/// <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 void Build(IList<int> seq, int sigma, int t = 16, BitmapFromList64 bitmap_builder = null)
{
this.sigma = sigma;
long n = seq.Count;
var L = new long[n];
var counters = new int[sigma + 1];
// counters.Add (0, sigma); <- if ListIFS
for (int i = 0; i < n; ++i) {
var sym = seq [i];
try {
counters [sym + 1] += 1;
} catch (Exception e) {
Console.WriteLine ("===== sigma: {0}, sym: {1}, i: {2}, n: {3}", sigma, sym, i, n);
throw e;
}
}
for (int i = 1; i <= sigma; ++i) {
counters [i] += counters [i - 1];
}
for (int i = 0; i < n; ++i) {
var sym = seq [i];
long long_sym = n * ((long)sym) + i;
L [counters [sym]] = long_sym;
counters [sym] += 1;
}
counters = null;
/**** slow construction ****/
/*****
for (int i = 0; i < n; ++i) {
long s = seq [i];
L [i] = n * s + i;
//L.Add (n * s + i);
}
Array.Sort (L);
*****/
if (bitmap_builder == null) {
bitmap_builder = BitmapBuilders.GetSArray64 ();
}
this.xl_bitmap = bitmap_builder (L, n * sigma);
// now building the permutation for access
var p = new ListGen_MRRR ();
p.Build (this.GetNotIdxPERM (), t, null);
this.perm = p;
}
public void Load(BinaryReader Input)
{
this.N = Input.ReadInt32 ();
int vocsize = Input.ReadInt32 ();
this.InvIndex = new Bitmap[vocsize];
for (int i = 0; i < vocsize; i++) {
this.InvIndex [i] = GenericIO<Bitmap>.Load (Input);
}
this.Lens = GenericIO<Bitmap>.Load (Input);
var p = new ListGen_MRRR ();
p.Load (Input);
p.SetPERM (this.GetNotIdxPERM ());
this.Perm = p;
}
public void Load(BinaryReader Input)
{
this.sigma = Input.ReadInt32 ();
this.xl_bitmap = GenericIO<Bitmap64>.Load (Input);
var p = new ListGen_MRRR ();
p.Load (Input);
p.SetPERM (this.GetNotIdxPERM ());
this.perm = p;
}