/// <summary>
/// Calculation method.
/// </summary>
/// <param name="chains">
/// The chains.
/// </param>
/// <param name="calculators">
/// The calculators.
/// </param>
/// <param name="links">
/// The links.
/// </param>
/// <param name="characteristicTypeLinkIds">
/// The characteristic type link ids.
/// </param>
/// <returns>
/// The <see cref="T:double[][]"/>.
/// </returns>
public static double[][] Calculate(Chain[][] chains, IFullCalculator[] calculators, Link[] links, int[] characteristicTypeLinkIds)
{
var newCharacteristics = new List<Characteristic>();
var characteristics = new double[chains.Length][];
var sequenceIds = chains.SelectMany(c => c).Select(c => c.Id).Distinct();
Dictionary<long, Dictionary<int, double>> dbCharacteristics;
using (var db = new LibiadaWebEntities())
{
dbCharacteristics = db.Characteristic
.Where(c => characteristicTypeLinkIds.Contains(c.CharacteristicTypeLinkId) && sequenceIds.Contains(c.SequenceId))
.ToArray()
.GroupBy(c => c.SequenceId)
.ToDictionary(c => c.Key, c => c.ToDictionary(ct => ct.CharacteristicTypeLinkId, ct => ct.Value));
}
for (int i = 0; i < chains.Length; i++)
{
characteristics[i] = new double[calculators.Length];
for (int j = 0; j < calculators.Length; j++)
{
long sequenceId = chains[i][j].Id;
chains[i][j].FillIntervalManagers();
Dictionary<int, double> sequenceDbCharacteristics;
if (!dbCharacteristics.TryGetValue(sequenceId, out sequenceDbCharacteristics))
{
sequenceDbCharacteristics = new Dictionary<int, double>();
}
if (!sequenceDbCharacteristics.TryGetValue(characteristicTypeLinkIds[j], out characteristics[i][j]))
{
characteristics[i][j] = calculators[j].Calculate(chains[i][j], links[j]);
var currentCharacteristic = new Characteristic
{
SequenceId = sequenceId,
CharacteristicTypeLinkId = characteristicTypeLinkIds[j],
Value = characteristics[i][j]
};
newCharacteristics.Add(currentCharacteristic);
}
}
}
// trying to save calculated characteristics to database
using (var db = new LibiadaWebEntities())
{
var characteristicRepository = new CharacteristicRepository(db);
characteristicRepository.TrySaveCharacteristicsToDatabase(newCharacteristics);
}
return characteristics;
}
/// <summary>
/// Calculation method.
/// </summary>
/// <param name="chainIds">
/// The chains ids.
/// </param>
/// <param name="characteristicLinkIds">
/// The characteristic type link ids.
/// </param>
/// <param name="rotate">
/// The rotate flag.
/// </param>
/// <param name="complementary">
/// The complementary flag.
/// </param>
/// <param name="rotationLength">
/// The rotation length.
/// </param>
/// <returns>
/// The <see cref="T:double[][]"/>.
/// </returns>
public static double[][] Calculate(long[][] chainIds, short[] characteristicLinkIds, bool rotate, bool complementary, uint?rotationLength)
{
var links = new Link[characteristicLinkIds.Length];
var calculators = new IFullCalculator[characteristicLinkIds.Length];
var characteristics = new double[chainIds.Length][];
long[] sequenceIds = chainIds.SelectMany(c => c).Distinct().ToArray();
var sequences = new Dictionary <long, Chain>();
using (var db = new LibiadaWebEntities())
{
var commonSequenceRepository = new CommonSequenceRepository(db);
for (int i = 0; i < sequenceIds.Length; i++)
{
sequences.Add(sequenceIds[i], commonSequenceRepository.GetLibiadaChain(sequenceIds[i]));
}
var characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
for (int k = 0; k < characteristicLinkIds.Length; k++)
{
links[k] = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkIds[k]);
FullCharacteristic characteristic = characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkIds[k]);
calculators[k] = FullCalculatorsFactory.CreateCalculator(characteristic);
}
}
for (int i = 0; i < chainIds.Length; i++)
{
characteristics[i] = new double[calculators.Length];
for (int j = 0; j < calculators.Length; j++)
{
long sequenceId = chainIds[i][j];
var sequence = (Chain)sequences[sequenceId].Clone();
if (complementary)
{
var sourceSequence = new Sequence(Alphabets.DNA, sequence.ToString());
ISequence complementarySequence = sourceSequence.GetReverseComplementedSequence();
sequence = new Chain(complementarySequence.ConvertToString());
}
if (rotate)
{
int[] building = sequence.Building.Rotate(rotationLength ?? 0);
List <IBaseObject> newSequence = building.Select(t => new ValueInt(t)).ToList <IBaseObject>();
sequence = new Chain(newSequence);
}
characteristics[i][j] = calculators[j].Calculate(sequence, links[j]);
}
}
return(characteristics);
}
/// <summary>
/// The calculate characteristic.
/// </summary>
/// <param name="characteristicLinkId">
/// The characteristic type and link id.
/// </param>
/// <param name="subsequences">
/// The subsequences.
/// </param>
/// <returns>
/// The <see cref="List{Subsequence}"/>.
