+
+ |
+
+ |
+ 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.
+ - 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.
- 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
@@ -69,48 +149,77 @@
- 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.
@@ -119,28 +228,33 @@
- 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
- - Find incrementally searches ID string matches as well as subsequence matches, and correctly reports total number of both.
- - 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.
+ - 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.
@@ -326,8 +440,7 @@
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.
|