protected override void Initialize()
{
// TODO: Add your initialization logic here
mapEd = new Map ();
drawMapSeg = new DrawMapSegment (mapEd.SegmentDefinitions, 500, 30, 50, 30, 40);
segIndex = -1;
mapSegIndex = -1;
currentLayer = 0f;
layer = new string[]{ "back", "mid", "front" };
selectType = new string[]{"col","select" };
layerName = layer[0];
selectName = selectType [1];
mouseClick = false;
dropSegment = false;
holdSegment = false;
mouseDrag = false;
drawType = DrawingMode.SegmentSelection;
//Components.Add (new CollisionRectangle (this));
base.Initialize ();
}
public static void CreateTestData (NHibernate.ISession session, IList<SpectrumTuple> testPsmSummary)
{
var dbGroups = new Map<string, SpectrumSourceGroup>();
foreach (var ssg in session.Query<SpectrumSourceGroup>())
dbGroups[ssg.Name] = ssg;
var dbSources = new Map<long, SpectrumSource>();
foreach (var ss in session.Query<SpectrumSource>())
dbSources[ss.Id.Value] = ss;
var dbAnalyses = new Map<long, Analysis>();
foreach (var a in session.Query<Analysis>())
dbAnalyses[a.Id.Value] = a;
var dbPeptides = new Map<string, Peptide>();
foreach (var pep in session.Query<Peptide>())
dbPeptides[pep.Sequence] = pep;
var bulkInserter = new BulkInserter(session.Connection);
long lastPsmId = session.CreateQuery("SELECT MAX(Id) FROM PeptideSpectrumMatch").UniqueResult<long?>().GetValueOrDefault();
long lastModId = session.CreateQuery("SELECT MAX(Id) FROM Modification").UniqueResult<long?>().GetValueOrDefault();
long lastPmId = session.CreateQuery("SELECT MAX(Id) FROM PeptideModification").UniqueResult<long?>().GetValueOrDefault();
long lastGroupId = session.CreateQuery("SELECT MAX(Id) FROM SpectrumSourceGroup").UniqueResult<long?>().GetValueOrDefault();
long lastSourceId = session.CreateQuery("SELECT MAX(Id) FROM SpectrumSource").UniqueResult<long?>().GetValueOrDefault();
long lastSglId = session.CreateQuery("SELECT MAX(Id) FROM SpectrumSourceGroupLink").UniqueResult<long?>().GetValueOrDefault();
foreach (SpectrumTuple row in testPsmSummary)
{
string groupName = row.Group;
string sourceName = "Source " + row.Source;
string analysisId = "Engine " + row.Analysis;
string peptideTuples = row.PeptideTuples;
SpectrumSourceGroup group = dbGroups[groupName];
if (String.IsNullOrEmpty(group.Name))
{
group.Id = ++lastGroupId;
group.Name = groupName;
bulkInserter.Add(group);
}
SpectrumSource source = dbSources[row.Source];
if (String.IsNullOrEmpty(source.Name))
{
source.Id = ++lastSourceId;
source.Name = sourceName;
source.Group = group;
source.Spectra = new List<Spectrum>();
bulkInserter.Add(source);
// add a source group link for the source's immediate group
bulkInserter.Add(new SpectrumSourceGroupLink() { Id = ++lastSglId, Group = group, Source = source });
#region add source group links for all of the immediate group's parent groups
if (groupName != "/")
{
string parentGroupName = groupName.Substring(0, groupName.LastIndexOf("/"));
while (true)
{
if (String.IsNullOrEmpty(parentGroupName))
parentGroupName = "/";
// add the parent group if it doesn't exist yet
SpectrumSourceGroup parentGroup = session.UniqueResult<SpectrumSourceGroup>(o => o.Name == parentGroupName);
if (parentGroup == null)
{
parentGroup = new SpectrumSourceGroup() { Id = ++lastGroupId, Name = parentGroupName };
bulkInserter.Add(parentGroup);
}
bulkInserter.Add(new SpectrumSourceGroupLink() { Id = ++lastSglId, Group = parentGroup, Source = source });
if (parentGroupName == "/")
break;
parentGroupName = parentGroupName.Substring(0, parentGroupName.LastIndexOf("/"));
}
}
#endregion
}
Spectrum spectrum = source.Spectra.SingleOrDefault(o => o.Source.Id == source.Id &&
o.Index == row.Spectrum - 1);
if (spectrum == null)
{
spectrum = new Spectrum()
{
Id = source.Id * 10000 + row.Spectrum,
Index = row.Spectrum - 1,
NativeID = "scan=" + row.Spectrum,
Source = source,
PrecursorMZ = 42
};
source.Spectra.Add(spectrum);
bulkInserter.Add(spectrum);
}
Analysis analysis = dbAnalyses[row.Analysis];
if (String.IsNullOrEmpty(analysis.Name))
{
analysis.Id = dbAnalyses.Max(o => o.Value.Id).GetValueOrDefault() + 1;
analysis.Name = analysisId + " 1.0";
analysis.Software = new AnalysisSoftware() {Name = analysisId, Version = "1.0"};
analysis.StartTime = DateTime.Today.AddHours(row.Analysis);
analysis.Type = AnalysisType.DatabaseSearch;
analysis.Parameters = new SortedSet<AnalysisParameter>()
{
new AnalysisParameter()
{
Id = analysis.Id * 10000,
Analysis = analysis,
Name = "Parameter 1",
Value = "Value 1"
}
};
bulkInserter.Add(analysis);
}
// make sure peptides are sorted by their score divider (which will determine rank)
var peptideList = new SortedList<int, List<PeptideTuple>>();
foreach (string tuple in peptideTuples.Split(" ".ToCharArray(), StringSplitOptions.RemoveEmptyEntries))
{
var peptideTuple = new PeptideTuple()
{
Sequence = tuple.Split('@', '/')[0],
Charge = Convert.ToInt32(tuple.Split('@', '/')[1]),
ScoreDivider = Convert.ToInt32(tuple.Split('@', '/')[2])
};
if (!peptideList.ContainsKey(peptideTuple.ScoreDivider))
peptideList[peptideTuple.ScoreDivider] = new List<PeptideTuple>();
peptideList[peptideTuple.ScoreDivider].Add(peptideTuple);
