private void LoadSpectralLibraries(out List <string> errors)
{
errors = new List <string>();
try
{
SpectralLibrary = new SpectralLibrary(SpectralLibraryPaths.ToList());
}
catch (Exception e)
{
SpectralLibrary = null;
errors.Add("Problem loading spectral library: " + e.Message);
}
}
public static void AnotherSpectralLibrarySearchTestDecoy()
{
var testDir = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch");
string myFile = Path.Combine(testDir, @"slicedMouse.raw");
MyFileManager myFileManager = new MyFileManager(true);
CommonParameters commonParameters = new CommonParameters(maxThreadsToUsePerFile: 1, scoreCutoff: 1);
MsDataFile myMsDataFile = myFileManager.LoadFile(myFile, commonParameters);
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein> {
new Protein("QTATIAHVTTMLGEVIGFNDHIVK", "P16858")
};
string targetSpectralLibrary = Path.Combine(testDir, @"P16858_target.msp");
string decoySpectralLibrary = Path.Combine(testDir, @"P16858_decoy.msp");
List <string> specLibs = new List <string> {
targetSpectralLibrary, decoySpectralLibrary
};
SpectralLibrary sl = new SpectralLibrary(specLibs);
var searchModes = new SinglePpmAroundZeroSearchMode(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
bool writeSpectralLibrary = false;
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchModes, commonParameters, null, sl, new List <string>(), writeSpectralLibrary).Run();
// Single search mode
Assert.AreEqual(7, allPsmsArray.Length);
Assert.IsTrue(allPsmsArray[5].Score > 38);
Assert.AreEqual("VIHDNFGIVEGLMTTVHAITATQK", allPsmsArray[5].BaseSequence);
Assert.IsTrue(allPsmsArray[5].IsDecoy);
SpectralLibrarySearchFunction.CalculateSpectralAngles(sl, allPsmsArray, listOfSortedms2Scans, commonParameters);
Assert.That(allPsmsArray[5].SpectralAngle, Is.EqualTo(0.69).Within(0.01));
}
public static void TestReverseDecoyGenerationDuringSearch()
{
CommonParameters CommonParameters = new CommonParameters();
MetaMorpheusTask.DetermineAnalyteType(CommonParameters);
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein>
{
new Protein("KKAEDGINK", ""), new Protein("AVNSISLK", ""), new Protein("EKAEAEAEK", ""), new Protein("DITANLR", ""), new Protein("QNAIGTAK", ""),
new Protein("FHKSQLNK", ""), new Protein("KQVAQWNK", ""), new Protein("NTRIEELK", ""), new Protein("RQPAQPR", ""),
};
var myMsDataFile = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SmallCalibratible_Yeast.mzML"));
var searchMode = new SinglePpmAroundZeroSearchMode(5);
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
var path = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\myPrositLib.msp");
var testLibrary = new SpectralLibrary(new List <string> {
path
});
//test when doing spectral library search without generating library
PeptideSpectralMatch[] allPsmsArray1 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray1, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchMode, CommonParameters, null, testLibrary, new List <string>(), false).Run();
var psm1 = allPsmsArray1.Where(p => p != null).ToList();
Assert.That(psm1[0].IsDecoy == false && psm1[0].FullSequence == "DITANLR");
Assert.That(psm1[1].IsDecoy == true && psm1[1].FullSequence == "LSISNVAK");
Assert.That(psm1[2].IsDecoy == true && psm1[2].FullSequence == "LSISNVAK");
Assert.That(psm1[3].IsDecoy == false && psm1[3].FullSequence == "RQPAQPR");
Assert.That(psm1[4].IsDecoy == false && psm1[4].FullSequence == "KKAEDGINK");
