[leetcode] Repeated DNA sequence

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.

最开始的思路是：存入hashmap所有10以后的10个字符, 然后从头遍历，存在则删掉，但是这样会memory limit exceed。代码如下

public class Solution {
    public ArrayList<String> findRepeatedDnaSequences(String s) {
        HashMap<String, Integer> map = new HashMap<String, Integer>();
        ArrayList<String> result = new ArrayList<String>();
        if(s.length() < 20)
            return result;
        for(int i = 10; i <= s.length() - 10; i++){
            map.put(s.substring(i, i+10), i);
        }
        for(int j = 0; j <= s.length() - 20; j++){
            if(map.containsKey(s.substring(j,j+10))){
                result.add(s.substring(j,j+10));
                map.remove(s.substring(j+10,j+20));
            }
        }
        return result;
    }
}

改进方案是：

hashmap的key是string，如果每次存入10个字符的string，很占空间，所以用2 bit数据来表示ACGT, 这样用20bit就能表示10个字符的字符串，此外用linkedlist代替ArrayList, 用boolean代替Integer。其中boolean，第一次加入hashmap是否为false，以后每当有相同string时，存入true，覆盖false，从而避免重复存取

public class Solution {
    public int myHash(String s){
        int code = 0;
        for(int i = 0; i < s.length(); i++){
            code <<= 2;
            if(s.charAt(i) == 'C'){
                code += 1;
            }else if(s.charAt(i) == 'G'){
                code += 2;
            }else if(s.charAt(i) == 'T'){
                code += 3;
            }
        }
        return code;
    }
    public List<String> findRepeatedDnaSequences(String s) {  
        List<String> list = new LinkedList<String>();  
        if(s == null || s.length() < 10) return list;  
  
        HashMap<Integer, Boolean> table = new HashMap<Integer, Boolean>();  
        int L = 10;  
        for(int i = 0; i <= s.length() - L; i++){  
            String sub = s.substring(i, i + L);  
            int hs = myHash(sub);  
            if(table.containsKey(hs)){  
                if(!table.get(hs)) list.add(sub);  
                table.put(hs, true);  
            }else{  
                table.put(hs, false);  
            }  
        }  
        return list;  
    }  
}