Jalview 2.5

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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.