Assert.That(psm1[5].IsDecoy == false && psm1[5].FullSequence == "EKAEAEAEK");
Assert.That(psm1[6].IsDecoy == false && psm1[6].FullSequence == "EKAEAEAEK");
proteinList.Add(new Protein("LSISNVAK", "", isDecoy: true));
//test when doing spectral library search with generating library; non spectral search won't generate decoy by "decoy on the fly" , so proteinlist used by non spectral library search would contain decoys
PeptideSpectralMatch[] allPsmsArray2 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray2, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchMode, CommonParameters, null, testLibrary, new List <string>(), true).Run();
var psm2 = allPsmsArray2.Where(p => p != null).ToList();
Assert.That(psm2[0].IsDecoy == false && psm2[0].FullSequence == "DITANLR");
Assert.That(psm2[1].IsDecoy == true && psm2[1].FullSequence == "LSISNVAK");
Assert.That(psm2[2].IsDecoy == true && psm2[2].FullSequence == "LSISNVAK");
Assert.That(psm2[3].IsDecoy == false && psm2[3].FullSequence == "RQPAQPR");
Assert.That(psm2[4].IsDecoy == false && psm2[4].FullSequence == "KKAEDGINK");
Assert.That(psm2[5].IsDecoy == false && psm2[5].FullSequence == "EKAEAEAEK");
Assert.That(psm2[6].IsDecoy == false && psm2[6].FullSequence == "EKAEAEAEK");
//test when doing non spectral library search without generating library
PeptideSpectralMatch[] allPsmsArray3 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray3, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchMode, CommonParameters, null, null, new List <string>(), false).Run();
var psm3 = allPsmsArray3.Where(p => p != null).ToList();
Assert.That(psm3[0].IsDecoy == false && psm3[0].FullSequence == "DITANLR");
Assert.That(psm3[1].IsDecoy == true && psm3[1].FullSequence == "LSISNVAK");
Assert.That(psm3[2].IsDecoy == true && psm3[2].FullSequence == "LSISNVAK");
Assert.That(psm3[3].IsDecoy == false && psm3[3].FullSequence == "RQPAQPR");
Assert.That(psm3[4].IsDecoy == false && psm3[4].FullSequence == "KKAEDGINK");
Assert.That(psm3[5].IsDecoy == false && psm3[5].FullSequence == "EKAEAEAEK");
Assert.That(psm3[6].IsDecoy == false && psm3[6].FullSequence == "EKAEAEAEK");
//test when doing non spectral library search with generating library
PeptideSpectralMatch[] allPsmsArray4 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray4, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchMode, CommonParameters, null, null, new List <string>(), true).Run();
var psm4 = allPsmsArray4.Where(p => p != null).ToList();
Assert.That(psm4[0].IsDecoy == false && psm4[0].FullSequence == "DITANLR");
Assert.That(psm4[1].IsDecoy == true && psm4[1].FullSequence == "LSISNVAK");
Assert.That(psm4[2].IsDecoy == true && psm4[2].FullSequence == "LSISNVAK");
Assert.That(psm4[3].IsDecoy == false && psm4[3].FullSequence == "RQPAQPR");
Assert.That(psm4[4].IsDecoy == false && psm4[4].FullSequence == "KKAEDGINK");
Assert.That(psm4[5].IsDecoy == false && psm4[5].FullSequence == "EKAEAEAEK");
Assert.That(psm4[6].IsDecoy == false && psm4[6].FullSequence == "EKAEAEAEK");
//compare psm's target/decoy results in 4 conditions. they should be same as new decoy methods shouldn't change the t/d results
for (int i = 0; i < psm1.Count; i++)
{
Assert.That(psm1[i].FullSequence == psm2[i].FullSequence && psm3[i].FullSequence == psm3[i].FullSequence && psm2[i].FullSequence == psm3[i].FullSequence);
Assert.That(psm1[i].IsDecoy == psm2[i].IsDecoy && psm3[i].IsDecoy == psm3[i].IsDecoy && psm2[i].IsDecoy == psm3[i].IsDecoy);
