annotation row column label formatting attributes stored in project file
  • Annotation row order for auto-calculated annotation rows preserved in Jalview project file
  • Visual progress indication when Jalview state is saved using Desktop window menu
  • Visual indication that command line arguments are still being processed
  • Groovy script execution from URL
  • Colour by annotation default min and max colours in preferences
  • Automatically associate PDB files dragged onto an alignment with sequences that have high similarity and matching IDs
  • Update JGoogleAnalytics to latest release (0.3)
  • 'view structures' option to open many structures in same window
  • Sort associated views menu option for tree panel
  • Group all JABA and non-JABA services for a particular analysis function in its own submenu
Applet
  • Userdefined and autogenerated annotation rows for groups
  • Adjustment of alignment annotation pane height
  • Annotation scrollbar for annotation panel
  • Drag to reorder annotation rows in annotation panel
  • 'automaticScrolling' parameter
  • Allow sequences with partial ID string matches to be annotated from GFF/Jalview features files
  • Sequence logo annotation row in applet
  • Absolute paths relative to host server in applet parameters are treated as such
  • New in the JalviewLite javascript API:
    • JalviewLite.js javascript library
    • Javascript callbacks for
      • Applet initialisation
      • Sequence/alignment mouse-overs and selections
    • scrollTo row and column alignment scrolling functions
    • Select sequence/alignment regions from javascript
    • javascript structure viewer harness to pass messages between Jmol and Jalview when running as distinct applets
    • sortBy method
    • Set of applet and application examples shipped with documentation
    • New example to demonstrate JalviewLite and Jmol javascript message exchange
General
  • Enable Jmol displays to be associated with multiple multiple alignments
  • Option to automatically sort alignment with new tree
  • User configurable link to enable redirects to a www.Jalview.org mirror
  • Jmol colours option for Jmol displays
  • Configurable newline string when writing alignment and other flat files
  • Allow alignment annotation description lines to contain html tags
Documentation and Development
  • Add groovy test harness for bulk load testing to examples
  • Groovy script to load and align a set of sequences using a web service before displaying the result in the Jalview desktop
  • Restructured javascript and applet api documentation
  • Ant target to publish example html files with applet archive
  • Netbeans project for building Jalview from source
  • ant task to create online javadoc for Jalview source
Application
  • User defined colourscheme throws exception when current built in colourscheme is saved as new scheme
  • AlignFrame->Save in application pops up save dialog for valid filename/format
  • Cannot view associated structure for UniProt sequence
  • PDB file association breaks for UniProt sequence P37173
  • Associate PDB from file dialog does not tell you which sequence is to be associated with the file
  • Find All raises null pointer exception when query only matches sequence IDs
  • Pre 2.6 Jalview project cannot be loaded into v2.6
  • Jalview project with Jmol views created with Jalview 2.4 cannot be loaded
  • Filetype associations not installed for webstart launch
  • Two or more chains in a single PDB file associated with sequences in different alignments do not get coloured by their associated sequence
  • Visibility status of autocalculated annotation row not preserved when project is loaded
  • Annotation row height and visibility attributes not stored in Jalview project
  • Tree bootstraps are not preserved when saved as a Jalview project
  • Envision2 workflow tooltips are corrupted
  • Enabling show group conservation also enables colour by conservation
  • Duplicate group associated conservation or consensus created on new view
  • Annotation scrollbar not displayed after 'show all hidden annotation rows' option selected
  • Alignment quality not updated after alignment annotation row is hidden then shown
  • Preserve colouring of structures coloured by sequences in pre Jalview 2.7 projects
  • Web service job parameter dialog is not laid out properly
  • Web services menu not refreshed after 'reset services' button is pressed in preferences
  • Annotation off by one in Jalview v2_3 example project
  • Structures imported from file and saved in project get name like jalview_pdb1234.txt when reloaded
  • Jalview does not always retrieve progress of a JABAWS job execution in full once it is complete
Applet
  • Alignment height set incorrectly when lots of annotation rows are displayed
  • Relative URLs in feature HTML text not resolved to codebase
  • View follows highlighting does not work for positions in sequences
  • <= shown as = in tooltip
  • Export features raises exception when no features exist
  • Separator string used for serialising lists of IDs for javascript api is modified when separator string provided as parameter
  • Null pointer exception when selecting tree leaves for alignment with no existing selection
  • Relative URLs for datasources assumed to be relative to applet's codebase
  • Status bar not updated after finished searching and search wraps around to first result
  • StructureSelectionManager instance shared between several Jalview applets causes race conditions and memory leaks
  • Hover tooltip and mouseover of position on structure not sent from Jmol in applet
  • Certain sequences of javascript method calls to applet API fatally hang browser
General
  • View follows structure mouseover scrolls beyond position with wrapped view and hidden regions
  • Find sequence position moves to wrong residue with/without hidden columns
  • Sequence length given in alignment properties window is off by 1
  • InvalidNumberFormat exceptions thrown when trying to import PDB like structure files
  • Positional search results are only highlighted between user-supplied sequence start/end bounds
  • End attribute of sequence is not validated
  • Find dialog only finds first sequence containing a given sequence position
  • Sequence numbering not preserved in MSF alignment output
  • Jalview PDB file reader does not extract sequence from nucleotide chains correctly
  • Structure colours not updated when tree partition changed in alignment
  • Sequence associated secondary structure not correctly parsed in interleaved stockholm
  • Colour by annotation dialog does not restore current state
  • Hiding (nearly) all sequences doesn't work properly
  • Sequences containing lowercase letters are not properly associated with their pdb files
Documentation and Development
  • schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright tool
2.6.1
15/11/2010
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
2.6
26/9/2010
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.
