public ActionResult Index(int length, int alphabetCardinality, bool generateStrict, short[] characteristicLinkIds)
{
return(CreateTask(() =>
{
var orderGenerator = new OrderGenerator();
var orders = generateStrict ?
orderGenerator.StrictGenerateOrders(length, alphabetCardinality) :
orderGenerator.GenerateOrders(length, alphabetCardinality);
var characteristics = new double[orders.Count][];
var sequencesCharacteristics = new List <SequenceCharacteristics>();
for (int i = 0; i < orders.Count; i++)
{
sequencesCharacteristics.Add(new SequenceCharacteristics());
}
for (int j = 0; j < orders.Count; j++)
{
var sequence = new Chain(orders[j].Select(Convert.ToInt16).ToArray());
characteristics[j] = 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[j][k] = calculator.Calculate(sequence, link);
}
sequencesCharacteristics[j] = new SequenceCharacteristics
{
MatterName = String.Join(",", orders[j].Select(n => n.ToString()).ToArray()),
Characteristics = characteristics[j]
};
}
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
};
}
sequencesCharacteristics.RemoveAll(el => el.Characteristics.Any(v => Double.IsInfinity(v) ||
Double.IsNaN(v) ||
Double.IsNegativeInfinity(v) ||
Double.IsPositiveInfinity(v)));
var index = new int[characteristicsList.Length];
for (int i = 0; i < index.Length; i++)
{
index[i] = i;
}
var result = new Dictionary <string, object>
{
{ "characteristics", sequencesCharacteristics.ToArray() },
{ "characteristicNames", characteristicNames },
{ "characteristicsList", characteristicsList },
{ "characteristicsIndex", index }
};
return new Dictionary <string, object>
{
{ "data", JsonConvert.SerializeObject(result) }
};
}));
}
public ActionResult Index(
long[] matterIds,
short[] characteristicLinkIds,
Notation[] notations,
Language?[] languages,
Translator?[] translators,
PauseTreatment?[] pauseTreatments,
bool?[] sequentialTransfers,
ImageOrderExtractor?[] trajectories,
bool rotate,
bool complementary,
uint?rotationLength)
{
return(CreateTask(() =>
{
Dictionary <long, string> mattersNames;
long[][] sequenceIds;
using (var db = new LibiadaWebEntities())
{
var commonSequenceRepository = new CommonSequenceRepository(db);
sequenceIds = commonSequenceRepository.GetSequenceIds(matterIds,
notations,
languages,
translators,
pauseTreatments,
sequentialTransfers,
trajectories);
mattersNames = Cache.GetInstance().Matters.Where(m => matterIds.Contains(m.Id)).ToDictionary(m => m.Id, m => m.Name);
}
double[][] characteristics;
if (!rotate && !complementary)
{
characteristics = SequencesCharacteristicsCalculator.Calculate(sequenceIds, characteristicLinkIds);
}
else
{
characteristics = SequencesCharacteristicsCalculator.Calculate(sequenceIds, characteristicLinkIds, rotate, complementary, rotationLength);
}
var sequencesCharacteristics = new SequenceCharacteristics[matterIds.Length];
for (int i = 0; i < matterIds.Length; i++)
{
sequencesCharacteristics[i] = new SequenceCharacteristics
{
MatterName = mattersNames[matterIds[i]],
Characteristics = characteristics[i]
};
}
var characteristicNames = new string[characteristicLinkIds.Length];
var characteristicsList = new SelectListItem[characteristicLinkIds.Length];
var characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
for (int k = 0; k < characteristicLinkIds.Length; k++)
{
characteristicNames[k] = characteristicTypeLinkRepository.GetCharacteristicName(characteristicLinkIds[k], notations[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, 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 Index(int length, int alphabetCardinality, int generateStrict, short[] characteristicLinkIds)
{
// TODO: Reafctor all of this
return(CreateTask(() =>
{
var orderGenerator = new OrderGenerator();
var orders = new List <int[]>();
switch (generateStrict)
{
case 0:
orders = orderGenerator.StrictGenerateOrders(length, alphabetCardinality);
break;
case 1:
orders = orderGenerator.GenerateOrders(length, alphabetCardinality);
break;
default: throw new ArgumentException("Invalid type of generate");
}
var characteristics = new double[orders.Count][];
var sequencesCharacteristics = new List <SequenceCharacteristics>();
for (int i = 0; i < orders.Count; i++)
{
sequencesCharacteristics.Add(new SequenceCharacteristics());
}
for (int j = 0; j < orders.Count; j++)
{
var sequence = new Chain(orders[j].Select(Convert.ToInt16).ToArray());
characteristics[j] = new double[characteristicLinkIds.Length];
for (int k = 0; k < characteristicLinkIds.Length; k++)
{
Link characteristicLink = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkIds[k]);
FullCharacteristic characteristic = characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkIds[k]);
IFullCalculator calculator = FullCalculatorsFactory.CreateCalculator(characteristic);
characteristics[j][k] = calculator.Calculate(sequence, characteristicLink);
}
sequencesCharacteristics[j] = new SequenceCharacteristics
{
MatterName = String.Join(",", orders[j].Select(n => n.ToString()).ToArray()),
Characteristics = characteristics[j]
};
}
sequencesCharacteristics.RemoveAll(el => el.Characteristics.Any(v => Double.IsInfinity(v) ||
Double.IsNaN(v) ||
Double.IsNegativeInfinity(v) ||
Double.IsPositiveInfinity(v)));
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 index = new int[characteristicsList.Length];
