Jalview 2.7

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New Features

Application

  • Jalview Desktop News Reader
  • Tweaked default layout of web services menu
  • View/alignment association menu to enable user to easily specify which alignment a multi-structure view takes its colours/correspondences from
  • Allow properties file location to be specified as URL
  • Extend Jalview project to preserve associations between many alignment views and a single Jmol display
  • Store annotation row height in Jalview project file
  • Annotation row column label formatting attributes stored in project file
  • Annotation row order for auto-calculated annotation rows preserved in Jalview project file
  • Visual progress indication when Jalview state is saved using Desktop window menu
  • Visual indication that command line arguments are still being processed
  • Groovy script execution from URL
  • Colour by annotation default min and max colours in preferences
  • Automatically associate PDB files dragged onto an alignment with sequences that have high similarity and matching IDs
  • Update JGoogleAnalytics to latest release (0.3)
  • ‘view structures’ option to open many structures in same window
  • Sort associated views menu option for tree panel
  • Group all JABA and non-JABA services for a particular analysis function in its own submenu

Applet

  • Userdefined and autogenerated annotation rows for groups
  • Adjustment of alignment annotation pane height
  • Annotation scrollbar for annotation panel
  • Drag to reorder annotation rows in annotation panel
  • ‘automaticScrolling’ parameter
  • Allow sequences with partial ID string matches to be annotated from GFF/Jalview features files
  • Sequence logo annotation row in applet
  • Absolute paths relative to host server in applet parameters are treated as such
  • New in the JalviewLite javascript API:
    • JalviewLite.js javascript library
    • Javascript callbacks for
      • Applet initialisation
      • Sequence/alignment mouse-overs and selections
    • scrollTo row and column alignment scrolling functions
    • Select sequence/alignment regions from javascript
    • javascript structure viewer harness to pass messages between Jmol and Jalview when running as distinct applets
    • sortBy method
    • Set of applet and application examples shipped with documentation
    • New example to demonstrate JalviewLite and Jmol javascript message exchange

General

  • Enable Jmol displays to be associated with multiple multiple alignments
  • Option to automatically sort alignment with new tree
  • User configurable link to enable redirects to a www.Jalview.org mirror
  • Jmol colours option for Jmol displays
  • Configurable newline string when writing alignment and other flat files
  • Allow alignment annotation description lines to contain html tags

Documentation and Development

  • Add groovy test harness for bulk load testing to examples
  • Groovy script to load and align a set of sequences using a web service before displaying the result in the Jalview desktop
  • Restructured javascript and applet api documentation
  • Ant target to publish example html files with applet archive
  • Netbeans project for building Jalview from source
  • ant task to create online javadoc for Jalview source

Issues Resolved

Application

  • User defined colourscheme throws exception when current built in colourscheme is saved as new scheme
  • AlignFrame->Save in application pops up save dialog for valid filename/format
  • Cannot view associated structure for UniProt sequence
  • PDB file association breaks for UniProt sequence P37173
  • Associate PDB from file dialog does not tell you which sequence is to be associated with the file
  • Find All raises null pointer exception when query only matches sequence IDs
  • Pre 2.6 Jalview project cannot be loaded into v2.6
  • Jalview project with Jmol views created with Jalview 2.4 cannot be loaded
  • Filetype associations not installed for webstart launch
  • Two or more chains in a single PDB file associated with sequences in different alignments do not get coloured by their associated sequence
  • Visibility status of autocalculated annotation row not preserved when project is loaded
  • Annotation row height and visibility attributes not stored in Jalview project
  • Tree bootstraps are not preserved when saved as a Jalview project
  • Envision2 workflow tooltips are corrupted
  • Enabling show group conservation also enables colour by conservation
  • Duplicate group associated conservation or consensus created on new view
  • Annotation scrollbar not displayed after ‘show all hidden annotation rows’ option selected
  • Alignment quality not updated after alignment annotation row is hidden then shown
  • Preserve colouring of structures coloured by sequences in pre Jalview 2.7 projects
  • Web service job parameter dialog is not laid out properly
  • Web services menu not refreshed after ‘reset services’ button is pressed in preferences
  • Annotation off by one in Jalview v2_3 example project
  • Structures imported from file and saved in project get name like jalview_pdb1234.txt when reloaded
  • Jalview does not always retrieve progress of a JABAWS job execution in full once it is complete

Applet

  • Alignment height set incorrectly when lots of annotation rows are displayed
  • Relative URLs in feature HTML text not resolved to codebase
  • View follows highlighting does not work for positions in sequences
  • <= shown as = in tooltip
  • Export features raises exception when no features exist
  • Separator string used for serialising lists of IDs for javascript api is modified when separator string provided as parameter
  • Null pointer exception when selecting tree leaves for alignment with no existing selection
  • Relative URLs for datasources assumed to be relative to applet’s codebase
  • Status bar not updated after finished searching and search wraps around to first result
  • StructureSelectionManager instance shared between several Jalview applets causes race conditions and memory leaks
  • Hover tooltip and mouseover of position on structure not sent from Jmol in applet
  • Certain sequences of javascript method calls to applet API fatally hang browser

General

  • View follows structure mouseover scrolls beyond position with wrapped view and hidden regions
  • Find sequence position moves to wrong residue with/without hidden columns
  • Sequence length given in alignment properties window is off by 1
  • InvalidNumberFormat exceptions thrown when trying to import PDB like structure files
  • Positional search results are only highlighted between user-supplied sequence start/end bounds
  • End attribute of sequence is not validated
  • Find dialog only finds first sequence containing a given sequence position
  • Sequence numbering not preserved in MSF alignment output
  • Jalview PDB file reader does not extract sequence from nucleotide chains correctly
  • Structure colours not updated when tree partition changed in alignment
  • Sequence associated secondary structure not correctly parsed in interleaved stockholm
  • Colour by annotation dialog does not restore current state
  • Hiding (nearly) all sequences doesn’t work properly
  • Sequences containing lowercase letters are not properly associated with their pdb files

Documentation and Development

  • schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright tool