}
int rank = 1;
int lastDivider = 1;
foreach (var peptideTupleList in peptideList.Values)
foreach (var peptideTuple in peptideTupleList)
{
using (PwizPeptide pwizPeptide = new PwizPeptide(peptideTuple.Sequence, ModParsing.ModificationParsing_Auto, ModDelimiter.ModificationDelimiter_Brackets))
{
Peptide peptide = dbPeptides[pwizPeptide.sequence];
if (String.IsNullOrEmpty(peptide.Sequence))
{
peptide = new TestPeptide(pwizPeptide.sequence);
peptide.Id = dbPeptides.Max(o => o.Value.Id).GetValueOrDefault() + 1;
peptide.MonoisotopicMass = pwizPeptide.monoisotopicMass(false);
peptide.MolecularWeight = pwizPeptide.molecularWeight(false);
dbPeptides[pwizPeptide.sequence] = peptide;
bulkInserter.Add(peptide);
createTestPeptideInstances(session, bulkInserter, peptide);
}
double neutralPrecursorMass = (spectrum.PrecursorMZ*peptideTuple.Charge) - (peptideTuple.Charge*Proton.Mass);
var psm = new PeptideSpectrumMatch()
{
Id = ++lastPsmId,
Peptide = peptide,
Spectrum = spectrum,
Analysis = analysis,
ObservedNeutralMass = neutralPrecursorMass,
MonoisotopicMassError = neutralPrecursorMass - pwizPeptide.monoisotopicMass(),
MolecularWeightError = neutralPrecursorMass - pwizPeptide.molecularWeight(),
Charge = peptideTuple.Charge,
Rank = (peptideTuple.ScoreDivider == lastDivider ? rank : ++rank),
QValue = (rank == 1 ? row.QValue : PeptideSpectrumMatch.DefaultQValue),
};
if (row.Score != null)
psm.Scores = new Dictionary<string, double>()
{
{"score1", (double) row.Score/peptideTuple.ScoreDivider},
{"score2", 1/((double) row.Score/peptideTuple.ScoreDivider)}
};
bulkInserter.Add(psm);
lastDivider = peptideTuple.ScoreDivider;
// add PeptideModifications and Modifications
foreach (KeyValuePair<int, ModList> itr in pwizPeptide.modifications())
{
foreach (PwizMod pwizMod in itr.Value)
{
Modification mod = session.UniqueResult<Modification>(o => o.Formula == pwizMod.formula());
if (mod == null)
{
mod = new Modification()
{
Id = ++lastModId,
Formula = pwizMod.formula(),
MonoMassDelta = pwizMod.monoisotopicDeltaMass(),
AvgMassDelta = pwizMod.averageDeltaMass(),
Name = pwizMod.formula()
};
bulkInserter.Add(mod);
}
bulkInserter.Add(new PeptideModification()
{
Id = ++lastPmId,
PeptideSpectrumMatch = psm,
Modification = mod,
Offset = itr.Key == ModMap.NTerminus() ? int.MinValue
: itr.Key == ModMap.CTerminus() ? int.MaxValue
: itr.Key
});
}
}
}
}
}
bulkInserter.Execute();
bulkInserter.Reset("");
}
public void Init()
{
map = new Map ();
map.AddSeg (1f, 1, 45, 45);
pallet =new DrawMapSegment (map.SegmentDefinitions, 500, 30, 50, 30, 40);
}
public void TestAdditionalPeptides ()
{
// each protein in the test scenarios is created from simple repeating motifs
var testProteinSequences = new string[]
{
createSimpleProteinSequence("A", 20), // PRO1
createSimpleProteinSequence("B", 20),
createSimpleProteinSequence("C", 20),
createSimpleProteinSequence("D", 20),
createSimpleProteinSequence("E", 20), // PRO5
createSimpleProteinSequence("E", 21),
createSimpleProteinSequence("F", 20),
createSimpleProteinSequence("F", 21),
createSimpleProteinSequence("G", 20),
createSimpleProteinSequence("G", 21), // PRO10
createSimpleProteinSequence("H", 20),
createSimpleProteinSequence("H", 21),
createSimpleProteinSequence("AAAABBBBCCCC", 24),
createSimpleProteinSequence("AAAABBBB", 24),
createSimpleProteinSequence("BBBBCCCC", 24), // PRO15
createSimpleProteinSequence("DDDDEEEEFFFF", 24),
createSimpleProteinSequence("DDDDEEEE", 24),
createSimpleProteinSequence("DDDDEEEE", 16),
createSimpleProteinSequence("GGGGHHHHIIII", 24),
createSimpleProteinSequence("GGGGHHHHIIII", 36), // PRO20
createSimpleProteinSequence("GGGGHHHH", 24),
createSimpleProteinSequence("HHHHIIII", 24),
createSimpleProteinSequence("KKKKLLLLMMMM", 24),
createSimpleProteinSequence("KKKKLLLLMMMM", 36),
createSimpleProteinSequence("LLLLMMMM", 24), // PRO25
createSimpleProteinSequence("LLLLMMMM", 16),
createSimpleProteinSequence("NNNNPPPPQQQQ", 24),
createSimpleProteinSequence("PPPPQQQQRRRR", 24),
createSimpleProteinSequence("SSSSTTTTUUUU", 24),
createSimpleProteinSequence("TTTTUUUUVVVV", 24), // PRO30
createSimpleProteinSequence("TTTTUUUUVVVV", 36),
createSimpleProteinSequence("WWWWYYYYZZZZ", 24),
createSimpleProteinSequence("WWWWYYYYZZZZ", 36),
createSimpleProteinSequence("YYYYZZZZFFFF", 24),
createSimpleProteinSequence("AAAACCCCEEEE", 24), // PRO35
createSimpleProteinSequence("AAAACCCCEEEE", 36),
createSimpleProteinSequence("CCCCEEEEGGGG", 24),
createSimpleProteinSequence("CCCCEEEEGGGG", 36),
createSimpleProteinSequence("BBBBBDDDDD", 20),
createSimpleProteinSequence("BBBBDDDD", 24), // PRO40
createSimpleProteinSequence("ZBBBBDDD", 24),
createSimpleProteinSequence("YBBBDDD", 20),
createSimpleProteinSequence("WBBDD", 21),
createSimpleProteinSequence("DDDDDFFFFF", 20),
createSimpleProteinSequence("FFFFFHHHHH", 20), // PRO45
createSimpleProteinSequence("HHHHHKKKKK", 20),
createSimpleProteinSequence("HHHHHKKKKK", 30),
createSimpleProteinSequence("KKKKKMMMMM", 20),
createSimpleProteinSequence("LLLLLNNNNN", 20),
createSimpleProteinSequence("NNNNNQQQQQ", 20), // PRO50
createSimpleProteinSequence("NNNNNQQQQQ", 30),
