X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=2d51647148790b1f8d7e7f117e3f2caaee111302;hb=e66bdc1c0086ab56c56979d9dc6635e81503eb84;hp=19bd13a6c963cd88eeca510536dfe90d2167ae5e;hpb=de934b6dd40469cccd6298a8de15829233b4fd93;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 19bd13a..2d51647 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -1,21 +1,21 @@
+-->
Release History
@@ -33,14 +33,524 @@
Issues Resolved
+
+ |
+ Application
+ Support for JABAWS 2.0 Services (AACon alignment
+ conservation, protein disorder and Clustal Omega)
+ JABAWS server status indicator in Web Services preferences
+
+ VARNA (http://varna.lri.fr) viewer for RNA structures in
+ Jalview alignment window
+ Updated Jalview build and deploy framework for OSX mountain
+ lion, windows 7, and 8
+ Nucleotide substitution matrix for PCA that supports RNA
+ and ambiguity codes
+
+ Improved sequence database retrieval GUI
+ Support fetching and database reference look up against
+ multiple DAS sources (Fetch all from in 'fetch db refs')
+ Jalview project improvements
+
+ - Store and retrieve the 'belowAlignment' flag for
+ annotation
+ - calcId attribute to group annotation rows on the
+ alignment
+ - Store AACon calculation settings for a view in Jalview
+ project
+
+
+
+ horizontal scrolling gesture support
+ Visual progress indicator when PCA calculation is running
+ Simpler JABA web services menus
+ visual indication that web service results are still being
+ retrieved from server
+ Serialise the dialogs that are shown when Jalview starts up
+ for first time
+ Jalview user agent string for interacting with HTTP
+ services
+ DAS 1.6 and DAS 2.0 source support using new JDAS client
+ library
+ Examples directory and Groovy library included in
+ InstallAnywhere distribution
+ Applet
+
+ - RNA alignment and secondary structure annotation
+ visualization applet example
+ General
+
+ - Normalise option for consensus sequence logo
+ - Reset button in PCA window to return dimensions to
+ defaults
+ - Allow seqspace or Jalview variant of alignment PCA
+ calculation
+ - PCA with either nucleic acid and protein substitution
+ matrices
+
- Allow windows containing HTML reports to be exported in
+ HTML
+ - Interactive display and editing of RNA secondary structure
+ contacts
+ - RNA Helix Alignment Colouring
+ - RNA base pair logo consensus
+ - Parse sequence associated secondary structure information
+ in Stockholm files
+ - HTML Export database accessions and annotation information
+ presented in tooltip for sequences
+ - Import secondary structure from LOCARNA clustalw style RNA
+ alignment files
+ - import and visualise T-COFFEE quality scores for an
+ alignment
+ - 'colour by annotation' per sequence option to
+ shade each sequence according to its associated alignment
+ annotation
+ - New Jalview Logo
+ Documentation and Development
+
+ - documentation for score matrices used in Jalview
+ - New Website!
+ |
+ Application
+
+ - PDB, Unprot and EMBL (ENA) databases retrieved via
+ wsdbfetch REST service
+ - Stop windows being moved outside desktop on OSX
+ - Filetype associations not installed for webstart launch
+ - Jalview does not always retrieve progress of a JABAWS job
+ execution in full once it is complete
+ - revise SHMR RSBS definition to ensure alignment is
+ uploaded via ali_file parameter
+ - Jalview 2.7 is incompatible with Jmol-12.2.2
+ - View all structures superposed fails with exception
+ - Jnet job queues forever if a very short sequence is
+ submitted for prediction
+ - Cut and paste menu not opened when mouse clicked on
+ desktop window
+ - Putting fractional value into integer text box in
+ alignment parameter dialog causes Jalview to hang
+ - Structure view highlighting doesn't work on windows 7
+
+ - View all structures fails with exception shown in
+ structure view
+ - Characters in filename associated with PDBEntry not
+ escaped in a platform independent way
+ - Jalview desktop fails to launch with exception when using
+ proxy
+ - Tree calculation reports 'you must have 2 or more
+ sequences selected' when selection is empty
+ - Jalview desktop fails to launch with jar signature failure
+ when java web start temporary file caching is disabled
+ - DAS Sequence retrieval with range qualification results in
+ sequence xref which includes range qualification
+ - Errors during processing of command line arguments cause
+ progress bar (JAL-898) to be removed
+ - Replace comma for semi-colon option not disabled for DAS
+ sources in sequence fetcher
+ - Cannot close news reader when JABAWS server warning dialog
+ is shown
+ - Option widgets not updated to reflect user settings
+ - Edited sequence not submitted to web service
+ - Jalview 2.7 Webstart does not launch on mountain lion
+ - InstallAnywhere installer doesn't unpack and run on
