private void Search_MouseLeftButtonUp(object sender, MouseButtonEventArgs e)
{
SearchTask st = new SearchTask();
st.SearchQuery = "31 Days of Windows Phone";
st.Show();
}
//Search the web for the URL
private void SearchWebURL(object sender, RoutedEventArgs e)
{
SearchTask task = new SearchTask();
task.SearchQuery = this.barcodeText;
task.Show();
}
public static void TestMetaDrawReadPsmFile()
{
SearchTask searchTask = new SearchTask();
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\PrunedDbSpectra.mzml");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\DbForPrunedDb.fasta");
string folderPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestMetaDrawReadPsmFile");
DbForTask db = new DbForTask(myDatabase, false);
Directory.CreateDirectory(folderPath);
searchTask.RunTask(folderPath, new List <DbForTask> {
db
}, new List <string> {
myFile
}, "metadraw");
string psmFile = Directory.GetFiles(folderPath).First(f => f.Contains("AllPSMs.psmtsv"));
List <PsmFromTsv> parsedPsms = PsmTsvReader.ReadTsv(psmFile, out var warnings);
Assert.AreEqual(11, parsedPsms.Count);
Assert.AreEqual(0, warnings.Count);
Directory.Delete(folderPath, true);
}
public IHttpActionResult GetAllTaskBySearch(SearchTask Search)
{
service = new TaskManagerService();
List <Task> tasks = service.GetAllTaskBySearchCriteria(Search);
return(Ok(tasks));
}
//Search the we for more information abut the product
private void SearchWeb(object ender, RoutedEventArgs e)
{
SearchTask searchTask = new SearchTask();
searchTask.SearchQuery = AppContext.appContext.itemEdit.barcodeNumber;
searchTask.Show();
}
public void FindAndExecute(SearchTask searchTask)
{
if (string.IsNullOrWhiteSpace(searchTask.SearchLine))
{
return;
}
if (File.Exists(searchTask.FullPath))
{
if (TryExecute(searchTask.FullPath, searchTask.SearchLine, searchTask.SearchDir))
{
return;
}
}
var files = Directory.GetFiles(searchTask.SearchDir, "*.*", SearchOption.AllDirectories).Where(IsCodeFile).ToArray();
foreach (var file in files)
{
if (TryExecute(file, searchTask.SearchLine, searchTask.SearchDir))
{
searchTask.FullPath = file;
return;
}
}
}
public static IEnumerable <ParsedClass> FindAndParse(SearchTask searchTask, string projName, string[] extensions, bool isApi)
{
var cashFile = Path.Combine(SubDirName, projName, $"{searchTask.SearchLine}.txt");
if (!Directory.Exists(SubDirName))
{
Directory.CreateDirectory(SubDirName);
}
if (!Directory.Exists(Path.Combine(SubDirName, projName)))
{
Directory.CreateDirectory(Path.Combine(SubDirName, projName));
}
if (!string.IsNullOrEmpty(searchTask.FullPath) && File.Exists(searchTask.FullPath))
{
if (File.Exists(cashFile))
{
var text = File.ReadAllText(cashFile);
yield return(JsonConvert.DeserializeObject <ParsedClass>(text));
}
}
var lines = Grabber.FindClass(searchTask, projName, extensions);
foreach (var text in lines)
{
var parcedClass = TryParseClass(text, isApi);
parcedClass.AbsPathToFile = searchTask.FullPath.Remove(0, searchTask.SearchDir.Length);
var json = JsonConvert.SerializeObject(parcedClass);
File.WriteAllText(cashFile, json);
yield return(parcedClass);
}
}
private void SearchClick(object sender, EventArgs e)
{
SearchTask task = new SearchTask();
task.SearchQuery = Constants.SearchStr + " " + _detailItem.ItemTitle;
task.Show();
}
public SearchTaskWindow()
{
InitializeComponent();
TheTask = new SearchTask();
PopulateChoices();
UpdateFieldsFromTask(TheTask);
this.saveButton.Content = "Add the Search Task";
dataContextForSearchTaskWindow = new DataContextForSearchTaskWindow
{
ExpanderTitle = string.Join(", ", SearchModesForThisTask.Where(b => b.Use).Select(b => b.Name)),
//ModExpanderTitle =
//"fixed: "
//+ string.Join(",", ModFileListInWindow.Where(b => b.Fixed).Select(b => b.FileName))
//+ " variable: "
//+ string.Join(",", ModFileListInWindow.Where(b => b.Variable).Select(b => b.FileName))
//+ " localize: "
//+ string.Join(",", ModFileListInWindow.Where(b => b.Localize).Select(b => b.FileName)),
AnalysisExpanderTitle = "Some analysis properties...",
SearchModeExpanderTitle = "Some search properties..."
