bio-maf 0.1.0-java

data/lib/bio/maf/parser.rb

@@ -0,0 +1,888 @@
+require 'strscan'
+require 'java' if RUBY_PLATFORM == 'java'
+
+# @api public
+module Bio
+  # @api public
+  module MAF
+
+    # @api public
+    class ParseError < Exception; end
+
+    # A MAF header, containing the variable-value pairs from the first
+    # line of the file as well as the alignment parameters.
+    # @api public
+    class Header
+      # Variable-value pairs from the ##maf line
+      # @return [Hash]
+      attr_accessor :vars
+      # Alignment parameters from the MAF header.
+      # @return [Hash]
+      attr_accessor :alignment_params
+
+      def initialize(vars, params)
+        @vars = vars
+        @alignment_params = params
+      end
+
+      # The required version parameter.
+      # @return [String]
+      def version
+        vars[:version]
+      end
+
+      # The optional scoring parameter, if present.
+      # @return [String]
+      def scoring
+        vars[:scoring]
+      end
+
+    end
+
+    # A MAF alignment block.
+    # @api public
+    class Block
+      # Parameters from the 'a' line starting the alignment block.
+      attr_reader :vars
+      # Sequences, one per 's' or 'e' line.
+      # @return [Array<Sequence>]
+      attr_reader :sequences
+      # Offset of the alignment block within the MAF file, in bytes.
+      # @return [Integer]
+      attr_reader :offset
+      # Size of the alignment block within the MAF file, in bytes.
+      # @return [Integer]
+      attr_reader :size
+
+      def initialize(*args)
+        @vars, @sequences, @offset, @size = args
+      end
+
+      def raw_seq(i)
+        sequences.fetch(i)
+      end
+
+      def each_raw_seq
+        sequences.each { |s| yield s }
+      end
+
+      # Text size of the alignment block. This is the number of text
+      # characters in each line of sequence data, including dashes and
+      # other gaps in the sequence.
+      def text_size
+        sequences.first.text.size
+      end
+
+    end
+
+    # A sequence within an alignment block.
+    # @api public
+    class Sequence
+      # @return [String] Source sequence name.
+      attr_reader :source
+      # @return [Integer] Zero-based start position.
+      attr_reader :start
+      # @return [Integer] Size of aligning region in source sequence.
+      attr_reader :size
+      # :+ or :-, indicating which strand the alignment is to.
+      # @return [Symbol]
+      attr_reader :strand
+      # Size of the entire source sequence, not just the aligning
+      # region.
+      # @return [Integer]
+      attr_reader :src_size
+      # Sequence data for the alignment, including insertions.
+      # @return [String]
+      attr_reader :text
+      # Array of raw synteny information from 'i' line.
+      # @return [Array<String>]
+      attr_accessor :i_data
+      # Quality string from 'q' line.
+      # @return [String]
+      attr_accessor :quality
+      alias_method :source_size, :src_size
+
+      def initialize(*args)
+        @source, @start, @size, @strand, @src_size, @text = args
+      end
+
+      # Whether this sequence is empty. Only true for {EmptySequence}
+      # instances from 'e' lines.
+      def empty?
+        false
+      end
+
+      def write_fasta(writer)
+        writer.write("#{source}:#{start}-#{start + size}",
+                     text)
+      end
+    end
+
+    # An empty sequence record from an 'e' line.
+    #
+    # This indicates that "there isn't aligning DNA for a species but
+    # that the current block is bridged by a chain that connects
+    # blocks before and after this block" (MAF spec).
+    # @api public
+    class EmptySequence < Sequence
+      attr_reader :status
+
+      def initialize(*args)
+        super(*args[0..4])
+        @status = args[5]
+      end
+
+      def text
+        ''
+      end
+
+      def empty?
+        true
+      end
+
+      def write_fasta(writer)
+        raise "empty sequence output not implemented!"
+      end
+    end
+
+    # Reads MAF files in chunks.
