Create a new configuration object

Create a new configuration object to specify how the Gesel database should be queried. This can be used by applications to point to a different Gesel database from the default.

newConfig(
  fetch.gene = NULL,
  fetch.gene.args = list(),
  fetch.file = NULL,
  fetch.file.args = list(),
  fetch.range = NULL,
  fetch.range.args = list()
)

Arguments

fetch.gene

Function that accepts the name of the file in the Gesel gene descriptions and returns an absolute path to the file. If NULL, it defaults to downloadGeneFile.

fetch.gene.args

Named list of arguments to pass to fetch.gene.

fetch.file

Function that accepts the name of the file in the Gesel database and returns an absolute path to the file. If NULL, it defaults to downloadDatabaseFile.

fetch.file.args

Named list of arguments to pass to fetch.file.

fetch.range

Function that accepts three arguments - the name of the file in the Gesel database, an integer vector containing the starts of the byte ranges, and another vector containing the ends of the byte ranges (see downloadDatabaseRanges for details). It should return a character vector containing the contents of the specified byte ranges. If NULL, it defaults to downloadDatabaseRanges.

fetch.range.args

Named list of arguments to pass to fetch.range.

Value

A list containing Gesel configuration settings.

Details

The configuration list returned by newConfig can be passed to each gesel function to alter its behavior in a consistent manner. For example, we can override fetch.file to retrieve database files from a shared filesystem instead of performing a HTTP request.

The configuration list also contains a cache of data structures that can be populated by gesel functions. This avoids unnecessary fetch requests upon repeated calls to the same function. If the cache becomes stale or too large, it can be cleared by calling flushMemoryCache.

If no configuration list is supplied to gesel functions, the default configuration is used. The default is created by calling newConfig without any arguments.

Author

Aaron Lun

Examples

config <- newConfig()