}
//compare MetaMorpheus scores in 4 conditions; for some psms, they should have a little higher score when "generating library" as they switch to all charges ions matching function
for (int j = 0; j < psm1.Count; j++)
{
if (psm1[j].FullSequence == psm2[j].FullSequence && psm1[j].MatchedFragmentIons.Count != psm2[j].MatchedFragmentIons.Count)
{
Assert.That(psm1[j].Score < psm2[j].Score);
}
}
}
public static void SpectralLibraryReaderTest_pDeep()
{
var path = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch\yeast2fake_pdeep_lib.msp");
var testLibraryWithoutDecoy = new SpectralLibrary(new List <string> {
path
});
var librarySpectra = testLibraryWithoutDecoy.GetAllLibrarySpectra().ToList();
Assert.That(librarySpectra.Count == 5);
Assert.That(testLibraryWithoutDecoy.TryGetSpectrum("VGIVPGEVIAPGM[Common Variable:Oxidation on M]R", 3, out var spectrum1));
Assert.That(testLibraryWithoutDecoy.TryGetSpectrum("C[Common Fixed:Carbamidomethyl on C]TSC[Common Fixed:Carbamidomethyl on C]NGQGIKFVTR", 3, out var spectrum2));
Assert.AreEqual(spectrum2.PrecursorMz, 543.2608252287667);
Assert.AreEqual(spectrum2.RetentionTime, 2789.812255859375);
testLibraryWithoutDecoy.TryGetSpectrum("YHPDKNPSEEAAEK", 3, out var test1);
Assert.AreEqual(test1.PrecursorMz, 538.9179945621);
Assert.AreEqual(test1.RetentionTime, 1361.375244140625);
Assert.AreEqual(test1.ChargeState, 3);
var frags = new List <(double mz, double intensity, ProductType ProductType, int fragmentNumber, int charge, double ppm)>
{
(301.1295080000, 10000.0, ProductType.b, 2, 1, 0.0),
(657.8122378432, 1102.3, ProductType.y, 12, 2, 0.0),
(974.4425296863, 1476.0, ProductType.y, 9, 1, 0.0),
(860.3996026863, 7228.2, ProductType.y, 8, 1, 0.0),
(763.3468386863, 1201.9, ProductType.y, 7, 1, 0.0),
(418.2296246863, 1178.9, ProductType.y, 4, 1, 0.0),
(347.1925106863, 1042.8, ProductType.y, 3, 1, 0.0)
};
for (int i = 0; i < frags.Count; i++)
{
var frag = frags[i];
var readFrag = test1.MatchedFragmentIons[i];
Assert.That(frag.mz == readFrag.Mz);
Assert.That(frag.intensity == readFrag.Intensity);
Assert.That(frag.ProductType == readFrag.NeutralTheoreticalProduct.ProductType);
Assert.That(frag.fragmentNumber == readFrag.NeutralTheoreticalProduct.FragmentNumber);
Assert.That(frag.charge == readFrag.Charge);
//Assert.That(frag.ppm == readFrag.MassErrorPpm);
}
// write the library w/ the ToString method
var writtenPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\testLibraryToString.msp");
var str = librarySpectra.SelectMany(p => p.ToString().Split(new char[] { '\n' }));
File.WriteAllLines(writtenPath, str);
testLibraryWithoutDecoy.CloseConnections();
// read the written library and make sure the results are readable
testLibraryWithoutDecoy = new SpectralLibrary(new List <string> {
writtenPath
});
librarySpectra = testLibraryWithoutDecoy.GetAllLibrarySpectra().ToList();
Assert.That(librarySpectra.Count == 5);
Assert.That(testLibraryWithoutDecoy.TryGetSpectrum("VGIVPGEVIAPGM[Common Variable:Oxidation on M]R", 3, out var spectrum3));
Assert.That(testLibraryWithoutDecoy.TryGetSpectrum("C[Common Fixed:Carbamidomethyl on C]TSC[Common Fixed:Carbamidomethyl on C]NGQGIKFVTR", 3, out var spectrum4));
Assert.AreEqual(spectrum4.PrecursorMz, 543.2608252287667);
Assert.AreEqual(spectrum4.RetentionTime, 2789.812255859375);
testLibraryWithoutDecoy.TryGetSpectrum("YHPDKNPSEEAAEK", 3, out test1);
