Class: Bio::MAF::AllSpeciesFilter

Inherits:

Filter

• Object
• Filter
• Bio::MAF::AllSpeciesFilter

Defined in:

lib/bio/maf/index.rb

Constant Summary

Constants included from KVHelpers

KVHelpers::CHROM_BIN_PREFIX_FMT, KVHelpers::KEY_FMT, KVHelpers::KEY_SCAN_FMT, KVHelpers::VAL_FMT, KVHelpers::VAL_IDX_OFFSET_FMT, KVHelpers::VAL_N_SEQ_FMT, KVHelpers::VAL_SPECIES_FMT, KVHelpers::VAL_TEXT_SIZE_FMT

Instance Attribute Summary

• #bs ⇒ Object readonly

  Returns the value of attribute bs.

Instance Method Summary

• #initialize(species, idx) ⇒ AllSpeciesFilter constructor

  A new instance of AllSpeciesFilter.

• #match(entry) ⇒ Object

Methods inherited from Filter

#call

Methods included from KVHelpers

bin_start_prefix, extract_index_offset, extract_n_sequences, extract_species_vec, extract_text_size, unpack_key

Constructor Details

#initialize(species, idx) ⇒ AllSpeciesFilter

Returns a new instance of AllSpeciesFilter.

# File 'lib/bio/maf/index.rb', line 885

def initialize(species, idx)
  ids = species.collect {|s| 1 << idx.species.fetch(s) }
  @mask = ids.reduce(0, :|)
end

Instance Attribute Details

#bs ⇒ Object (readonly)

Returns the value of attribute bs.

# File 'lib/bio/maf/index.rb', line 884

def bs
  @bs
end

Instance Method Details

#match(entry) ⇒ Object

# File 'lib/bio/maf/index.rb', line 890

def match(entry)
  vec = extract_species_vec(entry)
  (@mask & vec) == @mask
end