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Component Configuration Sections

Pregap4 Components may each contain their own configuration section. Where several components are mutually exclusive, such as components describing naming conventions, it makes sense to give each component the same configuration section. This will ensure that loading a new component will overwrite the old one. At present the only defined components both create a [naming_scheme] section.

Components may redefine items which could appear in other configuration sections. In this case the last definition of that setting will take priority. For instance if a component defines the TN_com procedure and this is also defined in the [global_variables] section then the component will only take priority if it is after the global section in the configuration file.

Components may also be used to define parameters for modules. Once again the components need to be listed after the module definitions being overridden. To define module components in this way, use the module command. An example follows.

module tag_repeats {set repeat_file repeats.list}

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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap4_44.html