X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_5.md;fp=help%2Fmarkdown%2Freleases%2Frelease-2_5.md;h=b6f6ebe83ffe1d77ca0c2a96edc61a9b312ae325;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=0000000000000000000000000000000000000000;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git diff --git a/help/markdown/releases/release-2_5.md b/help/markdown/releases/release-2_5.md new file mode 100644 index 0000000..b6f6ebe --- /dev/null +++ b/help/markdown/releases/release-2_5.md @@ -0,0 +1,81 @@ +--- +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 +- 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.