/// <summary>
/// The create.
/// </summary>
/// <param name="source">
/// The source.
/// </param>
/// <param name="link">
/// The link.
/// </param>
/// <returns>
/// The <see cref="Chain"/>.
/// </returns>
/// <exception cref="ArgumentException">
/// Thrown if link is unacceptable.
/// </exception>
public static Chain Create(Chain source, Link link)
{
if (link != Link.Start && link != Link.End && link != Link.CycleEnd && link != Link.CycleStart)
{
throw new ArgumentException("Unknown link", "link");
}
var result = new Chain(source.GetLength());
Alphabet sourceAlphabet = source.Alphabet;
var entries = new int[sourceAlphabet.Cardinality];
var intervals = new int[sourceAlphabet.Cardinality][];
for (int j = 0; j < sourceAlphabet.Cardinality; j++)
{
var intervalsManager = new CongenericIntervalsManager(source.CongenericChain(j));
intervals[j] = intervalsManager.GetIntervals(link);
}
for (int i = 0; i < source.GetLength(); i++)
{
var elementIndex = sourceAlphabet.IndexOf(source[i]);
int entry = entries[elementIndex]++;
var interval = intervals[elementIndex][entry];
result.Set(new ValueInt(interval), i);
}
return result;
}
public void WriteTest()
{
var messages = new List<ValueString>(12)
{
new ValueString('1'),
new ValueString('2'),
new ValueString('1'),
new ValueString('3'),
new ValueString('3'),
new ValueString('1'),
new ValueString('2'),
new ValueString('1'),
new ValueString('2'),
new ValueString('2'),
new ValueString('3'),
new ValueString('1')
};
var toWrite = new Chain(12);
var iteratorWrite = new IteratorWritableStart(toWrite);
int i = 0;
while (iteratorWrite.Next())
{
iteratorWrite.WriteValue(messages[i++]);
}
Assert.AreEqual(chainToIterate, toWrite);
}
public void Initialize()
{
// Creating sequence containing 12 elements.
// |a|d|b|a|a|c|b|b|a|a|c|a|
testChain = new Chain(12);
testChain.Set((ValueString)"a", 0);
testChain.Set((ValueString)"d", 1);
testChain.Set((ValueString)"b", 2);
testChain.Set((ValueString)"a", 3);
testChain.Set((ValueString)"a", 4);
testChain.Set((ValueString)"c", 5);
testChain.Set((ValueString)"b", 6);
testChain.Set((ValueString)"b", 7);
testChain.Set((ValueString)"a", 8);
testChain.Set((ValueString)"a", 9);
testChain.Set((ValueString)"c", 10);
testChain.Set((ValueString)"a", 11);
secondTestChain = new Chain(12);
secondTestChain.Set((ValueString)"a", 0);
secondTestChain.Set((ValueString)"a", 1);
secondTestChain.Set((ValueString)"a", 2);
secondTestChain.Set((ValueString)"a", 3);
secondTestChain.Set((ValueString)"a", 4);
secondTestChain.Set((ValueString)"a", 5);
secondTestChain.Set((ValueString)"b", 6);
secondTestChain.Set((ValueString)"a", 7);
secondTestChain.Set((ValueString)"a", 8);
secondTestChain.Set((ValueString)"a", 9);
secondTestChain.Set((ValueString)"b", 10);
secondTestChain.Set((ValueString)"a", 11);
}
/// <summary>
/// The compare sequences by subsequences.
/// </summary>
/// <param name="characteristicTypeLinkId">
/// The characteristic type link id.
/// </param>
/// <param name="notationId">
/// The notation id.
/// </param>
/// <param name="firstChains">
/// The first chains.
/// </param>
/// <param name="secondChains">
/// The second chains.
/// </param>
/// <param name="difference">
/// The difference.
/// </param>
/// <param name="excludeType">
/// The exclude type.
/// </param>
/// <returns>
/// The <see cref="double"/>.