Assert.AreEqual(test1.PrecursorMz, 538.9179945621);
Assert.AreEqual(test1.RetentionTime, 1361.375244140625);
Assert.AreEqual(test1.ChargeState, 3);
double maxOfIntensity = frags.Select(p => p.intensity).ToList().Max();
for (int i = 0; i < frags.Count; i++)
{
var frag = frags[i];
var readFrag = test1.MatchedFragmentIons[i];
Assert.That(frag.mz == readFrag.Mz);
Assert.That((frag.intensity / maxOfIntensity) == readFrag.Intensity);
Assert.That(frag.ProductType == readFrag.NeutralTheoreticalProduct.ProductType);
Assert.That(frag.fragmentNumber == readFrag.NeutralTheoreticalProduct.FragmentNumber);
Assert.That(frag.charge == readFrag.Charge);
//Assert.That(frag.ppm == readFrag.MassErrorPpm);
}
testLibraryWithoutDecoy.CloseConnections();
File.Delete(writtenPath);
}
public static void SpectralLibraryReaderTestNeutralLoss()
{
var path = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch\spectralLibraryNeutralLossTest.msp");
var testLibraryWithoutDecoy = new SpectralLibrary(new List <string> {
path
});
var librarySpectra = testLibraryWithoutDecoy.GetAllLibrarySpectra().ToList();
Assert.That(librarySpectra[0].MatchedFragmentIons[9].NeutralTheoreticalProduct.NeutralLoss == 97.976895573);
Assert.That(librarySpectra[0].MatchedFragmentIons[11].NeutralTheoreticalProduct.NeutralLoss == 97.976895573);
Assert.That(librarySpectra[0].MatchedFragmentIons[13].NeutralTheoreticalProduct.NeutralLoss == 97.976895573);
Assert.That(librarySpectra[0].MatchedFragmentIons[23].NeutralTheoreticalProduct.NeutralLoss == 97.976895573);
testLibraryWithoutDecoy.TryGetSpectrum("ASVSELAC[Common Fixed:Carbamidomethyl on C]IYSALILHDDEVTVTEDKINALIKAAGVNVEPFWPGLFAKALANVNIGSLIC[Common Fixed:Carbamidomethyl on C]NVGAGGPAPAAGAAPAGGPAPSTAAAPAEEKKVEAKKEES[Common Biological:Phosphorylation on S]EES[Common Biological:Phosphorylation on S]DDDMGFGLFD", 11, out var test1);
Assert.AreEqual(test1.ChargeState, 11);
var frags = new List <(double mz, double intensity, ProductType ProductType, int fragmentNumber, int charge, double neutralLoss)>
{
(474.22253552109225, 0.12327031966337068, ProductType.b, 5, 1, 0.0),
(598.2911881692844, 0.17637685313108434, ProductType.y, 5, 1, 0.0),
(587.3078660257297, 0.26448833020105406, ProductType.b, 6, 1, 0.0),
(655.3122852061485, 0.2573965224084584, ProductType.y, 6, 1, 0.0),
(786.3547054957799, 0.5973180470179946, ProductType.y, 7, 1, 0.0),
(901.3828669653562, 0.1394747476004537, ProductType.y, 8, 1, 0.0),
(931.4665832519531, 0.1434341615825174, ProductType.b, 9, 1, 0.0),
(1298.4420166015627, 0.04799051344737827, ProductType.y, 11, 1, 0.0),
(1194.1036493343909, 0.16497897552735782, ProductType.b, 22, 2, 0.0),
(1412.6153999317123, 0.059408140384558945, ProductType.y, 24, 2, 97.976895573),
(1610.16612195462, 0.06598126929193648, ProductType.y, 27, 2, 0.0),
(1561.176395469285, 0.3655719849041352, ProductType.y, 27, 2, 97.976895573),
(1596.6949731527957, 0.1196248007420883, ProductType.y, 28, 2, 97.976895573),
(1632.2140387967154, 0.1134099785167373, ProductType.y, 29, 2, 97.976895573),
(1239.8634635821659, 0.19969145903784855, ProductType.y, 33, 3, 0.0),
(1207.2033996967743, 0.4866798941848081, ProductType.y, 33, 3, 97.976895573),
(1810.301461311722, 0.2822226465462767, ProductType.y, 33, 2, 97.976895573),
(1282.2420159220214, 0.06365769264631967, ProductType.y, 36, 3, 97.976895573),
(1333.9057047796402, 0.04957330666530949, ProductType.y, 37, 3, 0.0),
