Bio::Tools::HMMER::Domain(3pm) User Contributed Perl Documentation Bio::Tools::HMMER::Domain(3pm)NAME
Bio::Tools::HMMER::Domain - One particular domain hit from HMMER
SYNOPSIS
Read the Bio::Tools::HMMER::Results docs
DESCRIPTION
A particular domain score. We reuse the Homol SeqFeature system here, so this inherits off Homol SeqFeature. As this code originally came
from a separate project, there are some backward compatibility stuff provided to keep this working with old code.
Don't forget this inherits off Bio::SeqFeature, so all your usual nice start/end/score stuff is ready for use.
CONTACT
Ewan Birney, birney@ebi.ac.uk
CONTRIBUTORS
Jason Stajich, jason@bioperl.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
add_alignment_line
Title : add_alignment_line
Usage : $domain->add_alignment_line($line_from_hmmer_output);
Function: add an alignment line to this Domain object
Returns : Nothing
Args : scalar
Adds an alignment line, mainly for storing the HMMER alignments
as flat text which can be reguritated. You're right. This is *not
nice* and not the right way to do it. C'est la vie.
each_alignment_line
Title : each_alignment_line
Usage : foreach $line ( $domain->each_alignment_line )
Function: reguritates the alignment lines as they were fed in.
only useful realistically for printing.
Example :
Returns :
Args : None
get_nse
Title : get_nse
Usage : $domain->get_nse()
Function: Provides a seqname/start-end format, useful
for unique keys. nse stands for name-start-end
It is used a lot in Pfam
Example :
Returns : A string
Args : Optional separator 1 and separator 2 (default / and -)
hmmacc
Title : hmmacc
Usage : $domain->hmmacc($newacc)
Function: set get for HMM accession number. This is placed in the homol
feature of the HMM
Example :
Returns :
Args :
hmmname
Title : hmmname
Usage : $domain->hmmname($newname)
Function: set get for HMM accession number. This is placed in the homol
feature of the HMM
Example :
Returns :
Args :
bits
Title : bits
Usage :
Function: backward compatibility. Same as score
Example :
Returns :
Args :
evalue
Title : evalue
Usage :
Function: $domain->evalue($value);
Example :
Returns :
Args :
seqbits
Title : seqbits
Usage :
Function: $domain->seqbits($value);
Example :
Returns :
Args :
seq_range
Title : seq_range
Usage :
Function: Throws an exception to catch scripts which need to upgrade
Example :
Returns :
Args :
hmm_range
Title : hmm_range
Usage :
Function: Throws an exception to catch scripts which need to upgrade
Example :
Returns :
Args :
perl v5.14.2 2012-03-02 Bio::Tools::HMMER::Domain(3pm)
Check Out this Related Man Page
Bio::Matrix::Scoring(3pm) User Contributed Perl Documentation Bio::Matrix::Scoring(3pm)NAME
Bio::Matrix::Scoring - Object which can hold scoring matrix information
SYNOPSIS
use Bio::Matrix::Scoring;
DESCRIPTION
An object which can handle AA or NT scoring matrix information. Some transformation properties are available too.
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 list. 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 of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::Matrix::Scoring->new();
Function: Builds a new Bio::Matrix::Scoring object
Returns : an instance of Bio::Matrix::Scoring
Args :
entropy
Title : entropy
Usage : $obj->entropy($newval)
Function:
Example :
Returns : value of entropy (a scalar)
Args : on set, new value (a scalar or undef, optional)
expected_score
Title : expected_score
Usage : $obj->expected_score($newval)
Function:
Example :
Returns : value of expected (a scalar)
Args : on set, new value (a scalar or undef, optional)
scale
Title : scale
Usage : $obj->scale($newval)
Function:
Example :
Returns : value of scale (a scalar)
Args : on set, new value (a scalar or undef, optional)
scale_value
Title : scale_value
Usage : $obj->scale_value($newval)
Function:
Example :
Returns : value of scale_value (a scalar)
Args : on set, new value (a scalar or undef, optional)
description
Title : description
Usage : $obj->description($newval)
Function:
Example :
Returns : value of description (a scalar)
Args : on set, new value (a scalar or undef, optional)
database
Title : database
Usage : $obj->database($newval)
Function:
Example :
Returns : value of database (a scalar)
Args : on set, new value (a scalar or undef, optional)
lowest_score
Title : lowest_score
Usage : $obj->lowest_score($newval)
Function:
Example :
Returns : value of lowest_score (a scalar)
Args : on set, new value (a scalar or undef, optional)
highest_score
Title : highest_score
Usage : $obj->highest_score($newval)
Function:
Example :
Returns : value of highest_score (a scalar)
Args : on set, new value (a scalar or undef, optional)
lambda
Title : lambda
Usage : $obj->lambda($newval)
Function:
Example :
Returns : value of lambda (a scalar)
Args : on set, new value (a scalar or undef, optional)
H
Title : H
Usage : $obj->H($newval)
Function:
Example :
Returns : value of H (a scalar)
Args : on set, new value (a scalar or undef, optional)
perl v5.14.2 2012-03-02 Bio::Matrix::Scoring(3pm)