/// </returns>
public double CompareSequencesBySubsequences(int characteristicTypeLinkId, int notationId, Chain[] firstChains, Chain[] secondChains, double difference, string excludeType)
{
var firstSequenceCharacteristics = CalculateCharacteristic(characteristicTypeLinkId, firstChains);
var secondSequenceCharacteristics = CalculateCharacteristic(characteristicTypeLinkId, secondChains);
var similarSubsequences = new List<IntPair>();
for (int i = 0; i < firstSequenceCharacteristics.Count; i++)
{
for (int j = 0; j < secondSequenceCharacteristics.Count; j++)
{
if (System.Math.Abs(firstSequenceCharacteristics[i] - secondSequenceCharacteristics[j]) <= difference)
{
similarSubsequences.Add(new IntPair(i, j));
if (excludeType == "Exclude")
{
firstSequenceCharacteristics[i] = double.NaN;
secondSequenceCharacteristics[j] = double.NaN;
}
}
}
}
return similarSubsequences.Count * 200d / (firstChains.Length + secondChains.Length);
}
public void LevelOneTest()
{
var cycleTestChainLevel1 = new Chain("adbaacbbaacaa");
var rebulder = new NullCycleSpaceReorganizer(1);
var result = rebulder.Reorganize(testChain);
Assert.AreEqual(cycleTestChainLevel1, result);
}
public void LevelFiveTest()
{
var cycleTestChainLevel5 = new Chain("adbaacbbaacaadbaa");
var reorganizer = new NullCycleSpaceReorganizer(5);
var result = reorganizer.Reorganize(testChain);
Assert.AreEqual(cycleTestChainLevel5, result);
}
public void ToStringTest()
{
var stringExpected = "abcabccc";
var chain = new Chain(stringExpected);
Assert.AreEqual(stringExpected, chain.ToString());
var baseChain = new BaseChain(stringExpected);
Assert.AreEqual(stringExpected, baseChain.ToString());
}
/// <summary>
/// The calculate characteristics.
/// </summary>
/// <param name="chain">
/// The chain.
/// </param>
/// <param name="characteristic">
/// The characteristic for calculation.
/// </param>
/// <returns>
/// The <see cref="List{Double}"/>.
/// </returns>
private List<double> CalculateCharacteristics(Chain chain, List<LinkedCharacteristic> characteristic)
{
var characteristics = new List<double>(characteristic.Count);
foreach (LinkedCharacteristic calculator in characteristic)
{
characteristics.Add(calculator.Calculator.Calculate(chain, calculator.Link));
}
return characteristics;
}
/// <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;
}
public void Initialize()
{
testChain = new Chain(8);
testChain.Set((ValueString)"A", 0);
testChain.Set((ValueString)"G", 1);
testChain.Set((ValueString)"T", 2);
testChain.Set((ValueString)"A", 3);
testChain.Set((ValueString)"A", 4);
testChain.Set((ValueString)"G", 5);
testChain.Set((ValueString)"T", 6);
testChain.Set((ValueString)"C", 7);
}
public void ToStringDelimiterTest()
{
var source = "abcabccc";
var chain = new Chain(source);
var baseChain = new BaseChain(source);
var expected = "a b c a b c c c";
Assert.AreEqual(expected, chain.ToString(" "));
Assert.AreEqual(expected, baseChain.ToString(" "));
expected = "acbcccacbcccccc";
Assert.AreEqual(expected, chain.ToString("c"));
Assert.AreEqual(expected, baseChain.ToString("c"));
}
public void ToStringLongDelimiterTest()
{
var source = "abcabccc";
var chain = new Chain(source);
var baseChain = new BaseChain(source);
var expected = "a - b - c - a - b - c - c - c";
Assert.AreEqual(expected, chain.ToString(" - "));
Assert.AreEqual(expected, baseChain.ToString(" - "));
expected = "a, b, c, a, b, c, c, c";
Assert.AreEqual(expected, chain.ToString(", "));
Assert.AreEqual(expected, baseChain.ToString(", "));
}
/// <summary>
/// Method that creates chain of "first occurrences of different elements".
/// </summary>
/// <param name="source">
/// Source chain.
/// </param>
/// <returns>/
/// Dissimilar chain.
/// </returns>
public static Chain Create(BaseChain source)
{
var result = new Chain(source.GetLength());
Alphabet sourceAlphabet = source.Alphabet;
var entries = new int[sourceAlphabet.Cardinality];
for (int i = 0; i < source.GetLength(); i++)
{
int elementIndex = sourceAlphabet.IndexOf(source[i]);
int entry = ++entries[elementIndex];
result.Set(new ValueInt(entry), i);
}
return result;
}
/// <summary>
/// The extract chains.
/// </summary>
/// <param name="subsequences">
/// The subsequences.
/// </param>
/// <param name="chainId">
/// The sequence id.
/// </param>
/// <returns>
/// The <see cref="List{Chain}"/>.
/// </returns>
public Chain[] ExtractChains(Subsequence[] subsequences, long chainId)
{
var parentChain = commonSequenceRepository.ToLibiadaBaseChain(chainId).ToString();
var sourceSequence = new Sequence(Alphabets.DNA, parentChain);
var result = new Chain[subsequences.Length];
for (int i = 0; i < subsequences.Length; i++)
{
result[i] = subsequences[i].Position.Count == 0
? ExtractSimpleSubsequence(sourceSequence, subsequences[i])
: ExtractJoinedSubsequence(sourceSequence, subsequences[i]);
}
return result;
}
/// <summary>
/// The is valid.
/// </summary>
/// <param name="building">
/// The building.
