X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=08ea3eb4294a42796e9a3795dcb144ab17cad6d4;hb=6e23a164b465e79b78230d042159f4c8cc1fa9f0;hp=e7ab682c3b65204770a6b8de6c2a5ae1fb8e1e2d;hpb=b5fd4f62a35039495e03fc69c82a0920d848e587;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index e7ab682..08ea3eb 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -1,4 +1,21 @@
+
Release History
@@ -16,13 +33,706 @@
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.
+
+ |
+
+
+ |
+
+ |
+ |
- 2.5
- Not Yet Released
+
+ - Alignment prettyprinter doesn't cope with long sequence IDs
+
+ - clustalx colourscheme colours Ds preferentially when both
+ D+E are present in over 50% of the column
+ - nucleic acid structures retrieved from PDB do not import
+ correctly
+ - More columns get selected than were clicked on when a number
+ of columns are hidden
+ - annotation label popup menu not providing correct
+ add/hide/show options when rows are hidden or none are present
+ - Stockholm format shown in list of readable formats, and
+ parser copes better with alignments from RFAM.
+ - CSV output of consensus only includes the percentage of all
+ symbols if sequence logo display is enabled
+
+
+ Applet
+
+ - annotation panel disappears when annotation is
+ hidden/removed
+
+ Application
+
+ - Alignment view not redrawn properly when new alignment
+ opened where annotation panel is visible but no annotations are
+ present on alignment
+ - pasted region containing hidden columns is incorrectly
+ displayed in new alignment window
+ - Jalview slow to complete operations when stdout is flooded
+ (fix is to close the Jalview console)
+ - typo in AlignmentFrame->View->Hide->all but
+ selected Rregions menu item.
+ - inconsistent group submenu and Format submenu entry 'Un' or
+ 'Non'conserved
+ - Sequence feature settings are being shared by multiple
+ distinct alignments
+ - group annotation not recreated when tree partition is
+ changed
+ - double click on group annotation to select sequences does
+ not propagate to associated trees
+ - Mac OSX specific issues:
+
+ - exception raised when mouse clicked on desktop window
+ background
+ - Desktop menu placed on menu bar and application name set
+ correctly
+ - sequence feature settings not wide enough for the save
+ feature colourscheme button
+
+
+
|
+
+
+
|
+
+ |
+ New Capabilities
- URL links generated from description line for
regular-expression based URL links (applet and application)
@@ -30,20 +740,15 @@
- 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 in order of average feature score or
- total feature count
+ - 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.
- 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
-
Application
- Fetch DB References capabilities and UI expanded to support
@@ -51,48 +756,77 @@
- 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).
+ 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
+ - 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
+ - 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
+ - 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.
+ - 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.
+ - 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).
+ - 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.
@@ -101,25 +835,33 @@
- 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)
+ - 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
- - Applet:
-
-
+ - 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 (application)
+ 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.
@@ -305,8 +1047,7 @@
list
annotation consisting of sequence associated scores can be
read and written correctly to annotation file
- Aligned cDNA translation to aligned peptide works correctly
-
+ 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.
|