+ OSX Mountain Lion
+ - Annotation panel not given a scroll bar when sequences
+ with alignment annotation are pasted into the alignment
+ - Sequence associated annotation rows not associated when
+ loaded from Jalview project
+ - Browser launch fails with NPE on java 1.7
+ - JABAWS alignment marked as finished when job was cancelled
+ or job failed due to invalid input
+ - NPE with v2.7 example when clicking on Tree associated
+ with all views
+ - Exceptions when copy/paste sequences with grouped
+ annotation rows to new window
+ Applet
+
+ - Sequence features are momentarily displayed before they
+ are hidden using hidefeaturegroups applet parameter
+ - loading features via javascript API automatically enables
+ feature display
+ - scrollToColumnIn javascript API method doesn't work
+ General
+
+ - Redundancy removal fails for rna alignment
+ - PCA calculation fails when sequence has been selected and
+ then deselected
+ - PCA window shows grey box when first opened on OSX
+ - Letters coloured pink in sequence logo when alignment
+ coloured with clustalx
+ - Choosing fonts without letter symbols defined causes
+ exceptions and redraw errors
+ - Initial PCA plot view is not same as manually reconfigured
+ view
+ - Grouped annotation graph label has incorrect line colour
+ - Grouped annotation graph label display is corrupted for
+ lots of labels
+
+ |
+
+ |
+
+ |
+ Application
+
+ - Jalview Desktop News Reader
+ - Tweaked default layout of web services menu
+ - View/alignment association menu to enable user to easily
+ specify which alignment a multi-structure view takes its
+ colours/correspondences from
+ - Allow properties file location to be specified as URL
+ - Extend Jalview project to preserve associations between
+ many alignment views and a single Jmol display
+ - Store annotation row height in Jalview project file
+ - Annotation row column label formatting attributes stored
+ in project file
+ - Annotation row order for auto-calculated annotation rows
+ preserved in Jalview project file
+ - Visual progress indication when Jalview state is saved
+ using Desktop window menu
+ - Visual indication that command line arguments are still
+ being processed
+ - Groovy script execution from URL
+ - Colour by annotation default min and max colours in
+ preferences
+ - Automatically associate PDB files dragged onto an
+ alignment with sequences that have high similarity and matching
+ IDs
+ - Update JGoogleAnalytics to latest release (0.3)
+ - 'view structures' option to open many structures
+ in same window
+ - Sort associated views menu option for tree panel
+ - Group all JABA and non-JABA services for a particular
+ analysis function in its own submenu
+ Applet
+
+ - Userdefined and autogenerated annotation rows for groups
+ - Adjustment of alignment annotation pane height
+ - Annotation scrollbar for annotation panel
+ - Drag to reorder annotation rows in annotation panel
+ - 'automaticScrolling' parameter
+ - Allow sequences with partial ID string matches to be
+ annotated from GFF/Jalview features files
+ - Sequence logo annotation row in applet
+ - Absolute paths relative to host server in applet
+ parameters are treated as such
+ - New in the JalviewLite javascript API:
+
+ - JalviewLite.js javascript library
+ - Javascript callbacks for
+
+ - Applet initialisation
+ - Sequence/alignment mouse-overs and selections
+
+
+ - scrollTo row and column alignment scrolling functions
+ - Select sequence/alignment regions from javascript
+ - javascript structure viewer harness to pass messages
+ between Jmol and Jalview when running as distinct applets
+ - sortBy method
+ - Set of applet and application examples shipped with
+ documentation
+ - New example to demonstrate JalviewLite and Jmol
+ javascript message exchange
+
+ General
+
+ - Enable Jmol displays to be associated with multiple
+ multiple alignments
+ - Option to automatically sort alignment with new tree
+ - User configurable link to enable redirects to a
+ www.Jalview.org mirror
+ - Jmol colours option for Jmol displays
+ - Configurable newline string when writing alignment and
+ other flat files
+ - Allow alignment annotation description lines to contain
+ html tags
+ Documentation and Development
+
+ - Add groovy test harness for bulk load testing to examples
+
+ - Groovy script to load and align a set of sequences using a
+ web service before displaying the result in the Jalview desktop
+ - Restructured javascript and applet api documentation
+ - Ant target to publish example html files with applet
+ archive
+ - Netbeans project for building Jalview from source
+ - ant task to create online javadoc for Jalview source
+ |
+ Application
+
+ - User defined colourscheme throws exception when current
+ built in colourscheme is saved as new scheme
