Class Bio::HMMER::Report::Hit
In: lib/bio/appl/hmmer/report.rb
Parent: Object

Container class for HMMER search hits.

Methods

append_hsp   each   each_hsp   new   target_def  

External Aliases

accession -> target_id
accession -> hit_id
accession -> entry_id
description -> definition
score -> bit_score

Attributes

accession  [R] 
description  [R] 
evalue  [R]  E-value
hsps  [R]  An Array of Bio::HMMER::Report::Hsp objects.
num  [R]  Number of domains
score  [R]  Matching scores (total of all HSPs).

Public Class methods

new(hit_data)

Sets hit data.

[Source]

     # File lib/bio/appl/hmmer/report.rb, line 391
391:       def initialize(hit_data)
392:         @hsps = Array.new
393:         if /^(\S+)\s+(.*?)\s+(\S+)\s+(\S+)\s+(\S+)$/ =~ hit_data
394:           @accession, @description, @score, @evalue, @num = \
395:           [$1, $2, $3.to_f, $4.to_f, $5.to_i]
396:         end
397:       end

Public Instance methods

append_hsp(hsp)

Appends a Bio::HMMER::Report::Hsp object.

[Source]

     # File lib/bio/appl/hmmer/report.rb, line 419
419:       def append_hsp(hsp)
420:         @hsps << hsp
421:       end
each() {|hsp| ...}

Iterates on each Hsp object (Bio::HMMER::Report::Hsp).

[Source]

     # File lib/bio/appl/hmmer/report.rb, line 401
401:       def each
402:         @hsps.each do |hsp|
403:           yield hsp
404:         end
405:       end
each_hsp()

Alias for each

target_def()

Shows the hit description.

[Source]

     # File lib/bio/appl/hmmer/report.rb, line 410
410:       def target_def
411:         if @hsps.size == 1
412:           "<#{@hsps[0].domain}> #{@description}"
413:         else
414:           "<#{@num.to_s}> #{@description}"
415:         end
416:       end

[Validate]