/// </returns>
private List <double> CalculateCharacteristic(short characteristicLinkId, Subsequence[] subsequences)
{
var characteristics = new List <double>();
var newCharacteristics = new List <CharacteristicValue>();
FullCharacteristic fullCharacteristic = characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkId);
IFullCalculator calculator = FullCalculatorsFactory.CreateCalculator(fullCharacteristic);
Link link = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkId);
var subsequenceIds = subsequences.Select(s => s.Id);
var existingCharacteristics = db.CharacteristicValue
.Where(cv => cv.CharacteristicLinkId == characteristicLinkId && subsequenceIds.Contains(cv.SequenceId))
.ToDictionary(cv => cv.SequenceId);
Dictionary <long, Chain> sequences = subsequenceExtractor.GetSubsequencesSequences(subsequences);
for (int i = 0; i < subsequences.Length; i++)
{
if (existingCharacteristics.ContainsKey(subsequences[i].Id))
{
characteristics.Add(existingCharacteristics[subsequences[i].Id].Value);
}
else
{
double value = calculator.Calculate(sequences[subsequences[i].Id], link);
var currentCharacteristic = new CharacteristicValue
{
SequenceId = subsequences[i].Id,
CharacteristicLinkId = characteristicLinkId,
Value = value
};
newCharacteristics.Add(currentCharacteristic);
characteristics.Add(value);
}
}
db.CharacteristicValue.AddRange(newCharacteristics);
db.SaveChanges();
return(characteristics);
}
/// <summary>
/// Calculation method.
/// </summary>
/// <param name="chains">
/// The chains.
/// </param>
/// <param name="calculator">
/// The calculator.
/// </param>
/// <param name="link">
/// The link.
/// </param>
/// <param name="characteristicTypeLinkId">
/// The characteristic type link id.
/// </param>
/// <returns>
/// The <see cref="T:double[]"/>.
/// </returns>
public static double[] Calculate(Chain[] chains, IFullCalculator calculator, Link link, int characteristicTypeLinkId)
{
var newCharacteristics = new List<Characteristic>();
var characteristics = new double[chains.Length];
var sequenceIds = chains.Select(c => c.Id);
Dictionary<long, double> dbCharacteristics;
using (var db = new LibiadaWebEntities())
{
dbCharacteristics = db.Characteristic
.Where(c => characteristicTypeLinkId == c.CharacteristicTypeLinkId && sequenceIds.Contains(c.SequenceId))
.ToArray()
.GroupBy(c => c.SequenceId)
.ToDictionary(c => c.Key, c => c.Single().Value);
}
for (int i = 0; i < chains.Length; i++)
{
chains[i].FillIntervalManagers();
long sequenceId = chains[i].Id;
if (!dbCharacteristics.TryGetValue(sequenceId, out characteristics[i]))
{
characteristics[i] = calculator.Calculate(chains[i], link);
var currentCharacteristic = new Characteristic
{
SequenceId = sequenceId,
CharacteristicTypeLinkId = characteristicTypeLinkId,
Value = characteristics[i]
};
newCharacteristics.Add(currentCharacteristic);
}
}
// trying to save calculated characteristics to database
using (var db = new LibiadaWebEntities())
{
var characteristicRepository = new CharacteristicRepository(db);
characteristicRepository.TrySaveCharacteristicsToDatabase(newCharacteristics);
}
return characteristics;
}
public ActionResult Index(
long[] matterIds,
short[] characteristicLinkIds,
Notation[] notations,
Language[] languages,
int clustersCount,
ClusterizationType clusterizationType,
double equipotencyWeight = 1,
double normalizedDistanceWeight = 1,
double distanceWeight = 1,
double bandwidth = 0,
int maximumClusters = 2)
{
return(CreateTask(() =>
{
var characteristicNames = new string[characteristicLinkIds.Length];
var mattersCharacteristics = new object[matterIds.Length];
var characteristics = new double[matterIds.Length][];
matterIds = matterIds.OrderBy(m => m).ToArray();
Dictionary <long, string> matters = db.Matter.Where(m => matterIds.Contains(m.Id)).ToDictionary(m => m.Id, m => m.Name);
for (int j = 0; j < matterIds.Length; j++)
{
long matterId = matterIds[j];
characteristics[j] = new double[characteristicLinkIds.Length];
for (int i = 0; i < characteristicLinkIds.Length; i++)
{
Notation notation = notations[i];
long sequenceId = db.Matter.Single(m => m.Id == matterId).Sequence.Single(c => c.Notation == notation).Id;
int characteristicLinkId = characteristicLinkIds[i];
if (db.CharacteristicValue.Any(c => c.SequenceId == sequenceId && c.CharacteristicLinkId == characteristicLinkId))
{
characteristics[j][i] = db.CharacteristicValue.Single(c => c.SequenceId == sequenceId && c.CharacteristicLinkId == characteristicLinkId).Value;
}
else
{
Chain tempChain = commonSequenceRepository.GetLibiadaChain(sequenceId);
Link link = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkId);
FullCharacteristic characteristic = characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkId);
IFullCalculator calculator = FullCalculatorsFactory.CreateCalculator(characteristic);
characteristics[j][i] = calculator.Calculate(tempChain, link);
}
}
}
for (int k = 0; k < characteristicLinkIds.Length; k++)
{
characteristicNames[k] = characteristicTypeLinkRepository.GetCharacteristicName(characteristicLinkIds[k], notations[k]);
}
var clusterizationParams = new Dictionary <string, double>
{
{ "clustersCount", clustersCount },
{ "equipotencyWeight", equipotencyWeight },
{ "normalizedDistanceWeight", normalizedDistanceWeight },
{ "distanceWeight", distanceWeight },
{ "bandwidth", bandwidth },
{ "maximumClusters", maximumClusters }
};
IClusterizator clusterizator = ClusterizatorsFactory.CreateClusterizator(clusterizationType, clusterizationParams);
int[] clusterizationResult = clusterizator.Cluster(clustersCount, characteristics);
for (int i = 0; i < clusterizationResult.Length; i++)
{
mattersCharacteristics[i] = new
{
MatterName = matters[matterIds[i]],
cluster = clusterizationResult[i] + 1,
Characteristics = characteristics[i]
};
}
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 result = new Dictionary <string, object>
{
{ "characteristicNames", characteristicNames },
{ "characteristics", mattersCharacteristics },
{ "characteristicsList", characteristicsList },
{ "clustersCount", clusterizationResult.Distinct().Count() }
};
return new Dictionary <string, object>
{
{ "data", JsonConvert.SerializeObject(result) }
};
}));
}
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) }
};
}));
}
/// <summary>
/// Initializes a new instance of the <see cref="LinkedCharacteristic"/> class.
