/// <summary>
/// Initializes a new instance of the <see cref="SequenceTransformerController"/> class.
/// </summary>
public SequenceTransformerController()
{
db = new LibiadaWebEntities();
dnaSequenceRepository = new GeneticSequenceRepository(db);
commonSequenceRepository = new CommonSequenceRepository(db);
elementRepository = new ElementRepository(db);
}
public ActionResult Index(
long matterId,
short characteristicLinkId,
Notation notation,
int step,
int initialLength,
string accuracy)
{
return(CreateTask(() =>
{
string characteristicName;
string matterName;
double[] characteristics;
Chain sequence;
IFullCalculator calculator;
Link link;
using (var db = new LibiadaWebEntities())
{
var commonSequenceRepository = new CommonSequenceRepository(db);
matterName = Cache.GetInstance().Matters.Single(m => matterId == m.Id).Name;
var sequenceId = db.CommonSequence.Single(c => matterId == c.MatterId && c.Notation == notation).Id;
sequence = commonSequenceRepository.GetLibiadaChain(sequenceId);
var characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
characteristicName = characteristicTypeLinkRepository.GetCharacteristicName(characteristicLinkId, notation);
FullCharacteristic characteristic = characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkId);
calculator = FullCalculatorsFactory.CreateCalculator(characteristic);
link = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkId);
}
// characteristics = SequencesCharacteristicsCalculator.Calculate( new[] { sequenceId }, characteristicLinkId);
AverageRemoteness averageRemotenessCalc = new AverageRemoteness();
double averageRemoteness = averageRemotenessCalc.Calculate(sequence, Link.Start);
Alphabet alphabet = sequence.Alphabet;
var doubleAccuracy = double.Parse(accuracy);
List <SequencePredictionData> sequencePredictionResult;
Chain chain;
(sequencePredictionResult, chain) = Predict(averageRemotenessCalc, sequence, initialLength, alphabet, averageRemoteness, doubleAccuracy);
var matching = FindPercentageOfMatching(sequence, chain, initialLength) * 100;
var result = new Dictionary <string, object>
{
{ "result", sequencePredictionResult },
{ "matterName", matterName },
{ "matching", matching }
};
return new Dictionary <string, string>
{
{ "data", JsonConvert.SerializeObject(result) }
};
}));
}
/// <summary>
/// Calculation method.
/// </summary>
/// <param name="chainCharacteristicsIds">
/// Dictionary with chain ids as a key
/// and characteristicLink ids array as value.
/// </param>
/// <returns>
/// The <see cref="T:double[][]"/>.
/// </returns>
public static Dictionary <long, Dictionary <short, double> > Calculate(Dictionary <long, short[]> chainCharacteristicsIds)
{
var newCharacteristics = new List <CharacteristicValue>();
var allCharacteristics = new Dictionary <long, Dictionary <short, double> >();
using (var db = new LibiadaWebEntities())
{
short[] characteristicLinkIds = chainCharacteristicsIds.SelectMany(c => c.Value).Distinct().ToArray();
var characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
var calculators = new Dictionary <short, LinkedFullCalculator>();
foreach (short characteristicLinkId in characteristicLinkIds)
{
Link link = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkId);
FullCharacteristic characteristic = characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkId);
calculators.Add(characteristicLinkId, new LinkedFullCalculator(characteristic, link));
}
var commonSequenceRepository = new CommonSequenceRepository(db);
long[] sequenceIds = chainCharacteristicsIds.Keys.ToArray();
foreach (long sequenceId in sequenceIds)
{
short[] sequenceCharacteristicLinkIds = chainCharacteristicsIds[sequenceId];
Dictionary <short, double> characteristics = db.CharacteristicValue
.Where(c => sequenceId == c.SequenceId && sequenceCharacteristicLinkIds.Contains(c.CharacteristicLinkId))
.ToDictionary(ct => ct.CharacteristicLinkId, ct => ct.Value);
allCharacteristics.Add(sequenceId, characteristics);
if (characteristics.Count < sequenceCharacteristicLinkIds.Length)
{
Chain sequence = commonSequenceRepository.GetLibiadaChain(sequenceId);
foreach (short sequenceCharacteristicLinkId in sequenceCharacteristicLinkIds)
{
if (!characteristics.ContainsKey(sequenceCharacteristicLinkId))
{
LinkedFullCalculator calculator = calculators[sequenceCharacteristicLinkId];
double characteristicValue = calculator.Calculate(sequence);
var characteristic = new CharacteristicValue
{
SequenceId = sequenceId,
CharacteristicLinkId = sequenceCharacteristicLinkId,
Value = characteristicValue
};
characteristics.Add(sequenceCharacteristicLinkId, characteristicValue);
newCharacteristics.Add(characteristic);
}
}
}
}
var characteristicRepository = new CharacteristicRepository(db);
characteristicRepository.TrySaveCharacteristicsToDatabase(newCharacteristics);
return(allCharacteristics);
}
}
/// <summary>
/// Initializes a new instance of the <see cref="SequenceMixerController"/> class.