};
this.DataContext = dataContextForSearchTaskWindow;
}
private ParsedClass FindAndParse(SearchTask task, string storeResultDir, bool enablePrint)
{
switch (task.Converter)
{
case KnownConverter.ApiConverter:
{
var converted = _apiConverter.FindAndParse(task, new[] { ".hpp" }, true);
if (enablePrint && converted != null)
{
var absPathToFile = task.FullPath.Remove(0, task.SearchDir.Length);
_apiConverter.PrintToFile(converted, task.SearchDir, absPathToFile, storeResultDir);
}
return(converted);
}
case KnownConverter.StructConverter:
{
var converted = _structConverter.FindAndParse(task, new[] { ".cpp", ".hpp" }, false);
if (enablePrint && converted != null)
{
var absPathToFile = task.FullPath.Remove(0, task.SearchDir.Length);
_structConverter.PrintToFile(converted, task.SearchDir, absPathToFile, storeResultDir);
}
return(converted);
}
}
return(null);
}
public static void GenerateDefaultTaskTomls(string folderLocation)
{
try
{
if (!Directory.Exists(folderLocation))
{
Directory.CreateDirectory(folderLocation);
}
CalibrationTask c = new CalibrationTask();
Toml.WriteFile(c, Path.Combine(folderLocation, @"CalibrationTask.toml"), MetaMorpheusTask.tomlConfig);
GptmdTask g = new GptmdTask();
Toml.WriteFile(g, Path.Combine(folderLocation, @"GptmdTask.toml"), MetaMorpheusTask.tomlConfig);
SearchTask s = new SearchTask();
Toml.WriteFile(s, Path.Combine(folderLocation, @"SearchTask.toml"), MetaMorpheusTask.tomlConfig);
XLSearchTask xl = new XLSearchTask();
Toml.WriteFile(xl, Path.Combine(folderLocation, @"XLSearchTask.toml"), MetaMorpheusTask.tomlConfig);
GlycoSearchTask glyco = new GlycoSearchTask();
Toml.WriteFile(glyco, Path.Combine(folderLocation, @"GlycoSearchTask.toml"), MetaMorpheusTask.tomlConfig);
}
catch (Exception e)
{
throw new MetaMorpheusException("Default tomls could not be written: " + e.Message);
}
}
public static void MassDiffAceptorTest()
{
SearchTask searchTask = new SearchTask();
var result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, searchTask.SearchParameters.MassDiffAcceptorType, searchTask.SearchParameters.CustomMdac);
Assert.That(result.FileNameAddition.Equals("1mm"));
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.TwoMM, searchTask.SearchParameters.CustomMdac);
Assert.That(result.FileNameAddition.Equals("2mm"));
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.ThreeMM, searchTask.SearchParameters.CustomMdac);
Assert.That(result.FileNameAddition.Equals("3mm"));
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.ModOpen, searchTask.SearchParameters.CustomMdac);
Assert.That(result.FileNameAddition.Equals("-187andUp"));
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Open, searchTask.SearchParameters.CustomMdac);
Assert.That(result.FileNameAddition.Equals("OpenSearch"));
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Custom, "custom ppmAroundZero 4");
Assert.That(result.FileNameAddition.Equals("4ppmAroundZero"));
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Exact, searchTask.SearchParameters.CustomMdac);
Assert.That(result.FileNameAddition.Equals("5ppmAroundZero"));
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.PlusOrMinusThreeMM, searchTask.SearchParameters.CustomMdac);
Assert.That(result.FileNameAddition.Equals("PlusOrMinus3Da"));
}
public static void PrunedDbWithContaminantsTest()
{
SearchTask searchTask = new SearchTask()
{
SearchParameters = new SearchParameters
{
WritePrunedDatabase = true
},
};
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\PrunedDbSpectra.mzml");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\DbForPrunedDb.fasta");
string folderPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestNormalization");
string filePath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\ExperimentalDesign.tsv");
// contaminant DB
DbForTask db = new DbForTask(myDatabase, true);
Directory.CreateDirectory(folderPath);
searchTask.RunTask(folderPath, new List <DbForTask> {
db
}, new List <string> {
myFile
}, "normal");
Assert.That(File.ReadAllLines(Path.Combine(folderPath, @"DbForPrunedDbproteinPruned.xml")).Length > 0);