for (int i = 0; i < index.Length; i++)
{
index[i] = i;
}
var resultIntervals = new Dictionary <string, Dictionary <Dictionary <int, int>, Dictionary <int[], SequenceCharacteristics> > >();
foreach (var link in EnumExtensions.ToArray <Link>())
{
if (link == Link.NotApplied)
{
continue;
}
var accordance = new Dictionary <Dictionary <int, int>, Dictionary <int[], SequenceCharacteristics> >();
for (int j = 0; j < orders.Count; j++)
{
var order = orders[j];
var sequence = new Chain(order.Select(Convert.ToInt16).ToArray());
var fullIntervals = new Dictionary <int, int>();
var alphabet = sequence.Alphabet.ToList();
foreach (var el in alphabet)
{
var congIntervals = sequence.CongenericChain(el).GetArrangement(link);
foreach (var interval in congIntervals)
{
if (fullIntervals.Any(e => e.Key == interval))
{
fullIntervals[interval]++;
}
else
{
fullIntervals.Add(interval, 1);
}
}
}
if (accordance.Keys.Any(intervals => intervals.All(i1 => fullIntervals.Any(i2 => i2.Key == i1.Key && i2.Value == i1.Value))))
{
accordance[accordance.Keys.First(intervals => intervals.All(i1 => fullIntervals.Any(i2 => i2.Key == i1.Key && i2.Value == i1.Value)))].Add(order, sequencesCharacteristics.First(el => el.MatterName.SequenceEqual(String.Join(",", orders[j].Select(n => n.ToString()).ToArray()))));
}
else
{
accordance.Add(fullIntervals, new Dictionary <int[], SequenceCharacteristics> {
{
order,
sequencesCharacteristics.First(el => el.MatterName.SequenceEqual(String.Join(",", orders[j].Select(n => n.ToString()).ToArray())))
}
});
}
}
resultIntervals.Add(EnumExtensions.GetDisplayValue <Link>(link), accordance);
}
var list = EnumHelper.GetSelectList(typeof(Link));
list.RemoveAt(0);
var result = new Dictionary <string, object>
{
{ "result", resultIntervals.Select(r => new
{
link = r.Key,
accordance = r.Value.Select(d => new {
distributionIntervals = d.Key.Select(pair => new
{
interval = pair.Key,
count = pair.Value
}).ToArray(),
orders = d.Value.Select(o => new
{
order = o.Key,
characteristics = o.Value
})
})
}) },
{ "linkList", list },
{ "characteristicNames", characteristicNames },
{ "characteristicsList", characteristicsList },
{ "characteristicsIndex", index }
};
return new Dictionary <string, string> {
{ "data", JsonConvert.SerializeObject(result) }
};
}));
}
public ActionResult Index(
long[] matterIds,
OrderTransformation[] transformationsSequence,
int iterationsCount,
short[] characteristicLinkIds,
Notation[] notations,
Language?[] languages,
Translator?[] translators,
PauseTreatment?[] pauseTreatments,
bool?[] sequentialTransfers,
ImageOrderExtractor?[] trajectories)
{
return(CreateTask(() =>
{
Dictionary <long, string> mattersNames = Cache.GetInstance().Matters.Where(m => matterIds.Contains(m.Id)).ToDictionary(m => m.Id, m => m.Name);
Chain[][] sequences = new Chain[matterIds.Length][];
using (var db = new LibiadaWebEntities())
{
var commonSequenceRepository = new CommonSequenceRepository(db);
long[][] sequenceIds = commonSequenceRepository.GetSequenceIds(matterIds,
notations,
languages,
translators,
pauseTreatments,
sequentialTransfers,
trajectories);
for (int i = 0; i < matterIds.Length; i++)
{
sequences[i] = new Chain[characteristicLinkIds.Length];
for (int j = 0; j < characteristicLinkIds.Length; j++)
{
sequences[i][j] = commonSequenceRepository.GetLibiadaChain(sequenceIds[i][j]);
}
}
}
var characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
var sequencesCharacteristics = new SequenceCharacteristics[matterIds.Length];
matterIds = matterIds.OrderBy(m => m).ToArray();
for (int i = 0; i < matterIds.Length; i++)
{
long matterId = matterIds[i];
var characteristics = new double[characteristicLinkIds.Length];
for (int j = 0; j < characteristicLinkIds.Length; j++)
{
Notation notation = notations[j];
Chain sequence = sequences[i][j];
for (int l = 0; l < iterationsCount; l++)
{
for (int k = 0; k < transformationsSequence.Length; k++)
{
sequence = transformationsSequence[k] == OrderTransformation.Dissimilar ? DissimilarChainFactory.Create(sequence)
: HighOrderFactory.Create(sequence, EnumExtensions.GetLink(transformationsSequence[k]));
}
}
int characteristicLinkId = characteristicLinkIds[j];
Link link = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkId);
FullCharacteristic characteristic = characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkId);
IFullCalculator calculator = FullCalculatorsFactory.CreateCalculator(characteristic);
characteristics[j] = calculator.Calculate(sequence, link);
}
sequencesCharacteristics[i] = new SequenceCharacteristics
{
MatterName = mattersNames[matterId],
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], notations[k]);
characteristicsList[k] = new SelectListItem
{
Value = k.ToString(),
Text = characteristicNames[k],
Selected = false
};
}
var transformations = transformationsSequence.Select(ts => ts.GetDisplayValue());
var result = new Dictionary <string, object>
{
{ "characteristics", sequencesCharacteristics },
{ "characteristicNames", characteristicNames },
{ "characteristicsList", characteristicsList },
{ "transformationsList", transformations },
{ "iterationsCount", iterationsCount }
};
return new Dictionary <string, string> {
{ "data", JsonConvert.SerializeObject(result) }
};
}));
}