/// </summary>
/// <param name="calculator">
/// The calculator of characteristic.
/// </param>
public LinkedCharacteristic(IFullCalculator calculator)
{
this.calculator = calculator;
link = Link.Start;
}
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(
long[] matterIds,
short[] characteristicLinkIds,
int length,
int step,
bool delta,
bool fourier,
bool growingWindow,
bool autocorrelation,
Notation notation,
Language?language,
Translator?translator,
PauseTreatment?pauseTreatment,
bool?sequentialTransfer,
ImageOrderExtractor?trajectory)
{
return(CreateTask(() =>
{
var characteristicNames = new string[characteristicLinkIds.Length];
var partNames = new List <string> [matterIds.Length];
var starts = new List <int> [matterIds.Length];
var lengthes = new List <int> [matterIds.Length];
var chains = new Chain[matterIds.Length];
var mattersCharacteristics = new object[matterIds.Length];
var calculators = new IFullCalculator[characteristicLinkIds.Length];
var links = new Link[characteristicLinkIds.Length];
matterIds = matterIds.OrderBy(m => m).ToArray();
Dictionary <long, Matter> matters = Cache.GetInstance().Matters.Where(m => matterIds.Contains(m.Id)).ToDictionary(m => m.Id);
for (int k = 0; k < matterIds.Length; k++)
{
long matterId = matterIds[k];
Nature nature = Cache.GetInstance().Matters.Single(m => m.Id == matterId).Nature;
long sequenceId = commonSequenceRepository.GetSequenceIds(new[] { matterId },
notation,
language,
translator,
pauseTreatment,
sequentialTransfer,
trajectory).Single();
chains[k] = commonSequenceRepository.GetLibiadaChain(sequenceId);
}
for (var i = 0; i < characteristicLinkIds.Length; i++)
{
int characteristicLinkId = characteristicLinkIds[i];
FullCharacteristic characteristic = characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkId);
calculators[i] = FullCalculatorsFactory.CreateCalculator(characteristic);
links[i] = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkId);
}
for (int i = 0; i < chains.Length; i++)
{
CutRule cutRule = growingWindow
? (CutRule) new CutRuleWithFixedStart(chains[i].Length, step)
: new SimpleCutRule(chains[i].Length, step, length);
CutRuleIterator iterator = cutRule.GetIterator();
var fragments = new List <Chain>();
partNames[i] = new List <string>();
starts[i] = new List <int>();
lengthes[i] = new List <int>();
while (iterator.Next())
{
int start = iterator.GetStartPosition();
int end = iterator.GetEndPosition();
var fragment = new List <IBaseObject>();
for (int k = 0; start + k < end; k++)
{
fragment.Add(chains[i][start + k]);
}
fragments.Add(new Chain(fragment));
partNames[i].Add(fragment.ToString());
starts[i].Add(iterator.GetStartPosition());
lengthes[i].Add(fragment.Count);
}
var fragmentsData = new FragmentData[fragments.Count];
for (int k = 0; k < fragments.Count; k++)
{
var characteristics = new double[calculators.Length];
for (int j = 0; j < calculators.Length; j++)
{
characteristics[j] = calculators[j].Calculate(fragments[k], links[j]);
}
fragmentsData[k] = new FragmentData(characteristics, fragments[k].ToString(), starts[i][k], fragments[k].Length);
}
double[][] differenceData = null;
double[][] fourierData = null;
double[][] autocorrelationData = null;
if (delta)
{
differenceData = CalculateDifference(fragmentsData.Select(f => f.Characteristics).ToArray());
}
if (fourier)
{
fourierData = FastFourierTransform.CalculateFastFourierTransform(fragmentsData.Select(f => f.Characteristics).ToArray());
}
if (autocorrelation)
{
autocorrelationData = AutoCorrelation.CalculateAutocorrelation(fragmentsData.Select(f => f.Characteristics).ToArray());
}
mattersCharacteristics[i] = new LocalCharacteristicsData(matters[matterIds[i]].Name,
fragmentsData,
differenceData,
fourierData,
autocorrelationData);
}
for (int l = 0; l < characteristicLinkIds.Length; l++)
{
characteristicNames[l] = characteristicTypeLinkRepository.GetCharacteristicName(characteristicLinkIds[l]);
}
var characteristicsList = new SelectListItem[characteristicLinkIds.Length];
for (int k = 0; k < characteristicLinkIds.Length; k++)
{
characteristicNames[k] = characteristicTypeLinkRepository.GetCharacteristicName(characteristicLinkIds[k], notation);
characteristicsList[k] = new SelectListItem
{
Value = k.ToString(),
Text = characteristicNames[k],
Selected = false
};
}
var result = new Dictionary <string, object>
{
{ "characteristics", mattersCharacteristics },
{ "notationName", notation.GetDisplayValue() },
