public int SearchWithDiff(string src, string sub, int diff)
{
int srcLen = src.Length;
int subLen = sub.Length;
if (srcLen < subLen)
return -1;
RkSearchHash hash = new RkSearchHash();
long target = hash.GenerateHash(sub);
long rolHash = hash.GenerateHash(src.Substring(0, subLen));
int i = 0;
int limit = srcLen - subLen;
int rolDiff = 0;
for (i = 0; i < limit; i++)
{
rolDiff = CountSetPairs((ulong)(target ^ rolHash));
if (rolDiff <= diff)
{
return i;
}
rolHash = hash.GenerateRollingHash(src[i], src[i + subLen], rolHash, subLen);
}
rolDiff = CountSetPairs((ulong)(target ^ rolHash));
if (rolDiff <= diff)
{
return i;
}
return -1;
}
public int Search(string src, string substr)
{
int srcLen = src.Length;
int subLen = substr.Length;
if (srcLen < subLen)
return -1;
RkSearchHash hash = new RkSearchHash();
long target = hash.GenerateHash(substr);
long rolHash = hash.GenerateHash(src.Substring(0, subLen));
int i = 0;
int limit = srcLen - subLen;
for (i = 0; i < limit; i++)
{
if (rolHash == target)
{
return i;
}
rolHash = hash.GenerateRollingHash(src[i], src[i + subLen], rolHash, subLen);
}
// Avoid per loop comparison, of i + susbstr.Length
if (rolHash == target)
{
return i;
}
return -1;
}
public void TestHash()
{
RkSearchHash hash = new RkSearchHash();
long h = hash.GenerateHash("ACGT");
Console.WriteLine("h: {0}", h);
//Generate rolling hash for CGTA
h = hash.GenerateRollingHash('A', 'A', h, 4);
Console.WriteLine("h: {0}", h);
Assert.AreEqual(h, hash.GenerateHash("CGTA"));
//Generate rolling hash for GTAG from CGTA
h = hash.GenerateRollingHash('C', 'G', h, 4);
Console.WriteLine("h: {0}", h);
Assert.AreEqual(h, hash.GenerateHash("GTAG"));
}