+ - AlignFrame->Save in application pops up save dialog for
+ valid filename/format
+ - Cannot view associated structure for Uniprot sequence
+ - PDB file association breaks for Uniprot sequence P37173
+ - Associate PDB from file dialog does not tell you which
+ sequence is to be associated with the file
+ - Find All raises null pointer exception when query only
+ matches sequence IDs
+ - Pre 2.6 Jalview project cannot be loaded into v2.6
+ - Jalview project with Jmol views created with Jalview 2.4
+ cannot be loaded
+ - Filetype associations not installed for webstart launch
+ - Two or more chains in a single PDB file associated with
+ sequences in different alignments do not get coloured by their
+ associated sequence
+ - Visibility status of autocalculated annotation row not
+ preserved when project is loaded
+ - Annotation row height and visibility attributes not stored
+ in Jalview project
+ - Tree bootstraps are not preserved when saved as a Jalview
+ project
+ - Envision2 workflow tooltips are corrupted
+ - Enabling show group conservation also enables colour by
+ conservation
+ - Duplicate group associated conservation or consensus
+ created on new view
+ - Annotation scrollbar not displayed after 'show all
+ hidden annotation rows' option selected
+ - Alignment quality not updated after alignment annotation
+ row is hidden then shown
+ - Preserve colouring of structures coloured by sequences in
+ pre Jalview 2.7 projects
+ - Web service job parameter dialog is not laid out properly
+
+ - Web services menu not refreshed after 'reset
+ services' button is pressed in preferences
+ - Annotation off by one in Jalview v2_3 example project
+ - Structures imported from file and saved in project get
+ name like jalview_pdb1234.txt when reloaded
+ - Jalview does not always retrieve progress of a JABAWS job
+ execution in full once it is complete
+ Applet
+
+ - Alignment height set incorrectly when lots of annotation
+ rows are displayed
+ - Relative URLs in feature HTML text not resolved to
+ codebase
+ - View follows highlighting does not work for positions in
+ sequences
+ - <= shown as = in tooltip
+ - Export features raises exception when no features exist
+ - Separator string used for serialising lists of IDs for
+ javascript api is modified when separator string provided as
+ parameter
+ - Null pointer exception when selecting tree leaves for
+ alignment with no existing selection
+ - Relative URLs for datasources assumed to be relative to
+ applet's codebase
+ - Status bar not updated after finished searching and search
+ wraps around to first result
+ - StructureSelectionManager instance shared between several
+ Jalview applets causes race conditions and memory leaks
+ - Hover tooltip and mouseover of position on structure not
+ sent from Jmol in applet
+ - Certain sequences of javascript method calls to applet API
+ fatally hang browser
+ General
+
+ - View follows structure mouseover scrolls beyond position
+ with wrapped view and hidden regions
+ - Find sequence position moves to wrong residue with/without
+ hidden columns
+ - Sequence length given in alignment properties window is
+ off by 1
+ - InvalidNumberFormat exceptions thrown when trying to
+ import PDB like structure files
+ - Positional search results are only highlighted between
+ user-supplied sequence start/end bounds
+ - End attribute of sequence is not validated
+ - Find dialog only finds first sequence containing a given
+ sequence position
+ - Sequence numbering not preserved in MSF alignment output
+ - Jalview PDB file reader does not extract sequence from
+ nucleotide chains correctly
+ - Structure colours not updated when tree partition changed
+ in alignment
+ - Sequence associated secondary structure not correctly
+ parsed in interleaved stockholm
+ - Colour by annotation dialog does not restore current state
+
+ - Hiding (nearly) all sequences doesn't work properly
+ - Sequences containing lowercase letters are not properly
+ associated with their pdb files
+ Documentation and Development
+
+ - schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
+ tool
+ |
+
+
+ |
+ |
+ Application
+
+ - New warning dialog when the Jalview Desktop cannot contact
+ web services
+ - JABA service parameters for a preset are shown in service
+ job window
+ - JABA Service menu entries reworded
+ |
+
+
+ - Modeller PIR IO broken - cannot correctly import a pir
+ file emitted by Jalview
+ - Existing feature settings transferred to new alignment
+ view created from cut'n'paste
+ - Improved test for mixed amino/nucleotide chains when
+ parsing PDB files
+ - Consensus and conservation annotation rows occasionally
+ become blank for all new windows
+ - Exception raised when right clicking above sequences in
+ wrapped view mode
+ Application
+