+    # @api private
+    class ChunkReader
+      # Size, in bytes, of the chunks to read. Must be a power of 2.
+      # @return [Integer]
+      attr_accessor :chunk_size
+      # Current position in the file.
+      # @return [Integer]
+      attr_accessor :pos
+      # {File} from which chunks are read.
+      # @return [File]
+      attr_reader :f
+      def initialize(f, chunk_size)
+        @f = f
+        self.chunk_size = chunk_size
+        @pos = 0
+      end
+
+      def chunk_size=(size)
+        check_chunk_size(size)
+        @chunk_size = size
+        # power of 2 so don't worry about rounding
+        # @chunk_shift = Math.log2(size).to_i
+      end
+
+      def check_chunk_size(size)
+        if size < 1
+          raise "Invalid chunk size: #{size}"
+        end
+        ## test whether it is a power of 2
+        ## cf. http://bit.ly/JExNc4
+        if size & (size - 1) != 0
+          raise "Invalid chunk size (not a power of 2): #{size}}"
+        end
+      end
+
+      # Reads the next chunk of the file.
+      # @return [String] Next {#chunk_size} bytes of MAF data.
+      def read_chunk
+        chunk = f.read(@chunk_size)
+        @pos += chunk.bytesize if chunk
+        return chunk
+      end
+
+      # Reads a chunk of the file.
+      #
+      # Currently always reads size_hint bytes but this may change
+      # with BGZF support.
+      #
+      # @param [Integer] offset file offset to read from.
+      # @param [Integer] size_hint desired size of chunk.
+      # @return [String] Chunk of MAF data.
+      def read_chunk_at(offset, size_hint=@chunk_size)
+        f.seek(offset)
+        chunk = f.read(size_hint)
+        @pos = offset + chunk.bytesize
+        return chunk
+      end
+    end
+
+    # Variant ChunkReader using a read-ahead thread with internal
+    # queue for sequential parsing. Not useful for random-access
+    # parsing.
+    #
+    # Only beneficial on JRuby.
+    class ThreadedChunkReader < ChunkReader
+
+      def initialize(f, chunk_size, buffer_size=64)
+        super(f, chunk_size)
+        @buffer = SizedQueue.new(buffer_size)
+        @eof_reached = false
+        start_read_ahead
+      end
+
+      # Spawn a read-ahead thread. Called from {#initialize}.
+      def start_read_ahead
+        @read_thread = Thread.new { read_ahead }
+      end
+
+      # Read ahead into queue.
+      def read_ahead
+        # n = 0
+        begin
+          f_pos = 0
+          until f.eof?
+            chunk = f.read(@chunk_size)
+            @buffer << [f_pos, chunk]
+            f_pos += chunk.bytesize
+            # n += 1
+            # if (n % 100) == 0
+            #   $stderr.puts "buffer size: #{@buffer.size}"
+            # end
+          end
+          @eof_reached = true
+        rescue Exception
+          @read_ahead_ex = $!
+          $stderr.puts "read_ahead aborting: #{$!}"
+        end
+      end
+
+      # (see ChunkReader#read_chunk)
+      def read_chunk
+        raise "readahead failed: #{@read_ahead_ex}" if @read_ahead_ex
+        if @eof_reached && @buffer.empty?
+          return nil
+        else
+          c_pos, chunk = @buffer.shift()
+          @pos = c_pos
+          return chunk
+        end
+      end
+
+    end
+
+    # MAF parsing code useful for sequential and random-access parsing.
+    module MAFParsing
+      
+      BLOCK_START = /^(?=a)/
+      BLOCK_START_OR_EOS = /(?:^(?=a))|\z/
+      EOL_OR_EOF = /\n|\z/
+
+      def set_last_block_pos!
+        @last_block_pos = s.string.rindex(BLOCK_START)
+      end
+
+      ## On finding the start of a block:
+      ## See whether we are at the last block in the chunk.
+      ##   If at the last block:
+      ##     If at EOF: last block.