/// </summary>
public SequenceMixerController()
{
db = new LibiadaWebEntities();
sequenceRepository = new CommonSequenceRepository(db);
dnaSequenceRepository = new GeneticSequenceRepository(db);
musicSequenceRepository = new MusicSequenceRepository(db);
literatureSequenceRepository = new LiteratureSequenceRepository(db);
dataSequenceRepository = new DataSequenceRepository(db);
elementRepository = new ElementRepository(db);
}
/// <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>
/// Initializes a new instance of the <see cref="SequenceElementsController"/> class.
/// </summary>
public SequenceElementsController()
{
db = new LibiadaWebEntities();
elementRepository = new ElementRepository(db);
sequenceRepository = new CommonSequenceRepository(db);
}
/// <summary>
/// The index.
/// </summary>
/// <returns>
/// The <see cref="ActionResult"/>.
/// </returns>
public ActionResult Index()
{
using (var db = new LibiadaWebEntities())
{
var matterRepository = new MatterRepository(db);
var dnaSequenceRepository = new GeneticSequenceRepository(db);
var commonSequenceRepository = new CommonSequenceRepository(db);
var elementRepository = new ElementRepository(db);
var matterIds = new long[] { 1332, 1333, 1339, 1330, 1337, 1342, 1331, 1338, 1340, 1943, 1945, 1334 };
DnaSequence[] sequences = db.DnaSequence.Include(d => d.Matter).Where(d => matterIds.Contains(d.MatterId)).ToArray();
for (int i = 0; i < sequences.Length; i++)
{
var newMatter = new Matter
{
Name = $"{sequences[i].Matter.Name} Cleaned of IS110",
Description = sequences[i].Matter.Description,
Nature = sequences[i].Matter.Nature,
Group = sequences[i].Matter.Group,
SequenceType = sequences[i].Matter.SequenceType
};
var newSequence = new CommonSequence
{
Notation = sequences[i].Notation,
Matter = newMatter,
Description = sequences[i].Description,
RemoteDb = sequences[i].RemoteDb,
RemoteId = sequences[i].RemoteId
};
var chain = commonSequenceRepository.GetLibiadaChain(sequences[i].Id);
matterRepository.CreateOrExtractExistingMatterForSequence(newSequence);
dnaSequenceRepository.Create(newSequence, false, elementRepository.ToDbElements(chain.Alphabet, Notation.Nucleotides, false), chain.Building);
var sequenceId = sequences[i].Id;
var subsequences = db.Subsequence.Include(s => s.Position).Include(s => s.SequenceAttribute).Where(s => s.SequenceId == sequenceId).ToList();
var subsequenceIds = subsequences.Select(s => s.Id);
var subsequencesIdsToRemove = db.SequenceAttribute
.Where(sa => subsequenceIds.Contains(sa.SequenceId) && sa.Value.Contains("IS110"))
.Select(sa => sa.SequenceId)
.Distinct()
.ToArray();
subsequences.RemoveAll(s => subsequencesIdsToRemove.Contains(s.Id));
var newSubsequences = new Subsequence[subsequences.Count];
var newSequenceAttributes = new List <SequenceAttribute>();
var newPositions = new List <Position>();
for (int j = 0; j < subsequences.Count; j++)
{
newSubsequences[j] = new Subsequence
{
Id = db.GetNewElementId(),
Feature = subsequences[j].Feature,
SequenceId = newSequence.Id,
Start = subsequences[j].Start,
Length = subsequences[j].Length,
RemoteId = subsequences[j].RemoteId,
Partial = subsequences[j].Partial
};
foreach (SequenceAttribute subsequenceAttribute in subsequences[j].SequenceAttribute.ToArray())
{
newSequenceAttributes.Add(new SequenceAttribute
{
SequenceId = newSubsequences[j].Id,
Attribute = subsequenceAttribute.Attribute,
Value = subsequenceAttribute.Value
});
}
foreach (Position position in subsequences[j].Position.ToArray())
{
newPositions.Add(new Position
{
SubsequenceId = newSubsequences[j].Id,
Length = position.Length,
Start = position.Start
});
}
}
db.Subsequence.AddRange(newSubsequences);
db.SequenceAttribute.AddRange(newSequenceAttributes);
