/* triple wave building codesnippet
*
* int length = (int)(SampleRate * BlockAlign * duration);
* byte[] buffer = new byte[length];
*
* double A = frequency * 2 * Math.PI / (double)SampleRate;
* for (int i = 0; i < length; i++)
* {
* if (i > 1) buffer[i] = (byte)(2 * Math.Cos(A) * buffer[i - 1] - buffer[i - 2]);
* else if (i > 0) buffer[i] = (byte)(2 * Math.Cos(A) * buffer[i - 1] - (Math.Cos(A)));
* else buffer[i] = (byte)(2 * Math.Cos(A) * Math.Cos(A) - Math.Cos(2 * A));
* }
*
* public double CalculateGoertzel(byte[] sample, double frequency, int samplerate)
* {
* double Skn, Skn1, Skn2;
* Skn = Skn1 = Skn2 = 0;
* for (int i = 0; i < sample.Length; i++)
* {
* Skn2 = Skn1;
* Skn1 = Skn;
* Skn = 2 * Math.Cos(2 * Math.PI * frequency / samplerate) * Skn1 - Skn2 + sample[i];
* }
*
* double WNk = Math.Exp(-2 * Math.PI * frequency / samplerate);
*
* return 20 * Math.Log10(Math.Abs((Skn - WNk * Skn1)));
* }
*
* public int TestGoertzel(int frequency, byte[] sample, int samplerate)
* {
* int stepsize = frequency / 5;
* Dictionary<int, double> res = new Dictionary<int, double>();
* for (int i = 0; i < 10; i++)
* {
* int freq = stepsize * i;
* res.Add(freq, CalculateGoertzel(sample, freq, samplerate));
* }
* }
*/
private void BuildDiagram(ZedGraph.ZedGraphControl zg, byte[] _data)
{
ZedGraph.GraphPane myPane = zg.GraphPane;
ZedGraph.LineItem curve = null;
if (myPane.CurveList.Count >= 1)
{
curve = myPane.CurveList[0] as ZedGraph.LineItem;
curve.Clear();
}
else
{
curve = new ZedGraph.LineItem("SPS");
}
// Make sure that the curvelist has at least one curve
for (int i = 0; i < _data.Length; i++)
{
curve.AddPoint(i, _data[i]);
}
ZedGraph.IPointList list = curve.Points as ZedGraph.IPointList;
if (myPane.CurveList.Count == 0)
{
myPane.AddCurve("Wave", list, Color.DimGray, ZedGraph.SymbolType.None);
}
zg.AxisChange();
zg.Invalidate();
}
public PointMap(ZedGraph.IPointList pointList)
{
for (int i = 0; i < pointList.Count; ++i)
{
Add(pointList[i].X, pointList[i].Y);
}
}
public void deltaScoreTest()
{
Spectrum rawSpectrum = spectrum.Element;
// Work around to have a sort function in List.
ZedGraph.IPointList peaks = spectrum.Points;
List <ScoringUtils.Peak> rawPeaks = new List <ScoringUtils.Peak>();
for (int i = 0; i < peaks.Count; ++i)
{
rawPeaks.Add(new ScoringUtils.Peak(peaks[i].X, peaks[i].Y));
}
// Remove the precursor and associated neutral loss peaks
double precursorMZ = rawSpectrum.precursors[0].selectedIons[0].cvParam(pwiz.CLI.cv.CVID.MS_selected_ion_m_z).value;
ScoringUtils.erasePrecursorIons(precursorMZ, ref rawPeaks);
// Filter the peaks and rank them based on increasing
// order of intensity: i.e. intense peaks get higher ranks
rawPeaks = ScoringUtils.filterByPeakCount(rawPeaks, 100);
Set <ScoringUtils.Peak> rankedPeaks = new Set <ScoringUtils.Peak>(rawPeaks);
//Set<Peak> rankedPeaks = rankPeaks(rawPeaks);
//string alt = "";
//InputBox("Alternative", "Enter Alt peptide", ref alt);
Peptide alternative;
try
{
alternative = new Peptide(annotation.SecondarySequence,
pwiz.CLI.proteome.ModificationParsing.ModificationParsing_Auto,
pwiz.CLI.proteome.ModificationDelimiter.ModificationDelimiter_Brackets);
}
catch (Exception) { return; }
Set <double> primaryMatchFragMasses = new Set <double>();
ScoringUtils.calculateSequenceIons(annotation.Peptide, 2, ref primaryMatchFragMasses);
Set <double> secondaryMatchFragMasses = new Set <double>();
ScoringUtils.calculateSequenceIons(alternative, 2, ref secondaryMatchFragMasses);
Set <ScoringUtils.Peak> primarySeqMatchedIons = new Set <ScoringUtils.Peak>();
double primarySeqMatchedIntens = 0.0;
foreach (var peak in primaryMatchFragMasses)
{
ScoringUtils.Peak match = ScoringUtils.findNear(rankedPeaks, peak, 0.5);
if (match != null)
{
primarySeqMatchedIons.Add(match);
primarySeqMatchedIntens += match.rankOrIntensity;
}
}
Set <ScoringUtils.Peak> secondarySeqMatchedIons = new Set <ScoringUtils.Peak>();
double secondarySeqMatchedIntens = 0;
foreach (var peak in secondaryMatchFragMasses)
{
ScoringUtils.Peak match = ScoringUtils.findNear(rankedPeaks, peak, 0.5);
if (match != null)
{
secondarySeqMatchedIons.Add(match);
secondarySeqMatchedIntens += match.rankOrIntensity;
}
}
double TIC = 0.0;
foreach (var peak in rankedPeaks)
{
TIC += peak.rankOrIntensity;
}
MessageBox.Show("PRS:" + primarySeqMatchedIntens + " SRS:" + secondarySeqMatchedIntens + " TIC:" + TIC);
}