X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Freleases.html;h=92cc453223be92895a18ae464df40223b7620b56;hb=95e0d29563438e76f0908a0eb8b263ab5d359065;hp=2f340ffce84c95008cd2b24bc70aa1f71a752430;hpb=244a1460b0d7ae9a7a8c57d3a767b327788e8bd3;p=jalview.git
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@@ -1,4 +1,21 @@
+
Release History
@@ -17,74 +34,425 @@
+ |
+
+ |
+ 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
+
+ |
- 2.4
- Feb/2008
+
+ - 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.
+
+ |
+
+
+ |
+
|
+ |
- - New VAMSAS capabilities in Jalview
+
- 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:
- - 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
+ - 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
- - Retrieval of cross-referenced sequences from other databases
-
- - export annotation rows as CSV for spreadsheet import
- - Jalview projects record alignment dataset associations, EMBL
- products, and cDNA sequence mappings
- - Linked highlighting of codon and amino acid from translation
- and protein products
- - JPred3 web service
- - Generalised database reference retrieval and validation to
- all fetchable databases
- - Fetch sequences from DAS sources supporting the sequence command
- - Fetch either seed alignment or full alignment from PFAM
- - Sequence Fetcher GUI provides example accession numbers and 'clear' button
- - URL Links created for matching database cross references as well as sequence ID
- - URL Links can be created using regular-expressions
- - Application command line
+
+ |
+
+
+
+ |
+
+ |
+ 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
- - -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
+ - 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
- - Trees passed as applet parameters can be passed to
- application (when using "View in full application")
- - MemoryMonitor added as an option under Desktop's Tools menu
-
- - allow reading of JPred concise files as a normal filetype
- - sort sequences by named annotation scores
- - Re-instated Full AMSA support and .amsa file association
- - Stockholm annotation parsing and alignment properties import
-
- - Applet Parameters
+
+ Applet
+
+ - Middle button resizes annotation row height
+ - New Parameters
- - feature group display control parameter
- - debug parameter
- - showbutton parameter
+ - 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.
- - Applet API methods
+
- 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:
- - newView public method
- - Window (current view) specific get/set public methods
- - Feature display control methods
+ - Better handling of exceptions during sequence retrieval
+ - Dasobert generated non-positional feature URL link text
+ excludes the start_end suffix
+ - DAS feature and source retrieval buttons disabled when
+ fetch or registry operations in progress.
+ - PDB files retrieved from URLs are cached properly
+ - Sequence description lines properly shared via VAMSAS
+ - Sequence fetcher fetches multiple records for all data
+ sources
+ - Ensured that command line das feature retrieval completes
+ before alignment figures are generated.
+ - Reduced time taken when opening file browser for first
+ time.
+ - isAligned check prior to calculating tree, PCA or
+ submitting an MSA to JNet now excludes hidden sequences.
+ - User defined group colours properly recovered from Jalview
+ projects.
+ |
+
+
+
+ |
+ 2.4.0.b2
+ 28/10/2009
+ |
+
+
+ - Experimental support for google analytics usage tracking.
+ - Jalview privacy settings (user preferences and docs).
+
+ |
+
+
+ - Race condition in applet preventing startup in jre1.6.0u12+.
+ - Exception when feature created from selection beyond length
+ of sequence.
+ - Allow synthetic PDB files to be imported gracefully
+ - Sequence associated annotation rows associate with all
+ sequences with a given id
+ - Find function matches case-insensitively for sequence ID
+ string searches
+ - Non-standard characters do not cause pairwise alignment to
+ fail with exception
+
+ Application Issues
+
+ - Sequences are now validated against EMBL database
+ - Sequence fetcher fetches multiple records for all data
+ sources
+
+ InstallAnywhere Issues
+
+ - Dock icon works for Mac OS X java (Mac 1.6 update issue with
+ installAnywhere mechanism)
+ - Command line launching of JARs from InstallAnywhere version
+ (java class versioning error fixed)
+
+ |
+
+
+ |
+
+ 2.4
+ 27/8/2008
+ |
+ User Interface
+
+ - Linked highlighting of codon and amino acid from translation
+ and protein products
+ - Linked highlighting of structure associated with residue
+ mapping to codon position
+ - Sequence Fetcher provides example accession numbers and
+ 'clear' button
+ - MemoryMonitor added as an option under Desktop's Tools menu
+ - Extract score function to parse whitespace separated numeric
+ data in description line
+ - Column labels in alignment annotation can be centred.
+ - Tooltip for sequence associated annotation give name of
+ sequence
+
+ Web Services and URL fetching
+
+ - JPred3 web service
+ - Prototype sequence search client (no public services
+ available yet)
+ - Fetch either seed alignment or full alignment from PFAM
+ - URL Links created for matching database cross references as
+ well as sequence ID
+ - URL Links can be created using regular-expressions
+
+ Sequence Database Connectivity
+
+ - Retrieval of cross-referenced sequences from other databases
+
+ - Generalised database reference retrieval and validation to
+ all fetchable databases
+ - Fetch sequences from DAS sources supporting the sequence
+ command
+
+ Import and Export
+ export annotation rows as CSV for spreadsheet import
+ Jalview projects record alignment dataset associations, EMBL
+ products, and cDNA sequence mappings
+ Sequence Group colour can be specified in Annotation File
+ Ad-hoc colouring of group in Annotation File using RGB
+ triplet as name of colourscheme
+
+ VAMSAS Client capabilities (Experimental)
+
+ - treenode binding for VAMSAS tree exchange
+ - local editing and update of sequences in VAMSAS alignments
+ (experimental)
+ - Create new or select existing session to join
+ - load and save of vamsas documents
+
+ Application command line
+
+ - -tree parameter to open trees (introduced for passing from
+ applet)
+ - -fetchfrom command line argument to specify nicknames of DAS
+ servers to query for alignment features
+ - -dasserver command line argument to add new servers that are
+ also automatically queried for features
+ - -groovy command line argument executes a given groovy script
+ after all input data has been loaded and parsed
+
+ Applet-Application data exchange
+
+ - Trees passed as applet parameters can be passed to
+ application (when using "View in full application")
+
+ Applet Parameters
+
+ - feature group display control parameter
+ - debug parameter
+ - showbutton parameter
+
+ Applet API methods
+
+ - newView public method
+ - Window (current view) specific get/set public methods
+ - Feature display control methods
+ - get list of currently selected sequences
+
New Jalview distribution features
+ - InstallAnywhere Installer upgraded to IA 2008 VP1
- RELEASE file gives build properties for the latest Jalview
release.
- Java 1.1 Applet build made easier and donotobfuscate
@@ -93,9 +461,10 @@
- Debug flag for javacc
- .jalview_properties file is documented (slightly) in
jalview.bin.Cache
- - Group colour can be given as an RGB triplet which is used to colour all non-gap characters
-
+ - Continuous Build Integration for stable and development
+ version of Application, Applet and source distribution
+
|
@@ -120,6 +489,8 @@
- 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
@@ -127,10 +498,14 @@
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
-
+ - 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.
@@ -139,14 +514,36 @@
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
+ - 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
|