{ "starts", starts },
{ "partNames", partNames },
{ "lengthes", lengthes },
{ "characteristicNames", characteristicNames },
{ "matterIds", matterIds },
{ "characteristicsList", characteristicsList },
{ "aligners", EnumHelper.GetSelectList(typeof(Aligner)) },
{ "distanceCalculators", EnumHelper.GetSelectList(typeof(DistanceCalculator)) },
{ "aggregators", EnumHelper.GetSelectList(typeof(Aggregator)) }
};
return new Dictionary <string, string> {
{ "data", JsonConvert.SerializeObject(result) }
};
}));
}
public ActionResult Index(long[] matterIds, int[] characteristicTypeLinkIds, int[] featureIds, string[] filters)
{
return Action(() =>
{
Dictionary<int, string> features;
var attributeValues = new List<AttributeValue>();
var characteristics = new Dictionary<string, SubsequenceData[]>(matterIds.Length);
var matterNames = new string[matterIds.Length];
var characteristicNames = new string[characteristicTypeLinkIds.Length];
long[] parentSequenceIds;
var calculators = new IFullCalculator[characteristicTypeLinkIds.Length];
var links = new LibiadaCore.Core.Link[characteristicTypeLinkIds.Length];
using (var db = new LibiadaWebEntities())
{
var featureRepository = new FeatureRepository(db);
features = featureRepository.Features.ToDictionary(f => f.Id, f => f.Name);
var parentSequences = db.DnaSequence.Include(s => s.Matter)
.Where(s => s.NotationId == Aliases.Notation.Nucleotide && matterIds.Contains(s.MatterId))
.Select(s => new { s.Id, MatterName = s.Matter.Name })
.ToDictionary(s => s.Id);
parentSequenceIds = parentSequences.Keys.ToArray();
for (int n = 0; n < parentSequenceIds.Length; n++)
{
matterNames[n] = parentSequences[parentSequenceIds[n]].MatterName;
}
var characteristicTypeLinkRepository = new CharacteristicTypeLinkRepository(db);
for (int k = 0; k < characteristicTypeLinkIds.Length; k++)
{
var characteristicTypeLinkId = characteristicTypeLinkIds[k];
characteristicNames[k] = characteristicTypeLinkRepository.GetCharacteristicName(characteristicTypeLinkId);
string className = characteristicTypeLinkRepository.GetCharacteristicType(characteristicTypeLinkId).ClassName;
calculators[k] = CalculatorsFactory.CreateFullCalculator(className);
links[k] = characteristicTypeLinkRepository.GetLibiadaLink(characteristicTypeLinkId);
}
}
// cycle through matters; first level of characteristics array
for (int i = 0; i < parentSequenceIds.Length; i++)
{
// all subsequence calculations
var subsequencesData = SubsequencesCharacteristicsCalculator.CalculateSubsequencesCharacteristics(
characteristicTypeLinkIds,
featureIds,
parentSequenceIds[i],
calculators,
links,
attributeValues,
filters);
subsequencesData = subsequencesData.OrderByDescending(s => s.CharacteristicsValues[0]).ToArray();
characteristics[matterNames[i]] = subsequencesData;
}
return new Dictionary<string, object>
{
{ "characteristics", characteristics },
{ "matterNames", matterNames },
{ "characteristicNames", characteristicNames },
{ "features", features },
{ "attributes", EnumExtensions.ToArray<LibiadaWeb.Attribute>().ToDictionary(a => (byte)a, a => a.GetDisplayValue()) },
{ "attributeValues", attributeValues.Select(sa => new { attribute = (byte)sa.AttributeId, value = sa.Value }) }
};
});
}
public ActionResult Index(
long[] matterIds,
int[] characteristicTypeLinkIds,
int[] notationIds,
int[] languageIds,
int?[] translatorIds,
bool rotate,
bool complementary,
uint? rotationLength)
{
return Action(() =>
{
var sequencesCharacteristics = new SequenceCharacteristics[matterIds.Length];
var characteristicNames = new string[characteristicTypeLinkIds.Length];
var characteristicsList = new SelectListItem[characteristicTypeLinkIds.Length];
var links = new Link[characteristicTypeLinkIds.Length];
var calculators = new IFullCalculator[characteristicTypeLinkIds.Length];
Dictionary<long, string> mattersNames;
double[][] characteristics;
Chain[][] chains;
using (var db = new LibiadaWebEntities())
{
mattersNames = db.Matter.Where(m => matterIds.Contains(m.Id)).ToDictionary(m => m.Id, m => m.Name);
var commonSequenceRepository = new CommonSequenceRepository(db);
chains = commonSequenceRepository.GetChains(matterIds, notationIds, languageIds, translatorIds);
var characteristicTypeLinkRepository = new CharacteristicTypeLinkRepository(db);
for (int k = 0; k < characteristicTypeLinkIds.Length; k++)
{
links[k] = characteristicTypeLinkRepository.GetLibiadaLink(characteristicTypeLinkIds[k]);
