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Bio::MAGETAB::Util::ReUser:Contributed PBio::MAGETAB::Util::Reader::Tabfile(3)

NAME
       Bio::MAGETAB::Util::Reader::Tabfile - An	abstract class providing
       methods for handling tab-delimited files.

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

DESCRIPTION
       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.

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
       Bio::MAGETAB::Util::Reader Bio::MAGETAB::Util::Reader::TagValueFile

AUTHOR
       Tim F. Rayner <tfrayner@gmail.com>

LICENSE
       This library is released	under version 2	of the GNU General Public
       License (GPL).

perl v5.24.1			  2013-0Bio::MAGETAB::Util::Reader::Tabfile(3)

NAME | SYNOPSIS | DESCRIPTION | ATTRIBUTES | METHODS | SEE ALSO | AUTHOR | LICENSE

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