1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
|
/* The Computer Language Benchmarks Game
http://shootout.alioth.debian.org/
contributed by Isaac Gouy
fixed by Iulian Dragos
fixed by Meiko Rachimow
*/
import java.io._
import scala.collection.mutable.{HashTable, HashEntry}
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): Unit = {
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
}
def generateFrequencies(length: Int) = {
val bag: HashBag[String] = new HashBag()
def kFrequency(offset: Int, j: Int) = {
val n = sequence.length - j + 1
var i = offset
while (i < n){ bag += sequence.substring(i,i+j); i = i+j }
}
for (val o <- Iterator.range(0,length)) kFrequency(o,length)
bag
}
def writeFrequencies(j: Int) = {
val bag = generateFrequencies(j)
val n = sequence.length - j + 1.0
val sortedValues = bag.elements.toList.sort(
(a,b) => if (a.value == b.value) a.key > b.key
else a.value > b.value )
for (val a <- sortedValues)
Console.printf("%s %.3f\n", a.key, a.value / n * 100.0)
Console.println
}
def writeCount(fragment: String) = {
val bag = generateFrequencies(fragment.length)
Console.println( bag.findOccurrences(fragment) + "\t" + fragment )
}
}
class HashBag[A] extends HashTable[A] {
protected type Entry = Counter[A]
protected def entryKey(e: Entry) = e.key
def elements = entries
def +=(elem: A): Unit = {
var bucket = table(index(elemHashCode(elem))).asInstanceOf[Entry]
while (bucket ne null) {
if (elemEquals(entryKey(bucket), elem)){
bucket.inc
return
}
bucket = bucket.next
}
addEntry(new Entry(elem, 1))
}
def findOccurrences(elem: A): Int = {
var bucket = table(index(elemHashCode(elem))).asInstanceOf[Entry]
while (bucket ne null) {
if (elemEquals(entryKey(bucket), elem)){
return bucket.value
}
bucket = bucket.next
}
return 0
}
/*
def -=(elem: A): Unit = {
var bucket = table(index(elemHashCode(elem)))
while (!bucket.isEmpty) {
if (elemEquals(entryKey(bucket.head), elem)){
bucket.head.dec
if (bucket.head.value == 0) removeEntry(elem)
return
}
bucket = bucket.tail
}
}
*/
}
protected class Counter[A](k: A, v: Int) extends AnyRef with HashEntry[A, Counter[A]] {
val key = k
var value = v
def inc = { value = value + 1 }
def dec = { value = value - 1 }
}
|
