public static SequenceBuilder GetIISketches(int sketch_blocksize,
BitmapFromList bitmap_builder = null)
{
if (bitmap_builder == null) {
bitmap_builder = BitmapBuilders.GetSArray();
}
return delegate (IList<int> seq, int sigma) {
var iis = new InvIndexSketches ();
iis.BitmapBuilder = bitmap_builder;
iis.Build (seq, sigma, sketch_blocksize);
return iis;
};
}
public void Build(KnrSeqSearch knr, int min_occ, BitmapFromList bitmap_builder = null)
{
this.DB = knr.DB;
this.K = knr.K;
this.MINOCC = min_occ;
// this.MAXCAND = knr.MAXCAND;
this.R = knr.R;
int sigma = this.R.DB.Count;
if (bitmap_builder == null) {
bitmap_builder = BitmapBuilders.GetDiffSetRL2(63, new EliasDelta());
}
this.INVINDEX = new IRankSelect[sigma];
var list = new List<int>();
for (int i = 0; i < sigma; ++i) {
list.Clear();
var unravel = knr.SEQ.Unravel(i);
var count = unravel.Count1;
for (int s = 1; s <= count; ++s) {
list.Add (unravel.Select1(s) / this.K);
}
this.INVINDEX[i] = bitmap_builder(list);
}
}
public void Build(string sa_name, BitmapFromList create_bitmap)
{
using (var Input = new BinaryReader (File.OpenRead (sa_name + ".structs"))) {
this.newF = RankSelectGenericIO.Load (Input);
int len = this.newF.Count1;
this.charT = new int[len];
// Console.WriteLine ("*****>> charT => {0} bytes", this.charT.Length * 4);
PrimitiveIO<int>.ReadFromFile (Input, len, this.charT);
}
using (var Input = new BinaryReader (File.OpenRead (sa_name + ".psi"))) {
this.InvIndex = new IRankSelect[this.AlphabetSize];
int curr = 0;
for (int i = 1; i <= this.AlphabetSize; i++) {
int next;
if (i == this.AlphabetSize) {
next = this.newF.Count;
} else {
next = this.newF.Select1 (i + 1);
}
int len = next - curr;
var L = new int[len];
PrimitiveIO<int>.ReadFromFile (Input, len, L);
this.InvIndex [i - 1] = create_bitmap (L);
curr = next;
}
}
using (var Input = new BinaryReader (File.OpenRead (sa_name + ".samples"))) {
this.SA_sample_step = Input.ReadInt16 ();
this.SA_marked = RankSelectGenericIO.Load (Input);
var _samples = new ListIFS ();
_samples.Load (Input);
var _invsamples = new ListIFS ();
_invsamples.Load (Input);
this.SA_samples = _samples;
this.SA_invsamples = _invsamples;
}
}
/// <summary>
/// Builds the index for the sequence
/// </summary>
public void Build(IList<int> sequence, int alphabet_size, int t = 16,
BitmapFromList rowbuilder = null, BitmapFromBitStream lenbuilder = null)
{
if (rowbuilder == null) {
rowbuilder = BitmapBuilders.GetSArray ();
}
if (lenbuilder == null) {
lenbuilder = BitmapBuilders.GetGGMN_wt (12);
}
var invindex = new IList<int>[alphabet_size];
for (int i = 0; i < alphabet_size; i++) {
invindex [i] = new List<int> ();
}
int pos = 0;
foreach (var c in sequence) {
invindex [c].Add (pos);
pos++;
}
pos = 0;
this.N = sequence.Count;
this.InvIndex = new Bitmap[alphabet_size];
var lens = new BitStream32 ();
for (int i = 0; i < alphabet_size; i++) {
if (i % 1000 == 0) {
if (i % 10000 == 0) {
Console.WriteLine ();
Console.Write ("*** InvIndexXLBSeq {0}/{1}", i, alphabet_size);
} else {
Console.Write (", {0}", i);
}
}
this.InvIndex [i] = rowbuilder (invindex [i]);
lens.Write (true);
lens.Write (false, invindex [i].Count);
invindex [i] = null;
}
lens.Write (true);
Console.WriteLine ();
Console.WriteLine ("done, now saving permutation and the Len bitmap");
this.Lens = lenbuilder (new FakeBitmap (lens));
var p = new ListGen_MRRR ();
p.Build (this.GetNotIdxPERM (), t, null);
Console.WriteLine ("done");
this.Perm = p;
}
public static SequenceBuilder GetInvIndexXLBSeq(short t = 16, BitmapFromList row_builder = null, BitmapFromBitStream len_builder = null)
{
if (row_builder == null) {
row_builder = BitmapBuilders.GetSArray ();
}
if (len_builder == null) {
len_builder = BitmapBuilders.GetGGMN_wt (12);
}
return delegate (IList<int> seq, int sigma) {
var iis = new InvIndexXLBSeq();
iis.Build (seq, sigma, t, row_builder, len_builder);
return iis;
};
}
public static SequenceBuilder GetIISketches(
BitmapFromList bitmap_builder, int sketch_blocksize
)
{
return delegate (IList<int> seq, int sigma) {
var iis = new InvIndexSketches ();
iis.BitmapBuilder = bitmap_builder;
iis.Build (seq, sigma, sketch_blocksize);
return iis;
};
}
public static SequenceBuilder GetIISeq(
BitmapFromList bitmap_builder
)
{
return delegate (IList<int> seq, int sigma) {
var iis = new InvIndexSeq ();
iis.BitmapBuilder = bitmap_builder;
iis.Build (seq, sigma);
return iis;
};
}