class ABSee

# File lib/absee.rb, line 81
def get_calledSequence()
  return @calledSequence
end

# File lib/absee.rb, line 91
def get_peakIndexes()
  return @peakIndexes
end

# File lib/absee.rb, line 86
def get_qualityScores()
  return @qualityScores
end

# File lib/absee.rb, line 61
def get_traceA()
  return @traceA
end

# File lib/absee.rb, line 76
def get_traceC()
  return @traceC
end

# File lib/absee.rb, line 66
def get_traceG()
  return @traceG
end

# File lib/absee.rb, line 71
def get_traceT()
  return @traceT
end

# File lib/absee.rb, line 33
def read(filename)
  if filename.instance_of?(StringIO) or filename.instance_of?(File)
    abFile = filename
  elsif filename.instance_of? String
    #opens ab1 as a File object
    abFile = open(filename)
  else
    raise "Don't know what to do with input type #{filename.class}"
  end

  byteArray = ""
  #// here we read the first four bytes. It is important
  #// to remember that we do not seek back the file, just
  #// because it is not necessary to do this.
  abFile.seek(0, IO::SEEK_SET)
  abFile.read(4, byteArray)
  #ABIF file indicator
  if byteArray == "ABIF"
    processAB(abFile)
  else
    raise "file not recognized as ABIF"
  end
end

# File lib/absee.rb, line 260
def gatherInformation(directory, numElements)
  numSamples = 0
  numBases = 0

  (0..(numElements-1)).each do |i|
    if (get(directory[i],"name") == "DATA") && (get(directory[i], "tag_number") == 9)
      numSamples = get(directory[i], "number_of_elements") #number of elements
    else
      if (get(directory[i], "name") == "PBAS") && (get(directory[i], "tag_number") == 2)
        numBases = get(directory[i], "number_of_elements") #number of elements
      end
    end
  end

  return numSamples, numBases
end

# File lib/absee.rb, line 232
def get(array, element)
  if element == "name"
    return array[0]
  elsif element == "tag_number"
    return array[1]
  elsif element == "element_type"
    return array[2]
  elsif element == "element_size"
    return array[3]
  elsif element == "number_of_elements"
    return array[4]
  elsif element == "data_size"
    return array[5]
  elsif element == "data_offset"
    return array[6]
  else
    return array[0]
  end
end

# File lib/absee.rb, line 337
def getCalledSequence(filestream, directory, numElements, numBases)
  calledSequence = []
  (0..numElements-1).each do |i|
    if (get(directory[i], "name") == "PBAS") && (get(directory[i], "tag_number") == 2)
      byteArray_seq = ""
      filestream.seek(get(directory[i], "data_offset"))
      filestream.read(numBases,byteArray_seq)
      (0..numBases-1).each do |j|
        calledSequence[j] = byteArray_seq.getbyte(j).chr
      end
    end
  end
  return calledSequence
end

# File lib/absee.rb, line 387
def getPeakIndexes(filestream, directory, numElements, numBases)
  peakIndexes = []
  (0..numElements-1).each do |i|
    if (get(directory[i], "name") == "PLOC") && (get(directory[i], "tag_number") == 2)
      byteArray_peak = ""
      filestream.seek(get(directory[i], "data_offset"), IO::SEEK_SET)
      filestream.read(get(directory[i], "number_of_elements")*4, byteArray_peak)
      pos = -1
      (0..numBases-1).each do |j|
        peakIndex = byteArray_peak.getbyte(pos+=1) << 8 | byteArray_peak.getbyte(pos+=1)
        peakIndexes[j] = peakIndex
      end
    end
  end
  return peakIndexes
end

# File lib/absee.rb, line 362
def getQualityScores(filestream, directory, numElements, numBases)
  qualityScore = []
  (0..numElements-1).each do |i|
    if (get(directory[i], "name") == "PCON") && (get(directory[i], "tag_number") == 2)
      byteArray_seq = ""
      filestream.seek(get(directory[i], "data_offset"))
      filestream.read(numBases,byteArray_seq)
      (0..numBases-1).each do |j|
        qualityScore[j] = byteArray_seq.getbyte(j)
      end
    end
  end
  return qualityScore
end

# File lib/absee.rb, line 287
def getSamples(filestream, directory, numElements, numSamples)
  samples_a = []
  samples_c = []
  samples_g = []
  samples_t = []

  #// we guess the order being GATC, as Ferreira and Staden does
  (0..numElements-1).each do |i|
    tag_number = get(directory[i], "tag_number")
    if (get(directory[i],"name") == "DATA") && ([9,10,11,12].include? tag_number)
      byteArray_samples = ""
      filestream.seek(get(directory[i],"data_offset"), IO::SEEK_SET)
      filestream.read(get(directory[i], "number_of_elements")*2, byteArray_samples)
      pos = -1
      if tag_number == 9 #G
        (0..numSamples-1).each do |j|
          value = byteArray_samples.getbyte(pos+=1) << 8 | byteArray_samples.getbyte(pos+=1)
          samples_g[j] = value
        end
      elsif tag_number == 10 #A
        (0..numSamples-1).each do |j|
          value = byteArray_samples.getbyte(pos+=1) << 8 | byteArray_samples.getbyte(pos+=1)
          samples_a[j] = value
        end
      elsif tag_number == 11 #T
        (0..numSamples-1).each do |j|
          value = byteArray_samples.getbyte(pos+=1) << 8 | byteArray_samples.getbyte(pos+=1)
          samples_t[j] = value
        end
      else #C
        (0..numSamples-1).each do |j|
          value = byteArray_samples.getbyte(pos+=1) << 8 | byteArray_samples.getbyte(pos+=1)
          samples_c[j] = value
        end
      end
    end
  end
  return samples_a, samples_c, samples_g, samples_t
end

