public SimpleGa(TextComparer posComparer, TextComparer negComparer, SimpleGaParams pars = null)
{
_pars = pars ?? new SimpleGaParams();
_posComparer = posComparer;
_negComparer = negComparer;
_rnd = new Random(_pars.Seed);
_pTotal = _posComparer.GetAllCites(new[] {(byte) Nucleotide.End}, 1).Count();
_nTotal = _negComparer.GetAllCites(new[] { (byte)Nucleotide.End }, 1).Count();
}
private static void TransTest(int origLen, IEnumerable<ElementGroup> groups, TextComparer cmp)
{
var cntOrig = 0;
var cntTrans = 0;
foreach (var gr in groups)
{
var cnt = cmp.GetAllCites(gr.Chain, gr.Chain.Length);
Console.WriteLine(gr + ", otherCnt=" + cnt.Length);
cntOrig += gr.Count;
cntTrans += cnt.Length;
}
Console.WriteLine("origFactor=" + cntOrig + ", transFactor=" + Math.Round((double)origLen * cntTrans / cmp.StrokeSize, 3));
}
private static void GetSfx(GetSfxParams pars, IEnumerable<Region> peaks, IEnumerable<Region> noises,
out TextComparer posComp, out TextComparer negComp)
{
var t = DateTime.Now;
var chrDic = new Dictionary<ChromosomeEnum, Chromosome>();
// peaks
var peaksTmp = peaks.Select(p =>
{
if (!chrDic.ContainsKey(p.Chr))
chrDic.Add(p.Chr, ChrManager.GetChromosome(p.Chr));
return chrDic[p.Chr].GetPack(p.Start, p.Size);
}).ToArray();
TextComparer sfxPeaks = SuffixBuilder.BuildMany2(peaksTmp, pars.MinGroupSize);
Console.WriteLine("Peaks sfx build, dt=" + (DateTime.Now - t) + ", size=" + sfxPeaks.StrokeSize);
// noise
var noiseTmp = noises.Select(p =>
{
if (!chrDic.ContainsKey(p.Chr))
chrDic.Add(p.Chr, ChrManager.GetChromosome(p.Chr));
return chrDic[p.Chr].GetPack(p.Start, p.Size);
}).ToArray();
TextComparer sfxNoise = SuffixBuilder.BuildMany2(noiseTmp, pars.MinGroupSize);
Console.WriteLine("Noise sfx build, dt=" + (DateTime.Now - t) + ", size=" + sfxNoise.StrokeSize);
posComp = sfxPeaks;
negComp = sfxNoise;
}