string className = characteristicTypeLinkRepository.GetCharacteristicType(characteristicTypeLinkIds[k]).ClassName;
calculators[k] = CalculatorsFactory.CreateFullCalculator(className);
characteristicNames[k] = characteristicTypeLinkRepository.GetCharacteristicName(characteristicTypeLinkIds[k], notationIds[k]);
characteristicsList[k] = new SelectListItem
{
Value = k.ToString(),
Text = characteristicNames[k],
Selected = false
};
}
}
if (!rotate && !complementary)
{
characteristics = SequencesCharacteristicsCalculator.Calculate(chains, calculators, links, characteristicTypeLinkIds);
}
else
{
characteristics = SequencesCharacteristicsCalculator.Calculate(chains, calculators, links, rotate, complementary, rotationLength);
}
for (int i = 0; i < matterIds.Length; i++)
{
sequencesCharacteristics[i] = new SequenceCharacteristics
{
MatterName = mattersNames[matterIds[i]],
Characteristics = characteristics[i]
};
}
var result = new Dictionary<string, object>
{
{ "characteristics", sequencesCharacteristics },
{ "characteristicNames", characteristicNames },
{ "characteristicsList", characteristicsList }
};
return new Dictionary<string, object>
{
{ "data", JsonConvert.SerializeObject(result) }
};
});
}
public ActionResult Index(
long[] matterIds,
OrderTransformation[] transformationsSequence,
int iterationsCount,
short characteristicLinkId,
Notation notation,
Language?language,
Translator?translator,
PauseTreatment?pauseTreatment,
bool?sequentialTransfer)
{
return(CreateTask(() =>
{
var db = new LibiadaWebEntities();
var characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
var commonSequenceRepository = new CommonSequenceRepository(db);
var mattersCharacteristics = new object[matterIds.Length];
matterIds = matterIds.OrderBy(m => m).ToArray();
Dictionary <long, Matter> matters = db.Matter.Where(m => matterIds.Contains(m.Id)).ToDictionary(m => m.Id);
for (int i = 0; i < matterIds.Length; i++)
{
long matterId = matterIds[i];
long sequenceId;
switch (matters[matterId].Nature)
{
case Nature.Literature:
sequenceId = db.LiteratureSequence.Single(l => l.MatterId == matterId &&
l.Notation == notation &&
l.Language == language &&
l.Translator == translator).Id;
break;
case Nature.Music:
sequenceId = db.MusicSequence.Single(m => m.MatterId == matterId &&
m.Notation == notation &&
m.PauseTreatment == pauseTreatment &&
m.SequentialTransfer == sequentialTransfer).Id;
break;
default:
sequenceId = db.CommonSequence.Single(c => c.MatterId == matterId && c.Notation == notation).Id;
break;
}
Link link = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkId);
FullCharacteristic characteristic = characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkId);
IFullCalculator calculator = FullCalculatorsFactory.CreateCalculator(characteristic);
Chain sequence = commonSequenceRepository.GetLibiadaChain(sequenceId);
var characteristics = new double[transformationsSequence.Length * iterationsCount];
for (int j = 0; j < iterationsCount; j++)
{
for (int k = 0; k < transformationsSequence.Length; k++)
{
sequence = transformationsSequence[k] == OrderTransformation.Dissimilar ? DissimilarChainFactory.Create(sequence)
: HighOrderFactory.Create(sequence, transformationsSequence[k].GetLink());
characteristics[transformationsSequence.Length * j + k] = calculator.Calculate(sequence, link);
}
}
mattersCharacteristics[i] = new { matterName = matters[matterId].Name, characteristics };
}
string characteristicName = characteristicTypeLinkRepository.GetCharacteristicName(characteristicLinkId, notation);
var result = new Dictionary <string, object>
{
{ "characteristics", mattersCharacteristics },
{ "characteristicName", characteristicName },
{ "transformationsList", transformationsSequence.Select(ts => ts.GetDisplayValue()) },
{ "iterationsCount", iterationsCount }
};
return new Dictionary <string, object>
{
{ "data", JsonConvert.SerializeObject(result) }
};
}));
}
/// <summary>
/// Calculates subsequences characteristics.
/// </summary>
/// <param name="characteristicIds">
/// The ids of characteristic types, arrangement types and links as <see cref="FullCharacteristicLink"/>.
/// </param>
/// <param name="features">
/// The features ids of subsequences to extract.
/// </param>
/// <param name="parentSequenceId">
/// The parent sequence id.
/// </param>
/// <param name="filters">
/// Textual search filters for subsequences products.
/// </param>
/// <returns>
/// The <see cref="T:SubsequenceData[]"/> .
