Bio::Search::HSP HSPI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Search::HSP::HSPI - Interface for a High Scoring Pair in a similarity search result
Package variables
No package variables defined.
Included modules
Bio::Root::RootI
Bio::SeqFeature::SimilarityPair
Carp
Inherit
Bio::Root::RootI Bio::SeqFeature::SimilarityPair
Synopsis
    $r_type = $hsp->algorithm

    $pvalue = $hsp->p();

    $evalue = $hsp->evalue();

    $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] );

    $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] );

    $gaps = $hsp->gaps( ['query'|'hit'|'total'] );

    $qseq = $hsp->query_string;

    $hseq = $hsp->hit_string;

    $homo_string = $hsp->homology_string;

    $len = $hsp->length( ['query'|'hit'|'total'] );
Description
Bio::Search::HSP::HSPI objects cannot be instantiated since this
module defines a pure interface.
Given an object that implements the Bio::Search::HSP::HSPI interface,
you can do the following things with it:
Methods
algorithmDescriptionCode
pvalueDescriptionCode
evalueDescriptionCode
frac_identicalDescriptionCode
frac_conservedDescriptionCode
gapsDescriptionCode
query_stringDescriptionCode
hit_stringDescriptionCode
homology_stringDescriptionCode
lengthDescriptionCode
percent_identityDescriptionCode
get_alnDescriptionCode
Methods description
algorithmcode    nextTop
 Title   : algorithm
 Usage   : my $r_type = $hsp->algorithm
 Function: Obtain the name of the algorithm used to obtain the HSP
 Returns : string (e.g., BLASTP)
 Args    : none
pvaluecodeprevnextTop
 Title   : pvalue
 Usage   : my $pvalue = $hsp->pvalue();
 Function: Returns the P-value for this HSP or undef 
 Returns : float or exponential (2e-10)
           P-value is not defined with NCBI Blast2 reports.
 Args    : none
evaluecodeprevnextTop
 Title   : evalue
 Usage   : my $evalue = $hsp->evalue();
 Function: Returns the e-value for this HSP
 Returns : float or exponential (2e-10)
 Args    : none
frac_identicalcodeprevnextTop
 Title   : frac_identical
 Usage   : my $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] );
 Function: Returns the fraction of identitical positions for this HSP 
 Returns : Float in range 0.0 -> 1.0
 Args    : 'query' = num identical / length of query seq (without gaps)
           'hit'   = num identical / length of hit seq (without gaps)
           'total' = num identical / length of alignment (with gaps)
           default = 'total'
frac_conservedcodeprevnextTop
 Title    : frac_conserved
 Usage    : my $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] );
 Function : Returns the fraction of conserved positions for this HSP.
            This is the fraction of symbols in the alignment with a 
            positive score.
 Returns : Float in range 0.0 -> 1.0
 Args    : 'query' = num conserved / length of query seq (without gaps)
           'hit'   = num conserved / length of hit seq (without gaps)
           'total' = num conserved / length of alignment (with gaps)
           default = 'total'
gapscodeprevnextTop
 Title    : gaps
 Usage    : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
 Function : Get the number of gaps in the query, hit, or total alignment.
 Returns  : Integer, number of gaps or 0 if none
 Args     : 'query' = num conserved / length of query seq (without gaps)
            'hit'   = num conserved / length of hit seq (without gaps)
            'total' = num conserved / length of alignment (with gaps)
            default = 'total'
query_stringcodeprevnextTop
 Title   : query_string
 Usage   : my $qseq = $hsp->query_string;
 Function: Retrieves the query sequence of this HSP as a string
 Returns : string
 Args    : none
hit_stringcodeprevnextTop
 Title   : hit_string
 Usage   : my $hseq = $hsp->hit_string;
 Function: Retrieves the hit sequence of this HSP as a string
 Returns : string
 Args    : none
homology_stringcodeprevnextTop
 Title   : homology_string
 Usage   : my $homo_string = $hsp->homology_string;
 Function: Retrieves the homology sequence for this HSP as a string.
         : The homology sequence is the string of symbols in between the 
         : query and hit sequences in the alignment indicating the degree