(1042.7038942258248, 0.10714201465676373, ProductType.y, 39, 4, 0.0),
(1389.9361001454733, 0.20027716863748268, ProductType.y, 39, 3, 0.0),
(1018.2100179729548, 0.23609364592477405, ProductType.y, 39, 4, 97.976895573),
(1357.2775984749799, 1, ProductType.y, 39, 3, 97.976895573),
(1503.354187325224, 0.060227438209151066, ProductType.y, 45, 3, 97.976895573)
};
for (int i = 0; i < frags.Count; i++)
{
var frag = frags[i];
var readFrag = test1.MatchedFragmentIons[i];
Assert.That(frag.mz == readFrag.Mz);
Assert.That(frag.intensity == readFrag.Intensity);
Assert.That(frag.ProductType == readFrag.NeutralTheoreticalProduct.ProductType);
Assert.That(frag.fragmentNumber == readFrag.NeutralTheoreticalProduct.FragmentNumber);
Assert.That(frag.charge == readFrag.Charge);
Assert.That(frag.neutralLoss == readFrag.NeutralTheoreticalProduct.NeutralLoss);
}
// write the library w/ the ToString method
var writtenPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\testLibraryToString.msp");
var str = librarySpectra.SelectMany(p => p.ToString().Split(new char[] { '\n' }));
File.WriteAllLines(writtenPath, str);
testLibraryWithoutDecoy.CloseConnections();
// read the written library and make sure the results are readable
testLibraryWithoutDecoy = new SpectralLibrary(new List <string> {
writtenPath
});
librarySpectra = testLibraryWithoutDecoy.GetAllLibrarySpectra().ToList();
Assert.That(librarySpectra.Count == 1);
testLibraryWithoutDecoy.TryGetSpectrum("ASVSELAC[Common Fixed:Carbamidomethyl on C]IYSALILHDDEVTVTEDKINALIKAAGVNVEPFWPGLFAKALANVNIGSLIC[Common Fixed:Carbamidomethyl on C]NVGAGGPAPAAGAAPAGGPAPSTAAAPAEEKKVEAKKEES[Common Biological:Phosphorylation on S]EES[Common Biological:Phosphorylation on S]DDDMGFGLFD", 11, out test1);
Assert.AreEqual(test1.ChargeState, 11);
double maxOfIntensity = frags.Select(p => p.intensity).ToList().Max();
for (int i = 0; i < frags.Count; i++)
{
var frag = frags[i];
var readFrag = test1.MatchedFragmentIons[i];
Assert.That(frag.mz == readFrag.Mz);
Assert.That((frag.intensity / maxOfIntensity) == readFrag.Intensity);
Assert.That(frag.ProductType == readFrag.NeutralTheoreticalProduct.ProductType);
Assert.That(frag.fragmentNumber == readFrag.NeutralTheoreticalProduct.FragmentNumber);
Assert.That(frag.charge == readFrag.Charge);
Assert.That(frag.neutralLoss == readFrag.NeutralTheoreticalProduct.NeutralLoss);
}
testLibraryWithoutDecoy.CloseConnections();
File.Delete(writtenPath);
}
public static void SpectralLibraryReaderTest()
{
var path = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\myPrositLib.msp");
var testLibraryWithoutDecoy = new SpectralLibrary(new List <string> {
path
});
var librarySpectra = testLibraryWithoutDecoy.GetAllLibrarySpectra().ToList();
Assert.That(librarySpectra.Count == 5);
Assert.That(testLibraryWithoutDecoy.TryGetSpectrum("QSQHM[Common Variable:Oxidation on M]TEVVR", 5, out var spectrum));
Assert.That(testLibraryWithoutDecoy.TryGetSpectrum("M[Common Variable:Oxidation on M]C[Common Fixed:Carbamidomethyl on C]SDSDGLAPPQHLIR", 2, out spectrum));
testLibraryWithoutDecoy.TryGetSpectrum("ALAVDGAGKPGAEE", 2, out var test1);
Assert.AreEqual(test1.ChargeState, 2);
var frags = new List <(double mz, double intensity, ProductType ProductType, int fragmentNumber, int charge, double ppm)>
{
(148.06044, 0.03711248, ProductType.y, 1, 1, 0.0),
(277.10303, 0.025135221, ProductType.y, 2, 1, 0.0),
