Bio::MAGETAB::Util::Reader::Tabfile - An abstract class providing methods for handling tab-delimited files.
use base qw(Bio::MAGETAB::Util::Reader::Tabfile);
This abstract class acts as a wrapper for the Text::CSV_XS module and line ending detection code used by the rest of the Bio::MAGETAB::Util::Reader modules. It is not designed to be used directly.
Required URI path to the file to be parsed.
The end-of-line character to use while parsing. Typically this is set by the Reader subclasses.
The filehandle for the file being parsed.
A Text::CSV_XS parser object.
A Bio::MAGETAB::Util::Builder object, used by subclasses to track MAGE-TAB object creation.
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).
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.
This method strips any whitespace surrounding the string values passed to it in an arrayref.
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.
the Bio::MAGETAB::Util::Reader manpage the Bio::MAGETAB::Util::Reader::TagValueFile manpage
Tim F. Rayner <tfrayner@gmail.com>
This library is released under version 2 of the GNU General Public License (GPL).