db.Position.AddRange(newPositions);
db.SaveChanges();
}
}
return(View());
}
/// <summary>
/// Initializes a new instance of the <see cref="OrderTransformerController"/> class.
/// </summary>
public OrderTransformerController() : base(TaskType.OrderTransformer)
{
db = new LibiadaWebEntities();
commonSequenceRepository = new CommonSequenceRepository(db);
}
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) }
};
}));
}
/// <summary>
/// Initializes a new instance of the <see cref="ClusterizationController"/> class.
/// </summary>
public ClusterizationController() : base(TaskType.Clusterization)
{
db = new LibiadaWebEntities();
commonSequenceRepository = new CommonSequenceRepository(db);
characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
}
public ActionResult Index(
long[] matterIds,
short[] characteristicLinkIds,
Notation[] notations,
Language?[] languages,
Translator?[] translators,
PauseTreatment?[] pauseTreatments,
bool?[] sequentialTransfers,
ImageOrderExtractor?[] trajectories,
bool sort,
bool theoretical)
{
return(CreateTask(() =>
{
var sequencesCharacteristics = new CongenericSequencesCharacteristics[matterIds.Length];
var characteristicNames = new string[characteristicLinkIds.Length];
var characteristicsList = new SelectListItem[characteristicLinkIds.Length];
Dictionary <long, string> mattersNames;
long[][] sequenceIds;
using (var db = new LibiadaWebEntities())
{
mattersNames = Cache.GetInstance().Matters.Where(m => matterIds.Contains(m.Id)).ToDictionary(m => m.Id, m => m.Name);
var commonSequenceRepository = new CommonSequenceRepository(db);
sequenceIds = commonSequenceRepository.GetSequenceIds(matterIds, notations, languages, translators, pauseTreatments, sequentialTransfers, trajectories);
var congenericCharacteristicRepository = CongenericCharacteristicRepository.Instance;
for (int k = 0; k < characteristicLinkIds.Length; k++)
{
characteristicNames[k] = congenericCharacteristicRepository.GetCharacteristicName(characteristicLinkIds[k], notations[k]);
characteristicsList[k] = new SelectListItem
{
Value = k.ToString(),
Text = characteristicNames[k],
Selected = false
};
}
}
double[][][] characteristics = CongenericSequencesCharacteristicsCalculator.Calculate(sequenceIds, characteristicLinkIds);
for (int i = 0; i < matterIds.Length; i++)
{
sequencesCharacteristics[i] = new CongenericSequencesCharacteristics
{
MatterName = mattersNames[matterIds[i]],
Elements = null,
Characteristics = characteristics[i]
};
}
var result = new Dictionary <string, object>
{
{ "characteristics", sequencesCharacteristics },
{ "characteristicNames", characteristicNames },
{ "characteristicsList", characteristicsList }
};
return new Dictionary <string, string> {
{ "data", JsonConvert.SerializeObject(result) }
};
//var theoreticalRanks = new List<List<List<double>>>();
//var elementNames = new List<List<string>>();
//var newCharacteristics = new List<CongenericCharacteristicValue>();
//var isLiteratureSequence = false;
//// cycle through matters; first level of characteristics array
//for (int w = 0; w < matterIds.Length; w++)
//{
// long matterId = matterIds[w];
// elementNames.Add(new List<string>());
// characteristics.Add(new List<List<KeyValuePair<int, double>>>());
// theoreticalRanks.Add(new List<List<double>>());
// // cycle through characteristics and notations; second level of characteristics array
// for (int i = 0; i < characteristicLinkIds.Length; i++)
// {
// Notation notation = notations[i];
// long sequenceId;
// if (db.Matter.Single(m => m.Id == matterId).Nature == Nature.Literature)
// {
// Language language = languages[i];
// Translator? translator = translators[i];
