Bio::Coordinate::ResultI(3pm) User Contributed Perl Documentation Bio::Coordinate::ResultI(3pm)NAME
Bio::Coordinate::ResultI - Interface to identify coordinate mapper results
SYNOPSIS
# not to be used directly
DESCRIPTION
ResultI identifies Bio::LocationIs returned by Bio::Coordinate::MapperI implementing classes from other locations.
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 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
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
perl v5.14.2 2012-03-02 Bio::Coordinate::ResultI(3pm)
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Bio::Coordinate::Utils(3pm) User Contributed Perl Documentation Bio::Coordinate::Utils(3pm)NAME
Bio::Coordinate::Utils - Additional methods to create Bio::Coordinate objects
SYNOPSIS
use Bio::Coordinate::Utils;
# get a Bio::Align::AlignI compliant object, $aln, somehow
# it could be a Bio::SimpleAlign
$mapper = Bio::Coordinate::Utils->from_align($aln, 1);
# Build a set of mappers which will map, for each sequence,
# that sequence position in the alignment (exon position to alignment
# position)
my @mappers = Bio::Coordinate::Utils->from_seq_to_alignmentpos($aln);
DESCRIPTION
This class is a holder of methods that work on or create Bio::Coordinate::MapperI- compliant objects. . These methods are not part of the
Bio::Coordinate::MapperI interface and should in general not be essential to the primary function of sequence objects. If you are thinking
of adding essential functions, it might be better to create your own sequence class. See Bio::PrimarySeqI, Bio::PrimarySeq, and Bio::Seq
for more.
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
Jason Stajich jason at bioperl.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
from_align
Title : from_align
Usage : $mapper = Bio::Coordinate::Utils->from_align($aln, 1);
Function:
Create a mapper out of an alignment.
The mapper will return a value only when both ends of
the input range find a match.
Note: This implementation works only on pairwise alignments
and is not yet well tested!
Returns : A Bio::Coordinate::MapperI
Args : Bio::Align::AlignI object
Id for the reference sequence, optional
from_seq_to_alignmentpos
Title : from_seq_to_alignmentpos
Usage : $mapper = Bio::Coordinate::Utils->from_seq_to_alignmentpos($aln, 1);
Function:
Create a mapper out of an alignment.
The mapper will map the position of a sequence into that position
in the alignment.
Will work on alignments of >= 2 sequences
Returns : An array of Bio::Coordinate::MapperI
Args : Bio::Align::AlignI object
perl v5.14.2 2012-03-02 Bio::Coordinate::Utils(3pm)