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();
        }
Пример #3
0
        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);
        }
Пример #4
0
        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();
        }
Пример #6
0
        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;
                }
            }
        }
Пример #7
0
        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);
            }
        }
Пример #8
0
        private void SearchClick(object sender, EventArgs e)
        {
            SearchTask task = new SearchTask();

            task.SearchQuery = Constants.SearchStr + " " + _detailItem.ItemTitle;
            task.Show();
        }
Пример #9
0
        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;
        }
Пример #10
0
        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);
        }
Пример #11
0
        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);
            }
        }
Пример #12
0
        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"));
        }
Пример #13
0
        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);
        }
Пример #14
0
        private void btnSearch_Click(object sender, RoutedEventArgs e)
        {
            SearchTask st = new SearchTask();

            st.SearchQuery = tbxSearch.Text;
            st.Show();
        }
Пример #15
0
        private void Button_Click(object sender, RoutedEventArgs e)
        {
            SearchTask searchTask = new SearchTask();

            searchTask.SearchQuery = txtKeyword.Text;
            searchTask.Show();
        }
Пример #16
0
        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);
        }
Пример #17
0
        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> {
Пример #18
0
        private void SearchClick(object sender, EventArgs e)
        {
            SearchTask task = new SearchTask();

            task.SearchQuery = blogDetail.ItemUser;
            task.Show();
        }
Пример #19
0
        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
    }
Пример #21
0
        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();
        }
Пример #23
0
 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;
         }
     }
 }
Пример #24
0
        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)
            },
Пример #25
0
        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);
        }
Пример #26
0
        private void SearchTask_MouseLeftButtonDown(object sender, MouseButtonEventArgs e)
        {
            SearchTask searchTask = new SearchTask();

            searchTask.SearchQuery = "driving music";
            searchTask.Show();
        }
Пример #27
0
        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>());
        }
Пример #28
0
        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> {
Пример #29
0
        private void SearchClick(object sender, EventArgs e)
        {
            SearchTask task = new SearchTask();

            task.SearchQuery = Constants.SearchStr;
            task.Show();
        }
Пример #30
0
        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();
     }
 }
Пример #33
0
 private void btnLaunchSearch_Click(object sender, RoutedEventArgs e)
 {
     SearchTask task = new SearchTask();
     task.SearchQuery = "Vangos Pterneas";
     task.Show();
 }
Пример #34
0
 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();
 }
Пример #36
0
 private void BingSearch_Click(object sender, RoutedEventArgs e)
 {
     SearchTask task = new SearchTask()
     {
         SearchQuery = "MobiPicasa bing.com"
     };
     task.Show();
 }
Пример #37
0
        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();
 }