public static void MakeChromatogramInfo(double precursorMz, LibraryChromGroup chromGroup, LibraryChromGroup.ChromData chromData, out ChromatogramInfo chromatogramInfo, out TransitionChromInfo transitionChromInfo)
{
var crawPeakFinder = new CrawdadPeakFinder();
crawPeakFinder.SetChromatogram(chromGroup.Times, chromData.Intensities);
var crawdadPeak =
crawPeakFinder.GetPeak(
FindNearestIndex(chromGroup.Times, (float)chromGroup.StartTime),
FindNearestIndex(chromGroup.Times, (float)chromGroup.EndTime));
var chromPeak = new ChromPeak(crawPeakFinder, crawdadPeak, 0, chromGroup.Times, chromData.Intensities, null);
transitionChromInfo = new TransitionChromInfo(null, 0, chromPeak, new float?[0], Annotations.EMPTY,
UserSet.FALSE);
var peaks = new[] { chromPeak };
var header = new ChromGroupHeaderInfo5(new ChromGroupHeaderInfo(
(float)precursorMz, 0, 1, 0, peaks.Length, 0, 0,
chromGroup.Times.Length, 0, 0));
chromatogramInfo = new ChromatogramInfo(header,
new Dictionary <Type, int>(), 0,
new ChromCachedFile[0],
new[] { new ChromTransition(chromData.Mz, 0, 0, 0, ChromSource.unknown), },
peaks, null,
chromGroup.Times, new[] { chromData.Intensities }, null, null);
}
public void FindPeaks(double[] retentionTimes, bool requireDocNode)
{
Finder = new CrawdadPeakFinder();
Finder.SetChromatogram(Times, Intensities);
if (requireDocNode && DocNode == null)
{
RawPeaks = new CrawdadPeak[0];
}
else
{
RawPeaks = Finder.CalcPeaks(MAX_PEAKS, TimesToIndices(retentionTimes));
// Calculate smoothing for later use in extending the Crawdad peaks
IntensitiesSmooth = ChromatogramInfo.SavitzkyGolaySmooth(Intensities);
}
}
public void TestData2Of2()
{
float[] rts = { 1473.55f, 1476.31f, 1479.08f, 1481.84f, 1484.61f, 1487.39f, 1490.15f, 1492.92f, 1495.69f, 1498.45f, 1501.23f, 1504f, 1506.76f, 1509.53f, 1512.29f, 1515.07f, 1517.84f, 1520.62f };
float[] intensities = { 3.44054f, 2142.31f, 3.58763f, 3076.97f, 6663.55f, 45681f, 157694f, 122844f, 86034.7f, 85391.1f, 15992.8f, 2293.94f, 6934.85f, 2735.18f, 459.413f, 3.93863f, 3.36564f, 3.44005f };
CrawdadPeakFinder pf = new CrawdadPeakFinder();
pf.SetChromatogram(rts, intensities);
IList <CrawdadPeak> res = pf.CalcPeaks();
Assert.IsTrue(res.Count == 1);
Assert.IsTrue(res[0].StartIndex == 2);
Assert.IsTrue(res[0].TimeIndex == 6);
Assert.IsTrue(res[0].EndIndex == 13);
}
public void TestData1Of2()
{
float[] rts = { 1474.34f, 1477.11f, 1479.88f, 1482.64f, 1485.41f, 1488.19f, 1490.95f, 1493.72f, 1496.48f, 1499.25f, 1502.03f, 1504.8f, 1507.56f, 1510.33f, 1513.09f, 1515.87f, 1518.64f, 1521.42f };
float[] intensities = { 3.26958f, 3.74189f, 3.31075f, 86.1901f, 3.47528f, 387.864f, 13281f, 6375.84f, 39852.6f, 2.66726f, 612.747f, 3.34313f, 793.12f, 3.29156f, 4.00586f, 4.1591f, 3.23035f, 3.90591f };
CrawdadPeakFinder pf = new CrawdadPeakFinder();
pf.SetChromatogram(rts, intensities);
IList <CrawdadPeak> res = pf.CalcPeaks();
Assert.IsTrue(res.Count == 1);
Assert.IsTrue(res[0].StartIndex == 2);
Assert.IsTrue(res[0].TimeIndex == 8);
Assert.IsTrue(res[0].EndIndex == 13);
}
public CrawPeakFinderWrapper()
{
_crawdadPeakFinder = new CrawdadPeakFinder();
}
public CrawPeakFinderWrapper()
{
_crawdadPeakFinder = new CrawdadPeakFinder();
}
