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Release
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New Features
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Issues Resolved
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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
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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
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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
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- 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
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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
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- 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.
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- 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
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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.
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- 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.
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- Experimental support for google analytics usage tracking.
- Jalview privacy settings (user preferences and docs).
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- 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)
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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
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- 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
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- 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
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- 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
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2.2.1
12/2/07
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- 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
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- Applet crash under certain Linux OS with Java 1.6
installed
- Annotation file export / import bugs fixed
- PNG / EPS image output bugs fixed
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2.2
28/11/06
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- 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'
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- 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.
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2.1.1
12/9/06
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- Copy consensus sequence to clipboard
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- 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
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2.1
22/8/06
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- 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"
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- Redundancy Panel reinstalled in the Applet
- Monospaced font - EPS / rescaling bug fixed
- Annotation files with sequence references bug fixed
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2.08.1
2/5/06
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- 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
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- Annotation Panel displays complete JNet results
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2.08b
18/4/06
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- Java 1.5 bug - InternalMessageDialog fix for threads
- Righthand label on wrapped alignments shows correct value
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2.08
10/4/06
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- 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
- Applet can read zipped data files
- Applet can be embedded in web page
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- Drag & Drop fixed on Linux
- Jalview Archive file faster to load/save, sequence
descriptions saved.
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2.07
12/12/05
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- 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
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- HTML output writes groups and features
- Group editing is Control and mouse click
- File IO bugs
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2.06
28/9/05
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- View annotations in wrapped mode
- More options for PCA viewer
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- GUI bugs resolved
- Runs with -nodisplay from command line
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2.05b
15/9/05
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- Choose EPS export as lineart or text
- Jar files are executable
- Can read in "U" - maps to unknown residue
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- Known OutOfMemory errors give warning message
- Overview window calculated more efficiently
- Several GUI bugs resolved
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2.05
30/8/05
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- Edit and annotate in "Wrapped" view
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- Several GUI bugs resolved
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2.04
24/8/05
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- Hold down mouse wheel & scroll to change font size
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- Improved JPred client reliability
- Improved loading of Jalview files
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2.03
18/8/05
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- 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
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- InstallAnywhere download for Sparc Solaris
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2.02
18/7/05
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- Copy & Paste order of sequences maintains alignment
order.
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2.01
12/7/05
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- 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.
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- 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.
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2.0
20/6/05
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