public static DataBundle New(string id) { DataBundle newDataBundle = New(); newDataBundle.id = id; return(newDataBundle); }
public void OpenGamePanel(bool pvpModel) { var datas = new DataBundle(); datas.PutData("pvpModel", pvpModel); StartPanel("GamePanel", null, datas); }
private static ExitCodes ProgramExecution() { var logger = new ConsoleLogger(); var bundle = DataBundle.GetDataBundle(_inputReferencePath, _inputPrefix); int numRefSeqs = bundle.SequenceReader.NumRefSeqs; var chromosome = ReferenceNameUtilities.GetChromosome(bundle.SequenceReader.RefNameToChromosome, _referenceName); bundle.Load(chromosome); string outputStub = GetOutputStub(chromosome, bundle.Source); var interval = new ChromosomeInterval(chromosome, _referencePosition, _referenceEndPosition); var transcripts = GetTranscripts(logger, bundle, interval); var sift = GetPredictionStaging(logger, "SIFT", transcripts, chromosome, bundle.SiftPredictions, bundle.SiftReader, x => x.SiftIndex, numRefSeqs); var polyphen = GetPredictionStaging(logger, "PolyPhen", transcripts, chromosome, bundle.PolyPhenPredictions, bundle.PolyPhenReader, x => x.PolyPhenIndex, numRefSeqs); string referenceBases = GetReferenceBases(logger, bundle.SequenceReader, interval); var regulatoryRegionIntervalArrays = GetRegulatoryRegionIntervalArrays(logger, bundle.TranscriptCache, interval, numRefSeqs); var transcriptIntervalArrays = PredictionUtilities.UpdateTranscripts(transcripts, bundle.SiftPredictions, sift.Predictions, bundle.PolyPhenPredictions, polyphen.Predictions, numRefSeqs); var transcriptStaging = GetTranscriptStaging(bundle.TranscriptCacheData.Header, transcriptIntervalArrays, regulatoryRegionIntervalArrays); WriteCache(logger, FileUtilities.GetCreateStream(CacheConstants.TranscriptPath(outputStub)), transcriptStaging, "transcript"); WriteCache(logger, FileUtilities.GetCreateStream(CacheConstants.SiftPath(outputStub)), sift.Staging, "SIFT"); WriteCache(logger, FileUtilities.GetCreateStream(CacheConstants.PolyPhenPath(outputStub)), polyphen.Staging, "PolyPhen"); WriteReference(logger, CacheConstants.BasesPath(outputStub), bundle.SequenceReader, chromosome, referenceBases, interval.Start); return(ExitCodes.Success); }
public static List <ITranscript> GetTranscripts(DataBundle bundle, IChromosomeInterval interval) { ITranscript[] overlappingTranscripts = bundle.TranscriptCache.TranscriptIntervalForest.GetAllOverlappingValues(interval.Chromosome.Index, interval.Start, interval.End); return(overlappingTranscripts?.ToList() ?? new List <ITranscript>()); }
private void CloseMessageDialog(bool confirm) { var datas = new DataBundle(); datas.PutData("confirm", confirm); Close(datas); }
/// <summary> /// Updates the DataBundleCollection, wherever possible updating only values and not changing the bound variables, to avoid reinjecting the collection. /// </summary> public void CopyValuesFrom(DataBundleCollection dataBundleCollection) { if (dataBundleCollection == this) { return; } List <DataBundle> remainingDataBundles = dataBundles.Where(db => dataBundleCollection.dataBundles.Contains(db)).ToList(); dataBundles.Clear(); foreach (DataBundle dataBundle in dataBundleCollection.dataBundles) { DataBundle existingDataBundle = remainingDataBundles.Find(db => db.id == dataBundle.id); if (existingDataBundle) { existingDataBundle.CopyValuesFrom(dataBundle); Add(existingDataBundle); } else { Add(dataBundle); } } }