+      ##     If not:
+      ##       Read the next chunk
+      ##       Find the start of the next block in that chunk
+      ##       Concatenate the two block fragments
+      ##       Parse the resulting block
+      ##       Promote the next scanner, positioned
+
+      # Parse the block at the current position, joining fragments
+      # across chunk boundaries if necessary.
+      #
+      # @return [Block] alignment block
+      # @api public
+      def parse_block
+        return nil if at_end
+        if s.pos != last_block_pos
+          # in non-trailing block
+          parse_block_data
+        else
+          # in trailing block fragment
+          parse_trailing_fragment
+        end
+      end
+
+      ## Read chunks and accumulate a leading fragment until we
+      ## encounter a block start or EOF.
+      def gather_leading_fragment
+        leading_frag = ''
+        while true
+          next_chunk_start = cr.pos
+          next_chunk = cr.read_chunk
+          if next_chunk
+            next_scanner = StringScanner.new(next_chunk)
+            # If this trailing fragment ends with a newline, then an
+            # 'a' at the beginning of the leading fragment is the
+            # start of the next alignment block.
+            if trailing_nl?(leading_frag) || trailing_nl?(s.string)
+              pat = BLOCK_START
+            else
+              pat = /(?:\n(?=a))/
+            end
+            frag = next_scanner.scan_until(pat)
+            if frag
+              # got block start
+              leading_frag << frag
+              break
+            else
+              # no block start in this
+              leading_frag << next_chunk
+            end
+          else
+            # EOF
+            @at_end = true
+            break
+          end
+        end
+        return leading_frag, next_scanner, next_chunk_start
+      end
+
+      # Join the trailing fragment of the current chunk with the
+      # leading fragment of the next chunk and parse the resulting
+      # block.
+      #
+      # @return [Block] the alignment block.
+
+      def parse_trailing_fragment
+        leading_frag, next_scanner, next_chunk_start = gather_leading_fragment
+        # join fragments and parse
+        trailing_frag = s.rest
+        joined_block = trailing_frag + leading_frag
+        @chunk_start = chunk_start + s.pos
+        @s = StringScanner.new(joined_block)
+        begin
+          block = parse_block_data
+        rescue ParseError => pe
+          parse_error "Could not parse joined fragments: #{pe}\nTRAILING: #{trailing_frag}\nLEADING: #{leading_frag}"
+        end
+        # Set up to parse the next block
+        @s = next_scanner
+        @chunk_start = next_chunk_start
+        unless @at_end
+          set_last_block_pos!
+        end
+        return block
+      end
+
+      # Raise a {ParseError}, indicating position within the MAF file
+      # and the chunk as well as the text surrounding the current
+      # scanner position.
+      #
+      # @param [String] msg the error message
+      def parse_error(msg)
+        s_start = [s.pos - 10, 0].max
+        s_end = [s.pos + 10, s.string.length].min
+        if s_start > 0
+          left = s.string[s_start..(s.pos - 1)]
+        else
+          left = ''
+        end
+        right = s.string[s.pos..s_end]
+        extra = "pos #{s.pos} [#{chunk_start + s.pos}], last #{last_block_pos}"
+
+        raise ParseError, "#{msg} at: '#{left}>><<#{right}' (#{extra})"
+      end
+
+      S = 's'.getbyte(0)
+      I = 'i'.getbyte(0)
+      E = 'e'.getbyte(0)
+      Q = 'q'.getbyte(0)
+      COMMENT = '#'.getbyte(0)
+
+      # Parse a {Block} from the current position. Requires that {#s}
+      # and {#chunk_start} be set correctly.
+      #
+      # @return [Block] the alignment block.
+      def parse_block_data
+        block_start_pos = s.pos
+        block_offset = chunk_start + block_start_pos
+        s.scan(/^a\s*/) || parse_error("bad a line")
+        block_vars = parse_maf_vars()
+        seqs = []
+        payload = s.scan_until(/^(?=a)/)
+        unless payload
+          payload = s.rest
+          s.pos = s.string.size # jump to EOS
+        end
+        lines = payload.split("\n")
+        until lines.empty?
