ZMap Config File Example

NB: this documentation may be quite old and need updating


# -----------------------------------------------------------------------------
#           ZMap config file format for views.
#
#



# -----------------------------------------------------------------------------
# "ZMap" stanza:
#   Specifies general properties.
#
[ZMap]

# replaced by views keyword and 'mapping' in the view stanza
# default_sequence = b0250

default_printer = n318bw


# names of view stanzas.
views = b0250

# new keyword, display listed views, single means all in one window,
# multiple means all in their own windows, default is multiple.
view_windows = < single | multiple >



# -----------------------------------------------------------------------------
# "View" stanza:
#   Specifies properties for fetching a feature context to display to the
# the user.
#
# Currently we support one of these but in the future there can be multiple
# views, all of which get displayed. Each view stanza must have a unique name
# and it must in turn name the source stanzas which will specify servers
# to fetch the view data.
#
[b0250]

# List of featuresets to be displayed, the order is the column order on the screen,
# reverse strand is displayed in reverse order.
featuresets_display_order = GeneFinderFeatures ; eds_column ; 3 Frame ; 3 Frame Translation ; and many more...


# features to be displayed in the navigator window.
navigator_sets = Locus ; scale ; genomic_canonical

# The _default_ mapping for the view (in the end this should specify blocks etc....)
mapping = 

# list specifying all sources for this view.
sources = b0250_acedb_server



# -----------------------------------------------------------------------------
# source stanzas specify the servers that fetch the data for sequence
# display. Each stanza must have a unique name.
#
[b0250_acedb_server]

url = acedb://any:any@cbi4c:20000

# list of feature sets for this source
# (optional, default list is featuresets_display_order from parent view stanza)
featuresets = GeneFinderFeatures ; eds_column ; pseudogene ; curated

# fetch styles ? (optional, default is true)
styles = false

# mapping for this source only (optional, default taken from parent view stanza)
mapping = 

# fetch sequence for mapping from this source (optional, default is true)
sequence = false