         : of conservation (e.g., identical, similar, not similar).
 Returns : string
 Args    : none
lengthcodeprevnextTop
 Title    : length
 Usage    : my $len = $hsp->length( ['query'|'hit'|'total'] );
 Function : Returns the length of the query or hit in the alignment (without gaps) 
            or the aggregate length of the HSP (including gaps;
            this may be greater than either hit or query )
 Returns  : integer
 Args     : 'query' = length of query seq (without gaps)
            'hit'   = length of hit seq (without gaps)
            'total' = length of alignment (with gaps)
            default = 'total' 
 Args    : none
percent_identitycodeprevnextTop
 Title   : percent_identity
 Usage   : my $percentid = $hsp->percent_identity()
 Function: Returns the calculated percent identity for an HSP
 Returns : floating point between 0 and 100 
 Args    : none
get_alncodeprevnextTop
 Title   : get_aln
 Usage   : my $aln = $hsp->gel_aln
 Function: Returns a Bio::SimpleAlign representing the HSP alignment
 Returns : Bio::SimpleAlign
 Args    : none
Methods code
algorithmdescriptionprevnextTop
sub algorithm {
   my ($self,@args) = @_;
   $self->throw_not_implemented;
}
pvaluedescriptionprevnextTop
sub pvalue {
   my ($self) = @_;
   $self->throw_not_implemented;
}
evaluedescriptionprevnextTop
sub evalue {
   my ($self) = @_;
   $self->throw_not_implemented;
}
frac_identicaldescriptionprevnextTop
sub frac_identical {
   my ($self, $type) = @_;
   $self->throw_not_implemented;
}
frac_conserveddescriptionprevnextTop
sub frac_conserved {
    my ($self, $type) = @_;
    $self->throw_not_implemented;
}
gapsdescriptionprevnextTop
sub gaps {
    my ($self, $type) = @_;
    $self->throw_not_implemented;
}
query_stringdescriptionprevnextTop
sub query_string {
   my ($self) = @_;
   $self->throw_not_implemented;
}
hit_stringdescriptionprevnextTop
sub hit_string {
   my ($self) = @_;
   $self->throw_not_implemented;
}
homology_stringdescriptionprevnextTop
sub homology_string {
   my ($self) = @_;
   $self->throw_not_implemented;
}
lengthdescriptionprevnextTop
sub length {
   my ($self, $type) = @_;
   $self->throw_not_implemented;
}
percent_identitydescriptionprevnextTop
sub percent_identity {
   my ($self) = @_;
   return $self->frac_identical('hsp') * 100;
}
get_alndescriptionprevnextTop
sub get_aln {
   my ($self) = @_;
   $self->throw_not_implemented;
}
General documentation
SEE ALSOTop
This interface inherits methods from these other modules:
Bio::SeqFeatureI,
Bio::SeqFeature::FeaturePair
Bio::SeqFeature::SimilarityPair
Please refer to these modules for documentation of the
many additional inherited methods.
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
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists
Reporting BugsTop
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
email or the web:
  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/
AUTHOR - Steve Chervitz, Jason StajichTop
Email sac@bioperl.org
Email jason@bioperl.org
COPYRIGHTTop
Copyright (c) 2001 Steve Chervitz, Jason Stajich. All Rights Reserved.
DISCLAIMERTop
This software is provided "as is" without warranty of any kind.
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Inherited from Bio::SeqFeature::SimilarityPairTop
These methods come from Bio::SeqFeature::SimilarityPair
queryTop
 Title   : query
 Usage   : my $query = $hsp->query
 Function: Returns a SeqFeature representing the query in the HSP
 Returns : Bio::SeqFeature::Similarity
 Args    : [optional] new value to set
hitTop
 Title   : hit
 Usage   : my $hit = $hsp->hit
 Function: Returns a SeqFeature representing the hit in the HSP
 Returns : Bio::SeqFeature::Similarity
 Args    : [optional] new value to set
significanceTop
 Title   : significance
 Usage   : $evalue = $obj->significance();
           $obj->significance($evalue);
 Function: 
 Returns : 
 Args    :
scoreTop
 Title   : score
 Usage   : my $score = $hsp->score();
 Function: Returns the score for this HSP or undef 
 Returns : numeric           
 Args    : [optional] numeric to set value
bitsTop
 Title   : bits
 Usage   : my $bits = $hsp->bits();
 Function: Returns the bit value for this HSP or undef 
 Returns : numeric
 Args    : none