public void GenerateDecoysTest()
{
TestFilesDir testFilesDir = new TestFilesDir(TestContext, @"TestA\SimpleDecoys.zip");
string docPath = testFilesDir.GetTestPath("SimpleDecoys.sky");
SrmDocument simpleDecoysDoc = ResultsUtil.DeserializeDocument(docPath);
AssertEx.IsDocumentState(simpleDecoysDoc, 0, 1, 18, 18, 56);
// First check right number of decoy peptide groups and transtions are generated
var refineSettings = new RefinementSettings();
int numDecoys = simpleDecoysDoc.PeptideCount;
var decoysDoc = refineSettings.GenerateDecoys(simpleDecoysDoc, numDecoys, DecoyGeneration.ADD_RANDOM);
ValidateDecoys(simpleDecoysDoc, decoysDoc, false);
// Second call to generate decoys to make sure that it removes the original Decoys group and generates a completely new one.
var newDecoysDoc = refineSettings.GenerateDecoys(decoysDoc, numDecoys, DecoyGeneration.ADD_RANDOM);
Assert.AreNotEqual(decoysDoc.PeptideGroups.First(nodePeptideGroup => nodePeptideGroup.IsDecoy),
newDecoysDoc.PeptideGroups.First(nodePeptideGroup => nodePeptideGroup.IsDecoy));
// MS1 document with precursors and variable modifications, shuffled
docPath = testFilesDir.GetTestPath("Ms1FilterTutorial.sky");
SrmDocument variableDecoysDoc = ResultsUtil.DeserializeDocument(docPath);
AssertEx.IsDocumentState(variableDecoysDoc, 0, 11, 50, 51, 153);
numDecoys = variableDecoysDoc.PeptideCount;
var decoysVariableShuffle = refineSettings.GenerateDecoys(variableDecoysDoc, numDecoys, DecoyGeneration.SHUFFLE_SEQUENCE);
ValidateDecoys(variableDecoysDoc, decoysVariableShuffle, true);
// Document with explicit modifications, reversed
SrmDocument docStudy7 = ResultsUtil.DeserializeDocument("Study7.sky", GetType());
AssertEx.IsDocumentState(docStudy7, 0, 7, 11, 22, 66);
numDecoys = docStudy7.PeptideCount;
var decoysExplicitReverse = refineSettings.GenerateDecoys(docStudy7, numDecoys, DecoyGeneration.REVERSE_SEQUENCE);
ValidateDecoys(docStudy7, decoysExplicitReverse, true);
// Random mass shifts with precursors (used to throw an exception due to bad range check that assumed product ions only)
while (true)
{
// As this is random we may need to make a few attempts before we get the values we need
SrmDocument doc = ResultsUtil.DeserializeDocument(testFilesDir.GetTestPath("precursor_decoy_test.sky"));
AssertEx.IsDocumentState(doc, null, 1, 1, 2, 6);
numDecoys = 2;
var decoysRandom = refineSettings.GenerateDecoys(doc, numDecoys, DecoyGeneration.ADD_RANDOM);
// Verify that we successfully set a precursor transition decoy mass outside the allowed range of product transitions
if (decoysRandom.PeptideTransitions.Any(x => x.IsDecoy &&
(x.Transition.DecoyMassShift > Transition.MAX_PRODUCT_DECOY_MASS_SHIFT ||
x.Transition.DecoyMassShift < Transition.MIN_PRODUCT_DECOY_MASS_SHIFT)))
{
break;
}
}
}
