Bio::Search::Hit HitI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Search::Hit::HitI - Interface for a hit in a similarity search result
Package variables
No package variables defined.
Included modules
Bio::Root::RootI
Inherit
Bio::Root::RootI
Synopsis
Bio::Search::Hit::HitI objects should not be instantiated since this
module defines a pure interface.
Given an object that implements the Bio::Search::Hit::HitI interface,
you can do the following things with it:
    $hit_name = $hit->name();

    $desc = $hit->description();

    $len = $hit->length

    $alg = $hit->algorithm();

    $score = $hit->raw_score();

    $significance = $hit->significance();

    while( $hsp = $obj->next_hsp()) { ... }

    while( $hsp = $obj->next_hsp()) { ... }
Description
    Bio::Search::Hit::* objects are data structures that contain information
about specific hits obtained during a library search.  Some information will
be algorithm-specific, but others will be generally defined.
Methods
nameDescriptionCode
descriptionDescriptionCode
accessionDescriptionCode
lengthDescriptionCode
algorithmDescriptionCode
raw_scoreDescriptionCode
significanceDescriptionCode
next_hspDescriptionCode
Methods description
namecode    nextTop
 Title   : name
 Usage   : $hit_name = $hit->name();
 Function: returns the name of the Hit sequence
 Returns : a scalar string
 Args    : none
descriptioncodeprevnextTop
 Title   : description
 Usage   : $desc = $hit->description();
 Function: Retrieve the description for the hit
 Returns : a scalar string
 Args    : none
accessioncodeprevnextTop
 Title   : accession
 Usage   : $acc = $hit->accession();
 Function: Retrieve the accession (if available) for the hit
 Returns : a scalar string (empty string if not set)
 Args    : none
lengthcodeprevnextTop
 Title   : length
 Usage   : my $len = $hit->length
 Function: Returns the length of the hit 
 Returns : integer
 Args    : none
algorithmcodeprevnextTop
 Title   : algorithm
 Usage   : $alg = $hit->algorithm();
 Function: Gets the algorithm specification that was used to obtain the hit
           For BLAST, the algorithm denotes what type of sequence was aligned 
           against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated 
           dna-prt, TBLASTN prt-translated dna, TBLASTX translated 
           dna-translated dna).
 Returns : a scalar string 
 Args    : none
raw_scorecodeprevnextTop
 Title   : raw_score
 Usage   : $score = $hit->raw_score();
 Function: Gets the "raw score" generated by the algorithm.  What
           this score is exactly will vary from algorithm to algorithm,
           returning undef if unavailable.
 Returns : a scalar value
 Args    : none
significancecodeprevnextTop
 Title   : significance
 Usage   : $significance = $hit->significance();
 Function: Used to obtain the E or P value of a hit, i.e. the probability that
           this particular hit was obtained purely by random chance.  If
           information is not available (nor calculatable from other
           information sources), return undef.
 Returns : a scalar value or undef if unavailable
 Args    : none
next_hspcodeprevnextTop
 Title    : next_hsp
 Usage    : while( $hsp = $obj->next_hsp()) { ... }
 Function : Returns the next available High Scoring Pair
 Example  : 
 Returns  : Bio::Search::HSP::HSPI object or null if finished
 Args     : none
Methods code
namedescriptionprevnextTop
sub name {
    my ($self,@args) = @_;
    $self->throw_not_implemented;
}
descriptiondescriptionprevnextTop
sub description {
    my ($self,@args) = @_;
    $self->throw_not_implemented;
}
accessiondescriptionprevnextTop
sub accession {
    my ($self,@args) = @_;
    $self->throw_not_implemented;
}
lengthdescriptionprevnextTop
sub length {
   my ($self,@args) = @_;
   $self->throw_not_implemented;
}
algorithmdescriptionprevnextTop
sub algorithm {
    my ($self,@args) = @_;
    $self->throw_not_implemented;
}
raw_scoredescriptionprevnextTop
sub raw_score {
    my ($self,@args) = @_;
    $self->throw_not_implemented;
}
significancedescriptionprevnextTop
sub significance {
    my ($self,@args) = @_;
    $self->throw_not_implemented;
}
next_hspdescriptionprevnextTop
sub next_hsp {
    my ($self,@args) = @_;
    $self->throw_not_implemented;
}
General documentation
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://bio.perl.org/MailList.html - About the mailing lists
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 email
or the web:
  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/
AUTHOR - Aaron Mackey, Steve ChervitzTop
Email amackey@virginia.edu (original author)
Email sac@bioperl.org
COPYRIGHTTop
Copyright (c) 1999-2001 Aaron Mackey, Steve Chervitz. 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 _