Repeated DNA Sequences

All DNA is composed of a series of nucleotides abbreviated as A, C, G, and T, for

example: "ACGAATTCCG". When studying DNA, it is sometimes useful to identify

repeated sequences within the DNA.

Write a function to find all the 10-letter-long sequences (substrings) that occur more

than once in a DNA molecule.

For example,

Given s = "AAAAACCCCCAAAAACCCCCCAAAAAGGGTTT",

Return:
["AAAAACCCCC", "CCCCCAAAAA"].

Java Solution

The key to solve this problem is that each of the 4 nucleotides can be stored in 2 bits.

So the 10-letter-long sequence can be converted to 20-bits-long integer.

2bits就可以区分4个不同的字符，所以20bits就可以区分10个长度的不同字符。

如果用暴力搜索，需要O(n*n)，就会出现超时。

public List<String> findRepeatedDnaSequences(String s) {
List<String> result = new ArrayList<String>();
int len = s.length();
if (len < 10)
return result;
Map<Character, Integer> map = new HashMap<Character, Integer>();
map.put('A', 0);
map.put('C', 1);
map.put('G', 2);
map.put('T', 3);
Set<Integer> temp = new HashSet<Integer>();
Set<Integer> added = new HashSet<Integer>();
int hash = 0;
for (int i = 0; i < len; i++) {
if (i < 9){
//each ACGT fit 2 bits, so left shift 2
hash = (hash << 2) + map.get(s.charAt(i));
}else {
hash = (hash << 2) + map.get(s.charAt(i));
//make length of hash to be 20
hash = hash &  (1 << 20) - 1;
if (temp.contains(hash) && !added.contains(hash)) {
result.add(s.substring(i - 9, i + 1));
added.add(hash); //track added
} else
temp.add(hash);
}
}
return result;
}