/// </returns>
public static SubsequenceData[] CalculateSubsequencesCharacteristics(
short[] characteristicIds,
Feature[] features,
long parentSequenceId,
string[] filters = null)
{
Dictionary <long, Chain> sequences;
long[] subsequenceIds;
SubsequenceData[] subsequenceData;
Dictionary <long, Dictionary <short, double> > characteristics;
var calculators = new IFullCalculator[characteristicIds.Length];
var links = new Link[characteristicIds.Length];
var newCharacteristics = new List <CharacteristicValue>();
// creating local context to avoid memory overflow due to possibly big cache of characteristics
using (var db = new LibiadaWebEntities())
{
var subsequenceExtractor = new SubsequenceExtractor(db);
Subsequence[] subsequences = filters == null?
subsequenceExtractor.GetSubsequences(parentSequenceId, features) :
subsequenceExtractor.GetSubsequences(parentSequenceId, features, filters);
subsequenceData = subsequences.Select(s => new SubsequenceData(s)).ToArray();
// converting to libiada sequences
subsequenceIds = subsequences.Select(s => s.Id).ToArray();
characteristics = db.CharacteristicValue
.Where(c => characteristicIds.Contains(c.CharacteristicLinkId) && subsequenceIds.Contains(c.SequenceId))
.ToArray()
.GroupBy(c => c.SequenceId)
.ToDictionary(c => c.Key, c => c.ToDictionary(ct => ct.CharacteristicLinkId, ct => ct.Value));
if (characteristics.Count == subsequences.Length && characteristics.All(c => c.Value.Count == characteristicIds.Length))
{
sequences = new Dictionary <long, Chain>();
}
else
{
sequences = subsequenceExtractor.GetSubsequencesSequences(subsequences);
}
}
var characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
for (int k = 0; k < characteristicIds.Length; k++)
{
short characteristicLinkId = characteristicIds[k];
FullCharacteristic characteristic = characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkId);
calculators[k] = FullCalculatorsFactory.CreateCalculator(characteristic);
links[k] = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkId);
}
// cycle through subsequences
for (int i = 0; i < subsequenceIds.Length; i++)
{
characteristics.TryGetValue(subsequenceIds[i], out Dictionary <short, double> sequenceDbCharacteristics);
sequenceDbCharacteristics = sequenceDbCharacteristics ?? new Dictionary <short, double>();
var values = new double[calculators.Length];
// cycle through characteristics and notations
for (int j = 0; j < calculators.Length; j++)
{
short characteristicLinkId = characteristicIds[j];
if (!sequenceDbCharacteristics.TryGetValue(characteristicLinkId, out values[j]))
{
values[j] = calculators[j].Calculate(sequences[subsequenceIds[i]], links[j]);
var currentCharacteristic = new CharacteristicValue
{
SequenceId = subsequenceIds[i],
CharacteristicLinkId = characteristicLinkId,
Value = values[j]
};
newCharacteristics.Add(currentCharacteristic);
}
}
subsequenceData[i].CharacteristicsValues = values;
}
using (var db = new LibiadaWebEntities())
{
// trying to save calculated characteristics to database
var characteristicRepository = new CharacteristicRepository(db);
characteristicRepository.TrySaveCharacteristicsToDatabase(newCharacteristics);
}
return(subsequenceData);
}
public void Initialization()
{
var testClassName = this.GetType().Name;
var calculatorName = testClassName.Substring(0, testClassName.Length - 5);
Calculator = CalculatorsFactory.CreateFullCalculator(calculatorName);
}
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) }
};
}));
}
/// <summary>
/// Calculates subsequences characteristics.
/// </summary>
/// <param name="characteristicTypeLinkIds">
/// The characteristic type link ids.
/// </param>
/// <param name="featureIds">
/// The features ids.
/// </param>
/// <param name="parentSequenceId">
/// The parent sequence id.
/// </param>
/// <param name="calculators">
/// The calculators.
/// </param>
/// <param name="links">
/// The links.
/// </param>
/// <param name="attributeValues">
/// Nonredundant array of all attributes.
/// </param>
/// <param name="filters">
/// Textual search filters for subsequences products.
/// </param>
/// <returns>
/// The <see cref="T:SubsequenceData[]"/>.
/// </returns>
public static SubsequenceData[] CalculateSubsequencesCharacteristics(
int[] characteristicTypeLinkIds,
int[] featureIds,
long parentSequenceId,
IFullCalculator[] calculators,
Link[] links,
List<AttributeValue> attributeValues,
string[] filters = null)
{
// creating local context to avoid memory overflow due to possibly big cache of characteristics
using (var context = new LibiadaWebEntities())
{
var subsequenceExtractor = new SubsequenceExtractor(context);
var sequenceAttributeRepository = new SequenceAttributeRepository(context);
var attributeRepository = new AttributeRepository();
var newCharacteristics = new List<Characteristic>();
// extracting data from database
var dbSubsequences = filters == null ? subsequenceExtractor.GetSubsequences(parentSequenceId, featureIds) : subsequenceExtractor.GetSubsequences(parentSequenceId, featureIds, filters);
var subsequenceIds = dbSubsequences.Select(s => s.Id).ToArray();
var dbSubsequencesAttributes = sequenceAttributeRepository.GetAttributes(subsequenceIds);
var dbCharacteristics = context.Characteristic.Where(c => characteristicTypeLinkIds.Contains(c.CharacteristicTypeLinkId) && subsequenceIds.Contains(c.SequenceId))
.ToArray()
.GroupBy(c => c.SequenceId)
.ToDictionary(c => c.Key, c => c.ToDictionary(ct => ct.CharacteristicTypeLinkId, ct => ct.Value));
// converting to libiada sequences
var sequences = subsequenceExtractor.ExtractChains(dbSubsequences, parentSequenceId);
var subsequenceData = new SubsequenceData[sequences.Length];
// cycle through subsequences
for (int i = 0; i < sequences.Length; i++)
{
var values = new double[characteristicTypeLinkIds.Length];
Dictionary<int, double> sequenceDbCharacteristics;
if (!dbCharacteristics.TryGetValue(dbSubsequences[i].Id, out sequenceDbCharacteristics))
{
sequenceDbCharacteristics = new Dictionary<int, double>();
}
// cycle through characteristics and notations
for (int j = 0; j < characteristicTypeLinkIds.Length; j++)
{
int characteristicTypeLinkId = characteristicTypeLinkIds[j];
if (!sequenceDbCharacteristics.TryGetValue(characteristicTypeLinkId, out values[j]))
{
values[j] = calculators[j].Calculate(sequences[i], links[j]);
var currentCharacteristic = new Characteristic
{
SequenceId = dbSubsequences[i].Id,
CharacteristicTypeLinkId = characteristicTypeLinkId,
Value = values[j]
};
newCharacteristics.Add(currentCharacteristic);
}
}
AttributeValue[] attributes;
if (!dbSubsequencesAttributes.TryGetValue(dbSubsequences[i].Id, out attributes))
{
attributes = new AttributeValue[0];
}
var attributeIndexes = new int[attributes.Length];
for (int j = 0; j < attributes.Length; j++)
{
if (!attributeValues.Contains(attributes[j]))
{
attributeValues.Add(attributes[j]);
}
attributeIndexes[j] = attributeValues.IndexOf(attributes[j]);
}
subsequenceData[i] = new SubsequenceData(dbSubsequences[i], values, attributeIndexes);
}
// trying to save calculated characteristics to database
var characteristicRepository = new CharacteristicRepository(context);
characteristicRepository.TrySaveCharacteristicsToDatabase(newCharacteristics);
return subsequenceData;
}
}
/// <summary>
/// Calculation method.
