/ 
bioperl-1.0.2
/ Bio::Search::HSP::GenericHSP

NAME

Bio::Search::HSP::GenericHSP - DESCRIPTION of Object

SYNOPSIS

    my $hsp = new Bio::Search::HSP::GenericHSP( -algorithm => 'blastp',
						-evalue    => '1e-30',
						);


    $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'] );

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

DESCRIPTION

Describe the object here

FEEDBACK

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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 email or the web:

bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/

AUTHOR - Jason Stajich and Steve Chervitz

Email jason@bioperl.org Email sac@bioperl.org

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

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 = new Bio::Search::HSP::GenericHSP();
 Function: Builds a new Bio::Search::HSP::GenericHSP object 
 Returns : Bio::Search::HSP::GenericHSP
 Args    : -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 comparisions; 
			    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)

Bio::Search::HSP::HSPI methods

Implementation of Bio::Search::HSP::HSPI methods follow

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

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

frac_identical

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    : arg 1:  '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' 
          arg 2: [optional] frac identical value to set for the type requested

frac_conserved

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    : arg 1: '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' 
          arg 2: [optional] frac conserved value to set for the type requested

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

percent_identity

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

frame

 Title   : frame
 Usage   : $hsp->frame($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 subjects if return type wants an array
           or query frame if defined or subject frame
 Args    : none
 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

These methods come 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