+          line = lines.shift
+          first = line.getbyte(0)
+          if first == S
+            seq = parse_seq_line(line, sequence_filter)
+            seqs << seq if seq
+          elsif first == E && parse_empty
+            e_seq = parse_empty_line(line, sequence_filter)
+            seqs << e_seq if e_seq
+          elsif first == I && parse_extended
+            parts = line.split
+            parse_error("wrong i source #{parts[1]}!") unless seqs.last.source == parts[1]
+            seqs.last.i_data = parts.slice(2..6)
+          elsif first == Q && parse_extended
+            _, src, quality = line.split
+            parse_error("wrong q source #{src}!") unless seqs.last.source == src
+            seqs.last.quality = quality
+          elsif [I, E, Q, COMMENT, nil].include? first
+            next
+          else
+            parse_error "unexpected line: '#{line}'"
+          end
+        end
+        return Block.new(block_vars,
+                         seqs,
+                         block_offset,
+                         s.pos - block_start_pos)
+      end
+
+      # Parse an 's' line.
+      # @return [Sequence]
+      def parse_seq_line(line, filter)
+        _, src, start, size, strand, src_size, text = line.split
+        return nil if filter && ! seq_filter_ok?(src, filter)
+        begin
+          Sequence.new(src,
+                       start.to_i,
+                       size.to_i,
+                       STRAND_SYM.fetch(strand),
+                       src_size.to_i,
+                       text)
+        rescue KeyError
+          parse_error "invalid sequence line: #{line}"
+        end
+      end
+
+      # Parse an 'e' line.
+      # @return [EmptySequence]
+      def parse_empty_line(line, filter)
+        _, src, start, size, strand, src_size, status = line.split
+        return nil if filter && ! seq_filter_ok?(src, filter)
+        begin
+          EmptySequence.new(src,
+                            start.to_i,
+                            size.to_i,
+                            STRAND_SYM.fetch(strand),
+                            src_size.to_i,
+                            status)
+        rescue KeyError
+          parse_error "invalid empty sequence line: #{line}"
+        end
+      end
+
+      # Indicates whether the given sequence source should be parsed,
+      # given the current sequence filters.
+      def seq_filter_ok?(src, filter)
+        if filter[:only_species]
+          src_sp = src.split('.', 2)[0]
+          m = filter[:only_species].find { |sp| src_sp == sp }
+          return m
+        else
+          return true
+        end
+      end
+
+      # Parse key-value pairs from the MAF header or an 'a' line.
+      # @return [Hash]
+      def parse_maf_vars
+        vars = {}
+        while s.scan(/(\w+)=(\S*)\s+/) do
+          vars[s[1].to_sym] = s[2]
+        end
+        vars
+      end
+
+      # Does `string` have a trailing newline?
+      def trailing_nl?(string)
+        if string.empty?
+          false
+        else
+          s.string[s.string.size - 1] == "\n"
+        end
+      end
+
+      STRAND_SYM = {
+        '+' => :+,
+        '-' => :-
+      }
+    end
+
+    # A MAF parsing context, used for random-access parsing.
+    class ParseContext
+      include MAFParsing
+      attr_accessor :f, :s, :cr, :parser
+      attr_accessor :chunk_start, :last_block_pos, :at_end
+
+      def initialize(fd, chunk_size, parser, opts)
+        @f = fd
+        @parser = parser
+        reader = opts[:chunk_reader] || ChunkReader
+        @cr = reader.new(@f, chunk_size)
+        @last_block_pos = -1
+      end
+
+      def sequence_filter
+        parser.sequence_filter
+      end
+
+      def parse_empty
+        parser.parse_empty
+      end
+
+      def parse_extended
+        parser.parse_extended
+      end
+
+      def set_last_block_pos!
+        @last_block_pos = s.string.rindex(BLOCK_START)
+      end
+
+      # Fetch and parse blocks at given `offset` and `len`
+      # @param [Integer] offset Offset to start parsing at.