/// </summary>
/// <param name="chains">
/// The chains.
/// </param>
/// <param name="calculators">
/// The calculators.
/// </param>
/// <param name="links">
/// The links.
/// </param>
/// <param name="rotate">
/// The rotate flag.
/// </param>
/// <param name="complementary">
/// The complementary flag.
/// </param>
/// <param name="rotationLength">
/// The rotation length.
/// </param>
/// <returns>
/// The <see cref="T:double[][]"/>.
/// </returns>
public static double[][] Calculate(Chain[][] chains, IFullCalculator[] calculators, Link[] links, bool rotate, bool complementary, uint? rotationLength)
{
var characteristics = new double[chains.Length][];
for (int i = 0; i < chains.Length; i++)
{
characteristics[i] = new double[calculators.Length];
for (int j = 0; j < calculators.Length; j++)
{
if (complementary)
{
var sourceSequence = new Sequence(Alphabets.DNA, chains[i][j].ToString());
var complementarySequence = sourceSequence.GetReverseComplementedSequence();
chains[i][j] = new Chain(complementarySequence.ConvertToString());
}
if (rotate)
{
var building = chains[i][j].Building.Rotate(rotationLength ?? 0);
var newSequence = building.Select(t => new ValueInt(t)).Cast<IBaseObject>().ToList();
chains[i][j] = new Chain(newSequence);
}
chains[i][j].FillIntervalManagers();
characteristics[i][j] = calculators[j].Calculate(chains[i][j], links[j]);
}
}
return characteristics;
}
public ActionResult Index(
long[] matterIds,
OrderTransformation[] transformationsSequence,
int iterationsCount,
short[] characteristicLinkIds,
Notation[] notations,
Language[] languages,
Translator?[] translators,
PauseTreatment[] pauseTreatments,
bool[] sequentialTransfers)
{
return(CreateTask(() =>
{
var db = new LibiadaWebEntities();
var characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
var commonSequenceRepository = new CommonSequenceRepository(db);
var mattersCharacteristics = new object[matterIds.Length];
matterIds = matterIds.OrderBy(m => m).ToArray();
Dictionary <long, Matter> matters = db.Matter.Where(m => matterIds.Contains(m.Id)).ToDictionary(m => m.Id);
for (int i = 0; i < matterIds.Length; i++)
{
long matterId = matterIds[i];
var characteristics = new double[characteristicLinkIds.Length];
for (int k = 0; k < characteristicLinkIds.Length; k++)
{
Notation notation = notations[k];
long sequenceId;
switch (matters[matterId].Nature)
{
case Nature.Literature:
Language language = languages[k];
Translator translator = translators[k] ?? Translator.NoneOrManual;
sequenceId = db.LiteratureSequence.Single(l => l.MatterId == matterId &&
l.Notation == notation &&
l.Language == language &&
l.Translator == translator).Id;
break;
case Nature.Music:
PauseTreatment pauseTreatment = pauseTreatments[k];
bool sequentialTransfer = sequentialTransfers[k];
sequenceId = db.MusicSequence.Single(m => m.MatterId == matterId &&
m.Notation == notation &&
m.PauseTreatment == pauseTreatment &&
m.SequentialTransfer == sequentialTransfer).Id;
break;
default:
sequenceId = db.CommonSequence.Single(c => c.MatterId == matterId && c.Notation == notation).Id;
break;
}
Chain sequence = commonSequenceRepository.GetLibiadaChain(sequenceId);
for (int l = 0; l < iterationsCount; l++)
{
for (int j = 0; j < transformationsSequence.Length; j++)
{
sequence = transformationsSequence[j] == OrderTransformation.Dissimilar ? DissimilarChainFactory.Create(sequence)
: HighOrderFactory.Create(sequence, EnumExtensions.GetLink(transformationsSequence[j]));
}
}
int characteristicLinkId = characteristicLinkIds[k];
Link link = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkId);
FullCharacteristic characteristic = characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkId);
IFullCalculator calculator = FullCalculatorsFactory.CreateCalculator(characteristic);
characteristics[k] = calculator.Calculate(sequence, link);
}
mattersCharacteristics[i] = new { matterName = matters[matterId].Name, characteristics };
}
var characteristicNames = new string[characteristicLinkIds.Length];
for (int k = 0; k < characteristicLinkIds.Length; k++)
{
characteristicNames[k] = characteristicTypeLinkRepository.GetCharacteristicName(characteristicLinkIds[k], notations[k]);
}
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", mattersCharacteristics },
{ "characteristicNames", characteristicNames },
