Class: Bio::Blat::Report::SeqDesc
Overview
Bio::Blat::Report::SeqDesc stores sequence information of query or subject of the BLAT report. It also includes some hit information.
Instance Attribute Summary collapse
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#end ⇒ Object
readonly
end position of the final segment.
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#gap_bases ⇒ Object
readonly
gap bases.
-
#gap_count ⇒ Object
readonly
gap count.
-
#name ⇒ Object
readonly
name of the sequence.
-
#seqs ⇒ Object
readonly
sequences of segments.
-
#size ⇒ Object
readonly
length of the sequence.
-
#start ⇒ Object
readonly
start position of the first segment.
-
#starts ⇒ Object
readonly
start positions of segments.
Instance Method Summary collapse
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#initialize(gap_count, gap_bases, name, size, st, ed, starts, seqs) ⇒ SeqDesc
constructor
Creates a new SeqDesc object.
Constructor Details
#initialize(gap_count, gap_bases, name, size, st, ed, starts, seqs) ⇒ SeqDesc
Creates a new SeqDesc object. It is designed to be called internally from Bio::Blat::Report class. Users shall not use it directly.
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# File 'lib/bio/appl/blat/report.rb', line 120 def initialize(gap_count, gap_bases, name, size, st, ed, starts, seqs) @gap_count = gap_count.to_i @gap_bases = gap_bases.to_i @name = name @size = size.to_i @start = st.to_i @end = ed.to_i @starts = starts.collect { |x| x.to_i } @seqs = seqs end |
Instance Attribute Details
#end ⇒ Object (readonly)
end position of the final segment
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# File 'lib/bio/appl/blat/report.rb', line 142 def end @end end |
#gap_bases ⇒ Object (readonly)
gap bases
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# File 'lib/bio/appl/blat/report.rb', line 134 def gap_bases @gap_bases end |
#gap_count ⇒ Object (readonly)
gap count
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# File 'lib/bio/appl/blat/report.rb', line 132 def gap_count @gap_count end |
#name ⇒ Object (readonly)
name of the sequence
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# File 'lib/bio/appl/blat/report.rb', line 136 def name @name end |
#seqs ⇒ Object (readonly)
sequences of segments. Returns an array of String. Returns nil if there are no sequence data.
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# File 'lib/bio/appl/blat/report.rb', line 149 def seqs @seqs end |
#size ⇒ Object (readonly)
length of the sequence
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# File 'lib/bio/appl/blat/report.rb', line 138 def size @size end |
#start ⇒ Object (readonly)
start position of the first segment
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# File 'lib/bio/appl/blat/report.rb', line 140 def start @start end |
#starts ⇒ Object (readonly)
start positions of segments. Returns an array of numbers.
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# File 'lib/bio/appl/blat/report.rb', line 145 def starts @starts end |