Assert.That(File.ReadAllLines(Path.Combine(folderPath, @"DbForPrunedDbPruned.xml")).Length > 0);
Directory.Delete(folderPath, true);
}
private void btnSearch_Click(object sender, RoutedEventArgs e)
{
SearchTask st = new SearchTask();
st.SearchQuery = tbxSearch.Text;
st.Show();
}
private void Button_Click(object sender, RoutedEventArgs e)
{
SearchTask searchTask = new SearchTask();
searchTask.SearchQuery = txtKeyword.Text;
searchTask.Show();
}
private void Button_Click(object sender, RoutedEventArgs e)
{
if (!TryGetOption(out var option))
{
return;
}
var task = new SearchTask();
var paths = InputTextBox.Text.Split(new[] { Environment.NewLine }, StringSplitOptions.RemoveEmptyEntries)
.AsParallel()
.Select(x => Directory.Exists(x) ? Directory.EnumerateFiles(x) : Enumerable.Repeat(x, 1))
.SelectMany(x => x)
.Where(x => FastImageFormatChecker.IsImageFormat(x))
.ToArray();
paths.ForEach(x => Log.Debug($"Add saucenao search path: {x}"));
task.Options = option;
task.SearchImageInstances = paths.Select(x => new SearchInstance()
{
ImagePath = x
});
if (paths.Length == 0)
{
return;
}
AskIfNeedSave(task);
BeginTask(task);
}
public void VariantSpecificOutputFiles()
{
string thisTaskOutputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantFileOutput");
SearchTask task = Toml.ReadFile <SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"VariantSearchTaskConfig.toml"), MetaMorpheusTask.tomlConfig);
task.SearchParameters.DecoyType = DecoyType.None;
DbForTask noVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestNoVariantDb.xml"), false);
DbForTask ambigVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantDb_ambiguous.xml"), false);
DbForTask frameshiftVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantDB_frameshift.xml"), false);
DbForTask missenseVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantDB_missense.xml"), false);
DbForTask SNVmissenseVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantDB_SNVmissense.xml"), false);
DbForTask stopGainedVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantDB_stopGained.xml"), false);
DbForTask conservativeInsertionVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantDB_conservativeInsertion.xml"), false);
DbForTask disruptiveInsertionVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantDB_disruptiveInsertion.xml"), false);
DbForTask conservativeDeletionVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantDB_conservativeDeletion.xml"), false);
DbForTask disruptiveDeletionVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantDB_disruptiveDeletion.xml"), false);
DbForTask stopLossVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantDB_stopLoss.xml"), false);
string raw = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantPep.mzML");
EverythingRunnerEngine noVariants = new EverythingRunnerEngine(new List <(string, MetaMorpheusTask)> {
("NoVariantOutput", task)
}, new List <string> {
private void SearchClick(object sender, EventArgs e)
{
SearchTask task = new SearchTask();
task.SearchQuery = blogDetail.ItemUser;
task.Show();
}
public static void TestLoadAndRunMgf()
{
//The purpose of this test is to ensure that mgfs can be run without crashing.
//Whenever a new feature is added that may require things an mgf does not have,
//there should be a check that prevents mgfs from using that feature.
string mgfName = @"TestData\ok.mgf";
string xmlName = @"TestData\okk.xml";
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestLoadAndRunMgf");
SearchTask task1 = new SearchTask
{
SearchParameters = new SearchParameters
{
DoParsimony = true,
DoQuantification = true
}
};
List <(string, MetaMorpheusTask)> taskList = new List <(string, MetaMorpheusTask)>
{
("task1", task1),
};
//run!
var engine = new EverythingRunnerEngine(taskList, new List <string> {
mgfName
}, new List <DbForTask> {
new DbForTask(xmlName, false)
}, outputFolder);
engine.Run();
//Just don't crash! There should also be at least one psm at 1% FDR, but can't check for that.
