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.\" ========================================================================
.\"
.IX Title "Bio::Search::HSP::HMMERHSP 3pm"
.TH Bio::Search::HSP::HMMERHSP 3pm "2019-10-29" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Search::HSP::HMMERHSP \- A HSP object for HMMER results
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&    use Bio::Search::HSP::HMMERHSP;
\&    # use it just like a Bio::Search::HSP::GenericHSP object
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object is a specialization of Bio::Search::HSP::GenericHSP.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.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
the Bioperl mailing list.  Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- 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
of 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 \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason\-at\-bioperl.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 "new"
.IX Subsection "new"
.Vb 5
\& Title   : new
\& Usage   : my $obj = Bio::Search::HSP::HMMERHSP\->new();
\& Function: Builds a new Bio::Search::HSP::HMMERHSP object
\& Returns : Bio::Search::HSP::HMMERHSP
\& Args    :
.Ve
.PP
Plus Bio::Search::HSP::GenericHSP methods
.PP
.Vb 10
\&    \-algorithm    => algorithm used (BLASTP, TBLASTX, FASTX, etc)
\&    \-evalue       => evalue
\&    \-pvalue       => pvalue
\&    \-bits         => bit value for HSP
\&    \-score        => score value for HSP (typically z\-score but depends on
\&                                                   analysis)
\&    \-hsp_length   => Length of the HSP (including gaps)
\&    \-identical    => # of residues that that matched identically
\&    \-conserved    => # of residues that matched conservatively
\&                     (only protein comparisons \-
\&                     conserved == identical in nucleotide comparisons)
\&    \-hsp_gaps     => # of gaps in the HSP
\&    \-query_gaps   => # of gaps in the query in the alignment
\&    \-hit_gaps     => # of gaps in the subject in the alignment
\&    \-query_name   => HSP Query sequence name (if available)
\&    \-query_start  => HSP Query start (in original query sequence coords)
\&    \-query_end    => HSP Query end (in original query sequence coords)
\&    \-hit_name     => HSP Hit sequence name (if available)
\&    \-hit_start    => HSP Hit start (in original hit sequence coords)
\&    \-hit_end      => HSP Hit end (in original hit sequence coords)
\&    \-hit_length   => total length of the hit sequence
\&    \-query_length => total length of the query sequence
\&    \-query_seq    => query sequence portion of the HSP
\&    \-hit_seq      => hit sequence portion of the HSP
\&    \-homology_seq => homology sequence for the HSP
\&    \-hit_frame    => hit frame (only if hit is translated protein)
\&    \-query_frame  => query frame (only if query is translated protein)
.Ve
.SS "Bio::Search::HSP::HSPI methods"
.IX Subsection "Bio::Search::HSP::HSPI methods"
Implementation of Bio::Search::HSP::HSPI methods follow
.SS "algorithm"
.IX Subsection "algorithm"
.Vb 5
\& 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    : [optional] scalar string to set value
.Ve
.SS "pvalue"
.IX Subsection "pvalue"
.Vb 6
\& 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    : [optional] numeric to set value
.Ve
.SS "evalue"
.IX Subsection "evalue"
.Vb 5
\& Title   : evalue
\& Usage   : my $evalue = $hsp\->evalue();
\& Function: Returns the e\-value for this HSP
\& Returns : float or exponential (2e\-10)
\& Args    : [optional] numeric to set value
.Ve
.SS "frac_identical"
.IX Subsection "frac_identical"
.Vb 9
\& Title   : frac_identical
\& Usage   : my $frac_id = $hsp\->frac_identical( [\*(Aqquery\*(Aq|\*(Aqhit\*(Aq|\*(Aqtotal\*(Aq] );
\& Function: Returns the fraction of identitical positions for this HSP
\& Returns : Float in range 0.0 \-> 1.0
\& Args    : arg 1:  \*(Aqquery\*(Aq = num identical / length of query seq (without gaps)
\&                   \*(Aqhit\*(Aq   = num identical / length of hit seq (without gaps)
\&                   \*(Aqtotal\*(Aq = num identical / length of alignment (with gaps)
\&                   default = \*(Aqtotal\*(Aq
\&           arg 2: [optional] frac identical value to set for the type requested
.Ve
.SS "frac_conserved"
.IX Subsection "frac_conserved"
.Vb 11
\& Title    : frac_conserved
\& Usage    : my $frac_cons = $hsp\->frac_conserved( [\*(Aqquery\*(Aq|\*(Aqhit\*(Aq|\*(Aqtotal\*(Aq] );
\& 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    : arg 1: \*(Aqquery\*(Aq = num conserved / length of query seq (without gaps)
\&                  \*(Aqhit\*(Aq   = num conserved / length of hit seq (without gaps)
\&                  \*(Aqtotal\*(Aq = num conserved / length of alignment (with gaps)
\&                  default = \*(Aqtotal\*(Aq
\&           arg 2: [optional] frac conserved value to set for the type requested
.Ve
.SS "gaps"
.IX Subsection "gaps"
.Vb 9
\& Title    : gaps
\& Usage    : my $gaps = $hsp\->gaps( [\*(Aqquery\*(Aq|\*(Aqhit\*(Aq|\*(Aqtotal\*(Aq] );
\& Function : Get the number of gaps in the query, hit, or total alignment.
