Class Bio::Blast::Report::Hsp
In: lib/bio/appl/blast/report.rb
Parent: Object

Methods

new  

Attributes

align_len  [RW]  Length of the alignment used
bit_score  [RW]  Score (in bits) of HSP
density  [RW]  Score density
evalue  [RW]  E-value of HSP
gaps  [RW]  Number of gaps in HSP
hit_frame  [RW]  Translation frame of subject
hit_from  [RW]  Start of HSP in subject
hit_to  [RW]  End of HSP
hseq  [RW]  Alignment string for subject (with gaps)
hsp  [R] 
identity  [RW]  Number of identities in HSP
midline  [RW]  Formating middle line
mismatch_count  [RW]  Available only for ’-m 8’ format outputs.
num  [RW]  HSP number
pattern_from  [RW]  Start of PHI-BLAST pattern
pattern_to  [RW]  End of PHI-BLAST pattern
percent_identity  [RW]  Available only for ’-m 8’ format outputs.
positive  [RW]  Number of positives in HSP
qseq  [RW]  Alignment string for the query (with gaps)
query_frame  [RW]  Translation frame of query
query_from  [RW]  Start of HSP in query
query_to  [RW]  End of HSP
score  [RW]  Sscore of HSP

Public Class methods

[Source]

     # File lib/bio/appl/blast/report.rb, line 314
314:     def initialize
315:       @hsp = {}
316:     end

[Validate]