Provided by: libbio-perl-perl_1.6.901-2_all bug

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://redmine.open-bio.org/projects/bioperl/

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 implentation. 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 implentation. 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: Retrives 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

       Implemeting 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.