\& Returns  : Integer, number of gaps or 0 if none
\& Args     : arg 1: \*(Aqquery\*(Aq = num gaps in query seq
\&                   \*(Aqhit\*(Aq   = num gaps in hit seq
\&                   \*(Aqtotal\*(Aq = num gaps in whole alignment
\&                   default = \*(Aqtotal\*(Aq
\&            arg 2: [optional] integer gap value to set for the type requested
.Ve
.SS "query_string"
.IX Subsection "query_string"
.Vb 5
\& Title   : query_string
\& Usage   : my $qseq = $hsp\->query_string;
\& Function: Retrieves the query sequence of this HSP as a string
\& Returns : string
\& Args    : [optional] string to set for query sequence
.Ve
.SS "hit_string"
.IX Subsection "hit_string"
.Vb 5
\& Title   : hit_string
\& Usage   : my $hseq = $hsp\->hit_string;
\& Function: Retrieves the hit sequence of this HSP as a string
\& Returns : string
\& Args    : [optional] string to set for hit sequence
.Ve
.SS "homology_string"
.IX Subsection "homology_string"
.Vb 8
\& 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    : [optional] string to set for homology sequence
.Ve
.SS "length"
.IX Subsection "length"
.Vb 12
\& Title    : length
\& Usage    : my $len = $hsp\->length( [\*(Aqquery\*(Aq|\*(Aqhit\*(Aq|\*(Aqtotal\*(Aq] );
\& 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     : arg 1: \*(Aqquery\*(Aq = length of query seq (without gaps)
\&                   \*(Aqhit\*(Aq   = length of hit seq (without gaps)
\&                   \*(Aqtotal\*(Aq = length of alignment (with gaps)
\&                   default = \*(Aqtotal\*(Aq
\&            arg 2: [optional] integer length value to set for specific type
.Ve
.SS "percent_identity"
.IX Subsection "percent_identity"
.Vb 5
\& Title   : percent_identity
\& Usage   : my $percentid = $hsp\->percent_identity()
\& Function: Returns the calculated percent identity for an HSP
\& Returns : floating point between 0 and 100
\& Args    : none
.Ve
.SS "frame"
.IX Subsection "frame"
.Vb 10
\& Title   : frame
\& Usage   : my ($qframe, $hframe) = $hsp\->frame(\*(Aqlist\*(Aq,$queryframe,$subjectframe)
\& Function: Set the Frame for both query and subject and insure that
\&           they agree.
\&           This overrides the frame() method implementation in
\&           FeaturePair.