# File lib/absee.rb, line 106
def processAB(filestream)
  #// here, we can read the ABIF header information
  version = readUnsignedByte_2(4, filestream)
  #// major versions greater than 1 are not supported
  #// Applied Biosystems rules
  if (version / 100 > 1)
    raise "ABIF version #{version} not supported (only supported for version less than 1)"
  end
  #// we just read ABIF, so we don't need more information than that
  numElements = readUnsignedByte_4(18, filestream)
  dataOffset = readUnsignedByte_4(26, filestream)
  directory = readDirectoryEntry(filestream, dataOffset, numElements)
  numSamples, numBases = gatherInformation(directory, numElements)
  samples_a, samples_c, samples_g, samples_t = getSamples(filestream, directory, numElements, numSamples)
  called_sequence = getCalledSequence(filestream, directory, numElements, numBases)
  quality_scores = getQualityScores(filestream, directory, numElements, numBases)
  peak_indexes = getPeakIndexes(filestream, directory, numElements, numBases)
  ##return samples_a, samples_c, samples_g, samples_t, called_sequence, peak_indexes, quality_scores
  @traceA = samples_a
  @traceC = samples_c
  @traceG = samples_g
  @traceT = samples_t
  @calledSequence = called_sequence
  @qualityScores = quality_scores
  @peakIndexes = peak_indexes
  nil
end

# File lib/absee.rb, line 178
def readDirectoryEntry(filestream, dataOffset, numElements)
  filestream.seek(dataOffset, IO::SEEK_SET)
  byteArray = ""
  filestream.read(28*numElements, byteArray)
  directory = []
  pos = -1


  #directory structure
  #[name, tag number, element type, element size, number of elements, data size, data offset]
  (0..(numElements-1)).each do |i|
    directory[i] = []
    #// name
    name = ""
    name << byteArray.getbyte(pos+=1).chr
    name << byteArray.getbyte(pos+=1).chr
    name << byteArray.getbyte(pos+=1).chr
    name << byteArray.getbyte(pos+=1).chr
    directory[i] << name
    #// tag number
    tag_number = byteArray.getbyte(pos+=1)<<24 | byteArray.getbyte(pos+=1)<<16 | byteArray.getbyte(pos+=1)<<8 | byteArray.getbyte(pos+=1)
    directory[i] << tag_number
    #// element type
    element_type = byteArray.getbyte(pos+=1)<<8 | byteArray.getbyte(pos+=1)
    directory[i] << element_type
    #// element size
    element_size = byteArray.getbyte(pos+=1)<<8 | byteArray.getbyte(pos+=1)
    directory[i] << element_size
    #// number of elements
    number_of_elements = byteArray.getbyte(pos+=1)<<24 | byteArray.getbyte(pos+=1)<<16 | byteArray.getbyte(pos+=1)<<8 | byteArray.getbyte(pos+=1)
    directory[i] << number_of_elements
    #// data size
    data_size = byteArray.getbyte(pos+=1)<<24 | byteArray.getbyte(pos+=1)<<16 | byteArray.getbyte(pos+=1)<<8 | byteArray.getbyte(pos+=1)
    directory[i] << data_size
    #// data offset
    data_offset = byteArray.getbyte(pos+=1)<<24 | byteArray.getbyte(pos+=1)<<16 | byteArray.getbyte(pos+=1)<<8 | byteArray.getbyte(pos+=1)
    directory[i] << data_offset
    #// we do not save the dataHandle field
    pos += 4;
  end
  return directory
end

# File lib/absee.rb, line 142
def readUnsignedByte_2(offset, filestream)
  #// most significant byte first
  #// |byte0|byte1| <= |unsigned int|
  byteArray = ""
  filestream.seek(offset, IO::SEEK_SET)
  byteArray = filestream.read(2, byteArray)
  return (byteArray.getbyte(0) << 8) | byteArray.getbyte(1)
end

# File lib/absee.rb, line 159
def readUnsignedByte_4(offset, filestream)
  byteArray = ""
  filestream.seek(offset, IO::SEEK_SET)
  byteArray = filestream.read(4, byteArray)
  #// most significant byte first
  #// |byte0|byte1|byte2|byte3| <= |unsigned int|
  return (byteArray.getbyte(0)<<24) | (byteArray.getbyte(1)<<16) | (byteArray.getbyte(2)<<8) | byteArray.getbyte(3)
end