+ - multiple multiply aligned structure views cause cpu usage
+ to hit 100% and computer to hang
+ - Web Service parameter layout breaks for long user
+ parameter names
+ - Jaba service discovery hangs desktop if Jaba server is
+ down
+ |
+
+
+ |
+
+ |
+ Application
+
+ - Support for Java bioinformatics
+ analysis web services (JABAWS)
+ - Web Services preference tab
+ - Analysis parameters dialog box and user defined preferences
+ - Improved speed and layout of Envision2 service menu
+ - Superpose structures using associated sequence alignment
+ - Export coordinates and projection as CSV from PCA viewer
+
+ Applet
+
+ - enable javascript: execution by the applet via the link out
+ mechanism
+
+ Other
+
+ - Updated the Jmol Jalview interface to work with Jmol series
+ 12
+ - The Jalview Desktop and JalviewLite applet now require Java
+ 1.5
+ - Allow Jalview feature colour specification for GFF sequence
+ annotation files
+ - New 'colour by label' keword in Jalview feature file type
+ colour specification
+ - New Jalview Desktop Groovy API method that allows a script
+ to check if it being run in an interactive session or in a batch
+ operation from the Jalview command line
+
+ |
+
+
+ - clustalx colourscheme colours Ds preferentially when both
+ D+E are present in over 50% of the column
+
+
+ Application
+
+ - typo in AlignmentFrame->View->Hide->all but
+ selected Regions menu item
+ - sequence fetcher replaces ',' for ';' when the ',' is part
+ of a valid accession ID
+ - fatal OOM if object retrieved by sequence fetcher runs out
+ of memory
+ - unhandled Out of Memory Error when viewing pca analysis
+ results
+ - InstallAnywhere builds fail to launch on OS X java 10.5
+ update 4 (due to apple Java 1.6 update)
+ - Installanywhere Jalview silently fails to launch
+
+ Applet
+
+ - Jalview.getFeatureGroups() raises an
+ ArrayIndexOutOfBoundsException if no feature groups are defined.
+
+ |
+
+
+ |
+
+ |
+ |
+
+
+ - Alignment prettyprinter doesn't cope with long sequence IDs
+
+ - clustalx colourscheme colours Ds preferentially when both
+ D+E are present in over 50% of the column
+ - nucleic acid structures retrieved from PDB do not import
+ correctly
+ - More columns get selected than were clicked on when a number
+ of columns are hidden
+ - annotation label popup menu not providing correct
+ add/hide/show options when rows are hidden or none are present
+ - Stockholm format shown in list of readable formats, and
+ parser copes better with alignments from RFAM.
+ - CSV output of consensus only includes the percentage of all
+ symbols if sequence logo display is enabled
+
+
+ Applet
+
+ - annotation panel disappears when annotation is
+ hidden/removed
+
+ Application
+
+ - Alignment view not redrawn properly when new alignment
+ opened where annotation panel is visible but no annotations are
+ present on alignment
+ - pasted region containing hidden columns is incorrectly
+ displayed in new alignment window
+ - Jalview slow to complete operations when stdout is flooded
+ (fix is to close the Jalview console)
+ - typo in AlignmentFrame->View->Hide->all but
+ selected Rregions menu item.
+ - inconsistent group submenu and Format submenu entry 'Un' or
+ 'Non'conserved
+ - Sequence feature settings are being shared by multiple
+ distinct alignments
+ - group annotation not recreated when tree partition is
+ changed
+ - double click on group annotation to select sequences does
+ not propagate to associated trees
+ - Mac OSX specific issues:
+
+ - exception raised when mouse clicked on desktop window
+ background
+ - Desktop menu placed on menu bar and application name set
+ correctly
+ - sequence feature settings not wide enough for the save
+ feature colourscheme button
+
+
+
+ |
+
|
- |
-
- New Capabilities
+ | New Capabilities
- URL links generated from description line for
regular-expression based URL links (applet and application)
@@ -48,126 +558,132 @@
- 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.
+ - 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.
+ - 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
- - 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.
- - Applet:
-
-
- - Application:
-
- - Better handling of exceptions during sequence retrieval
- - Dasobert generated non-positional feature URL link text
- excludes the start_end suffix (application)
- - 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.
-
-
-
- |
+ 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.
+
+
+
+ |
@@ -256,523 +772,525 @@
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
-
+
+ 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
-
- |
+
+
+
+ - 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
- |
-
-
- |
- |
-
+
+
+ |
+ 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
+ |
+
+
+ |
+ |
+