/// <summary> /// updates a regulatory region /// mini-cache filename example: ENSR00000079256_chr1_Ensembl72_reg.ndb /// </summary> public UpdateStatus Update(DataBundle bundle, string outputCacheDir, ushort desiredVepVersion, List <string> outputFiles) { var regulatoryElement = MiniCacheUtilities.GetDesiredRegulatoryElement(bundle, _regulatoryId); if (regulatoryElement == null) { return(UpdateStatus.IdNotFound); } bundle.Load(regulatoryElement.ReferenceIndex); var outputCache = CreateCache(bundle.Cache.Header, new[] { regulatoryElement }); var outputStub = GetOutputStub(outputCacheDir, _regulatoryId, bundle.Sequence.Renamer.UcscReferenceNames[regulatoryElement.ReferenceIndex], TranscriptDataSource, desiredVepVersion); var refIndices = new HashSet <ushort> { regulatoryElement.ReferenceIndex }; MiniCacheUtilities.WriteTranscriptCache(outputCache, outputStub, outputFiles); MiniCacheUtilities.WriteEmptyBases(bundle, refIndices, outputStub, outputFiles); return(UpdateStatus.Current); }
public static void WriteBases(DataBundle bundle, List <TranscriptPacket> packets, string outputStub, List <string> outputFiles) { var refPath = outputStub + ".bases" + TempCacheExt; outputFiles.Add(refPath); const int flankingLength = 500; using (var writer = new CompressedSequenceWriter(refPath, bundle.SequenceReader.Metadata, bundle.Sequence.CytogeneticBands, bundle.Cache.Header.GenomeAssembly)) { for (ushort refIndex = 0; refIndex < bundle.Sequence.Renamer.NumRefSeqs; refIndex++) { var interval = GetBoundingInterval(packets, refIndex, flankingLength); if (interval == null) { continue; } LoadSequence(bundle, refIndex); var bases = bundle.Sequence.Substring(interval.Start, interval.End - interval.Start + 1); var ensemblRefName = bundle.Sequence.Renamer.EnsemblReferenceNames[refIndex]; writer.Write(ensemblRefName, bases, interval.Start); } } }
public void OnCancelClicked() { var datas = new DataBundle(); datas.PutData("confirm", false); Close(datas); }
public override void OnEscapeDown() { var datas = new DataBundle(); datas.PutData("confirm", false); Close(datas); }
public override void InitDialog(DataBundle datas = null) { if (datas != null) { var message = datas.ContainsKey("message") ? (string)datas.GetData("message") : ""; messageText.SetText(message); } }
protected virtual void Output(DataBundle dataBundle, bool copyValues = true) { DataBundleCollection dataBundleCollection = new DataBundleCollection(); dataBundleCollection.Add(dataBundle); Output(dataBundleCollection, copyValues); }
public DialogBase(string name, int?resultCode = null, DataBundle datas = null, bool blockFlag = true, bool modelFlag = true) { Name = name; ResultCode = resultCode; Datas = datas; BlockFlag = blockFlag; ModelFlag = modelFlag; }
public void OnConfirmClicked() { var datas = new DataBundle(); datas.PutData("confirm", true); datas.PutData("animeFlag", animeFlag); datas.PutData("selectFlag", selectFlag); Close(datas); }
private static void LoadSequence(DataBundle bundle, ushort refIndex) { if (refIndex == bundle.CurrentRefIndex) { return; } bundle.SequenceReader.GetCompressedSequence(bundle.Sequence.Renamer.EnsemblReferenceNames[refIndex]); bundle.CurrentRefIndex = refIndex; }
private static Transcript[] GetDesiredTranscripts(DataBundle bundle, Tuple <ushort, int, int> variantInterval) { var overlappingTranscripts = new List <Transcript>(); bundle.TranscriptForest.GetAllOverlappingValues(variantInterval.Item1, variantInterval.Item2, variantInterval.Item3, overlappingTranscripts); return(overlappingTranscripts.ToArray()); }
