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/* The Computer Language Shootout
http://shootout.alioth.debian.org/
contributed by Isaac Gouy
*/
import java.io._
import scala.collection.mutable.HashMap
import scala.Console
object knucleotide {
var sequence: String = _
def main(args: Array[String]) = {
val r = new BufferedReader(new InputStreamReader(System.in))
findSequence(">THREE", r)
sequence = nextSequence(r)
r.close
writeFrequencies(1)
writeFrequencies(2)
writeCount("GGT")
writeCount("GGTA")
writeCount("GGTATT")
writeCount("GGTATTTTAATT")
writeCount("GGTATTTTAATTTATAGT")
}
def findSequence(id: String, r: BufferedReader) {
var line = r.readLine
while (line != null) {
val c = line.charAt(0)
if (c == '>' && line.startsWith(id)) return
line = r.readLine
}
}
def nextSequence(r: BufferedReader): String = {
val b = new StringBuffer()
var line = r.readLine
while (line != null) {
val c = line.charAt(0)
if (c == '>') {
return b.toString
} else {
if (c != ';') b.append(line.toUpperCase)
}
line = r.readLine
}
b.toString
}
class Counter(_value: Int) {
var value = _value
def ++() = { value += 1 }
}
def generateFrequencies(length: Int) = {
val d: HashMap[String,Counter] = new HashMap()
def kFrequency(offset: Int, j: Int) = {
val n = sequence.length - j + 1
var i = offset
while (i < n){
val k = sequence.substring(i, i+j)
d.get(k) match {
case None => d += (k -> new Counter(1))
case Some(c) => c++
}
i += j
}
}
for (o <- Iterator.range(0,length)) kFrequency(o,length)
d
}
def writeFrequencies(j: Int) {
val d = generateFrequencies(j)
val n = sequence.length - j + 1.0
val sortedValues = d.toList.sort(
(a,b) => if (a._2.value == b._2.value) a._1 > b._1
else a._2.value > b._2.value )
for (a <- sortedValues)
Console.printf("%s %.3f\n", a._1, a._2.value / n * 100.0)
Console.println
}
def writeCount(fragment: String) {
val d = generateFrequencies(fragment.length)
val count = if (d.contains(fragment)) d(fragment).value else 0
Console.println(count + "\t" + fragment)
}
}
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