2.5.1
14/6/2010
  • 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
2.5
30/4/2010
New Capabilities
  • URL links generated from description line for regular-expression based URL links (applet and application)
  • Non-positional feature URL links are shown in link menu
  • Linked viewing of nucleic acid sequences and structures
  • Automatic Scrolling option in View menu to display the currently highlighted region of an alignment.
  • Order an alignment by sequence length, or using the average score or total feature count for each sequence.
  • Shading features by score or associated description
  • Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).
  • New hide/show options including Shift+Control+H to hide everything but the currently selected region.
Application
  • Fetch DB References capabilities and UI expanded to support retrieval from DAS sequence sources
  • Local DAS Sequence sources can be added via the command line or via the Add local source dialog box.
  • DAS Dbref and DbxRef feature types are parsed as database references and protein_name is parsed as description line (BioSapiens terms).
  • Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.
  • Group-associated consensus, sequence logos and conservation plots
  • Symbol distributions for each column can be exported and visualized as sequence logos
  • Optionally scale multi-character column labels to fit within each column of annotation row
  • Optional automatic sort of associated alignment view when a new tree is opened.
  • Jalview Java Console
  • Better placement of desktop window when moving between different screens.
  • New preference items for sequence ID tooltip and consensus annotation
  • Client to submit sequences and IDs to Envision2 Workflows
  • Vamsas Capabilities
    • Improved VAMSAS synchronization (Jalview archive used to preserve views, structures, and tree display settings)
    • Import of vamsas documents from disk or URL via command line
    • Sharing of selected regions between views and with other VAMSAS applications (Experimental feature!)
    • Updated API to VAMSAS version 0.2
Applet
  • Middle button resizes annotation row height
  • New Parameters
    • sortByTree (true/false) - automatically sort the associated alignment view by the tree when a new tree is opened.
    • showTreeBootstraps (true/false) - show or hide branch bootstraps (default is to show them if available)
    • showTreeDistances (true/false) - show or hide branch lengths (default is to show them if available)
    • showUnlinkedTreeNodes (true/false) - indicate if unassociated nodes should be highlighted in the tree view
    • heightScale and widthScale (1.0 or more) - increase the height or width of a cell in the alignment grid relative to the current font size.
  • Non-positional features displayed in sequence ID tooltip
Other
  • Features format: graduated colour definitions and specification of feature scores
  • Alignment Annotations format: new keywords for group associated annotation (GROUP_REF) and annotation row display properties (ROW_PROPERTIES)
  • XML formats extended to support graduated feature colourschemes, group associated annotation, and profile visualization settings.
  • Source field in GFF files parsed as feature source rather than description
  • Non-positional features are now included in sequence feature and gff files (controlled via non-positional feature visibility in tooltip).
  • URL links generated for all feature links (bugfix)
  • Added URL embedding instructions to features file documentation.
  • Codons containing ambiguous nucleotides translated as 'X' in peptide product
  • Match case switch in find dialog box works for both sequence ID and sequence string and query strings do not have to be in upper case to match case-insensitively.
  • AMSA files only contain first column of multi-character column annotation labels
  • Jalview Annotation File generation/parsing consistent with documentation (e.g. Stockholm annotation can be exported and re-imported)
  • PDB files without embedded PDB IDs given a friendly name
  • Find incrementally searches ID string matches as well as subsequence matches, and correctly reports total number of both.