createSimpleProteinSequence("MMMMMPPPPP", 20),
createSimpleProteinSequence("PPPPPRRRRR", 20),
createSimpleProteinSequence("PPPPPRRRR", 24),
createSimpleProteinSequence("QQQQSSSSUUUU", 24), // PRO55
createSimpleProteinSequence("SSSSUUUUYYYY", 24),
createSimpleProteinSequence("RRRRTTTTWWWWZZZZ", 32),
createSimpleProteinSequence("TTTTWWWWZZZZBBBB", 32),
createSimpleProteinSequence("RRRRTTTTZZZZBBBBTTTTWWWW", 24),
createSimpleProteinSequence("AAAADDDDGGGGKKKK", 32), // PRO60
createSimpleProteinSequence("DDDDGGGGKKKKNNNN", 32),
createSimpleProteinSequence("AAAADDDDKKKKNNNN", 32),
createSimpleProteinSequence("BBBBEEEEHHHH", 24),
createSimpleProteinSequence("EEEEHHHHLLLL", 24),
createSimpleProteinSequence("HHHHLLLLPPPP", 24), // PRO65
createSimpleProteinSequence("CCCCFFFFIIII", 24),
createSimpleProteinSequence("FFFFIIIIMMMM", 24),
createSimpleProteinSequence("IIIIMMMMQQQQ", 24),
createSimpleProteinSequence("NNNNRRRRUUUU", 24),
createSimpleProteinSequence("RRRRUUUUZZZZ", 24), // PRO70
createSimpleProteinSequence("UUUUZZZZCCCC", 24),
};
string idpDbName = System.Reflection.MethodInfo.GetCurrentMethod().Name + ".idpDB";
File.Delete(idpDbName);
sessionFactory = SessionFactoryFactory.CreateSessionFactory(idpDbName, new SessionFactoryConfig { CreateSchema = true });
var session = sessionFactory.OpenSession();
TestModel.CreateTestProteins(session, testProteinSequences);
const int analysisCount = 2;
const int sourceCount = 1;
const int chargeCount = 2;
for (int analysis = 1; analysis <= analysisCount; ++analysis)
for (int source = 1; source <= sourceCount; ++source)
for (int charge = 1; charge <= chargeCount; ++charge)
{
int scan = 0;
List<SpectrumTuple> testPsmSummary = new List<SpectrumTuple>()
{
// Columns: Group Source Spectrum Analysis Score Q List of Peptide@Charge/ScoreDivider
// 1 protein (PRO1) to 1 peptide to 1 spectrum = 1 additional peptide
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("AAAAAAAAAA@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO2) to 1 peptide to 2 spectra = 1 additional peptide
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBBBBBBB@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBBBBBBB@{0}/1 CCCCCCCCCC@{0}/8", charge)),
// 1 protein (PRO3) to 2 peptides to 1 spectrum (each) = 2 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("CCCCCCCCCC@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("CCCCCCCCC@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO4) to 2 peptides to 2 spectra (each) = 2 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDDDDDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDDDDDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDDDDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDDDDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO5,6) to 1 peptide to 1 spectrum = 1 additional peptide (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("EEEEEEEEEE@{0}/1 AAAAAAAAAA@{0}/8", charge)),
// 2 proteins (PRO7,8) to 1 peptide to 2 spectra = 1 additional peptide (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("FFFFFFFFFF@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("FFFFFFFFFF@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO9,10) to 2 peptides to 1 spectrum (each) = 2 additional peptides (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("GGGGGGGGGG@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("GGGGGGGGG@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO11,12) to 2 peptides to 2 spectra (each) = 2 additional peptides (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHHHHHH@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHHHHHH@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHHHHH@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHHHHH@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO13) to 2 peptides = 2 additional peptide
// 1 protein (PRO14) to 1 of the above peptides = 0 additional peptides (subsumed protein)
// 1 protein (PRO15) to the other above peptide = 0 additional peptides (subsumed protein)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("AAAABBBB@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBCCCC@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO16) to 2 peptides = 2 additional peptide
// 2 proteins (PRO17,18) to 1 of the above peptides = 0 additional peptides (subsumed ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDEEEE@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("EEEEFFFF@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO19,20) to 2 peptides = 2 additional peptide (ambiguous protein group)
// 1 protein (PRO21) to 1 of the above peptides = 0 additional peptides (subsumed protein)
// 1 protein (PRO22) to the other above peptide = 0 additional peptides (subsumed protein)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("GGGGHHHH@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHIIII@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO23,24) to 2 peptides = 2 additional peptides (ambiguous protein group)
