public DnaBwt(ISaisString text, LongSuffixArray suffixArray)
{
Length = text.Length;
_bwt = new byte[Length / 4 + (Length % 4 != 0 ? 1 : 0)];
for (long i = 1; i < suffixArray.Length; i++)
{
if (((long)suffixArray[i]) - 1 >= 0) continue;
_sentinelIndex = i;
break;
}
for (long i = 0; i < suffixArray.Length; i++)
{
var textIndex = ((long)suffixArray[i]) - 1;
if (textIndex < 0) continue;
var character = text[textIndex] - 1;
this[i] = (int)character; // ISaisString values range from 0 to 4, 0 being sentinel
}
}
private static void SA_IS(ISaisString s, LongSuffixArray SA, long n, long alphabetSize)
{
DateTime typeStart = DateTime.Now;
TypeArray T = new TypeArray(n);
T[n - 2] = SaisType.L;
T[n - 1] = SaisType.S;
for (long textIndex = n - 3; textIndex >= 0; textIndex--)
{
T[textIndex] = s[textIndex] < s[textIndex + 1] ||
(s[textIndex] == s[textIndex + 1] && T[textIndex + 1] == SaisType.S)
? SaisType.S
: SaisType.L;
}
Console.WriteLine("Type assigning took {0} seconds", DateTime.Now.Subtract(typeStart).TotalSeconds);
uint[] bucket = new uint[alphabetSize + 1];
DateTime lmsSortStart = DateTime.Now;
// Set bucket pointers to ends
GetBucketHeads(s, bucket, alphabetSize, true);
for (long saIndex = 0; saIndex < n; saIndex++)
SA[saIndex] = -1;
for (long textIndex = 1; textIndex < n; textIndex++)
if (IsLmsCharacter(T, textIndex))
{
var textChar = s[textIndex];
bucket[textChar] = bucket[textChar] - 1;
var saIndex = bucket[textChar];
SA[saIndex] = textIndex;
}
InduceSaL(T, SA, s, bucket, n, alphabetSize, false);
InduceSaS(T, SA, s, bucket, n, alphabetSize, true);
Console.WriteLine("LMS-substring sorting took {0} seconds", DateTime.Now.Subtract(lmsSortStart).TotalSeconds);
// Move LMS characters into first half of SA array
long n1 = 0;
for (long saIndex = 0; saIndex < n; saIndex++)
if (IsLmsCharacter(T, SA[saIndex]))
SA[n1++] = SA[saIndex];
// Name the LMS-substrings according to their order
DateTime namingStart = DateTime.Now;
for (long saIndex = n1; saIndex < n; saIndex++)
SA[saIndex] = -1;
long name = 0, prev = -1; // TODO: change?
for (long saIndex = 0; saIndex < n1; saIndex++)
{
long pos = SA[saIndex];
bool diff = false;
for (long d = 0; d < n; d++)
if (prev == -1 || s[pos + d] != s[prev + d]
|| T[pos + d] != T[prev + d])
{
diff = true;
break;
}
else if (d > 0 && (IsLmsCharacter(T, pos + d) || IsLmsCharacter(T, prev + d)))
break;
if (diff)
{
name++;
prev = pos;
}
pos = (pos % 2 == 0) ? pos / 2 : (pos - 1) / 2;
SA[n1 + pos] = name - 1;
}
for (long i = n - 1, j = n - 1; i >= n1; i--)
if (SA[i] >= 0)
SA[j--] = SA[i];
Console.WriteLine("Naming took {0} seconds", DateTime.Now.Subtract(namingStart).TotalSeconds);
// Recursive call if names are not unique
LongSuffixArray SA1 = new LongSuffixArray(SA.ParentArray, 0, n1);
LongLevelNString s1 = new LongLevelNString(SA.ParentArray, SA.Offset + n - n1, n1);
if (name < n1)
SA_IS(s1, SA1, n1, name - 1);
else // Otherwise SA1 can be solved directly
for (long i = 0; i < n1; i++)
SA1[s1[i]] = i;
// Set bucket pointers to end of buckets
bucket = new uint[alphabetSize + 1];
GetBucketHeads(s, bucket, alphabetSize, true);
// Replace s1 with P
for (long i = 1, j = 0; i < n; i++)
if (IsLmsCharacter(T, i))
s1[j++] = i;
// Replace SA1 with sorted P
for (int i = 0; i < n1; i++)
SA1[i] = s1[SA1[i]];
// Place sorted LMS characters
DateTime step1Start = DateTime.Now;
for (long i = n1; i < n; i++)
SA[i] = -1;
for (long i = n1 - 1; i >= 0; i--)
{
var textPos = SA[i];
SA[i] = -1;
var character = s[textPos];
bucket[character] = bucket[character] - 1;
var saIndex = bucket[character];
SA[saIndex] = textPos;
}
Console.WriteLine("Step 1 took {0} seconds", DateTime.Now.Subtract(step1Start).TotalSeconds);
// Induce sort L characters from LMS characters
DateTime step2Start = DateTime.Now;
InduceSaL(T, SA, s, bucket, n, alphabetSize, false);
Console.WriteLine("Step 2 took {0} seconds", DateTime.Now.Subtract(step2Start).TotalSeconds);
// Induce sort remaining S characters
DateTime step3Start = DateTime.Now;
InduceSaS(T, SA, s, bucket, n, alphabetSize, true);
Console.WriteLine("Step 3 took {0} seconds", DateTime.Now.Subtract(step3Start).TotalSeconds);
}
public static LongSuffixArray CreateSuffixArray(ISaisString text)
{
LongSuffixArray suffixArray = new LongSuffixArray(new ulong[text.Length / 2 + (text.Length % 2 == 0 ? 0 : 1)], 0, text.Length);
SA_IS(text, suffixArray, suffixArray.Length, 4);
return suffixArray;
}
private static void InduceSaS(TypeArray T, LongSuffixArray SA, ISaisString s, uint[] bucket, long n, long alphabetSize, bool end)
{
GetBucketHeads(s, bucket, alphabetSize, end);
for (long i = n - 1; i >= 0; i--)
{
long textPos = SA[i] - 1;
if (textPos >= 0 && T[textPos] == SaisType.S)
{
var character = s[textPos];
bucket[character] = bucket[character] - 1;
var saIndex = bucket[character];
SA[saIndex] = textPos;
}
}
}