  • Application:
    • Better handling of exceptions during sequence retrieval
    • Dasobert generated non-positional feature URL link text excludes the start_end suffix
    • DAS feature and source retrieval buttons disabled when fetch or registry operations in progress.
    • PDB files retrieved from URLs are cached properly
    • Sequence description lines properly shared via VAMSAS
    • Sequence fetcher fetches multiple records for all data sources
    • Ensured that command line das feature retrieval completes before alignment figures are generated.
    • Reduced time taken when opening file browser for first time.
    • isAligned check prior to calculating tree, PCA or submitting an MSA to JNet now excludes hidden sequences.
    • User defined group colours properly recovered from Jalview projects.
2.4.0.b2
28/10/2009
  • Experimental support for google analytics usage tracking.
  • Jalview privacy settings (user preferences and docs).
  • Race condition in applet preventing startup in jre1.6.0u12+.
  • Exception when feature created from selection beyond length of sequence.
  • Allow synthetic PDB files to be imported gracefully
  • Sequence associated annotation rows associate with all sequences with a given id
  • Find function matches case-insensitively for sequence ID string searches
  • Non-standard characters do not cause pairwise alignment to fail with exception
Application Issues
  • Sequences are now validated against EMBL database
  • Sequence fetcher fetches multiple records for all data sources
InstallAnywhere Issues
  • Dock icon works for Mac OS X java (Mac 1.6 update issue with installAnywhere mechanism)
  • Command line launching of JARs from InstallAnywhere version (java class versioning error fixed)
2.4
27/8/2008
User Interface
  • Linked highlighting of codon and amino acid from translation and protein products
  • Linked highlighting of structure associated with residue mapping to codon position
  • Sequence Fetcher provides example accession numbers and 'clear' button
  • MemoryMonitor added as an option under Desktop's Tools menu
  • Extract score function to parse whitespace separated numeric data in description line
  • Column labels in alignment annotation can be centred.
  • Tooltip for sequence associated annotation give name of sequence
Web Services and URL fetching
  • JPred3 web service
  • Prototype sequence search client (no public services available yet)
  • Fetch either seed alignment or full alignment from PFAM
  • URL Links created for matching database cross references as well as sequence ID
  • URL Links can be created using regular-expressions
Sequence Database Connectivity
  • Retrieval of cross-referenced sequences from other databases
  • Generalised database reference retrieval and validation to all fetchable databases
  • Fetch sequences from DAS sources supporting the sequence command
Import and Export
  • export annotation rows as CSV for spreadsheet import
  • Jalview projects record alignment dataset associations, EMBL products, and cDNA sequence mappings
  • Sequence Group colour can be specified in Annotation File
  • Ad-hoc colouring of group in Annotation File using RGB triplet as name of colourscheme
  • VAMSAS Client capabilities (Experimental)
    • treenode binding for VAMSAS tree exchange
    • local editing and update of sequences in VAMSAS alignments (experimental)
    • Create new or select existing session to join
    • load and save of vamsas documents
    Application command line
    • -tree parameter to open trees (introduced for passing from applet)
    • -fetchfrom command line argument to specify nicknames of DAS servers to query for alignment features
    • -dasserver command line argument to add new servers that are also automatically queried for features
    • -groovy command line argument executes a given groovy script after all input data has been loaded and parsed
    Applet-Application data exchange
    • Trees passed as applet parameters can be passed to application (when using "View in full application")
    Applet Parameters
    • feature group display control parameter
    • debug parameter
    • showbutton parameter
    Applet API methods
    • newView public method
    • Window (current view) specific get/set public methods
    • Feature display control methods
    • get list of currently selected sequences
    New Jalview distribution features
    • InstallAnywhere Installer upgraded to IA 2008 VP1
    • RELEASE file gives build properties for the latest Jalview release.
    • Java 1.1 Applet build made easier and donotobfuscate property controls execution of obfuscator
    • Build target for generating source distribution
    • Debug flag for javacc
    • .jalview_properties file is documented (slightly) in jalview.bin.Cache
    • Continuous Build Integration for stable and development version of Application, Applet and source distribution
    • selected region output includes visible annotations (for certain formats)
    • edit label/displaychar contains existing label/char for editing
    • update PDBEntries when DBRefEntries change (vamsas)
    • shorter peptide product names from EMBL records
    • Newick string generator makes compact representations
    • bootstrap values parsed correctly for tree files with comments
    • pathological filechooser bug avoided by not allowing filenames containing a ':'
    • Fixed exception when parsing GFF files containing global sequence features
    • Alignment datasets are finalized only when number of references from alignment sequences goes to zero
    • Close of tree branch colour box without colour selection causes cascading exceptions
    • occasional negative imgwidth exceptions
    • better reporting of non-fatal warnings to user when file parsing fails.
