Bio::Seq MetaI
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Summary
Bio::Seq::MetaI - Interface for sequence objects with residue-based
meta information
Package variables
No package variables defined.
Inherit
Bio::Root::RootI
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. 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.
Methods
metaDescriptionCode
meta_textDescriptionCode
named_metaDescriptionCode
named_meta_textDescriptionCode
submetaDescriptionCode
submeta_textDescriptionCode
named_submetaDescriptionCode
named_submeta_textDescriptionCode
meta_namesDescriptionCode
force_flushDescriptionCode
is_flushDescriptionCode
meta_lengthDescriptionCode
named_meta_lengthDescriptionCode
revcomDescriptionCode
truncDescriptionCode
Methods description
metacode    nextTop
 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
           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_textcodeprevnextTop
 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 meta.
 Returns : a string
 Args    : new value, optional
named_metacodeprevnextTop
 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 meta_names.
 Returns : a string
 Args    : scalar, name of the meta data set
           new value, optional
named_meta_textcodeprevnextTop
 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 meta.
 Returns : a string
 Args    : scalar, name of the meta data set
           new value, optional
submetacodeprevnextTop
 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 submeta_text.

 Returns : A reference to an array or a string
 Args    : integer, start position, optional
           integer, end position, optional
           new value, optional
submeta_textcodeprevnextTop
 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 meta.
 Returns : a string
 Args    : integer, start position, optional
           integer, end position, optional
           new value, optional
named_submetacodeprevnextTop
 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 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_textcodeprevnextTop
 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 meta.
 Returns : a string
 Args    : scalar, name of the meta data
 Args    : integer, start position, optional
           integer, end position, optional
           new value, optional
meta_namescodeprevnextTop
 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_flushcodeprevnextTop
 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_flushcodeprevnextTop
 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_lengthcodeprevnextTop
 Title   : meta_length()
 Usage   : $meeta_len  = $obj->meta_length();
 Function: return the number of elements in the meta set
 Returns : integer
 Args    : -
named_meta_lengthcodeprevnextTop
 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    : -
revcomcodeprevnextTop
 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
trunccodeprevnextTop
 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.
Methods code
metadescriptionprevnextTop
sub meta {
 shift->throw_not_implemented
}
meta_textdescriptionprevnextTop
sub meta_text {
 shift->throw_not_implemented
}
named_metadescriptionprevnextTop
sub named_meta {
 shift->throw_not_implemented
}
named_meta_textdescriptionprevnextTop
sub named_meta_text {
 shift->throw_not_implemented
}
submetadescriptionprevnextTop
sub submeta {
 shift->throw_not_implemented
}
submeta_textdescriptionprevnextTop
sub submeta_text {
 shift->throw_not_implemented
}
named_submetadescriptionprevnextTop
sub named_submeta {
 shift->throw_not_implemented
}
named_submeta_textdescriptionprevnextTop
sub named_submeta_text {
 shift->throw_not_implemented
}
meta_namesdescriptionprevnextTop
sub meta_names {
 shift->throw_not_implemented
}
force_flushdescriptionprevnextTop
sub force_flush {
 shift->throw_not_implemented
}
is_flushdescriptionprevnextTop
sub is_flush {
 shift->throw_not_implemented
}
meta_lengthdescriptionprevnextTop
sub meta_length {
 shift->throw_not_implemented
}
named_meta_lengthdescriptionprevnextTop
sub named_meta_length {
 shift->throw_not_implemented
}
revcomdescriptionprevnextTop
sub revcom {
 shift->throw_not_implemented
}
truncdescriptionprevnextTop
sub trunc {
 shift->throw_not_implemented
}
General documentation
SEE ALSOTop
Bio::Seq::Meta,
Bio::Seq::Meta::Array,
Bio::Seq::EncodedSeq,
Bio::Tools::OddCodes,
Bio::Seq::Quality
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 LehvaslaihoTop
Email heikki-at-bioperl-dot-org
CONTRIBUTORSTop
Chad Matsalla, bioinformatics@dieselwurks.com;
Aaron Mackey, amackey@virginia.edu;
Peter Schattner schattner@alum.mit.edu;
Richard Adams, Richard.Adams@ed.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Bio::PrimarySeqI methodsTop
Implemeting classes will need to rewrite these Bio::PrimaryI methods.