X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=92cc453223be92895a18ae464df40223b7620b56;hb=95e0d29563438e76f0908a0eb8b263ab5d359065;hp=ea956968522a950f7889e12b72a8ef66e5610da3;hpb=12fdd79d25527a93ee20ffa562899ec5b703e4d5;p=jalview.git
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@@ -1,4 +1,21 @@
+
Release History
@@ -17,73 +34,257 @@
+ |
+
+ |
+ 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
+
|
+ |
- - 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.
- - Enable or disable non-positional feature and database
- references in sequence ID tooltip from View menu in application.
- - Parsing of Dbref and DbxRef feature types as database
- references
+ - 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)
- 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.
- - Optionally scale multi-character column labels to fit within each column
+ - 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
- - New hidden columns and rows and representatives capabilities
- in annotations file (in progress - not yet fully implemented)
- - Order an alignment in order of average feature score or
- total feature count
- - Shading features by score or associated description
- - Group-associated automatic and user-defined alignment
- annotation
+ - 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
+ - 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
- - parameter to enable automatic sort of associated alignment view when a
- new tree is opened.
- - Non-positional features displayed in sequence ID tooltip
+ - 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
- - 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).
- URL links generated for all feature links (bugfix)
- Added URL embedding instructions to features file
documentation.
@@ -92,24 +293,33 @@
- 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
+ - 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.
@@ -295,8 +505,7 @@
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.
|