Directory.Delete(outputFolder, true);
}
public void Typing()
{
dropDown.interactable = false;
string s = input.text;
task = map.map.Search(s); // initiate search task
}
public static void TestQValueFilter()
{
SearchTask searchTask = new SearchTask()
{
CommonParameters = new CommonParameters
(
qValueOutputFilter: 1
)
};
SearchTask searchTask2 = new SearchTask()
{
CommonParameters = new CommonParameters
(
qValueOutputFilter: 0
)
};
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestPSMOutput");
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\PrunedDbSpectra.mzml");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\DbForPrunedDb.fasta");
var engine = new EverythingRunnerEngine(new List <(string, MetaMorpheusTask)> {
("QValueTest", searchTask)
}, new List <string> {
//Search the we for more information abut the product
private void SearchWeb(object ender, RoutedEventArgs e)
{
SearchTask searchTask = new SearchTask();
searchTask.SearchQuery = NewCodeWrapper.infoResult.Text;
searchTask.Show();
}
void Update()
{
if (nav == null)
{
nav = FindObjectOfType <UnityEngine.Camera>().GetComponent <VtsNavigation>().Navigation;
return;
}
if (map.GetMapconfigAvailable() && map.GetSearchable())
{
input.interactable = true;
// the check method will update the results list if the data are already available
if (task != null && task.Check())
{
dropDown.options.Clear();
results.Clear();
foreach (string sr in task.results)
{
Item it = JsonUtility.FromJson <Item>(sr);
results.Add(it);
Dropdown.OptionData o = new Dropdown.OptionData(it.title);
dropDown.options.Add(o);
}
dropDown.value = -1;
dropDown.interactable = true;
task = null;
}
}
}
public static void ExperimentalDesignCalibrationAndSearch(string nonCalibratedFile)
{
// set up output directories
string unitTestFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"ExperimentalDesignCalibrationAndSearch");
string outputFolder = Path.Combine(unitTestFolder, @"TaskOutput");
Directory.CreateDirectory(unitTestFolder);
Directory.CreateDirectory(outputFolder);
// set up original spectra file (input to calibration)
string nonCalibratedFilePath = Path.Combine(unitTestFolder, nonCalibratedFile);
File.Copy(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SmallCalibratible_Yeast.mzML"), nonCalibratedFilePath, true);
// set up original experimental design (input to calibration)
SpectraFileInfo fileInfo = new SpectraFileInfo(nonCalibratedFilePath, "condition", 0, 0, 0);
var experimentalDesignFilePath = ExperimentalDesign.WriteExperimentalDesignToFile(new List <SpectraFileInfo> {
fileInfo
});
// set up tasks (calibration + search)
CalibrationTask calibrationTask = new CalibrationTask();
SearchTask searchTask = new SearchTask();
// protein db
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\smalldb.fasta");
// run the tasks
EverythingRunnerEngine a = new EverythingRunnerEngine(
new List <(string, MetaMorpheusTask)> {
("", calibrationTask), ("", searchTask)
},
public static void ProteinGroupsNoParsimonyTest()
{
SearchTask searchTask = new SearchTask()
{
SearchParameters = new SearchParameters
{
DoParsimony = false
},
};
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\PrunedDbSpectra.mzml");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\DbForPrunedDb.fasta");
string folderPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestProteinGroupsNoParsimony");
DbForTask db = new DbForTask(myDatabase, false);
Directory.CreateDirectory(folderPath);
searchTask.RunTask(folderPath, new List <DbForTask> {
db
}, new List <string> {
myFile
}, "normal");
Directory.Delete(folderPath, true);
}
private void SearchTask_MouseLeftButtonDown(object sender, MouseButtonEventArgs e)
{
SearchTask searchTask = new SearchTask();
searchTask.SearchQuery = "driving music";
searchTask.Show();
}
public static void ParseSearchModeTest()
{
SearchTask searchTask = new SearchTask();
var result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Custom, "TestCustom dot 5 ppm 0,1.0029,2.0052");
Assert.That(result.NumNotches == 3);
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Custom, "TestCustom dot 5 da 0,1.0029,2.0052");
Assert.That(result.NumNotches == 3);
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Custom, "TestCustom interval [0,5];[0,5]");
Assert.That(result.NumNotches == 1);
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Custom, "TestCustom OpenSearch 5");
Assert.That(result.FileNameAddition.Equals("OpenSearch"));
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Custom, "TestCustom daltonsAroundZero 5");
Assert.That(result.FileNameAddition.Equals("5daltonsAroundZero"));
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Custom, "TestCustom ppmAroundZero 5");
Assert.That(result.FileNameAddition.Equals("5ppmAroundZero"));
Assert.That(() => SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Custom, "TestCustom Test 5"),