// isLiteratureSequence = true;
// sequenceId = db.LiteratureSequence.Single(l => l.MatterId == matterId
// && l.Notation == notation
// && l.Language == language
// && translator == l.Translator).Id;
// }
// else
// {
// sequenceId = db.CommonSequence.Single(c => c.MatterId == matterId && c.Notation == notation).Id;
// }
// Chain chain = commonSequenceRepository.GetLibiadaChain(sequenceId);
// chain.FillIntervalManagers();
// characteristics.Last().Add(new List<KeyValuePair<int, double>>());
// short characteristicLinkId = characteristicLinkIds[i];
// CongenericCharacteristic congenericCharacteristic = characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkId);
// ICongenericCalculator calculator = CongenericCalculatorsFactory.CreateCalculator(congenericCharacteristic);
// Link link = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkId);
// List<long> sequenceElements = db.GetElementIds(sequenceId);
// int calculated = db.CongenericCharacteristicValue.Count(c => c.SequenceId == sequenceId && c.CharacteristicLinkId == characteristicLinkId);
// if (calculated < chain.Alphabet.Cardinality)
// {
// for (int j = 0; j < chain.Alphabet.Cardinality; j++)
// {
// long elementId = sequenceElements[j];
// CongenericChain tempChain = chain.CongenericChain(j);
// if (!db.CongenericCharacteristicValue.Any(b => b.SequenceId == sequenceId
// && b.CharacteristicLinkId == characteristicLinkId
// && b.ElementId == elementId))
// {
// double value = calculator.Calculate(tempChain, link);
// var currentCharacteristic = new CongenericCharacteristicValue
// {
// SequenceId = sequenceId,
// CharacteristicLinkId = characteristicLinkId,
// ElementId = elementId,
// Value = value
// };
// newCharacteristics.Add(currentCharacteristic);
// }
// }
// }
// // cycle through all alphabet elements; third level of characteristics array
// for (int d = 0; d < chain.Alphabet.Cardinality; d++)
// {
// long elementId = sequenceElements[d];
// double characteristic = db.CongenericCharacteristicValue.Single(c => c.SequenceId == sequenceId
// && c.CharacteristicLinkId == characteristicLinkId
// && c.ElementId == elementId).Value;
// characteristics.Last().Last().Add(new KeyValuePair<int, double>(d, characteristic));
// if (i == 0)
// {
// elementNames.Last().Add(chain.Alphabet[d].ToString());
// }
// }
// // theoretical frequencies of orlov criterion
// if (theoretical)
// {
// theoreticalRanks[w].Add(new List<double>());
// ICongenericCalculator countCalculator = CongenericCalculatorsFactory.CreateCalculator(CongenericCharacteristic.ElementsCount);
// var counts = new List<int>();
// for (int f = 0; f < chain.Alphabet.Cardinality; f++)
// {
// counts.Add((int)countCalculator.Calculate(chain.CongenericChain(f), Link.NotApplied));
// }
// ICongenericCalculator frequencyCalculator = CongenericCalculatorsFactory.CreateCalculator(CongenericCharacteristic.Probability);
// var frequency = new List<double>();
// for (int f = 0; f < chain.Alphabet.Cardinality; f++)
// {
// frequency.Add(frequencyCalculator.Calculate(chain.CongenericChain(f), Link.NotApplied));
// }
// double maxFrequency = frequency.Max();
// double k = 1 / Math.Log(counts.Max());
// double b = (k / maxFrequency) - 1;
// int n = 1;
// double plow = chain.Length;
// double p = k / (b + n);
// while (p >= (1 / plow))
// {
// theoreticalRanks.Last().Last().Add(p);
// n++;
// p = k / (b + n);
// }
// }
// }
//}
//db.CongenericCharacteristicValue.AddRange(newCharacteristics);
//db.SaveChanges();
//// characteristics names
//for (int k = 0; k < characteristicLinkIds.Length; k++)
//{
// string characteristicType = characteristicTypeLinkRepository.GetCharacteristicName(characteristicLinkIds[k], notations[k]);
