ZMap reads resource files to control various aspects of its configuration. Currently this only occurs at start up, but in the future will be dynamic and hopefully complete with an editor. The following is a description of the various files that ZMap reads and how configuration is specified in those files.
The format of the files follows a stanza based layout.
StanzaName { property = "value" numeric = 1.0 number = 32000 truth = true list = "one two three four" } NamedStanza { foreground_colour = "blue" background_colour = "white" }
The main configuration files are held in the .ZMap directory which must be a subdirectory of the users home directory. Within this directory are a series of files that control how zmap works.
This is the default directory, in which, ZMap searches for the configuration files. The user may change this by passing ZMap an alternate directory on the command line when starting ZMap using the --conf_dir option (command line options).
ZMap looks in the configuration directory for a file named ZMap. Without this file ZMap will exit.
Stanzas:
This file should be located in the the configuration directory and named according to the value of the stylesfile option in the source stanza of the main configuration file.
Stanzas:
Describes a data source to ZMap. Multiple source stanzas allowed.
Members:
The url where the data source is accessible. This follows usual url standards. Possible protocols are acedb, file and http. Username and passwords maybe specified for sources as with basic http authentication. e.g. acedb://username:password@host. Ports may also be appended to the hostname separated by a colon e.g. host:8080.
a boolean to specify whether the data source can supply dna.
a boolean to specify whether the data source can accept data to store.
a filename for the styles file
a list of types for ZMap to display. This acts as a filter and orders the columns.
Members:
a boolean to tell ZMap whether to display empty columns
A stop gap to specify alignments...
Describes a style type. Multiple Type stanzas allowed.
The name of the type
The colour ZMap should use for the outline of features with this type [black]
The colour ZMap should use for the background of features with this type [black]
The colour ZMap should use for the foreground of features with this type [white]
The width of the features.
boolean to tell ZMap to display reverse as well as forward stranded features
boolean to control strand ...
boolean to control frame ...
int to control the minimum magnification at which features of this type are visible
boolean to tell ZMap features with this type are bumpable.
boolean to tell ZMap to display the indels of alignments
boolean to control parsing of gap arrays (Currently forced true)