GBrowse Persistent Variables

[[GBrowse]] uses a few persistent variables to store data for a user. The following is an explanation of the structure of the commonly-used ones:

• $state is a large hash containing information regarding the current configured state of the browser (hence the name). It contains the following key->value pairs:
  • width [string] - The width of the final image, in pixels, as set on the preferences tab.
  • source [string] - The current data source name.
  • ks [string] - ?
  • tracks [array] - An array of the labels of all the tracks for the
  • userid [string] - The currently-logged-in user's ID, corresponding to the main GBrowse user database.
  • uploadid [string] - The currently-logged-in user's uploads ID, corresponding to the folder containing their uploaded files.
  • seg_max [number] - The upper bound of the region currently being viewed; the right side of the image, unless flipped.
  • seg_min [number] - The lower bound of the region currently being viewed; the left side of the image, unless flipped.
  • flip [boolean] - True if the genome view has been flipped horizontally from the default left-to-right method.
  • show_tooltips [boolean] - Whether or not to show the helper tooltips in the main browser.
  • valid_region [boolean] - Whether the region requested is valid, or not. If not, the karotype is shown.
  • uploads [hash] - Contains all uploaded (not imported) files as keys, the values are arrays containing: ["uploaded file's name", "?"]
  • track_collapsed [hash] - ? "between"
  • region_size [number] - The size (in base pairs) of the region being viewed.
  • max segment [number] - ? 5000000
  • head [boolean] - ? 1
  • grid [boolean] - Whether or not to display the grid behind the rendered images
  • features [hash] - All the features available; the feature name is the key and the value is another hash containing 3 flags:
    • visible [boolean] - Whether or not the feature is visible in the browser display.
    • options [boolean] - ? 0
    • limit [boolean] - ? 0
  • version [number] - ? 100
  • stop [number] - ? 203999
  • ref [string] - The named region being displayed (?)
  • name [string] - The displayed name of the region (as seen in the "Landmark or Region" input field), "chrI:98000..203999" for example.
  • v [number] - ? 2
  • subtracks [hash] - ? {}
  • ins [boolean] - ? 1
  • stp [boolean] - ? 1
  • sk [string] - ? "sorted"
  • section_visible [hash] - A hash containing each section as a key and a boolean flag indicating whether a section is visible (true) or not (false).
  • cache [boolean] - Whether or not to cache the rendered images.
  • start [number] - 98000'

• $session is a blessed hash containing information regarding the current user's session. It contains the following key->value pairs:
  • pid [number] - The process ID number of the session.
  • lockdir [string] - The directory path holding the lock information.
  • locktype [string] - The type of lock used.
  • lockobj [hash] - The [File::NFSLock http://search.cpan.org/~bbb/File-NFSLock-1.20/lib/File/NFSLock.pm] details of the session.
  • session [hash] - A hash containing the session data: