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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

  https://github.com/bioperl/bioperl-live/issues

new

 Title   : new
 Usage   : my $obj = Bio::Search::HSP::ModelHSP->new();
 Function: Builds a new Bio::Search::HSP::ModelHSP object 
 Returns : Bio::Search::HSP::ModelHSP
 Args    :

Plus Bio::Seach::HSP::ModelHSP methods

           -algorithm => algorithm used (Infernal, RNAMotif, ERPIN, 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)
           -meta        => optional meta data (sec structure, markup, etc)
           -custom_score=> custom score data

meta

 Title   : meta
 Usage   : my $meta = $hsp->meta();
 Function: Returns meta data for this HSP or undef
 Returns : string of meta data or undef
 Args    : [optional] string to set value
 Note    : At some point very soon this will likely be a Bio::AnnotationI.
           Don't get used to a simple string!

noncanonical_string

 Title   : noncanonical_string
 Usage   : my $nc_seq = $hsp->noncanonical_string();
 Function: Returns noncanonical string (NC) data for this HSP or undef
 Returns : string of noncanonical data or undef
 Args    : [optional] string to set value

custom_score

 Title   : custom_score
 Usage   : my $data = $hsp->custom_score();
 Function: Returns custom_score data for this HSP, or undef
 Returns : custom_score data or undef
 Args    : [optional] custom_score
 Note    : This is a Get/Set used to deal with odd score-like data generated
           from RNAMotif (and other programs) where the score section
           can be customized to include non-standard data, including sequence
           data, user-based scores, and other values.

Bio::Search::HSP::HSPI methods

algorithm

 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

strand

 Title   : strand
 Usage   : $hsp->strand('hit')
 Function: Retrieves the strand for the HSP component requested
 Returns : +1 or -1 (0 if unknown)
 Args    : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject.
           There is no strand available for 'query', as the query is a model
           and not a true sequence.

seq

 Usage     : $hsp->seq( [seq_type] );
 Purpose   : Get the query or sbjct sequence as a Bio::Seq.pm object.
 Example   : $seqObj = $hsp->seq('sbjct');
 Returns   : Object reference for a Bio::Seq.pm object.
 Argument  : seq_type = 'query' or 'hit' or 'sbjct' (default = 'sbjct').
           :  ('sbjct' is synonymous with 'hit') 
           : default is 'sbjct'
           : Note: if there is no sequence available (eg for a model-based
           : search), this returns a LocatableSeq object w/o a sequence
 Throws    : Propagates any exception that occurs during construction
           : of the Bio::Seq.pm object.
 Comments  : The sequence is returned in an array of strings corresponding
           : to the strings in the original format of the Blast alignment.
           : (i.e., same spacing).

See Also : seq_str(), Bio::Seq

pvalue

 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

evalue

 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

gaps

 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     : arg 1: 'query' = num gaps in query seq
                   'hit'   = num gaps in hit seq
                   'total' = num gaps in whole alignment 
                   default = 'total' 
            arg 2: [optional] integer gap value to set for the type requested

query_string

 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

hit_string

 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

homology_string

 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

length

 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     : arg 1: 'query' = length of query seq (without gaps)
                   'hit'   = length of hit seq (without gaps)
                   'total' = length of alignment (with gaps)
                   default = 'total' 
            arg 2: [optional] integer length value to set for specific type

frame

 Title   : frame
 Usage   : my ($qframe, $hframe) = $hsp->frame('list',$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    : 'hit' or 'subject' or 'sbjct' to retrieve the frame of the subject (default)
           'query' to retrieve the query frame 
           'list' or 'array' 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)

get_aln

 Title   : get_aln
 Usage   : my $aln = $hsp->gel_aln
 Function: Returns a Bio::SimpleAlign representing the HSP alignment
 Returns : Bio::SimpleAlign
 Args    : none

Inherited from Bio::SeqFeature::SimilarityPair

query

 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

hit

 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

significance

 Title   : significance
 Usage   : $evalue = $obj->significance();
           $obj->significance($evalue);
 Function: Get/Set the significance value
 Returns : numeric
 Args    : [optional] new value to set

score

 Title   : score
 Usage   : my $score = $hsp->score();
 Function: Returns the score for this HSP or undef 
 Returns : numeric           
 Args    : [optional] numeric to set value

bits

 Title   : bits
 Usage   : my $bits = $hsp->bits();
 Function: Returns the bit value for this HSP or undef 
 Returns : numeric
 Args    : none

seq_inds

frac_identical

frac_conserved

matches

num_conserved

num_identical

cigar_string

generate_cigar_string

percent_identity