public CompressedSuffixArray(uint[] compressedSuffixArray, DnaBwt bwt, OccurrenceArray[] occ, uint[] c)
{
_baseArray = compressedSuffixArray;
_bwt = bwt;
_occ = occ;
_c = c;
Length = bwt.Length;
}
public static CompressedSuffixArray CreateFromFile(string fileName, DnaBwt bwt, OccurrenceArray[] occ, uint[] c)
{
var buffer = File.ReadAllBytes(fileName);
uint[] compressedSufArray = new uint[buffer.Length/4];
for (int i = 0; i < compressedSufArray.Length; i++)
{
compressedSufArray[i] = BitConverter.ToUInt32(buffer, i*4);
}
CompressedSuffixArray csa = new CompressedSuffixArray(compressedSufArray, bwt, occ, c);
return csa;
}
public Sequencer(uint[] c, OccurrenceArray[] occurrences, OccurrenceArray[] occurrencesRev,
CompressedSuffixArray suffixArray, CompressedSuffixArray suffixArrayRev,
int threadCount)
{
_c = c;
_occurrences = occurrences;
_occurrencesRev = occurrencesRev;
_suffixArray = suffixArray;
_suffixArrayRev = suffixArrayRev;
_database = new AlignmentDatabase("temp.db");
_threadCount = threadCount;
}
public static void WriteToFile(string fileName, OccurrenceArray[] occ)
{
using (var file = File.Open(fileName, FileMode.Create))
{
BinaryWriter writer = new BinaryWriter(file);
for (int i = 0; i < occ[0]._compressedOcc.Length; i++)
{
for (int dnaBase = 0; dnaBase < 4; dnaBase++)
{
var value = occ[dnaBase]._compressedOcc[i];
writer.Write(value);
}
}
}
}
public static OccurrenceArray[] CreateOccurrenceArrays(DnaBwt bwt)
{
OccurrenceArray[] occArrays = new OccurrenceArray[4]
{
new OccurrenceArray(bwt, 0, new int[bwt.Length/CompressFactor+1]),
new OccurrenceArray(bwt, 1, new int[bwt.Length/CompressFactor+1]),
new OccurrenceArray(bwt, 2, new int[bwt.Length/CompressFactor+1]),
new OccurrenceArray(bwt, 3, new int[bwt.Length/CompressFactor+1])
};
int[] sums = new int[4];
for (long i = 0; i < bwt.Length; i++)
{
if (bwt[i] >= 0)
sums[bwt[i]]++;
if (i%CompressFactor == 0)
{
occArrays[0][i] = sums[0];
occArrays[1][i] = sums[1];
occArrays[2][i] = sums[2];
occArrays[3][i] = sums[3];
}
}
return occArrays;
}
public Sequencer(uint[] c, OccurrenceArray[] occurrences, OccurrenceArray[] occurrencesRev,
CompressedSuffixArray suffixArray, CompressedSuffixArray suffixArrayRev)
: this(c, occurrences, occurrencesRev,
suffixArray, suffixArrayRev, Environment.ProcessorCount + 2)
{
}