// 2 proteins (PRO25,26) to 1 of the above peptides = 0 additional peptides (subsumed ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("KKKKLLLL@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("LLLLMMMM@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO27) to 3 peptides = 3 additional peptides
// 1 protein (PRO28) to 1 of the above peptides and 1 extra peptide = 1 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("NNNNPPPP@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("NNNNPPP@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("PPPPQQQQ@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("QQQQRRRR@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO29) to 3 peptides = 3 additional peptides
// 2 proteins (PRO30,31) to 1 of the above peptides and 1 extra peptide = 1 additional peptides (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("SSSSTTTT@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("SSSSTTT@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("TTTTUUUU@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("UUUUVVVV@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO32,33) to 3 peptides = 3 additional peptides (ambiguous protein group)
// 1 protein (PRO34) to 1 of the above peptides and 1 extra peptide = 1 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("WWWWYYYY@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("WWWWYYY@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("YYYYZZZZ@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("ZZZZFFFF@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO35,36) to 3 peptides = 3 additional peptides (ambiguous protein group)
// 2 proteins (PRO37,38) to 1 of the above peptides and 1 extra peptide = 1 additional peptides (ambiguous protein group)
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("AAAACCCC@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("AAAACCC@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("CCCCEEEE@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("EEEEGGGG@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO39) to 5 peptides = 5 additional peptides
// 1 protein (PRO40) to 4 of the above peptides = 0 additional peptides
// 1 protein (PRO41) to 3 of the above peptides and 1 extra peptides = 1 additional peptides
// 1 protein (PRO42) to 2 of the above peptides and 2 extra peptides = 2 additional peptides
// 1 protein (PRO43) to 1 of the above peptides and 3 extra peptides = 3 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBBDDDDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBDDDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBDDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("ZBBBBDDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("YBBBDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("YBBBDDD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("WBB@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("WBBD@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("WBBDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
// 1 protein (PRO44) to 3 peptides, 1 of which is evidenced by an ambiguous spectrum = 3 additional peptides
// 1 protein (PRO45) to 1 peptide evidenced by the ambiguous spectrum above and 1 extra peptide = 1 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDFFFFF@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDDFFFF@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DFFFFF@{0}/1 FFFFFH@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("FFFFFHHHHH@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 2 proteins (PRO46,47) to 3 peptides, 1 of which is evidenced by an ambiguous spectrum = 3 additional peptides
// 1 protein (PRO48) to 1 peptide evidenced by the ambiguous spectrum above and 1 extra peptide = 1 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHKKKKK@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHHKKKK@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HKKKKK@{0}/1 KKKKKM@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("KKKKKMMMMM@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO49) to 3 peptides, 1 of which is evidenced by an ambiguous spectrum = 3 additional peptides
// 2 proteins (PRO50,51) to 1 peptide evidenced by the ambiguous spectrum above and 1 extra peptide = 1 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("LLLLLNNNNN@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("LLLLLNNNN@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("LNNNNN@{0}/1 NNNNNQ@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("NNNNNQQQQQ@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// 1 protein (PRO52) to 3 peptides, 2 of which are evidenced by ambiguous spectra = 3 additional peptides
// 1 protein (PRO53) to 1 peptide evidenced by an ambiguous spectrum above and 1 extra peptide = 1 additional peptides
// 1 protein (PRO54) to 1 peptide evidenced by the other ambiguous spectrum above and 1 extra peptide = 1 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("MMMMMPPPPP@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("MPPPPP@{0}/1 PRRRRR@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("PPPPPRRRRR@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("MPPPP@{0}/1 PRRRRP@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("PPPPRRRRP@{0}/1 AAAAAAAAAA@{0}/8", charge)),