(185.12845, 0.8128169, ProductType.b, 2, 1, 0.0),
(348.14014, 0.008474186, ProductType.y, 3, 1, 0.0),
(256.16556, 1.0, ProductType.b, 3, 1, 0.0),
(405.1616, 0.006187536, ProductType.y, 4, 1, 0.0),
(203.08444, 0.00014141058, ProductType.y, 4, 2, 0.0),
(355.23398, 0.1165214, ProductType.b, 4, 1, 0.0),
(178.12064, 0.010349626, ProductType.b, 4, 2, 0.0),
(502.21436, 0.7401104, ProductType.y, 5, 1, 0.0),
(470.26093, 0.055574868, ProductType.b, 5, 1, 0.0),
(235.6341, 0.005631463, ProductType.b, 5, 2, 0.0),
(630.3093, 0.0679749, ProductType.y, 6, 1, 0.0),
(527.2824, 0.02713329, ProductType.b, 6, 1, 0.0),
(264.14484, 0.002669461, ProductType.b, 6, 2, 0.0),
(687.3308, 0.38598263, ProductType.y, 7, 1, 0.0),
(598.3195, 0.016116723, ProductType.b, 7, 1, 0.0),
(758.3679, 0.1706151, ProductType.y, 8, 1, 0.0),
(655.34094, 0.007904499, ProductType.b, 8, 1, 0.0),
(815.3894, 0.5167622, ProductType.y, 9, 1, 0.0),
(408.19833, 0.0012127026, ProductType.y, 9, 2, 0.0),
(783.4359, 0.01972321, ProductType.b, 9, 1, 0.0),
(930.4163, 0.8694488, ProductType.y, 10, 1, 0.0),
(465.7118, 0.026939344, ProductType.y, 10, 2, 0.0),
(1029.4847, 0.27091113, ProductType.y, 11, 1, 0.0),
(515.24603, 0.020846518, ProductType.y, 11, 2, 0.0),
(1100.5219, 0.22043262, ProductType.y, 12, 1, 0.0),
(550.7646, 0.0036459658, ProductType.y, 12, 2, 0.0),
(1008.5473, 0.0029647197, ProductType.b, 12, 1, 0.0),
(1137.5898, 0.009047425, ProductType.b, 13, 1, 0.0),
(569.2986, 7.061393e-05, ProductType.b, 13, 2, 0.0)
};
for (int i = 0; i < frags.Count; i++)
{
var frag = frags[i];
var readFrag = test1.MatchedFragmentIons[i];
Assert.That(frag.mz == readFrag.Mz);
Assert.That(frag.intensity == readFrag.Intensity);
Assert.That(frag.ProductType == readFrag.NeutralTheoreticalProduct.ProductType);
Assert.That(frag.fragmentNumber == readFrag.NeutralTheoreticalProduct.FragmentNumber);
Assert.That(frag.charge == readFrag.Charge);
//Assert.That(frag.ppm == readFrag.MassErrorPpm);
}
// write the library w/ the ToString method
var writtenPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\testLibraryToString.msp");
var str = librarySpectra.SelectMany(p => p.ToString().Split(new char[] { '\n' }));
File.WriteAllLines(writtenPath, str);
testLibraryWithoutDecoy.CloseConnections();
// read the written library and make sure the results are readable
testLibraryWithoutDecoy = new SpectralLibrary(new List <string> {
writtenPath
});
librarySpectra = testLibraryWithoutDecoy.GetAllLibrarySpectra().ToList();
Assert.That(librarySpectra.Count == 5);
Assert.That(testLibraryWithoutDecoy.TryGetSpectrum("QSQHM[Common Variable:Oxidation on M]TEVVR", 5, out spectrum));
Assert.That(testLibraryWithoutDecoy.TryGetSpectrum("M[Common Variable:Oxidation on M]C[Common Fixed:Carbamidomethyl on C]SDSDGLAPPQHLIR", 2, out spectrum));
testLibraryWithoutDecoy.TryGetSpectrum("ALAVDGAGKPGAEE", 2, out test1);
Assert.AreEqual(test1.ChargeState, 2);
for (int i = 0; i < frags.Count; i++)
{
var frag = frags[i];
var readFrag = test1.MatchedFragmentIons[i];
Assert.That(frag.mz == readFrag.Mz);
Assert.That(frag.intensity == readFrag.Intensity);
Assert.That(frag.ProductType == readFrag.NeutralTheoreticalProduct.ProductType);
Assert.That(frag.fragmentNumber == readFrag.NeutralTheoreticalProduct.FragmentNumber);
Assert.That(frag.charge == readFrag.Charge);
//Assert.That(frag.ppm == readFrag.MassErrorPpm);
}
testLibraryWithoutDecoy.CloseConnections();
File.Delete(writtenPath);
}