+      # @param [Integer] len Number of bytes to read.
+      # @param [Array] block_offsets Offsets of blocks to parse.
+      # @return [Array<Block>]
+      def fetch_blocks(offset, len, block_offsets)
+        start_chunk_read_if_needed(offset, len)
+        # read chunks until we have the entire merged set of
+        # blocks ready to parse
+        # to avoid fragment joining
+        append_chunks_to(len)
+        # parse the blocks
+        Enumerator.new do |y|
+          block_offsets.each do |expected_offset|
+            block = parse_block
+            ctx.parse_error("expected a block at offset #{expected_offset} but could not parse one!") unless block
+            ctx.parse_error("got block with offset #{block.offset}, expected #{expected_offset}!") unless block.offset == expected_offset
+            y << block
+          end
+        end
+      end
+
+      def start_chunk_read_if_needed(offset, len)
+        if chunk_start \
+          && (chunk_start <= offset) \
+          && (offset < (chunk_start + s.string.size))
+          ## the selected offset is in the current chunk
+          s.pos = offset - chunk_start
+        else
+          chunk = cr.read_chunk_at(offset, len)
+          @chunk_start = offset
+          @s = StringScanner.new(chunk)
+        end
+      end
+
+      def append_chunks_to(len)
+        # XXX: need to rethink this for BGZF; prefetching ChunkReader
+        while s.string.size < len
+          s.string << cr.read_chunk()
+        end
+      end
+
+    end
+
+    # MAF parser, used for sequential and random-access parsing.
+    #
+    # Options:
+    #
+    #  * `:parse_extended`: whether to parse 'i' and 'q' lines
+    #  * `:parse_empty`: whether to parse 'e' lines
+    #  * `:chunk_size`: read MAF file in chunks of this many bytes
+    #  * `:random_chunk_size`: as above, but for random access ({#fetch_blocks})
+    #  * `:merge_max`: merge up to this many bytes of blocks for
+    #    random access
+    #  * `:chunk_reader`: use the specified class to read
+    #    chunks. (Only useful with {ThreadedChunkReader}).
+    #  * `:threads`: number of threads to use for parallel
+    #    parsing. Only useful under JRuby.
+    # @api public
+    
+    class Parser
+      include MAFParsing
+
+      # @return [Header] header of the MAF file being parsed.
+      attr_reader :header
+      # @return [String] path of MAF file being parsed.
+      attr_reader :file_spec
+      # @return [File] file handle for MAF file.
+      attr_reader :f
+      # @return [StringScanner] scanner for parsing.
+      attr_reader :s
+      # @return [ChunkReader] ChunkReader.
+      attr_reader :cr
+      # @return [Boolean] whether EOF has been reached.
+      attr_reader :at_end
+      # @return [Hash] parser options.
+      attr_reader :opts
+      # @return [Integer] starting offset of the current chunk.
+      attr_reader :chunk_start
+      # @return [Integer] offset of the last block start in this chunk.
+      attr_reader :last_block_pos
+      # Sequence filter to apply.
+      # @api public
+      attr_accessor :sequence_filter
+
+      # @api private
+      attr_accessor :parse_extended
+      attr_accessor :parse_empty
+
+      SEQ_CHUNK_SIZE = 131072
+      RANDOM_CHUNK_SIZE = 4096
+      MERGE_MAX = SEQ_CHUNK_SIZE
+
+      # Create a new parser instance.
+      #
+      # @param [String] file_spec path of file to parse.
+      # @param [Hash] opts parser options.
+      # @api public
+      def initialize(file_spec, opts={})
+        @opts = opts
+        chunk_size = opts[:chunk_size] || SEQ_CHUNK_SIZE
+        @random_access_chunk_size = opts[:random_chunk_size] || RANDOM_CHUNK_SIZE
+        @merge_max = opts[:merge_max] || MERGE_MAX
+        @parse_extended = opts[:parse_extended] || false
+        @parse_empty = opts[:parse_empty] || false
+        @chunk_start = 0
+        @file_spec = file_spec
+        @f = File.open(file_spec)
+        reader = opts[:chunk_reader] || ChunkReader
+        @cr = reader.new(@f, chunk_size)
+        @s = StringScanner.new(cr.read_chunk())
+        set_last_block_pos!