// PRO55 -> QQQQSSSS, SSSSUUUU = 2 additional peptides
// PRO56 -> UUUUYYYY, SSSSUUUU = 2 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("QQQQSSSS@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("SSSSUUUU@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("UUUUYYYY@{0}/1 AAAAAAAAAA@{0}/8", charge)),
// PRO57 -> RRRRTTTT, WWWWZZZZ, TTTTWWWW = 3 additional peptides
// PRO58 -> ZZZZBBBB, WWWWZZZZ, TTTTWWWW = 3 additional peptides
// PRO59 -> RRRRTTTT, ZZZZBBBB, TTTTWWWW = 3 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("RRRRTTTT@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("WWWWZZZZ@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("TTTTWWWW@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("ZZZZBBBB@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// PRO60 -> AAAADDDD, DDDDGGGG, GGGGKKKK = 3 additional peptides
// PRO61 -> DDDDGGGG, GGGGKKKK, KKKKNNNN = 3 additional peptides
// PRO62 -> AAAADDDD, KKKKNNNN = 0 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("AAAADDDD@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("DDDDGGGG@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("GGGGKKKK@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("KKKKNNNN@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// PRO63 -> BBBBEEEE, EEEEHHHH = 2 additional peptides
// PRO64 -> EEEEHHHH, HHHHLLLL = 0 additional peptides
// PRO65 -> HHHHLLLL, LLLLPPPP = 2 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("BBBBEEEE@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("EEEEHHHH@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("HHHHLLLL@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("LLLLPPPP@{0}/1 BBBBBBBBBB@{0}/8", charge)),
// PRO66 -> CCCCFFFF, CFFFFI, FFFFIIII = 3 additional peptides
// PRO67 -> FFFFIIII, FIIIIM, IIIIMMMM = 1 additional peptides
// PRO68 -> IIIIMMMM, IMMMMQ, MMMMQQQQ = 3 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("CCCCFFFF@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("CFFFFI@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("FFFFIIII@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("FIIIIM@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("IIIIMMMM@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("IMMMMQ@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("MMMMQQQQ@{0}/1 AAAAAAAAAA@{0}/8", charge)),
// PRO69 -> NNNNRRRR, RRRRUUUU, RRRRUUU = 3 additional peptides
// PRO70 -> RRRRUUUU, RRRRUUU, UUUUZZZZ = 0 additional peptides
// PRO71 -> UUUUZZZZ, UZZZZC, ZZZZCCCC = 3 additional peptides
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("NNNNRRRR@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("RRRRUUUU@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("RRRRUUU@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("UUUUZZZZ@{0}/1 BBBBBBBBBB@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("UZZZZC@{0}/1 AAAAAAAAAA@{0}/8", charge)),
new SpectrumTuple("/", source, ++scan, analysis, 1, 1, String.Format("ZZZZCCCC@{0}/1 BBBBBBBBBB@{0}/8", charge)),
};
TestModel.CreateTestData(session, testPsmSummary);
}
var dataFilter = new DataFilter()
{
MaximumQValue = 1,
MinimumDistinctPeptides = 0,
MinimumSpectra = 0,
MinimumAdditionalPeptides = 1
};
dataFilter.ApplyBasicFilters(session);
// clear session so objects are loaded from database
session.Clear();
var additionalPeptidesByProteinId = new Map<long, int>();
foreach (object[] row in session.CreateSQLQuery("SELECT ProteinId, AdditionalMatches FROM AdditionalMatches").List<object[]>())
additionalPeptidesByProteinId[Convert.ToInt64(row[0])] = Convert.ToInt32(row[1]);
// 1 protein to 1 peptide to 1 spectrum = 1 additional peptide
Assert.AreEqual(1, additionalPeptidesByProteinId[1]);
// 1 protein to 1 peptide to 2 spectra = 1 additional peptide
Assert.AreEqual(1, additionalPeptidesByProteinId[2]);
// 1 protein to 2 peptides to 1 spectrum (each) = 2 additional peptides
Assert.AreEqual(2, additionalPeptidesByProteinId[3]);
// 1 protein to 2 peptides to 2 spectra (each) = 2 additional peptides
Assert.AreEqual(2, additionalPeptidesByProteinId[4]);
// 2 proteins to 1 peptide to 1 spectrum = 1 additional peptide (ambiguous protein group)
Assert.AreEqual(1, additionalPeptidesByProteinId[5]);
Assert.AreEqual(1, additionalPeptidesByProteinId[6]);
// 2 proteins to 1 peptide to 2 spectra = 1 additional peptide (ambiguous protein group)
Assert.AreEqual(1, additionalPeptidesByProteinId[7]);
Assert.AreEqual(1, additionalPeptidesByProteinId[8]);
// 2 proteins to 2 peptides to 1 spectrum (each) = 2 additional peptides (ambiguous protein group)
Assert.AreEqual(2, additionalPeptidesByProteinId[9]);
Assert.AreEqual(2, additionalPeptidesByProteinId[10]);
// 2 proteins to 2 peptides to 2 spectra (each) = 2 additional peptides (ambiguous protein group)
Assert.AreEqual(2, additionalPeptidesByProteinId[11]);
Assert.AreEqual(2, additionalPeptidesByProteinId[12]);
// 1 protein to 2 peptides to 1 spectrum (each) = 2 additional peptide
