NAME

SYNOPSIS

 use base qw(Bio::MAGETAB::Util::Reader::Tabfile);

DESCRIPTION

ATTRIBUTES

uri

Required URI path to the file to be parsed.

eol_char

The end-of-line character to use while parsing. Typically this is set by the Reader subclasses.

filehandle

The filehandle for the file being parsed.

csv_parser

A Text::CSV_XS parser object.

builder

A Bio::MAGETAB::Util::Builder object, used by subclasses to track MAGE-TAB object creation.

METHODS

getline

A simple wrapper for the Text::CSV_XS "getline()" method which takes an optional filehandle argument, using the cached filehandle returned by "get_filehandle()" as the default. This filehandle argument can be useful when explicitly controlling the read position of the script within the file (e.g. as in ADF parsing).

can_ignore

When passed an arrayref of column values for a given line, returns 1 if the line is ignorable (typically blank or commented lines fall into this category) or undef if not.

strip_whitespace

This method strips any whitespace surrounding the string values passed to it in an arrayref.

confirm_full_parse

Raises an exception if the file has not been parsed to completion (i.e., EOF). Takes a line arrayref as returned by "$self->getline()" as an optional argument to allow testing for either (a) the existence of a next line in the file, or (b) EOF. This is useful when pausing parsing partway through a file, e.g. after parsing the ADF header section.

In addition, each attribute has accessor (get_*) and mutator (set_*) methods.

SEE ALSO

AUTHOR

LICENSE