\& Returns : array of query and subject frame if return type wants an array
\&           or query frame if defined or subject frame if not defined
\& Args    : \*(Aqhit\*(Aq or \*(Aqsubject\*(Aq or \*(Aqsbjct\*(Aq to retrieve the frame of the subject (default)
\&           \*(Aqquery\*(Aq to retrieve the query frame
\&           \*(Aqlist\*(Aq or \*(Aqarray\*(Aq to retrieve both query and hit frames together
\& Note    : Frames are stored in the GFF way (0\-2) not 1\-3
\&           as they are in BLAST (negative frames are deduced by checking
\&                                 the strand of the query or hit)
.Ve
.SS "get_aln"
.IX Subsection "get_aln"
.Vb 5
\& Title   : get_aln
\& Usage   : my $aln = $hsp\->gel_aln
\& Function: Returns a Bio::SimpleAlign representing the HSP alignment
\& Returns : Bio::SimpleAlign
\& Args    : none
.Ve
.SS "num_conserved"
.IX Subsection "num_conserved"
.Vb 5
\& Title   : num_conserved
\& Usage   : $obj\->num_conserved($newval)
\& Function: returns the number of conserved residues in the alignment
\& Returns : inetger
\& Args    : integer (optional)
.Ve
.SS "num_identical"
.IX Subsection "num_identical"
.Vb 5
\& Title   : num_identical
\& Usage   : $obj\->num_identical($newval)
\& Function: returns the number of identical residues in the alignment
\& Returns : integer
\& Args    : integer (optional)
.Ve
.SS "seq_inds"
.IX Subsection "seq_inds"
.Vb 10
\& Title   : seq_inds
\& Purpose   : Get a list of residue positions (indices) for all identical
\&           : or conserved residues in the query or sbjct sequence.
\& Example   : @s_ind = $hsp\->seq_inds(\*(Aqquery\*(Aq, \*(Aqidentical\*(Aq);
\&           : @h_ind = $hsp\->seq_inds(\*(Aqhit\*(Aq, \*(Aqconserved\*(Aq);
\&           : @h_ind = $hsp\->seq_inds(\*(Aqhit\*(Aq, \*(Aqconserved\*(Aq, 1);
\& Returns   : List of integers
\&           : May include ranges if collapse is true.
\& Argument  : seq_type  = \*(Aqquery\*(Aq or \*(Aqhit\*(Aq or \*(Aqsbjct\*(Aq  (default = query)
\&           :  (\*(Aqsbjct\*(Aq is synonymous with \*(Aqhit\*(Aq)
\&           : class     = \*(Aqidentical\*(Aq or \*(Aqconserved\*(Aq or \*(Aqnomatch\*(Aq or \*(Aqgap\*(Aq
\&           :              (default = identical)
\&           :              (can be shortened to \*(Aqid\*(Aq or \*(Aqcons\*(Aq)
\&           :
\&           : collapse  = boolean, if true, consecutive positions are merged
\&           :             using a range notation, e.g., "1 2 3 4 5 7 9 10 11"
\&           :             collapses to "1\-5 7 9\-11". This is useful for
\&           :             consolidating long lists. Default = no collapse.
\& Throws    : n/a.
\& Comments  :
.Ve
.PP
See Also   : \fBBio::Search::BlastUtils::collapse_nums()\fR,
\&\fBBio::Search::Hit::HitI::seq_inds()\fR
.SS "Inherited from Bio::SeqFeature::SimilarityPair"
.IX Subsection "Inherited from Bio::SeqFeature::SimilarityPair"
These methods come from Bio::SeqFeature::SimilarityPair
.SS "query"
.IX Subsection "query"
.Vb 5
\& 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
.Ve
.SS "hit"
.IX Subsection "hit"
.Vb 5
\& 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
.Ve
.SS "significance"
.IX Subsection "significance"
.Vb 6
\& Title   : significance
\& Usage   : $evalue = $obj\->significance();
\&           $obj\->significance($evalue);
\& Function: Get/Set the significance value
\& Returns : numeric
\& Args    : [optional] new value to set
.Ve
.SS "score"
.IX Subsection "score"
.Vb 5
\& Title   : score
\& Usage   : my $score = $hsp\->score();
\& Function: Returns the score for this HSP or undef
\& Returns : numeric
\& Args    : [optional] numeric to set value
.Ve
.SS "bits"
.IX Subsection "bits"
.Vb 5
\& Title   : bits
\& Usage   : my $bits = $hsp\->bits();
\& Function: Returns the bit value for this HSP or undef
\& Returns : numeric
\& Args    : none
.Ve