// 1 protein to 1 of the above peptides = 0 additional peptides (subsumed protein)
// 1 protein to the other above peptide = 0 additional peptides (subsumed protein)
Assert.AreEqual(2, additionalPeptidesByProteinId[13]);
Assert.AreEqual(0, additionalPeptidesByProteinId[14]);
Assert.AreEqual(0, additionalPeptidesByProteinId[15]);
// 1 protein to 2 peptides to 1 spectrum (each) = 2 additional peptide
// 2 proteins to 1 of the above peptides = 0 additional peptides (subsumed ambiguous protein group)
Assert.AreEqual(2, additionalPeptidesByProteinId[16]);
Assert.AreEqual(0, additionalPeptidesByProteinId[17]);
Assert.AreEqual(0, additionalPeptidesByProteinId[18]);
// 2 proteins to 2 peptides to 1 spectrum (each) = 2 additional peptide (ambiguous protein group)
// 1 protein to 1 of the above peptides = 0 additional peptides (subsumed protein)
// 1 protein to the other above peptide = 0 additional peptides (subsumed protein)
Assert.AreEqual(2, additionalPeptidesByProteinId[19]);
Assert.AreEqual(2, additionalPeptidesByProteinId[20]);
Assert.AreEqual(0, additionalPeptidesByProteinId[21]);
Assert.AreEqual(0, additionalPeptidesByProteinId[22]);
// 2 proteins to 2 peptides to 1 spectrum (each) = 2 additional peptides (ambiguous protein group)
// 2 proteins to 1 of the above peptides = 0 additional peptides (subsumed ambiguous protein group)
Assert.AreEqual(2, additionalPeptidesByProteinId[23]);
Assert.AreEqual(2, additionalPeptidesByProteinId[24]);
Assert.AreEqual(0, additionalPeptidesByProteinId[25]);
Assert.AreEqual(0, additionalPeptidesByProteinId[26]);
// 1 protein to 3 peptides to 1 spectrum (each) = 3 additional peptides
// 1 protein to 1 of the above peptides and 1 extra peptide to 1 spectrum = 1 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[27]);
Assert.AreEqual(1, additionalPeptidesByProteinId[28]);
// 1 protein to 3 peptides to 1 spectrum (each) = 3 additional peptides
// 2 proteins to 1 of the above peptides and 1 extra peptide to 1 spectrum = 1 additional peptides (ambiguous protein group)
Assert.AreEqual(3, additionalPeptidesByProteinId[29]);
Assert.AreEqual(1, additionalPeptidesByProteinId[30]);
Assert.AreEqual(1, additionalPeptidesByProteinId[31]);
// 2 proteins to 3 peptides to 1 spectrum (each) = 3 additional peptides (ambiguous protein group)
// 1 protein to 1 of the above peptides and 1 extra peptide to 1 spectrum = 1 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[32]);
Assert.AreEqual(3, additionalPeptidesByProteinId[33]);
Assert.AreEqual(1, additionalPeptidesByProteinId[34]);
// 2 proteins to 3 peptides to 1 spectrum (each) = 3 additional peptides (ambiguous protein group)
// 2 proteins to 1 of the above peptides and 1 extra peptide to 1 spectrum = 1 additional peptides (ambiguous protein group)
Assert.AreEqual(3, additionalPeptidesByProteinId[35]);
Assert.AreEqual(3, additionalPeptidesByProteinId[36]);
Assert.AreEqual(1, additionalPeptidesByProteinId[37]);
Assert.AreEqual(1, additionalPeptidesByProteinId[38]);
// 1 protein (PRO39) to 5 peptides = 5 additional peptides
// 1 protein (PRO40) to 4 of the above peptides = 0 additional peptides
// 1 protein (PRO41) to 3 of the above peptides and 1 extra peptides = 1 additional peptides
// 1 protein (PRO42) to 2 of the above peptides and 2 extra peptides = 2 additional peptides
// 1 protein (PRO43) to 1 of the above peptides and 3 extra peptides = 3 additional peptides
Assert.AreEqual(5, additionalPeptidesByProteinId[39]);
Assert.AreEqual(0, additionalPeptidesByProteinId[40]);
Assert.AreEqual(1, additionalPeptidesByProteinId[41]);
Assert.AreEqual(2, additionalPeptidesByProteinId[42]);
Assert.AreEqual(3, additionalPeptidesByProteinId[43]);
// 1 protein (PRO44) to 3 peptides, 1 of which is evidenced by an ambiguous spectrum = 3 additional peptides
// 1 protein (PRO45) to 1 peptide evidenced by the ambiguous spectrum above and 1 extra peptide = 1 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[44]);
Assert.AreEqual(1, additionalPeptidesByProteinId[45]);
// 2 proteins (PRO46,47) to 3 peptides, 1 of which is evidenced by an ambiguous spectrum = 3 additional peptides
// 1 protein (PRO48) to 1 peptide evidenced by the ambiguous spectrum above and 1 extra peptide = 1 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[46]);
Assert.AreEqual(3, additionalPeptidesByProteinId[47]);
Assert.AreEqual(1, additionalPeptidesByProteinId[48]);
// 1 protein (PRO49) to 3 peptides, 1 of which is evidenced by an ambiguous spectrum = 3 additional peptides
// 2 proteins (PRO50,51) to 1 peptide evidenced by the ambiguous spectrum above and 1 extra peptide = 1 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[49]);
Assert.AreEqual(1, additionalPeptidesByProteinId[50]);
Assert.AreEqual(1, additionalPeptidesByProteinId[51]);
// 1 protein (PRO52) to 3 peptides, 2 of which are evidenced by ambiguous spectra = 3 additional peptides
// 1 protein (PRO53) to 1 peptide evidenced by an ambiguous spectrum above and 1 extra peptide = 1 additional peptides
// 1 protein (PRO54) to 1 peptide evidenced by the other ambiguous spectrum above and 1 extra peptide = 1 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[52]);
