Class: Bio::FlatFileIndex::BDB_1::BDBMappingFile

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/io/flatfile/bdb.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(filename, flag = BDBdefault.flag_read, permission = BDBdefault.permission) ⇒ BDBMappingFile

Returns a new instance of BDBMappingFile.



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# File 'lib/bio/io/flatfile/bdb.rb', line 110

def initialize(filename, flag = BDBdefault.flag_read,
               permission = BDBdefault.permission)
  @filename = filename
  @flag = flag
  @permission = permission
  #@bdb = BDB::Btree.open(@filename, nil, @flag, @permission)
end

Instance Attribute Details

#filename ⇒ Object (readonly)

Returns the value of attribute filename.



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# File 'lib/bio/io/flatfile/bdb.rb', line 117

def filename
  @filename
end

#flag ⇒ Object

Returns the value of attribute flag.



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# File 'lib/bio/io/flatfile/bdb.rb', line 118

def flag
  @flag
end

#permission ⇒ Object

Returns the value of attribute permission.



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# File 'lib/bio/io/flatfile/bdb.rb', line 118

def permission
  @permission
end

Class Method Details

.open(*arg) ⇒ Object 



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# File 'lib/bio/io/flatfile/bdb.rb', line 106

def self.open(*arg)
  self.new(*arg)
end

Instance Method Details

#add(key, val) ⇒ Object

methods for writing



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# File 'lib/bio/io/flatfile/bdb.rb', line 145

def add(key, val)
  open
  val = val.to_a.join("\t")
  s = @bdb[key]
  if s then
    s << "\t"
    s << val
    val = s
  end
  @bdb[key] = val
  #DEBUG.print "add: key=#{key.inspect}, val=#{val.inspect}\n"
  val
end

#add_exclusive(key, val) ⇒ Object 



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# File 'lib/bio/io/flatfile/bdb.rb', line 159

def add_exclusive(key, val)
  open
  val = val.to_a.join("\t")
  s = @bdb[key]
  if s then
    raise RuntimeError, "keys must be unique, but key #{key.inspect} already exists"
  end
  @bdb[key] = val
  #DEBUG.print "add_exclusive: key=#{key.inspect}, val=#{val.inspect}\n"
  val
end

#add_nr(key, val) ⇒ Object 



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# File 'lib/bio/io/flatfile/bdb.rb', line 183

def add_nr(key, val)
  open
  s = @bdb[key]
  if s then
    a = s.split("\t")
  else
    a = []
  end
  a.concat val.to_a
  a.sort!
  a.uniq!
  str = a.join("\t")
  @bdb[key] = str
  #DEBUG.print "add_nr: key=#{key.inspect}, val=#{str.inspect}\n"
  str
end

#add_overwrite(key, val) ⇒ Object 



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# File 'lib/bio/io/flatfile/bdb.rb', line 171

def add_overwrite(key, val)
  open
  val = val.to_a.join("\t")
  s = @bdb[key]
  if s then
    DEBUG.print "Warining: overwrote unique id #{key.inspect}\n"
  end
  @bdb[key] = val
  #DEBUG.print "add_overwrite: key=#{key.inspect}, val=#{val.inspect}\n"
  val
end

#close ⇒ Object 



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# File 'lib/bio/io/flatfile/bdb.rb', line 130

def close
  if @bdb then
    DEBUG.print "BDBMappingFile: close #{@filename}\n"
    @bdb.close
    @bdb = nil
  end
  nil
end

#open ⇒ Object 



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# File 'lib/bio/io/flatfile/bdb.rb', line 120

def open
  unless @bdb then
    DEBUG.print "BDBMappingFile: open #{@filename}\n"
    @bdb = BDB::Btree.open(@filename, nil, @flag, @permission)
    true
  else
    nil
  end
end

#records ⇒ Object Also known as: size 



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# File 'lib/bio/io/flatfile/bdb.rb', line 139

def records
  @bdb.size
end

#search(key) ⇒ Object

methods for searching



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# File 'lib/bio/io/flatfile/bdb.rb', line 201

def search(key)
  open
  s = @bdb[key]
  if s then
    a = s.split("\t")
    a
  else
    []
  end
end