// if (isLiteratureSequence)
// {
// Language language = languages[k];
// characteristicNames.Add(characteristicType + " " + language.GetDisplayValue());
// }
// else
// {
// characteristicNames.Add(characteristicType);
// }
//}
//// rank sorting
//if (sort)
//{
// for (int f = 0; f < matterIds.Length; f++)
// {
// for (int p = 0; p < characteristics[f].Count; p++)
// {
// SortKeyValuePairList(characteristics[f][p]);
// }
// }
//}
//return new Dictionary<string, object>
//{
// { "characteristics", characteristics },
// { "elementNames", elementNames },
// { "characteristicNames", characteristicNames },
// { "matterIds", matterIds },
// { "theoreticalRanks", theoreticalRanks },
// { "characteristicsList", characteristicsList }
//};
}));
}
/// <summary>
/// Initializes a new instance of the <see cref="AccordanceCalculationController"/> class.
/// </summary>
public AccordanceCalculationController() : base(TaskType.AccordanceCalculation)
{
db = new LibiadaWebEntities();
commonSequenceRepository = new CommonSequenceRepository(db);
characteristicTypeLinkRepository = AccordanceCharacteristicRepository.Instance;
}
/// <summary>
/// Initializes a new instance of the <see cref="SubsequenceExtractor"/> class.
/// </summary>
/// <param name="db">
/// The db.
/// </param>
public SubsequenceExtractor(LibiadaWebEntities db)
{
this.db = db;
commonSequenceRepository = new CommonSequenceRepository(db);
}
public ActionResult Index(
long matterId,
short characteristicLinkId,
Notation notation,
int step,
int initialLength,
double accuracy)
{
return(CreateTask(() =>
{
string characteristicName;
string mattersName;
double[] characteristics;
Chain sequence;
IFullCalculator calculator;
Link link;
using (var db = new LibiadaWebEntities())
{
var commonSequenceRepository = new CommonSequenceRepository(db);
mattersName = db.Matter.Single(m => matterId == m.Id).Name;
var sequenceId = db.CommonSequence.Single(c => matterId == c.MatterId && c.Notation == notation).Id;
sequence = commonSequenceRepository.GetLibiadaChain(sequenceId);
var characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
characteristicName = characteristicTypeLinkRepository.GetCharacteristicName(characteristicLinkId, notation);
FullCharacteristic characteristic = characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkId);
calculator = FullCalculatorsFactory.CreateCalculator(characteristic);
link = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkId);
}
// characteristics = SequencesCharacteristicsCalculator.Calculate( new[] { sequenceId }, characteristicLinkId);
CutRule cutRule = new CutRuleWithFixedStart(sequence.Length, step);
Depth depthCaulc = new Depth();
CutRuleIterator iter = cutRule.GetIterator();
var fragments = new List <Chain>();
var partNames = new List <string>();
var lengthes = new List <int>();
var teoreticalDepht = new List <double>();
while (iter.Next())
{
var fragment = new Chain(iter.GetEndPosition() - iter.GetStartPosition());
for (int k = 0; iter.GetStartPosition() + k < iter.GetEndPosition(); k++)
{
fragment.Set(sequence[iter.GetStartPosition() + k], k);
}
fragments.Add(fragment);
partNames.Add(fragment.ToString());
lengthes.Add(fragment.Length);
teoreticalDepht.Add(depthCaulc.Calculate(fragment, Link.Start));
}
characteristics = new double[fragments.Count];
for (int k = 0; k < fragments.Count; k++)
{
characteristics[k] = calculator.Calculate(fragments[k], link);
// fragmentsData[k] = new FragmentData(characteristics, fragments[k].ToString(), starts[i][k], fragments[k].Length);
}
// var predicted = new List<Chain>();
//int[] startingPart = new int[initialLength];
Chain predicted = new Chain(initialLength);
for (int i = 0; i < initialLength; i++)