Assert.AreEqual(1, additionalPeptidesByProteinId[53]);
Assert.AreEqual(1, additionalPeptidesByProteinId[54]);
// PRO55 -> QQQQSSSS, SSSSUUUU = 2 additional peptides
// PRO56 -> UUUUYYYY, SSSSUUUU = 2 additional peptides
Assert.AreEqual(2, additionalPeptidesByProteinId[55]);
Assert.AreEqual(2, additionalPeptidesByProteinId[56]);
// PRO57 -> RRRRTTTT, WWWWZZZZ, TTTTWWWW = 3 additional peptides
// PRO58 -> QQQQKKKK, WWWWZZZZ, TTTTWWWW = 3 additional peptides
// PRO59 -> RRRRTTTT, TTTTZZZZ, TTTTWWWW = 3 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[57]);
Assert.AreEqual(3, additionalPeptidesByProteinId[58]);
Assert.AreEqual(3, additionalPeptidesByProteinId[59]);
// PRO60 -> AAAADDDD, DDDDGGGG, GGGGKKKK = 3 additional peptides
// PRO61 -> DDDDGGGG, GGGGKKKK, KKKKNNNN = 3 additional peptides
// PRO62 -> AAAADDDD, KKKKNNNN = 0 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[60]);
Assert.AreEqual(3, additionalPeptidesByProteinId[61]);
Assert.AreEqual(0, additionalPeptidesByProteinId[62]);
// PRO63 -> BBBBEEEE, EEEEHHHH = 2 additional peptides
// PRO64 -> EEEEHHHH, HHHHLLLL = 0 additional peptides
// PRO65 -> HHHHLLLL, LLLLPPPP = 2 additional peptides
Assert.AreEqual(2, additionalPeptidesByProteinId[63]);
Assert.AreEqual(0, additionalPeptidesByProteinId[64]);
Assert.AreEqual(2, additionalPeptidesByProteinId[65]);
// PRO66 -> CCCCFFFF, CFFFFI, FFFFIIII = 3 additional peptides
// PRO67 -> FFFFIIII, FIIIIM, IIIIMMMM = 1 additional peptides
// PRO68 -> IIIIMMMM, IMMMMQ, MMMMQQQQ = 3 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[66]);
Assert.AreEqual(1, additionalPeptidesByProteinId[67]);
Assert.AreEqual(3, additionalPeptidesByProteinId[68]);
// PRO69 -> NNNNRRRR, RRRRUUUU, RRRRUUU = 3 additional peptides
// PRO70 -> RRRRUUUU, RRRRUUU, UUUUZZZZ = 0 additional peptides
// PRO71 -> UUUUZZZZ, UZZZZC, ZZZZCCCC = 3 additional peptides
Assert.AreEqual(3, additionalPeptidesByProteinId[69]);
Assert.AreEqual(0, additionalPeptidesByProteinId[70]);
Assert.AreEqual(3, additionalPeptidesByProteinId[71]);
// test that the MinimumAdditionalPeptidesPerProtein filter is applied correctly;
// proteins filtered out by it should cascade to PeptideInstances, Peptides, and PSMs
dataFilter.MinimumAdditionalPeptides = 1;
dataFilter.ApplyBasicFilters(session);
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO55"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO56"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO57"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO58"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO59"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO60"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO61"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO62"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO62"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "AAAADDDD"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "KKKKNNNN"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO63"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO64"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO65"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO64"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "EEEEHHHH"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "HHHHLLLL"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO66"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO67"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO68"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO69"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO70"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO71"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO70"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "RRRRUUUU"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "RRRRUUU"));
Assert.IsNotNull(session.UniqueResult<Peptide>(o => o.Sequence == "UUUUZZZZ"));
dataFilter.MinimumAdditionalPeptides = 2;
dataFilter.ApplyBasicFilters(session);
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO55"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO56"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO57"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO58"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO59"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO60"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO61"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO62"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO62"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO63"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO64"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO65"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO64"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO66"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO67"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO68"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO67"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "FIIIIM"));