public VerfiyScreen(DataBundle dataBundle) { InitializeComponent(); DataBundle = dataBundle; ValidDataConetet.Content = _ValidDataList; _selected = RefereeButton; ChangeList(dataBundle.Referees); }
public void Remove(string id) { DataBundle dataBundle = GetDataBundle(id); if (dataBundle != null) { dataBundles.Remove(dataBundle); } }
private void FinishWithDataIfConnected(bool isHost) { if (Bluetooth.Instance.IsConnected()) { var datas = new DataBundle(); datas.PutData("isHost", isHost); Finish(datas); } }
public void Inject(DataBundle dataBundle) { this.dataBundle.Value = dataBundle; // If SetOnValueChanged is true, this will be called automatically if (SetOnValueChanged == false) { Set(); } }
public void OnConfirmClicked() { var datas = new DataBundle(); datas.PutData("confirm", true); datas.PutData("initiative", initiative); datas.PutData("fusionModel", fusionFlag); datas.PutData("hiddenModel", hiddenFlag); Close(datas); }
public static PredictionCacheStaging GetStaging(DataBundle bundle, bool useSift, List <TranscriptPacket> packets, int numRefSeqs) { var cache = useSift ? bundle.SiftCache : bundle.PolyPhenCache; if (cache == null || packets.Count == 0) { return(null); } return(GetStagingWithPredictionIndices(cache, useSift, packets, numRefSeqs)); }
public override void InitDialog(DataBundle datas = null) { Bluetooth.SetBluetoothVisible(); var listener = Bluetooth.GetBluetoothListener(); listener.OnGetSocketConnectDelegate = delegate { closeFlag = true; }; Bluetooth.StartAcceptThread(); }
protected SpawnedInjector GetSpawnedInjector(DataBundle dataBundle) { foreach (SpawnedInjector spawnedInjector in spawnedChildren) { if (spawnedInjector.dataBundle.id == dataBundle.id) { return(spawnedInjector); } } return(null); }
private async void VerfiyClick(object sender, RoutedEventArgs e) { if (_workHistoryBundlePath != null) { DataBundle dataBundle = await Utils.ReadFromJson <DataBundle>(_workHistoryBundlePath); VerfiyScreen verfiyScreen = new VerfiyScreen(dataBundle); Main main = (Main)Window.GetWindow(this); main.Content = verfiyScreen; } }
/// <summary> /// Copies the values from all variables in the provided DataBundle, without overriding the variables themselves. /// </summary> public void CopyValuesFrom(DataBundle dataBundle) { foreach (var dataKeyPair in dataBundle.data) { SetOrUpdateValue(dataKeyPair.key, dataKeyPair.data); } foreach (var eventKeyPair in dataBundle.events) { Set(eventKeyPair.key, eventKeyPair.gameEvent); } }
public override void InitPanel(DataBundle datas = null) { LoadConfig(); PVPModel = (bool)datas.GetData("pvpModel"); if (PVPModel) { OpenBluetoothPanel(); } else { OpenNewOkDialog(); } }
public override void OnPanelResult(int?resultCode, DataBundle datas) { switch (resultCode) { case (int)ResultCode.HostDialog: FinishWithDataIfConnected(true); break; case (int)ResultCode.JoinDialog: FinishWithDataIfConnected(false); break; } }
protected void UpdateChildDataBundle(SpawnedInjector spawnedInjector, DataBundle newDataBundle) { if (newDataBundle != spawnedInjector.dataBundle) { if (logUpdates) { Debug.Log("DataInjectorCollection: Updating child DataBundle: " + spawnedInjector.dataBundle.id, this); } spawnedInjector.dataBundle = newDataBundle; spawnedInjector.injector?.Inject(spawnedInjector.dataBundle); } }
public override void OnPanelResult(int?resultCode, DataBundle datas) { switch (resultCode) { case (int)ResultCode.ExitDialog: bool confirm = (bool)datas.GetData("confirm"); if (confirm) { Application.Quit(); } break; } }