Throws.TypeOf <MetaMorpheusException>());
}
public static void TestContaminantAmbiguity()
{
//create an ms file and a database for the peptide
Protein targetProtein = new Protein("PEPTIDE", "target");
string xmlName = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\PEPTIDE.xml");
ProteinDbWriter.WriteXmlDatabase(null, new List <Protein> {
targetProtein
}, xmlName);
PeptideWithSetModifications pepWithSetMods = targetProtein.Digest(new DigestionParams(), null, null).First();
TestDataFile msFile = new TestDataFile(pepWithSetMods);
string mzmlName = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\PEPTIDE.mzML");
IO.MzML.MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(msFile, mzmlName, false);
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestContaminantAmbiguityOutput");
//run a full modern search using two databases (the same database) but one is called a target and the other is called a contaminant
//KEEP BOTH TARGET AND CONTAMINANT
SearchParameters modernSearchParams = new SearchParameters();
modernSearchParams.SearchType = SearchType.Modern;
modernSearchParams.TCAmbiguity = TargetContaminantAmbiguity.RenameProtein;
SearchTask modernTask = new SearchTask();
modernTask.SearchParameters = modernSearchParams;
EverythingRunnerEngine engine = new EverythingRunnerEngine(new List <(string, MetaMorpheusTask)> {
("task1", modernTask)
}, new List <string> {
private void SearchClick(object sender, EventArgs e)
{
SearchTask task = new SearchTask();
task.SearchQuery = Constants.SearchStr;
task.Show();
}
public static void AddCompIonsCommonParams()
{
CommonParameters cp = new CommonParameters(null, DissociationType.HCD, DissociationType.Unknown, true, true, 3, 12, true, true, 1,
5, 200, 0.01, null, null, false, false, true, false, null, null, null, -1, null, null, null, 1, true, 4, 1);
var myMsDataFile = new TestDataFile();
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var localizeableModifications = new List <Modification>();
Dictionary <Modification, ushort> modsDictionary = new Dictionary <Modification, ushort>();
foreach (var mod in fixedModifications)
{
modsDictionary.Add(mod, 0);
}
int ii = 1;
foreach (var mod in variableModifications)
{
modsDictionary.Add(mod, (ushort)ii);
ii++;
}
foreach (var mod in localizeableModifications)
{
modsDictionary.Add(mod, (ushort)ii);
ii++;
}
var proteinList = new List <Protein> {
new Protein("MNNNKQQQ", null)
};
SearchParameters SearchParameters = new SearchParameters
{
MassDiffAcceptorType = MassDiffAcceptorType.Exact,
SearchTarget = true,
};
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease protease = new Protease("Test", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
var indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, new List <SilacLabel>(),
1, DecoyType.Reverse, cp, SearchParameters.MaxFragmentSize, false, new List <FileInfo>(), new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
MassDiffAcceptor massDiffAcceptor = SearchTask.GetMassDiffAcceptor(cp.PrecursorMassTolerance, SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac);
// without complementary ions
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
var mse = new ModernSearchEngine(allPsmsArray, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, cp, massDiffAcceptor, SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, new List <string>()).Run();
}
private void BingSearchButton_Click(object sender, RoutedEventArgs e)
{
SearchTask task = new SearchTask()
{
SearchQuery = "Windows Phone 7 in Action domain:manning.com"
};
task.Show();
}
protected void Company_Tap(object sender, EventArgs e)
{
if (_viewModel.User != null && !string.IsNullOrWhiteSpace(_viewModel.User.Company))
{
var searchTask = new SearchTask();
searchTask.SearchQuery = _viewModel.User.Company;
searchTask.Show();
}
}
private void btnLaunchSearch_Click(object sender, RoutedEventArgs e)
{
SearchTask task = new SearchTask();
task.SearchQuery = "Vangos Pterneas";
task.Show();
}
private void btnLaunchSearch_Click(object sender, RoutedEventArgs e)
{
SearchTask task = new SearchTask();
task.SearchQuery = "Test Testerovich";
task.Show();
}
private void btnSearch_Click(object sender, RoutedEventArgs e)
{
SearchTask stask = new SearchTask();
stask.SearchQuery = "abhishek";
stask.Show();
}
private void BingSearch_Click(object sender, RoutedEventArgs e)
{
SearchTask task = new SearchTask()
{
SearchQuery = "MobiPicasa bing.com"
};
task.Show();
}
public SearchTaskViewModel GetSearchViewModel(string search)
{
if (search == null)
throw new ArgumentNullException("search");
var pattern = search + "%";
var task = new SearchTask(logger, pattern, mediaItemRepository);
return new SearchTaskViewModel(logger, task, search);
}
private void btnSearch_Click(object sender, RoutedEventArgs e)
{
SearchTask searchTask = new SearchTask();
searchTask.SearchQuery = txtInput.Text;
searchTask.Show();
}
