Class: Bio::Blast::Default::Report::F0dbstat
- Defined in:
- lib/bio/appl/blast/format0.rb
Overview
Stores format0 database statistics. Internal use only. Users must not use the class.
Direct Known Subclasses
Instance Attribute Summary collapse
-
#f0dbstat ⇒ Object
readonly
Returns the value of attribute f0dbstat.
-
#f0params ⇒ Object
Returns the value of attribute f0params.
Instance Method Summary collapse
-
#database ⇒ Object
Returns name (title or filename) of the database.
-
#db_len ⇒ Object
Returns number of letters in database.
-
#db_num ⇒ Object
Returns number of sequences in database.
-
#eff_space ⇒ Object
Returns effective length of the database.
-
#expect ⇒ Object
Returns e-value threshold specified when BLAST was executed.
-
#gap_extend ⇒ Object
Returns gap extend penalty value.
-
#gap_open ⇒ Object
Returns gap open penalty value.
-
#initialize(ary) ⇒ F0dbstat
constructor
Creates new F0dbstat class.
-
#matrix ⇒ Object
Returns name of the matrix.
-
#num_hits ⇒ Object
Returns number of hits.
-
#posted_date ⇒ Object
Returns posted date of the database.
-
#sc_match ⇒ Object
Returns the match score of the matrix.
-
#sc_mismatch ⇒ Object
Returns the mismatch score of the matrix.
Constructor Details
#initialize(ary) ⇒ F0dbstat
Creates new F0dbstat class. Internal use only.
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# File 'lib/bio/appl/blast/format0.rb', line 335 def initialize(ary) @f0dbstat = ary @hash = {} end |
Instance Attribute Details
#f0dbstat ⇒ Object (readonly)
Returns the value of attribute f0dbstat.
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# File 'lib/bio/appl/blast/format0.rb', line 339 def f0dbstat @f0dbstat end |
#f0params ⇒ Object
Returns the value of attribute f0params.
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# File 'lib/bio/appl/blast/format0.rb', line 340 def f0params @f0params end |
Instance Method Details
#database ⇒ Object
Returns name (title or filename) of the database.
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# File 'lib/bio/appl/blast/format0.rb', line 458 def database unless defined?(@database); parse_dbstat; end; @database end |
#db_len ⇒ Object
Returns number of letters in database.
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# File 'lib/bio/appl/blast/format0.rb', line 468 def db_len unless defined?(@db_len); parse_dbstat; end; @db_len end |
#db_num ⇒ Object
Returns number of sequences in database.
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# File 'lib/bio/appl/blast/format0.rb', line 473 def db_num unless defined?(@db_num); parse_dbstat; end; @db_num end |
#eff_space ⇒ Object
Returns effective length of the database.
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# File 'lib/bio/appl/blast/format0.rb', line 411 def eff_space; parse_params; @eff_space; end |
#expect ⇒ Object
Returns e-value threshold specified when BLAST was executed.
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# File 'lib/bio/appl/blast/format0.rb', line 414 def expect; parse_params; @expect; end |
#gap_extend ⇒ Object
Returns gap extend penalty value.
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# File 'lib/bio/appl/blast/format0.rb', line 408 def gap_extend; parse_params; @gap_extend; end |
#gap_open ⇒ Object
Returns gap open penalty value.
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# File 'lib/bio/appl/blast/format0.rb', line 406 def gap_open; parse_params; @gap_open; end |
#matrix ⇒ Object
Returns name of the matrix.
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# File 'lib/bio/appl/blast/format0.rb', line 399 def matrix; parse_params; @matrix; end |
#num_hits ⇒ Object
Returns number of hits.
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# File 'lib/bio/appl/blast/format0.rb', line 417 def num_hits; parse_params; @num_hits; end |
#posted_date ⇒ Object
Returns posted date of the database.
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# File 'lib/bio/appl/blast/format0.rb', line 463 def posted_date unless defined?(@posted_date); parse_dbstat; end; @posted_date end |
#sc_match ⇒ Object
Returns the match score of the matrix.
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# File 'lib/bio/appl/blast/format0.rb', line 401 def sc_match; parse_params; @sc_match; end |
#sc_mismatch ⇒ Object
Returns the mismatch score of the matrix.
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# File 'lib/bio/appl/blast/format0.rb', line 403 def sc_mismatch; parse_params; @sc_mismatch; end |