public KnrFP(KnrFP inputDB, int new_n, int new_K = -1)
{
this.K = new_K;
this.Fingerprints = new StringSpace<int> ();
this.Fingerprints.seqs.Capacity = new_n;
this.IdxRefs = inputDB.IdxRefs;
if (new_K <= 0) {
for (int i = 0; i < new_n; ++i) {
var u = inputDB.Fingerprints.seqs [i];
this.Fingerprints.Add (u);
}
} else {
if (new_K > inputDB.Fingerprints.seqs [0].Length) {
throw new ArgumentOutOfRangeException("new_K > old_K need a complete re-construction of the transformation");
}
for (int i = 0; i < new_n; ++i) {
var u = inputDB.Fingerprints.seqs [i];
var v = new int[new_K];
for (int j = 0; j < new_K; ++j) {
v [j] = u [j];
}
this.Fingerprints.Add (v);
}
}
}
public void Load(BinaryReader Input)
{
this.Name = Input.ReadString ();
this.IdxRefs = IndexGenericIO.Load (Input);
this.Fingerprints = SpaceGenericIO.SmartLoad (Input, false) as StringSpace<int>;
this.K = Input.ReadInt32 ();
}
public virtual void Build(MetricDB original, Index refs, int k)
{
this.K = k;
this.Fingerprints = new StringSpace<int> ();
this.Fingerprints.seqs.Capacity = original.Count;
this.IdxRefs = refs;
var n = original.Count;
var A = new int[n][];
int blocksize = 10000;
int pc = original.Count / 100 + 1;
int advance = 0;
var create_block = new Action<int> (delegate(int blockID) {
var sp = blockID * blocksize;
var ep = Math.Min (n, sp + blocksize);
for (; sp < ep; ++sp) {
var fp = this.GetFP(original[sp]);
A[sp] = fp;
if (advance % pc == 0) {
Console.WriteLine ("KnrFP {0} ({1}/{2}), db: {3}, num_refs: {4}, timestamp: {5}", this, advance, n, original.Name, this.IdxRefs.DB.Count, DateTime.Now);
}
advance++;
}
});
ParallelOptions ops = new ParallelOptions();
ops.MaxDegreeOfParallelism = -1;
Parallel.For (0, 1+n/blocksize, create_block);
foreach (var fp in A) {
this.Fingerprints.Add( fp );
}
}
