1 files changed, 0 insertions, 147 deletions
diff --git a/test/pending/shootout/revcomp.scala-3.scala b/test/pending/shootout/revcomp.scala-3.scala
deleted file mode 100644
index 39a0409127..0000000000
--- a/test/pending/shootout/revcomp.scala-3.scala
+++ /dev/null
@@ -1,147 +0,0 @@
-/* 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)
-         }
-      }
-   }
-
-}