public ActionResult Index( OrderTransformation[] transformationsSequence, int iterationsCount, string[] customSequences, bool localFile, HttpPostedFileBase[] file) { return(CreateTask(() => { int sequencesCount = localFile ? Request.Files.Count : customSequences.Length; var sourceSequences = new string[sequencesCount]; var sequences = new Chain[sequencesCount]; var names = new string[sequencesCount]; for (int i = 0; i < sequencesCount; i++) { if (localFile) { var sequenceStream = FileHelper.GetFileStream(file[i]); var fastaSequence = NcbiHelper.GetFastaSequence(sequenceStream); sourceSequences[i] = fastaSequence.ConvertToString(); names[i] = fastaSequence.ID; } else { sourceSequences[i] = customSequences[i]; names[i] = $"Custom sequence {i + 1}. Length: {customSequences[i].Length}"; } } for (int k = 0; k < sequencesCount; k++) { sequences[k] = new Chain(sourceSequences[k]); for (int j = 0; j < iterationsCount; j++) { for (int i = 0; i < transformationsSequence.Length; i++) { sequences[k] = transformationsSequence[i] == OrderTransformation.Dissimilar ? DissimilarChainFactory.Create(sequences[k]) : HighOrderFactory.Create(sequences[k], EnumExtensions.GetLink(transformationsSequence[i])); } } } var transformations = transformationsSequence.Select(ts => ts.GetDisplayValue()); var result = new Dictionary <string, object> { { "names", names }, { "sequences", sequences.Select((s, i) => new { name = names[i], value = s.ToString(" ") }).ToArray() }, { "transformationsList", transformations }, { "iterationsCount", iterationsCount } }; return new Dictionary <string, string> { { "data", JsonConvert.SerializeObject(result) } }; })); }
public ActionResult Index(short[] characteristicLinkIds, string[] customSequences, bool localFile, string fileType, bool toLower, bool removePunctuation) { return(CreateTask(() => { int sequencesCount = localFile ? Request.Files.Count : customSequences.Length; var sequencesNames = new string[sequencesCount]; var sequences = new Chain[sequencesCount]; if (localFile) { for (int i = 0; i < sequencesCount; i++) { Stream sequenceStream = FileHelper.GetFileStream(Request.Files[i]); sequencesNames[i] = Request.Files[i].FileName; switch (fileType) { case "text": using (var sr = new StreamReader(sequenceStream)) { string stringTextSequence = sr.ReadToEnd(); if (toLower) { stringTextSequence = stringTextSequence.ToLower(); } if (removePunctuation) { stringTextSequence = Regex.Replace(stringTextSequence, @"[^\w\s]", ""); } sequences[i] = new Chain(stringTextSequence); } break; case "image": var image = Image.Load(sequenceStream); var sequence = ImageProcessor.ProcessImage(image, new IImageTransformer[0], new IMatrixTransformer[0], new LineOrderExtractor()); var alphabet = new Alphabet { NullValue.Instance() }; var incompleteAlphabet = sequence.Alphabet; for (int j = 0; j < incompleteAlphabet.Cardinality; j++) { alphabet.Add(incompleteAlphabet[j]); } sequences[i] = new Chain(sequence.Building, alphabet); break; case "genetic": ISequence fastaSequence = NcbiHelper.GetFastaSequence(sequenceStream); var stringSequence = fastaSequence.ConvertToString(); sequences[i] = new Chain(stringSequence); sequencesNames[i] = fastaSequence.ID; break; case "wavFile": var reader = new BinaryReader(Request.Files[i].InputStream); int chunkID = reader.ReadInt32(); int fileSize = reader.ReadInt32(); int riffType = reader.ReadInt32(); int fmtID = reader.ReadInt32(); int fmtSize = reader.ReadInt32(); int fmtCode = reader.ReadInt16(); int channels = reader.ReadInt16(); int sampleRate = reader.ReadInt32(); int fmtAvgBPS = reader.ReadInt32(); int fmtBlockAlign = reader.ReadInt16(); int bitDepth = reader.ReadInt16(); if (fmtSize == 18) { // Read any extra values int fmtExtraSize = reader.ReadInt16(); reader.ReadBytes(fmtExtraSize); } int dataID = reader.ReadInt32(); int dataSize = reader.ReadInt32(); byte[] byteArray = reader.ReadBytes(dataSize); var shortArray = new short[byteArray.Length / 2]; Buffer.BlockCopy(byteArray, 0, shortArray, 0, byteArray.Length); //shortArray = Amplitude(shortArray, 20); shortArray = Sampling(shortArray, 50); //shortArray = shortArray.Select(s => (short)(s / 10)).ToArray(); sequences[i] = new Chain(shortArray); break; default: throw new ArgumentException("Unknown file type", nameof(fileType)); } } } else { for (int i = 0; i < sequencesCount; i++) { sequences[i] = new Chain(customSequences[i]); sequencesNames[i] = $"Custom sequence {i + 1}. Length: {customSequences[i].Length}"; } } var sequencesCharacteristics = new SequenceCharacteristics[sequences.Length]; for (int j = 0; j < sequences.Length; j++) { var characteristics = new double[characteristicLinkIds.Length]; for (int k = 0; k < characteristicLinkIds.Length; k++) { Link link = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkIds[k]); FullCharacteristic characteristic = characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkIds[k]); IFullCalculator calculator = FullCalculatorsFactory.CreateCalculator(characteristic); characteristics[k] = calculator.Calculate(sequences[j], link); } sequencesCharacteristics[j] = new SequenceCharacteristics { MatterName = sequencesNames[j], Characteristics = characteristics }; } var characteristicNames = new string[characteristicLinkIds.Length]; var characteristicsList = new SelectListItem[characteristicLinkIds.Length]; for (int k = 0; k < characteristicLinkIds.Length; k++) { characteristicNames[k] = characteristicTypeLinkRepository.GetCharacteristicName(characteristicLinkIds[k]); characteristicsList[k] = new SelectListItem { Value = k.ToString(), Text = characteristicNames[k], Selected = false }; } var result = new Dictionary <string, object> { { "characteristics", sequencesCharacteristics }, { "characteristicNames", characteristicNames }, { "characteristicsList", characteristicsList } }; return new Dictionary <string, object> { { "data", JsonConvert.SerializeObject(result) } }; })); }
public ActionResult Index( OrderTransformation[] transformationsSequence, int iterationsCount, short[] characteristicLinkIds, string[] customSequences, bool localFile, HttpPostedFileBase[] file) { return(CreateTask(() => { var characteristicTypeLinkRepository = FullCharacteristicRepository.Instance; int sequencesCount = localFile ? Request.Files.Count : customSequences.Length; var sequences = new string[sequencesCount]; var sequencesNames = new string[sequencesCount]; for (int i = 0; i < sequencesCount; i++) { if (localFile) { Stream sequenceStream = FileHelper.GetFileStream(file[i]); ISequence fastaSequence = NcbiHelper.GetFastaSequence(sequenceStream); sequences[i] = fastaSequence.ConvertToString(); sequencesNames[i] = fastaSequence.ID; } else { sequences[i] = customSequences[i]; sequencesNames[i] = $"Custom sequence {i + 1}. Length: {customSequences[i].Length}"; } } var sequencesCharacteristics = new SequenceCharacteristics[sequences.Length]; for (int j = 0; j < sequences.Length; j++) { var characteristics = new double[characteristicLinkIds.Length]; for (int k = 0; k < characteristicLinkIds.Length; k++) { var sequence = new Chain(sequences[j]); for (int l = 0; l < iterationsCount; l++) { for (int w = 0; w < transformationsSequence.Length; w++) { sequence = transformationsSequence[w] == OrderTransformation.Dissimilar ? DissimilarChainFactory.Create(sequence) : HighOrderFactory.Create(sequence, EnumExtensions.GetLink(transformationsSequence[w])); } } Link link = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkIds[k]); FullCharacteristic characteristic = characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkIds[k]); IFullCalculator calculator = FullCalculatorsFactory.CreateCalculator(characteristic); characteristics[k] = calculator.Calculate(sequence, link); } sequencesCharacteristics[j] = new SequenceCharacteristics { MatterName = sequencesNames[j], Characteristics = characteristics }; } string[] characteristicNames = characteristicLinkIds.Select(c => characteristicTypeLinkRepository.GetCharacteristicName(c)).ToArray(); var characteristicsList = new SelectListItem[characteristicLinkIds.Length]; for (int i = 0; i < characteristicNames.Length; i++) { characteristicsList[i] = new SelectListItem { Value = i.ToString(), Text = characteristicNames[i], Selected = false }; } var transformations = new Dictionary <int, string>(); for (int i = 0; i < transformationsSequence.Length; i++) { transformations.Add(i, transformationsSequence[i].GetDisplayValue()); } var result = new Dictionary <string, object> { { "characteristics", sequencesCharacteristics }, { "characteristicNames", characteristicNames }, { "characteristicsList", characteristicsList }, { "transformationsList", transformations }, { "iterationsCount", iterationsCount } }; return new Dictionary <string, object> { { "data", JsonConvert.SerializeObject(result) } }; })); }
public ActionResult Create( [Bind(Include = "Id,Notation,RemoteDb,RemoteId,Description,Matter,MatterId")] CommonSequence commonSequence, bool localFile, Language?language, bool?original, Translator?translator, bool?partial, int?precision) { return(CreateTask(() => { var db = new LibiadaWebEntities(); try { if (!ModelState.IsValid) { throw new Exception("Model state is invalid"); } Stream sequenceStream; Nature nature = commonSequence.Notation.GetNature(); if (nature == Nature.Genetic && !localFile) { sequenceStream = NcbiHelper.GetFastaFileStream(commonSequence.RemoteId); } else { sequenceStream = FileHelper.GetFileStream(Request.Files[0]); } switch (nature) { case Nature.Genetic: ISequence bioSequence = NcbiHelper.GetFastaSequence(sequenceStream); var dnaSequenceRepository = new GeneticSequenceRepository(db); dnaSequenceRepository.Create(commonSequence, bioSequence, partial ?? false); break; case Nature.Music: var musicSequenceRepository = new MusicSequenceRepository(db); musicSequenceRepository.Create(commonSequence, sequenceStream); break; case Nature.Literature: var literatureSequenceRepository = new LiteratureSequenceRepository(db); literatureSequenceRepository.Create(commonSequence, sequenceStream, language ?? Language.Russian, original ?? true, translator ?? Translator.NoneOrManual); break; case Nature.MeasurementData: var dataSequenceRepository = new DataSequenceRepository(db); dataSequenceRepository.Create(commonSequence, sequenceStream, precision ?? 0); break; case Nature.Image: var matterRepository = new MatterRepository(db); int fileSize = Request.Files[0].ContentLength; var file = new byte[fileSize]; Request.Files[0].InputStream.Read(file, 0, fileSize); var matter = new Matter { Nature = Nature.Image, SequenceType = commonSequence.Matter.SequenceType, Name = commonSequence.Matter.Name, Source = file, Group = commonSequence.Matter.Group }; matterRepository.SaveToDatabase(matter); break; default: throw new InvalidEnumArgumentException(nameof(nature), (int)nature, typeof(Nature)); } string multisequenceName = db.Multisequence.SingleOrDefault(ms => ms.Id == commonSequence.Matter.MultisequenceId).Name; var result = new ImportResult(commonSequence, language, original, translator, partial, precision, multisequenceName); return new Dictionary <string, string> { { "data", JsonConvert.SerializeObject(result) } }; } catch (Exception) { long matterId = commonSequence.MatterId; if (matterId != 0) { List <Matter> orphanMatter = db.Matter .Include(m => m.Sequence) .Where(m => m.Id == matterId && m.Sequence.Count == 0) .ToList(); if (orphanMatter.Count > 0) { db.Matter.Remove(orphanMatter[0]); db.SaveChanges(); } } throw; } finally { Dispose(true); } })); }