+        @at_end = false
+        _parse_header()
+      end
+
+      # Create a {ParseContext} for random access, using the given
+      # chunk size.
+      #
+      # @return [ParseContext]
+      # @api private
+      def context(chunk_size)
+        # IO#dup calls dup(2) internally, but seems broken on JRuby...
+        fd = File.open(file_spec)
+        ParseContext.new(fd, chunk_size, self, @opts)
+      end
+
+      # Execute the given block with a {ParseContext} using the given
+      # `chunk_size` as an argument.
+      #
+      # @see #context
+      # @api private
+      def with_context(chunk_size)
+        ctx = context(chunk_size)
+        begin
+          yield ctx
+        ensure
+          ctx.f.close
+        end
+      end
+
+      # Fetch and parse blocks given by `fetch_list`.
+      #
+      # `fetch_list` should be an array of `[offset, length]` tuples.
+      #
+      # @param [Array] fetch_list the fetch list
+      # @return [Array<Block>] the requested alignment blocks
+      def fetch_blocks(fetch_list)
+        merged = merge_fetch_list(fetch_list)
+        if RUBY_PLATFORM == 'java' && @opts.fetch(:threads, 1) > 1
+          fetch_blocks_merged_parallel(merged)
+        else
+          fetch_blocks_merged(merged)
+        end
+      end
+
+      # Fetch and parse the blocks given by the merged fetch list.
+      #
+      # @param [Array] fetch_list merged fetch list from {#merge_fetch_list}.
+      # @return [Array<Block>] the requested alignment blocks
+      def fetch_blocks_merged(fetch_list)
+        Enumerator.new do |y|
+          start = Time.now
+          total_size = fetch_list.collect { |e| e[1] }.reduce(:+)
+          with_context(@random_access_chunk_size) do |ctx|
+            fetch_list.each do |e|
+              ctx.fetch_blocks(*e).each do |block|
+                y << block
+                #total_size += block.size
+              end
+            end
+          end
+          elapsed = Time.now - start
+          rate = (total_size / 1048576.0) / elapsed
+          $stderr.printf("Fetched blocks in %.3fs, %.1f MB/s.\n",
+                         elapsed, rate)
+        end
+      end
+
+      # Fetch and parse the blocks given by the merged fetch list, in
+      # parallel. Uses the number of threads specified by the
+      # `:threads` parser option.
+      #
+      # @param [Array] fetch_list merged fetch list from {#merge_fetch_list}.
+      # @return [Array<Block>] the requested alignment blocks
+      def fetch_blocks_merged_parallel(fetch_list)
+        Enumerator.new do |y|
+          total_size = fetch_list.collect { |e| e[1] }.reduce(:+)
+          start = Time.now
+          n_threads = @opts.fetch(:threads, 1)
+          # TODO: break entries up into longer runs for more
+          # sequential I/O
+          jobs = java.util.concurrent.ConcurrentLinkedQueue.new(fetch_list)
+          completed = java.util.concurrent.LinkedBlockingQueue.new(128)
+          threads = []
+          n_threads.times { threads << make_worker(jobs, completed) }
+
+          n_completed = 0
+          while (n_completed < fetch_list.size)
+            c = completed.poll(5, java.util.concurrent.TimeUnit::SECONDS)
+            if c.nil?
+              if threads.find { |t| t.alive? }
+                next
+              else
+                raise "No threads alive, completed #{n_completed}/#{fetch_list.size} jobs!"
