Begone t1737...

1 files changed, 147 insertions, 0 deletions

diff --git a/test/pending/shootout/revcomp.scala-3.scala b/test/pending/shootout/revcomp.scala-3.scala
new file mode 100644
index 0000000000..ae12f0499b
--- /dev/null
+++ b/test/pending/shootout/revcomp.scala-3.scala
@@ -0,0 +1,147 @@
+/* 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(): Pair[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 Pair(header,lines)
+            }
+         } else {
+            if (c != sc) lines push line       // ';'
+         }
+         line = readLine()
+      }
+      return Pair(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 Pair(i,v) => iub(i) = v }
+
+      iub
+   }
+
+   def writeReverseComplement(sequence: Pair[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 Pair(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)
+         }
+      }
+   }
+
+}