Class: Bio::Blast::Default::Report::HSP
- Defined in:
- lib/bio/appl/blast/format0.rb
Overview
Bio::Blast::Default::Report::HSP holds information about the hsp (high-scoring segment pair).
Direct Known Subclasses
Instance Attribute Summary collapse
-
#align_len ⇒ Object
readonly
aligned length.
-
#bit_score ⇒ Object
readonly
bit score.
-
#evalue ⇒ Object
readonly
e-value.
-
#gaps ⇒ Object
readonly
Gaps (number of gaps).
-
#hit_frame ⇒ Object
readonly
frame of the hit.
-
#hit_from ⇒ Object
readonly
start position of the hit (the first position is 1).
-
#hit_strand ⇒ Object
readonly
strand of the hit (“Plus” or “Minus” or nil).
-
#hit_to ⇒ Object
readonly
end position of the hit (including its position).
-
#hseq ⇒ Object
readonly
hit sequence (with gaps) of the alignment of the hsp.
-
#identity ⇒ Object
readonly
Identity (number of identical nucleotides or amino acids).
-
#midline ⇒ Object
readonly
middle line of the alignment of the hsp.
-
#percent_gaps ⇒ Object
readonly
percent of gaps.
-
#percent_identity ⇒ Object
readonly
percent of identical nucleotides or amino acids.
-
#percent_positive ⇒ Object
readonly
percent of positive hit amino acids or nucleotides.
-
#positive ⇒ Object
readonly
Positives (number of positive hit amino acids or nucleotides).
-
#qseq ⇒ Object
readonly
query sequence (with gaps) of the alignment of the hsp.
-
#query_frame ⇒ Object
readonly
frame of the query.
-
#query_from ⇒ Object
readonly
start position of the query (the first position is 1).
-
#query_strand ⇒ Object
readonly
strand of the query (“Plus” or “Minus” or nil).
-
#query_to ⇒ Object
readonly
end position of the query (including its position).
-
#score ⇒ Object
readonly
score.
-
#stat_method ⇒ Object
readonly
statistical method for calculating evalue and/or score (nil or a string) (note that composition-based statistics for blastp or tblastn were enabled by default after NCBI BLAST 2.2.17).
Instance Method Summary collapse
-
#initialize(data) ⇒ HSP
constructor
Creates new HSP object.
Constructor Details
#initialize(data) ⇒ HSP
Creates new HSP object. It is designed to be called only internally from the Bio::Blast::Default::Report::Hit class. Users should not call the method directly.
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# File 'lib/bio/appl/blast/format0.rb', line 962 def initialize(data) @f0score = data.shift @f0alignment = [] while r = data[0] and /^(Query|Sbjct)\:/ =~ r @f0alignment << data.shift end end |
Instance Attribute Details
#align_len ⇒ Object (readonly)
aligned length
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# File 'lib/bio/appl/blast/format0.rb', line 1104 def align_len @align_len end |
#bit_score ⇒ Object (readonly)
bit score
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# File 'lib/bio/appl/blast/format0.rb', line 1065 def bit_score @bit_score end |
#evalue ⇒ Object (readonly)
e-value
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# File 'lib/bio/appl/blast/format0.rb', line 1072 def evalue @evalue end |
#gaps ⇒ Object (readonly)
Gaps (number of gaps)
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# File 'lib/bio/appl/blast/format0.rb', line 1097 def gaps @gaps end |
#hit_frame ⇒ Object (readonly)
frame of the hit
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# File 'lib/bio/appl/blast/format0.rb', line 1079 def hit_frame @hit_frame end |
#hit_from ⇒ Object (readonly)
start position of the hit (the first position is 1)
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# File 'lib/bio/appl/blast/format0.rb', line 1220 def hit_from @hit_from end |
#hit_strand ⇒ Object (readonly)
strand of the hit (“Plus” or “Minus” or nil)
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# File 'lib/bio/appl/blast/format0.rb', line 1112 def hit_strand @hit_strand end |
#hit_to ⇒ Object (readonly)
end position of the hit (including its position)
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# File 'lib/bio/appl/blast/format0.rb', line 1224 def hit_to @hit_to end |
#hseq ⇒ Object (readonly)
hit sequence (with gaps) of the alignment of the hsp
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# File 'lib/bio/appl/blast/format0.rb', line 1204 def hseq @hseq end |
#identity ⇒ Object (readonly)
Identity (number of identical nucleotides or amino acids)
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# File 'lib/bio/appl/blast/format0.rb', line 1083 def identity @identity end |
#midline ⇒ Object (readonly)
middle line of the alignment of the hsp
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# File 'lib/bio/appl/blast/format0.rb', line 1208 def midline @midline end |
#percent_gaps ⇒ Object (readonly)
percent of gaps
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# File 'lib/bio/appl/blast/format0.rb', line 1100 def percent_gaps @percent_gaps end |
#percent_identity ⇒ Object (readonly)
percent of identical nucleotides or amino acids
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# File 'lib/bio/appl/blast/format0.rb', line 1086 def percent_identity @percent_identity end |
#percent_positive ⇒ Object (readonly)
percent of positive hit amino acids or nucleotides
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# File 'lib/bio/appl/blast/format0.rb', line 1093 def percent_positive @percent_positive end |
#positive ⇒ Object (readonly)
Positives (number of positive hit amino acids or nucleotides)
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# File 'lib/bio/appl/blast/format0.rb', line 1090 def positive @positive end |
#qseq ⇒ Object (readonly)
query sequence (with gaps) of the alignment of the hsp
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# File 'lib/bio/appl/blast/format0.rb', line 1201 def qseq @qseq end |
#query_frame ⇒ Object (readonly)
frame of the query
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# File 'lib/bio/appl/blast/format0.rb', line 1076 def query_frame @query_frame end |
#query_from ⇒ Object (readonly)
start position of the query (the first position is 1)
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# File 'lib/bio/appl/blast/format0.rb', line 1212 def query_from @query_from end |
#query_strand ⇒ Object (readonly)
strand of the query (“Plus” or “Minus” or nil)
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# File 'lib/bio/appl/blast/format0.rb', line 1108 def query_strand @query_strand end |
#query_to ⇒ Object (readonly)
end position of the query (including its position)
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# File 'lib/bio/appl/blast/format0.rb', line 1216 def query_to @query_to end |
#score ⇒ Object (readonly)
score
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# File 'lib/bio/appl/blast/format0.rb', line 1068 def score @score end |
#stat_method ⇒ Object (readonly)
statistical method for calculating evalue and/or score (nil or a string) (note that composition-based statistics for blastp or tblastn were enabled by default after NCBI BLAST 2.2.17)
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# File 'lib/bio/appl/blast/format0.rb', line 1119 def stat_method @stat_method end |