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/* The Computer Language Shootout
http://shootout.alioth.debian.org/
contributed by Isaac Gouy
*/
import java.io._
import scala.collection.mutable.Stack
object revcomp {
def main(args: Array[String]) = {
val out = new FastaOutputStream(System.out)
val in = new FastaInputStream(System.in)
out.writeReverseComplement( in.readSequenceStack )
out.writeReverseComplement( in.readSequenceStack )
out.writeReverseComplement( in.readSequenceStack )
in.close
out.close
}
}
trait FastaByteStream {
val nl = '\n'.toByte
type Line = Array[Byte]
type LineStack = Stack[Line]
}
// extend the Java BufferedInputStream class
final class FastaInputStream(in: InputStream)
extends BufferedInputStream(in) with FastaByteStream {
val gt = '>'.toByte
val sc = ';'.toByte
def readSequenceStack(): Tuple2[Line,LineStack] = {
var header: Line = null
val lines: LineStack = new Stack
var line = readLine()
while (line != null) {
val c = line(0)
if (c == gt){ // '>'
if (header == null){
header = line
} else {
pos = pos - line.length - 1 // reposition to start of line
return (header,lines)
}
} else {
if (c != sc) lines push line // ';'
}
line = readLine()
}
return (header,lines)
}
def readLine() = {
var bytes: Line = null
if (in == null) bytes
else {
mark(128) // mark the start of the line
if (count == 0) read() // fill buffer
var i = markpos
while (i < count && buf(i) != nl) i = i + 1
if (i >= count){ // line extends past end of buffer
pos = i; read(); i = pos; // fill buffer again
while (i < count && buf(i) != nl) i = i + 1
}
if (i < count){
bytes = new Array(i - markpos)
System.arraycopy(buf, markpos, bytes, 0, i - markpos);
pos = i+1
}
}
bytes
}
}
// extend the Java BufferedOutputStream class
final class FastaOutputStream(in: OutputStream)
extends BufferedOutputStream(in) with FastaByteStream {
private val IUB = IUBCodeComplements
private def IUBCodeComplements() = {
val code = "ABCDGHKMNRSTVWYabcdghkmnrstvwy".getBytes
val comp = "TVGHCDMKNYSABWRTVGHCDMKNYSABWR".getBytes
val iub: Array[Byte] = new Array( 'z'.toByte )
for (indexValue <- code zip comp)
indexValue match { case (i,v) => iub(i) = v }
iub
}
def writeReverseComplement(sequence: Tuple2[Line,LineStack]) = {
def inplaceComplementReverse(b: Array[Byte]) = {
var i = 0
var j = b.length - 1
while (i < j){
val swap = b(i)
b(i) = IUB( b(j) )
b(j) = IUB( swap )
i = i + 1
j = j - 1
}
if (i == j) b(i) = IUB( b(i) )
}
sequence match {
case (header,lines) => {
write(header); write(nl)
val k = if (lines.isEmpty) 0 else lines.top.length
val LineLength = 60
val isSplitLine = k < LineLength
var isFirstLine = true
while (!lines.isEmpty) {
val line = lines.pop
inplaceComplementReverse(line)
if (isSplitLine){
if (isFirstLine){ write(line); isFirstLine = false }
else { write(line,0,LineLength-k); write(nl); write(line,LineLength-k,k) }
}
else { write(line); write(nl) }
}
if (isSplitLine && !isFirstLine) write(nl)
}
}
}
}
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