reopen.rtmsBrukerMCFReader {rtms}

Manage an MCF reader file connection

Description

Closes the open connection to the main data file in a Bruker MCF reader object.

Usage

## S3 method for class 'rtmsBrukerMCFReader'
reopen(x, ...)

## S3 method for class 'rtmsBrukerMCFReader'
close(con, ...)

closeBrukerMCFReader(reader)

reopenBrukerMCFReader(reader)

Arguments

x

The reader object to reopen

...

Included for S3 compatibility

con

The reader object to be closed

reader

An RTMS reader object of class rtmsBrukerMCFReader

Details

Because Bruker MCF directories contain a potentially large number of spectra, reopening a connection to the main data file when reading many spectra or samples from it is inefficient and slow, especially if the file is being accessed over a network connection. The rtmsBrukerMCFReader object therefore maintains an open connection to the main binary data file until it is closed by the user. Of course, the reader object still maintains all the index and calibration data, making it possible to reopen a connection to the MCF directory without all the preprocessing required when first opening. Unfortunately, taking advantage of this fact is a little tricky.

In most cases, R is a functional language, with limited side effects on R objects; so it is difficult to alter the state of reader object without returning it explicitly. However, one of the few cases where side-effects are quite important is R's management of open file connections, with functions like close. Thus, calling closeBrukerMCFReader (and the S3 function close which wraps it) will in fact close the connection, but will not return an altered copy of the reader object reflecting that it is closed. So if the user wishes to close a reader object with the possibility of reopening it, they must close the reader AND assign the returned reader object to the relevant name. This will store the fact the connection has been closed, and allow the reopen function to operate correctly.

Value

The same reader object with a closed connection

Functions

• reopen(rtmsBrukerMCFReader): The S3 method close for objects of class rtmsBrukerMCFReader; calls closeBrukerMCFReader

• close(rtmsBrukerMCFReader): The S3 method reopen for objects of class rtmsBrukerMCFReader; calls reopenBrukerMCFReader

• reopenBrukerMCFReader(): Reopens a file connection to the main binary data file in a Bruker MCF directgry so that data can be extracted