Assert.IsNull(session.UniqueResult<PeptideSpectrumMatch>(o => o.Peptide.Sequence == "FIIIIM"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO69"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO70"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO71"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO70"));
dataFilter.MinimumAdditionalPeptides = 3;
dataFilter.ApplyBasicFilters(session);
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO55"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO56"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO55"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO56"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "QQQQSSSS"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "SSSSUUUU"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "UUUUYYYY"));
Assert.IsNull(session.UniqueResult<PeptideSpectrumMatch>(o => o.Peptide.Sequence == "QQQQSSSS"));
Assert.IsNull(session.UniqueResult<PeptideSpectrumMatch>(o => o.Peptide.Sequence == "SSSSUUUU"));
Assert.IsNull(session.UniqueResult<PeptideSpectrumMatch>(o => o.Peptide.Sequence == "UUUUYYYY"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO57"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO58"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO59"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO60"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO61"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO62"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO62"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO63"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO64"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO65"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO63"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO64"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO65"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "BBBBEEEE"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "EEEEHHHH"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "HHHHLLLL"));
Assert.IsNull(session.UniqueResult<Peptide>(o => o.Sequence == "LLLLPPPP"));
Assert.IsNull(session.UniqueResult<PeptideSpectrumMatch>(o => o.Peptide.Sequence == "BBBBEEEE"));
Assert.IsNull(session.UniqueResult<PeptideSpectrumMatch>(o => o.Peptide.Sequence == "EEEEHHHH"));
Assert.IsNull(session.UniqueResult<PeptideSpectrumMatch>(o => o.Peptide.Sequence == "HHHHLLLL"));
Assert.IsNull(session.UniqueResult<PeptideSpectrumMatch>(o => o.Peptide.Sequence == "LLLLPPPP"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO66"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO67"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO68"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO67"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO69"));
Assert.IsNull(session.UniqueResult<Protein>(o => o.Accession == "PRO70"));
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO71"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession == "PRO70"));
dataFilter.MinimumAdditionalPeptides = 4;
dataFilter.ApplyBasicFilters(session);
Assert.AreEqual(1, session.Query<Protein>().Count());
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO39"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession != "PRO39"));
var remainingPeptides = new string[] { "BBBBBDDDDD", "BBBBDDDD", "BBBBDDD", "BBBDD", "BBDD" };
Assert.AreEqual(5, session.Query<Peptide>().Count());
Assert.AreEqual(5, session.Query<Peptide>().Count(o => remainingPeptides.Contains(o.Sequence)));
Assert.AreEqual(0, session.Query<Peptide>().Count(o => !remainingPeptides.Contains(o.Sequence)));
Assert.AreNotEqual(0, session.Query<PeptideSpectrumMatch>().Count(o => remainingPeptides.Contains(o.Peptide.Sequence)));
Assert.AreEqual(0, session.Query<PeptideSpectrumMatch>().Count(o => !remainingPeptides.Contains(o.Peptide.Sequence)));
dataFilter.MinimumAdditionalPeptides = 5;
dataFilter.ApplyBasicFilters(session);
Assert.AreEqual(1, session.Query<Protein>().Count());
Assert.IsNotNull(session.UniqueResult<Protein>(o => o.Accession == "PRO39"));
Assert.IsNull(session.UniqueResult<PeptideInstance>(o => o.Protein.Accession != "PRO39"));
dataFilter.MinimumAdditionalPeptides = 6;
dataFilter.ApplyBasicFilters(session);
Assert.AreEqual(0, session.Query<Protein>().Count());
Assert.AreEqual(0, session.Query<PeptideInstance>().Count());
Assert.AreEqual(0, session.Query<Peptide>().Count());
Assert.AreEqual(0, session.Query<PeptideSpectrumMatch>().Count());
session.Close();
}
public void Initialize()
{
//Objekte der Klassen werden initialisiert.
map = new Map(new System.Drawing.Bitmap("Collision-Maps/Collision-Bitmap.bmp"));
player = new Player("Cookie2", new Vector2f(200, 1400));
enemy = new Enemy01();
checkPointList = checkPointList01();
text = new Texture("Collision-Maps/Collision-Bitmap.bmp");
sprite = new Sprite(text);
sprite.Scale = new Vector2f(50, 50);
powerups = new Powerups01();
hud = new Hud();
start = new TimeSpan(0, 0, 3);
Stopwatch timer = new Stopwatch();
TimeSpan time = new TimeSpan();
timer.Start();
time = new TimeSpan(0, 0, 1);
pH = new ParticleHandler();
}
public void Init()
{
Map map = new Map ();
}
