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Bio::Seq::MetaI(3)    User Contributed Perl Documentation   Bio::Seq::MetaI(3)

NAME
       Bio::Seq::MetaI - Interface for sequence	objects	with residue-based
       meta information

SYNOPSIS
	 # get a Bio::Seq::MetaI compliant object somehow

	 # to test this	is a meta seq object
	 $obj->isa("Bio::Seq::MetaI")
	    || $obj->throw("$obj not a Bio::Seq::MetaI");

	 # accessors
	 $string     = $obj->meta;
	 $string     = $obj->meta_text;
	 $substring  = $obj->submeta(12,50);
	 $unique_key = $obj->accession_number();

DESCRIPTION
       This class defines an abstract interface	for basic residue-based	meta
       information. Examples of	this kind of meta data are secondary
       structures (RNA and protein), protein hydrophobicity assignments, or
       other alternative alphabets for polypeptides, sequence quality data and
       nucleotide alignments with translations.

       The length of the meta data sequence is not dependent on	the amount of
       the meta	information. The meta information always covers	all the
       residues, but a blank value is used to denote unavailable information.
       If necessary the	implementation quietly truncates or extends meta
       information with	blank values. Definition of blank is implementation
       dependent. Gaps in MSAs should not have meta information.

       At this point a residue in a sequence object can	have only one meta
       value. If you need more,	use multiple copies of the sequence object.

       Meta data storage can be	implemented in various ways, e.g: string,
       array of	scalars, array of hashes, array	of objects.

       If the implementation so	chooses, there can be more then	one meta
       values associated to each residue. See named_meta and names_submeta.
       Note that use of	arbitrary names	is very	prone to typos leading to
       creation	of additional copies of	meta data sets.

       Bio::Seq::Meta provides basic, pure perl	implementation of sequences
       with meta information. See Bio::Seq::Meta. Application specific
       implementations will override and add to	these methods.

   Method naming
       Character based meta data is read and set by method meta() and its
       variants. These are the suffixes	and prefixes used in the variants:

	   [named_] [sub] meta [_text]

       _text
	  Suffix _text guaranties that output is a string. Note	that it	does
	  not limit the	input.

       sub
	  Prefix sub, like in subseq(),	means that the method applies to sub
	  region of the	sequence range and takes start and end as arguments.
	  Unlike subseq(), these methods are able to set values.  If the range
	  is not defined, it defaults to the complete sequence.

       named_
	  Prefix named_	in method names	allows the used	to attach multiple
	  meta strings to one sequence by explicitly naming them. The name is
	  always the first argument to the method. The "unnamed" methods use
	  the class wide default name for the meta data	and are	thus special
	  cases	"named"	methods.

	  Note that internally names are keys in a hash	and any	misspelling of
	  a name will silently store the data under a wrong name. The used
	  names	(keys) can be retrieved	using method meta_names(). See
	  meta_names.

SEE ALSO
       Bio::Seq::Meta, Bio::Seq::Meta::Array, Bio::Seq::EncodedSeq,
       Bio::Tools::OddCodes, Bio::Seq::Quality

FEEDBACK
   Mailing Lists
       User feedback is	an integral part of the	evolution of this and other
       Bioperl modules.	Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About	the mailing lists

   Support
       Please direct usage questions or	support	issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and
       reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the	problem	with code and
       data examples if	at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track
       the bugs	and their resolution.  Bug reports can be submitted via	the
       web:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR - Heikki	Lehvaslaiho
       Email heikki-at-bioperl-dot-org

CONTRIBUTORS
       Chad Matsalla, bioinformatics@dieselwurks.com; Aaron Mackey,
       amackey@virginia.edu; Peter Schattner schattner@alum.mit.edu; Richard
       Adams, Richard.Adams@ed.ac.uk

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   meta
	Title	: meta
	Usage	: $meta_values	= $obj->meta($values_string);
	Function:

		  Get and set method for the unnamed meta data starting	from
		  residue position one.	Since it is dependent on the length
		  of the sequence, it needs to be manipulated after the
		  sequence.

		  The implementation may choose	to accept argument values in
		  a string or in an array (reference) or in a hash
		  (reference).

		  The return value may be a string or an array reference,
		  depending on the implementation. If in doubt,	use meta_text()
		  which	is a variant guarantied	to return a string.  See
		  L<meta_text>.

		  The length of	the returned value always matches the length
		  of the sequence.