{
predicted.Set(sequence[i], i);
}
Alphabet alphabet = sequence.Alphabet;
IEnumerator enumerator = alphabet.GetEnumerator();
var sequencePredictionResult = new List <SequencePredictionData>();
for (int i = initialLength; i < sequence.Length; i++)
{
Chain temp = new Chain(i + 1);
for (int j = 0; j < i; j++)
{
temp.Set(predicted[j], j);
}
predicted = temp;
double depth = 0;
/* do
* {
* predicted.Set((IBaseObject)enumerator.Current, i);
* depth = depthCaulc.Calculate(predicted, Link.Start);
* if (System.Math.Abs(depth - teoreticalDepht.ElementAt(i)) <= accuracy)
* {
* break;
* }
* } while (enumerator.MoveNext());*/
IBaseObject predictedLetter = null;
foreach (IBaseObject letter in alphabet)
{
predicted.Set(letter, i);
depth = depthCaulc.Calculate(predicted, Link.Start);
if (System.Math.Abs(depth - teoreticalDepht.ElementAt(i)) <= accuracy)
{
predictedLetter = letter;
break;
}
}
sequencePredictionResult.Add(new SequencePredictionData
{
Fragment = fragments.ElementAt(i).ToString(),
Predicted = /*enumerator.Current.ToString()*/ predicted.ToString(),
ActualCharacteristic = depth,
TheoreticalCharacteristic = teoreticalDepht.ElementAt(i)
});
}
/*int equal = 0;
* for (int i = initialLength; i < sequence.Length; i++)
* {
* if (sequence[i] == predicted[i])
* {
* equal++;
* }
* }
*
*
* double accuracyPercentage = equal / (sequence.Length - initialLength);*/
// TODO: sequence prediction
var result = new Dictionary <string, object>
{
{ "result", sequencePredictionResult }
};
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,
short[] characteristicLinkIds,
Notation[] notations,
Language?[] languages,
Translator?[] translators,
PauseTreatment?[] pauseTreatments,
bool?[] sequentialTransfers,
ImageOrderExtractor?[] trajectories,
int clustersCount,
ClusterizationType clusterizationType,
double equipotencyWeight = 1,
double normalizedDistanceWeight = 1,
double distanceWeight = 1,
double bandwidth = 0,
int maximumClusters = 2)
{
return(CreateTask(() =>
{
Dictionary <long, string> mattersNames;
Dictionary <long, string> matters = Cache.GetInstance()
.Matters
.Where(m => matterIds.Contains(m.Id))
.ToDictionary(m => m.Id, m => m.Name);
long[][] sequenceIds;
using (var db = new LibiadaWebEntities())
{
var commonSequenceRepository = new CommonSequenceRepository(db);
sequenceIds = commonSequenceRepository.GetSequenceIds(matterIds,
notations,
languages,
translators,
pauseTreatments,
sequentialTransfers,
trajectories);
mattersNames = db.Matter.Where(m => matterIds.Contains(m.Id)).ToDictionary(m => m.Id, m => m.Name);
}
double[][] characteristics;
characteristics = SequencesCharacteristicsCalculator.Calculate(sequenceIds, characteristicLinkIds);
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);
var mattersCharacteristics = new object[matterIds.Length];
for (int i = 0; i < clusterizationResult.Length; i++)
{
mattersCharacteristics[i] = new
{
MatterName = mattersNames[matterIds[i]],
cluster = clusterizationResult[i] + 1,
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>
{
{ "characteristicNames", characteristicNames },
{ "characteristics", mattersCharacteristics },
{ "characteristicsList", characteristicsList },
{ "clustersCount", clusterizationResult.Distinct().Count() }
};
return new Dictionary <string, string> {
{ "data", JsonConvert.SerializeObject(result) }
};
}));
}
public ActionResult Index(long matterId, string[] file)
{
return(CreateTask(() =>
{
var myFile = Request.Files[0];
if (myFile == null || myFile.ContentLength == 0)
{
throw new ArgumentNullException(nameof(file), "Sequence file not found or empty.");
}
int fileLen = myFile.ContentLength;
var input = new byte[fileLen];
// Initialize the stream.