    • Save works when Jalview project is default format
    • Save as dialog opened if current alignment format is not a valid output format
    • UniProt canonical names introduced for both das and vamsas
    • Histidine should be midblue (not pink!) in Zappo
    • error messages passed up and output when data read fails
    • edit undo recovers previous dataset sequence when sequence is edited
    • allow PDB files without pdb ID HEADER lines (like those generated by MODELLER) to be read in properly
    • allow reading of JPred concise files as a normal filetype
    • Stockholm annotation parsing and alignment properties import fixed for PFAM records
    • Structure view windows have correct name in Desktop window list
    • annotation consisting of sequence associated scores can be read and written correctly to annotation file
    • Aligned cDNA translation to aligned peptide works correctly
    • Fixed display of hidden sequence markers and non-italic font for representatives in Applet
    • Applet Menus are always embedded in applet window on Macs.
    • Newly shown features appear at top of stack (in Applet)
    • Annotations added via parameter not drawn properly due to null pointer exceptions
    • Secondary structure lines are drawn starting from first column of alignment
    • UniProt XML import updated for new schema release in July 2008
    • Sequence feature to sequence ID match for Features file is case-insensitive
    • Sequence features read from Features file appended to all sequences with matching IDs
    • PDB structure coloured correctly for associated views containing a sub-sequence
    • PDB files can be retrieved by applet from Jar files
    • feature and annotation file applet parameters referring to different directories are retrieved correctly
    • Fixed application hang whilst waiting for splash-screen version check to complete
    • Applet properly URLencodes input parameter values when passing them to the launchApp service
    • display name and local features preserved in results retrieved from web service
    • Visual delay indication for sequence retrieval and sequence fetcher initialisation
    • updated Application to use DAS 1.53e version of dasobert DAS client
    • Re-instated Full AMSA support and .amsa file association
    • Fixed parsing of JNet Concise annotation sans sequences
    2.3
    9/5/07
    • Jmol 11.0.2 integration
    • PDB views stored in Jalview XML files
    • Slide sequences
    • Edit sequence in place
    • EMBL CDS features
    • DAS Feature mapping
    • Feature ordering
    • Alignment Properties
    • Annotation Scores
    • Sort by scores
    • Feature/annotation editing in applet
    • Headless state operation in 2.2.1
    • Incorrect and unstable DNA pairwise alignment
    • Cut and paste of sequences with annotation
    • Feature group display state in XML
    • Feature ordering in XML
    • blc file iteration selection using filename # suffix
    • Stockholm alignment properties
    • Stockhom alignment secondary structure annotation
    • 2.2.1 applet had no feature transparency
    • Number pad keys can be used in cursor mode
    • Structure Viewer mirror image resolved
    2.2.1
    12/2/07
    • Non standard characters can be read and displayed
    • Annotations/Features can be imported/exported to the applet via textbox
    • Applet allows editing of sequence/annotation/group name & description
    • Preference setting to display sequence name in italics
    • Annotation file format extended to allow Sequence_groups to be defined
    • Default opening of alignment overview panel can be specified in preferences
    • PDB residue numbering annotation added to associated sequences
    • Applet crash under certain Linux OS with Java 1.6 installed
    • Annotation file export / import bugs fixed
    • PNG / EPS image output bugs fixed
    2.2
    27/11/06
    • Multiple views on alignment
    • Sequence feature editing
    • "Reload" alignment
    • "Save" to current filename
    • Background dependent text colour
    • Right align sequence ids
    • User-defined lower case residue colours
    • Format Menu
    • Select Menu
    • Menu item accelerator keys
    • Control-V pastes to current alignment
    • Cancel button for DAS Feature Fetching
    • PCA and PDB Viewers zoom via mouse roller
    • User-defined sub-tree colours and sub-tree selection
    • 'New Window' button on the 'Output to Text box'
    • New memory efficient Undo/Redo System
    • Optimised symbol lookups and conservation/consensus calculations
    • Region Conservation/Consensus recalculated after edits
    • Fixed Remove Empty Columns Bug (empty columns at end of alignment)
    • Slowed DAS Feature Fetching for increased robustness.