	Returns	: A reference to an array or a string
	Args	: new value, optional

   meta_text
	Title	: meta_text()
	Usage	: $meta_values	= $obj->meta_text($values_arrayref);
	Function: Variant of meta() guarantied to return a textual
		  representation of the	meta data. For details,	see L<meta>.
	Returns	: a string
	Args	: new value, optional

   named_meta
	Title	: named_meta()
	Usage	: $meta_values	= $obj->named_meta($name, $values_arrayref);
	Function: A more general version of meta(). Each meta data set needs
		  to be	named. See also	L<meta_names>.
	Returns	: a string
	Args	: scalar, name of the meta data	set
		  new value, optional

   named_meta_text
	Title	: named_meta_text()
	Usage	: $meta_values	= $obj->named_meta_text($name, $values_arrayref);
	Function: Variant of named_meta() guarantied to	return a textual
		  representation  of the named meta data.
		  For details, see L<meta>.
	Returns	: a string
	Args	: scalar, name of the meta data	set
		  new value, optional

   submeta
	Title	: submeta
	Usage	: $subset_of_meta_values = $obj->submeta(10, 20, $value_string);
		  $subset_of_meta_values = $obj->submeta(10, undef, $value_string);
	Function:

		  Get and set method for meta data for subsequences.

		  Numbering starts from	1 and the number is inclusive, ie 1-2
		  are the first	two residue of the sequence. Start cannot be
		  larger than end but can be equal.

		  If the second	argument is missing the	returned values
		  should extend	to the end of the sequence.

		  If implementation tries to set values	beyond the current
		  sequence, they should	be ignored.

		  The return value may be a string or an array reference,
		  depending on the implementation. If in doubt,	use
		  submeta_text() which is a variant guarantied to return a
		  string.  See L<submeta_text>.

	Returns	: A reference to an array or a string
	Args	: integer, start position, optional
		  integer, end position, optional
		  new value, optional

   submeta_text
	Title	: submeta_text
	Usage	: $meta_values	= $obj->submeta_text(20, $value_string);
	Function: Variant of submeta() guarantied to return a textual
		  representation  of meta data.	For details, see L<meta>.
	Returns	: a string
	Args	: integer, start position, optional
		  integer, end position, optional
		  new value, optional

   named_submeta
	Title	: named_submeta
	Usage	: $subset_of_meta_values = $obj->named_submeta($name, 10, 20, $value_string);
		  $subset_of_meta_values = $obj->named_submeta($name, 10);
	Function: Variant of submeta() guarantied to return a textual
		  representation  of meta data.	For details, see L<meta>.
	Returns	: A reference to an array or a string
	Args	: scalar, name of the meta data	set
		  integer, start position
		  integer, end position, optional when a third argument	present
		  new value, optional

   named_submeta_text
	Title	: named_submeta_text
	Usage	: $meta_values	= $obj->named_submeta_text($name, 20, $value_string);
	Function: Variant of submeta() guarantied to return a textual
		  representation  of meta data.	For details, see L<meta>.
	Returns	: a string
	Args	: scalar, name of the meta data
	Args	: integer, start position, optional
		  integer, end position, optional
		  new value, optional

   meta_names
	Title	: meta_names
	Usage	: @meta_names  = $obj->meta_names()
	Function: Retrieves an array of	meta data set names. The default (unnamed)
		  set name is guarantied to be the first name.
	Returns	: an array of names
	Args	: none

   force_flush
	Title	: force_flush()
	Usage	: $force_flush = $obj->force_flush(1);
	Function: Automatically	pad with empty values or truncate meta values to
		   sequence length
	Returns	: boolean 1 or 0
	Args	: optional boolean value

   is_flush
	Title	: is_flush
	Usage	: $is_flush  = $obj->is_flush()
		  or  $is_flush	= $obj->is_flush($my_meta_name)
	Function: Boolean to tell if all meta values are in
		  flush	with the sequence length.
		  Returns true if force_flush()	is set
		  Set verbosity	to a positive value to see failed meta sets
	Returns	: boolean 1 or 0
	Args	: optional name	of the meta set

   meta_length
	Title	: meta_length()
	Usage	: $meeta_len  =	$obj->meta_length();
	Function: return the number of elements	in the meta set
	Returns	: integer
	Args	: -

   named_meta_length
	Title	: named_meta_length()
	Usage	: $meeta_len  =	$obj->named_meta_length($name);
	Function: return the number of elements	in the named meta set
	Returns	: integer
	Args	: -

Bio::PrimarySeqI methods
       Implementing classes will need to rewrite these Bio::PrimaryI methods.

   revcom
	Title	: revcom
	Usage	: $newseq = $seq->revcom();
	Function: Produces a new Bio::Seq::MetaI implementing object where
		  the order of residues	and their meta information is reversed.
	Returns	: A new	(fresh)	Bio::Seq::MetaI	object
	Args	: none

   trunc
	Title	: trunc
	Usage	: $subseq = $myseq->trunc(10,100);
	Function: Provides a truncation	of a sequence
	Returns	: a fresh Bio::Seq::MetaI implementing object
	Args	: Two integers denoting	first and last residue of the sub-sequence.

perl v5.32.0			  2019-12-07		    Bio::Seq::MetaI(3)

NAME | SYNOPSIS | DESCRIPTION | SEE ALSO | FEEDBACK | AUTHOR - Heikki Lehvaslaiho | CONTRIBUTORS | APPENDIX | Bio::PrimarySeqI methods

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