{ "characteristicsList", characteristicsList },
{ "transformationsList", transformations },
{ "iterationsCount", iterationsCount }
};
return new Dictionary <string, object>
{
{ "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) }
};
}));
}
public ActionResult Index(long[] matterIds, int characteristicTypeLinkId, int[] characteristicTypeLinkIds, int[] featureIds)
{
return Action(() =>
{
var matterNames = new string[matterIds.Length];
var remoteIds = new string[matterIds.Length];
var subsequencesCharacteristicsNames = new string[characteristicTypeLinkIds.Length];
var calculators = new IFullCalculator[characteristicTypeLinkIds.Length];
var links = new Link[characteristicTypeLinkIds.Length];
var subsequencesCharacteristicsList = new SelectListItem[characteristicTypeLinkIds.Length];
var attributeValues = new List<AttributeValue>();
IEnumerable<SelectListItem> featuresSelectList;
Chain[] chains;
long[] parentSequenceIds;
string sequenceCharacteristicName;
IFullCalculator calculator;
Link link;
using (var db = new LibiadaWebEntities())
{
var featureRepository = new FeatureRepository(db);
featuresSelectList = featureRepository.GetFeaturesById(featureIds).Select(f => new SelectListItem { Value = f.Id.ToString(), Text = f.Name, Selected = true });
var parentSequences = db.DnaSequence.Include(s => s.Matter)
.Where(s => s.NotationId == Aliases.Notation.Nucleotide && matterIds.Contains(s.MatterId))
.Select(s => new { s.Id, MatterName = s.Matter.Name, s.RemoteId })
.ToDictionary(s => s.Id);
parentSequenceIds = parentSequences.Keys.ToArray();
for (int n = 0; n < parentSequenceIds.Length; n++)
{
matterNames[n] = parentSequences[parentSequenceIds[n]].MatterName;
remoteIds[n] = parentSequences[parentSequenceIds[n]].RemoteId;
}
var commonSequenceRepository = new CommonSequenceRepository(db);
chains = commonSequenceRepository.GetNucleotideChains(matterIds);
var characteristicTypeLinkRepository = new CharacteristicTypeLinkRepository(db);
sequenceCharacteristicName = characteristicTypeLinkRepository.GetCharacteristicName(characteristicTypeLinkId);
calculator = CalculatorsFactory.CreateFullCalculator(characteristicTypeLinkRepository.GetCharacteristicType(characteristicTypeLinkId).ClassName);
link = characteristicTypeLinkRepository.GetLibiadaLink(characteristicTypeLinkId);
for (int k = 0; k < characteristicTypeLinkIds.Length; k++)
{
links[k] = characteristicTypeLinkRepository.GetLibiadaLink(characteristicTypeLinkIds[k]);
string className = characteristicTypeLinkRepository.GetCharacteristicType(characteristicTypeLinkIds[k]).ClassName;
calculators[k] = CalculatorsFactory.CreateFullCalculator(className);
subsequencesCharacteristicsNames[k] = characteristicTypeLinkRepository.GetCharacteristicName(characteristicTypeLinkIds[k]);
subsequencesCharacteristicsList[k] = new SelectListItem
{
Value = k.ToString(),
Text = subsequencesCharacteristicsNames[k],
Selected = false
};
}
}
var characteristics = SequencesCharacteristicsCalculator.Calculate(chains, calculator, link, characteristicTypeLinkId);
var sequenceData = new SequenceData[parentSequenceIds.Length];
for (int i = 0; i < parentSequenceIds.Length; i++)
{
// all subsequence calculations
var subsequencesData = SubsequencesCharacteristicsCalculator.CalculateSubsequencesCharacteristics(
characteristicTypeLinkIds,
featureIds,
parentSequenceIds[i],
calculators,
links,
attributeValues);
sequenceData[i] = new SequenceData(matterIds[i], matterNames[i], remoteIds[i], characteristics[i], subsequencesData);
}
// sorting organisms by their characteristic
sequenceData = sequenceData.OrderBy(r => r.Characteristic).ToArray();
var resultData = new Dictionary<string, object>
{
{ "result", sequenceData },
{ "subsequencesCharacteristicsNames", subsequencesCharacteristicsNames },
{ "subsequencesCharacteristicsList", subsequencesCharacteristicsList },
{ "sequenceCharacteristicName", sequenceCharacteristicName },
{ "features", featuresSelectList.ToDictionary(f => f.Value) },
{ "attributes", EnumExtensions.ToArray<Attribute>().ToDictionary(a => (byte)a, a => a.GetDisplayValue()) },
{ "attributeValues", attributeValues.Select(sa => new { attribute = sa.AttributeId, value = sa.Value }) }
};
return new Dictionary<string, object>
{
{ "data", JsonConvert.SerializeObject(resultData) }
};
});
}
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) }
};
}));
}