var fileStream = myFile.InputStream;
// Read the file into the byte array.
fileStream.Read(input, 0, fileLen);
// Copy the byte array into a string.
string stringSequence = Encoding.ASCII.GetString(input);
string[] tempString = stringSequence.Split('\n', '\r');
var sequenceStringBuilder = new StringBuilder();
for (int j = 1; j < tempString.Length; j++)
{
sequenceStringBuilder.Append(tempString[j]);
}
string resultStringSequence = DataTransformers.CleanFastaFile(sequenceStringBuilder.ToString());
var chain = new BaseChain(resultStringSequence);
string message;
string status;
BaseChain dbChain;
using (var db = new LibiadaWebEntities())
{
long sequenceId = db.CommonSequence.Single(c => c.MatterId == matterId).Id;
var commonSequenceRepository = new CommonSequenceRepository(db);
dbChain = commonSequenceRepository.GetLibiadaBaseChain(sequenceId);
}
if (dbChain.Equals(chain))
{
message = "Sequence in db and in file are equal";
status = "Success";
}
else
{
status = "Error";
if (chain.Alphabet.Cardinality != dbChain.Alphabet.Cardinality)
{
message = $"Alphabet sizes are not equal. In db - {dbChain.Alphabet.Cardinality}. In file - {chain.Alphabet.Cardinality}";
return new Dictionary <string, string> {
{ "data", JsonConvert.SerializeObject(new { message }) }
};
}
for (int i = 0; i < chain.Alphabet.Cardinality; i++)
{
if (!chain.Alphabet[i].ToString().Equals(dbChain.Alphabet[i].ToString()))
{
message = $"{i} elements in alphabet are not equal. In db - {dbChain.Alphabet[i]}. In file - {chain.Alphabet[i]}";
return new Dictionary <string, string> {
{ "data", JsonConvert.SerializeObject(new { message }) }
};
}
}
if (chain.Length != dbChain.Length)
{
message = $"Sequence length in db {dbChain.Length}, and sequence length from file{chain.Length}";
return new Dictionary <string, string> {
{ "data", JsonConvert.SerializeObject(new { message, status }) }
};
}
int[] libiadaBuilding = chain.Building;
int[] dataBaseBuilding = dbChain.Building;
for (int j = 0; j < chain.Length; j++)
{
if (libiadaBuilding[j] != dataBaseBuilding[j])
{
message = $"{j} sequences elements are not equal. In db {dataBaseBuilding[j]}. In file {libiadaBuilding[j]}";
return new Dictionary <string, string> {
{ "data", JsonConvert.SerializeObject(new { message, status }) }
};
}
}
message = "Sequences are equal and not equal at the same time.";
}
return new Dictionary <string, string> {
{ "data", JsonConvert.SerializeObject(new { message, status }) }
};
}));
}
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 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) }
};
}));
}
