--- /dev/null
+---
+channel: release
+version: 2.5
+date: 2010-04-30
+---
+
+## New Features
+
+
+
+### 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
+- <!-- todo for applet --> 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.
+
+
+## Issues Resolved
+
+- 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.
git://source.jalview.org / jalview.git / blobdiff