public void TestSearchWithTagGeneration()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rawFilePath = @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(rawFilePath);
const string fastaFilePath = @"D:\MSPathFinder\Fasta\ID_002216_235ACCEA.fasta";
//const string fastaFilePath = @"D:\MassSpecFiles\60k\ID_004973_9BA6912F.fasta";
if (!File.Exists(fastaFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, fastaFilePath);
}
var fastaDb = new FastaDatabase(fastaFilePath);
var tolerance = new Tolerance(10);
var modsFilePath = @"D:\MSPathFinder\Fasta\Mods.txt";
if (!File.Exists(modsFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, modsFilePath);
}
var aaSet = new AminoAcidSet(modsFilePath);
//TestTagBasedSearch(run, fastaDb, tolerance, aaSet);
var tagSearchEngine = new ScanBasedTagSearchEngine(run, new SequenceTagGenerator(run, new Tolerance(8)), new LcMsPeakMatrix(run), fastaDb, tolerance,aaSet);
var matchedTags = tagSearchEngine.RunSearch(4672);
foreach (var match in matchedTags)
{
Console.Write(match.Sequence);
Console.WriteLine("\t{0}\t{1}\t{2}", match.TagMatch.StartIndex, match.TagMatch.EndIndex, match.TagMatch.Mass);
}
}
private void TestTagBasedSearch(LcMsRun run,
FastaDatabase fastaDb, Tolerance tolerance, AminoAcidSet aaSet)
{
var engine = new ScanBasedTagSearchEngine(run, new SequenceTagGenerator(run, new Tolerance(8)), new LcMsPeakMatrix(run), fastaDb, tolerance, aaSet);
// engine.MinScan = 3400;
// engine.MaxScan = 3900;
engine.RunSearch();
}