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.\" ========================================================================
.\"
.IX Title "Bio::DB::ReferenceI 3pm"
.TH Bio::DB::ReferenceI 3pm "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::DB::ReferenceI \- A RandomAccessI\-like abstract interface for
retrieving Reference data from a sequence database and returning
Bio::Annotation::Reference objects
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\&  #
\&  # get a database object somehow using a concrete class
\&  #
\&
\&  $ref = $db\->get_Reference_by_id(\*(Aq123456\*(Aq);
\&
\&  #
\&  # $ref is a Bio::Annotation::Reference object
\&  #
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a pure interface class \- in other words, all this does is define
methods which other (concrete) classes will actually implement.
.PP
The Bio::DB::ReferenceI class defines methods used to retrieve reference data
from a sequence.  This is returned in the form of Bio::Annotation::Reference
objects.
.PP
At the moment it is just the ability to make Bio::Annotation::Reference
objects from a name or unique id (id), an accession number (acc), and so on.
.SH "CONTACT"
.IX Header "CONTACT"
Ewan Birney originally wrote Bio::DB::RandomAccessI, from which this class
is based.
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@lists.open\-bio.org               \- General discussion
\&  http://bioperl.org/Support.html  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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.
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Email cjfields at bioperl dot org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _
.SS "get_Reference_by_id"
.IX Subsection "get_Reference_by_id"
.Vb 5
\& Title   : get_Reference_by_id
\& Usage   : $ref = $db\->get_Reference_by_id(\*(Aq123456\*(Aq)
\& Function: Gets a Bio::Annotation::Reference\-implementing object by its name (id)
\& Returns : a Bio::Annotation::Reference object or undef if not found
\& Args    : the id (as a string) of a sequence
.Ve
.SS "get_Reference_by_acc"
.IX Subsection "get_Reference_by_acc"
.Vb 8
\& Title   : get_Reference_by_acc
\& Usage   : $ref = $db\->get_Reference_by_acc(\*(AqX77802\*(Aq);
\& Function: Gets a Bio::Annotation::Reference object by accession number
\& Returns : A Bio::Annotation::Reference object or undef if not found
\& Args    : accession number (as a string)
\& Throws  : "more than one sequences correspond to this accession"
\&            if the accession maps to multiple primary ids and
\&            method is called in a scalar context
.Ve
.SS "get_Reference_by_version"
.IX Subsection "get_Reference_by_version"
.Vb 6
\& Title   : get_Reference_by_version
\& Usage   : $ref = $db\->get_Reference_by_version(\*(AqX77802.1\*(Aq);
\& Function: Gets a Bio::Annotation::Reference object by sequence version
\& Returns : A Bio::Annotation::Reference object
\& Args    : accession.version (as a string)
\& Throws  : "acc.version does not exist" exception
.Ve