+              end
+            end
+            raise "worker failed: #{c}" if c.is_a? Exception
+            c.each do |block|
+              y << block
+            end
+            n_completed += 1
+          end
+          threads.each { |t| t.join }
+          elapsed = Time.now - start
+          $stderr.printf("Fetched blocks from %d threads in %.1fs.\n",
+                         n_threads,
+                         elapsed)
+          mb = total_size / 1048576.0
+          $stderr.printf("%.3f MB processed (%.1f MB/s).\n",
+                         mb,
+                         mb / elapsed)
+        end
+      end
+
+      # Create a worker thread for parallel parsing.
+      #
+      # @see #fetch_blocks_merged_parallel
+      def make_worker(jobs, completed)
+        Thread.new do
+          with_context(@random_access_chunk_size) do |ctx|
+            while true
+              req = jobs.poll
+              break unless req
+              begin
+                n_blocks = req[2].size
+                blocks = ctx.fetch_blocks(*req).to_a
+                if blocks.size != n_blocks
+                  raise "expected #{n_blocks}, got #{blocks.size}: #{e.inspect}"
+                end
+                completed.put(blocks)
+              rescue Exception => e
+                completed.put(e)
+                $stderr.puts "Worker failing: #{e.class}: #{e}"
+                $stderr.puts e.backtrace.join("\n")
+                raise e
+              end
+            end
+          end
+        end
+      end
+
+      # Merge contiguous blocks in the given fetch list, up to
+      # `:merge_max` bytes.
+      #
+      # Returns `[offset, size, [offset1, offset2, ...]]` tuples.
+      def merge_fetch_list(orig_fl)
+        fl = orig_fl.dup
+        r = []
+        until fl.empty? do
+          cur = fl.shift
+          if r.last \
+            && (r.last[0] + r.last[1]) == cur[0] \
+            && (r.last[1] + cur[1]) <= @merge_max
+            # contiguous with the previous one
+            # add to length and increment count
+            r.last[1] += cur[1]
+            r.last[2] << cur[0]
+          else
+            cur << [cur[0]]
+            r << cur
+          end
+        end
+        return r
+      end
+
+      # Parse the header of the MAF file.
+      def _parse_header
+        parse_error("not a MAF file") unless s.scan(/##maf\s*/)
+        vars = parse_maf_vars()
+        align_params = nil
+        while s.scan(/^#\s*(.+?)\n/)
+          if align_params == nil
+            align_params = s[1]
+          else
+            align_params << ' ' << s[1]
+          end
+        end
+        @header = Header.new(vars, align_params)
+        s.skip_until BLOCK_START || parse_error("Cannot find block start!")
+      end
+
+      # Parse all alignment blocks until EOF.
+      #
+      # Delegates to {#parse_blocks_parallel} if `:threads` is set
+      # under JRuby.
+      #
+      # @return [Enumerator<Block>] enumerator of alignment blocks.
+      # @api public
+      def parse_blocks
+        if RUBY_PLATFORM == 'java' && @opts.has_key?(:threads)
+          parse_blocks_parallel
+        else
+          Enumerator.new do |y|
+            until at_end
+              y << parse_block()
+            end
+          end
+        end
+      end
+
+      # Parse alignment blocks with a worker thread.
+      #
+      # @return [Enumerator<Block>] enumerator of alignment blocks.
+      # @api private
+      def parse_blocks_parallel
+        queue = java.util.concurrent.LinkedBlockingQueue.new(128)
+        worker = Thread.new do
+          begin
+            until at_end
+              queue.put(parse_block())
+            end
+            queue.put(:eof)
+          rescue
+            $stderr.puts "worker exiting: #{$!.class}: #{$!}"
+            $stderr.puts $!.backtrace.join("\n")
+          end
+        end
+        Enumerator.new do |y|
+          saw_eof = false
+          while worker.alive?
+            block = queue.poll(1, java.util.concurrent.TimeUnit::SECONDS)
+            if block == :eof
+              saw_eof = true
+              break
+            elsif block
+              y << block
+            end
+          end
+          unless saw_eof
+            raise "worker exited unexpectedly!"
+          end
+        end
+      end
+
+      def each_block
+        until at_end
+          yield parse_block()
+        end
+      end
+
+    end
+
+  end
+  
+end