    • Made angle brackets in ASCII feature descriptions display correctly
    • Re-instated Zoom function for PCA
    • Sequence descriptions conserved in web service analysis results
    • UniProt ID discoverer uses any word separated by ∣
    • WsDbFetch query/result association resolved
    • Tree leaf to sequence mapping improved
    • Smooth fonts switch moved to FontChooser dialog box.
    2.1.1
    12/9/06
    • Copy consensus sequence to clipboard
    • Image output - rightmost residues are rendered if sequence id panel has been resized
    • Image output - all offscreen group boundaries are rendered
    • Annotation files with sequence references - all elements in file are relative to sequence position
    • Mac Applet users can use Alt key for group editing
    2.1
    22/8/06
    • MAFFT Multiple Alignment in default Web Service list
    • DAS Feature fetching
    • Hide sequences and columns
    • Export Annotations and Features
    • GFF file reading / writing
    • Associate structures with sequences from local PDB files
    • Add sequences to exisiting alignment
    • Recently opened files / URL lists
    • Applet can launch the full application
    • Applet has transparency for features (Java 1.2 required)
    • Applet has user defined colours parameter
    • Applet can load sequences from parameter "sequencex"
    • Redundancy Panel reinstalled in the Applet
    • Monospaced font - EPS / rescaling bug fixed
    • Annotation files with sequence references bug fixed
    2.08.1
    2/5/06
    • Change case of selected region from Popup menu
    • Choose to match case when searching
    • Middle mouse button and mouse movement can compress / expand the visible width and height of the alignment
    • Annotation Panel displays complete JNet results
    2.08b
    18/4/06
     
    • Java 1.5 bug - InternalMessageDialog fix for threads
    • Righthand label on wrapped alignments shows correct value
    2.08
    10/4/06
    • Editing can be locked to the selection area
    • Keyboard editing
    • Create sequence features from searches
    • Precalculated annotations can be loaded onto alignments
    • Features file allows grouping of features
    • Annotation Colouring scheme added
    • Smooth fonts off by default - Faster rendering
    • Choose to toggle Autocalculate Consensus On/Off
    • Drag & Drop fixed on Linux
    • Jalview Archive file faster to load/save, sequence descriptions saved.
    2.07
    12/12/05
    • PDB Structure Viewer enhanced
    • Sequence Feature retrieval and display enhanced
    • Choose to output sequence start-end after sequence name for file output
    • Sequence Fetcher WSDBFetch@EBI
    • Applet can read feature files, PDB files and can be used for HTML form input
    • HTML output writes groups and features
    • Group editing is Control and mouse click
    • File IO bugs
    2.06
    28/9/05
    • View annotations in wrapped mode
    • More options for PCA viewer
    • GUI bugs resolved
    • Runs with -nodisplay from command line
    2.05b
    15/9/05
    • Choose EPS export as lineart or text
    • Jar files are executable
    • Can read in Uracil - maps to unknown residue
    • Known OutOfMemory errors give warning message
    • Overview window calculated more efficiently
    • Several GUI bugs resolved
    2.05
    30/8/05
    • Edit and annotate in "Wrapped" view
    • Several GUI bugs resolved
    2.04
    24/8/05
    • Hold down mouse wheel & scroll to change font size
    • Improved JPred client reliability
    • Improved loading of Jalview files
    2.03
    18/8/05
    • Set Proxy server name and port in preferences
    • Multiple URL links from sequence ids
    • User Defined Colours can have a scheme name and added to Colour Menu
    • Choose to ignore gaps in consensus calculation
    • Unix users can set default web browser
    • Runs without GUI for batch processing
    • Dynamically generated Web Service Menus
    • InstallAnywhere download for Sparc Solaris
    2.02
    18/7/05
     
    • Copy & Paste order of sequences maintains alignment order.
    2.01
    12/7/05
    • Use delete key for deleting selection.
    • Use Mouse wheel to scroll sequences.
    • Help file updated to describe how to add alignment annotations.
    • Version and build date written to build properties file.
    • InstallAnywhere installation will check for updates at launch of Jalview.
    • Delete gaps bug fixed.
    • FileChooser sorts columns.
    • Can remove groups one by one.
    • Filechooser icons installed.
    • Finder ignores return character when searching. Return key will initiate a search.
    2.0
    20/6/05
    • New codebase