/// </param>
/// <returns>
/// true if
/// </returns>
public bool IsValid(string building)
{
var chain = new Chain(building);
var countCalculator = new ElementsCount();
var firstCount = (int)countCalculator.Calculate(chain.CongenericChain(0), Link.Start);
for (int i = 1; i < chain.Alphabet.Cardinality; i++)
{
if (firstCount != (int)countCalculator.Calculate(chain.CongenericChain(i), Link.Start))
{
return false;
}
}
return true;
}
public void CustomIteratorTest()
{
var starts = new List<List<int>> { new List<int> { 0 }, new List<int> { 3 }, new List<int> { 5, 9 } };
var lengthes = new List<List<int>> { new List<int> { 2 }, new List<int> { 3 }, new List<int> { 2, 1 } };
var source = new Chain("abcdefghij");
List<Chain> expected = new List<Chain> { new Chain("ab"), new Chain("def"), new Chain("fgj") };
var iterator = new CustomIterator(source, starts, lengthes);
for (int i = 0; iterator.Next(); i++)
{
Chain result = (Chain)iterator.Current();
Assert.AreEqual(expected[i], result);
}
}
public void GetBinaryIntervalIncompleteChainTest()
{
// A C A _ C C _ A A A C C A
// A _ A _ _ _ _ A A A _ _ A
// _ C _ _ C C _ _ _ _ C C _
var chain = new Chain(13);
chain.Set(elements["A"], 0);
chain.Set(elements["C"], 1);
chain.Set(elements["A"], 2);
chain.Set(elements["C"], 4);
chain.Set(elements["C"], 5);
chain.Set(elements["A"], 7);
chain.Set(elements["A"], 8);
chain.Set(elements["A"], 9);
chain.Set(elements["C"], 10);
chain.Set(elements["C"], 11);
chain.Set(elements["A"], 12);
var intervalManager = chain.GetRelationIntervalsManager(elements["A"], elements["C"]);
Assert.AreEqual(1, intervalManager.GetBinaryInterval(1));
Assert.AreEqual(2, intervalManager.GetBinaryInterval(2));
Assert.AreEqual(-1, intervalManager.GetBinaryInterval(3));
Assert.AreEqual(-1, intervalManager.GetBinaryInterval(4));
Assert.AreEqual(1, intervalManager.GetBinaryInterval(5));
Assert.AreEqual(-1, intervalManager.GetBinaryInterval(6));
Assert.AreEqual(-1, intervalManager.GetBinaryInterval(7));
intervalManager = chain.GetRelationIntervalsManager(elements["C"], elements["A"]);
Assert.AreEqual(1, intervalManager.GetBinaryInterval(1));
Assert.AreEqual(-1, intervalManager.GetBinaryInterval(2));
Assert.AreEqual(2, intervalManager.GetBinaryInterval(3));
Assert.AreEqual(-1, intervalManager.GetBinaryInterval(4));
Assert.AreEqual(1, intervalManager.GetBinaryInterval(5));
Assert.AreEqual(-1, intervalManager.GetBinaryInterval(6));
}
public ActionResult Index(
int[] transformationLinkIds,
int[] transformationIds,
int iterationsCount,
string[] customSequences,
bool localFile,
HttpPostedFileBase[] file)
{
return Action(() =>
{
int sequencesCount = localFile ? Request.Files.Count : customSequences.Length;
var sourceSequences = new string[sequencesCount];
var sequences = new string[sequencesCount];
var names = new string[sequencesCount];
for (int i = 0; i < sequencesCount; i++)
{
if (localFile)
{
var sequenceStream = FileHelper.GetFileStream(file[i]);
var fastaSequence = NcbiHelper.GetFastaSequence(sequenceStream);
sourceSequences[i] = fastaSequence.ConvertToString();
names[i] = fastaSequence.ID;
}
else
{
sourceSequences[i] = customSequences[i];
names[i] = "Custom sequence " + (i + 1) + ". Length: " + customSequences[i].Length;
}
}
for (int k = 0; k < iterationsCount; k++)
{
var sequence = new Chain(sourceSequences[k]);
for (int j = 0; j < iterationsCount; j++)
{
for (int i = 0; i < transformationIds.Length; i++)
{
if (transformationIds[i] == 1)
{
sequence = DissimilarChainFactory.Create(sequence);
}
else
{
sequence = HighOrderFactory.Create(sequence, (Link)transformationLinkIds[i]);
}
}
}
}
var transformations = new Dictionary<int, string>();
for (int i = 0; i < transformationIds.Length; i++)
{
var link = ((Link)transformationLinkIds[i]).GetDisplayValue();
transformations.Add(i, transformationIds[i] == 1 ? "dissimilar" : "higher order " + link);
}
var result = new Dictionary<string, object>
{
{ "names", names },
{ "sequences", sequences },
{ "transformationsList", transformations },
{ "iterationsCount", iterationsCount }
};
return result;
});
}
public void Initialization()
{
chain = new Chain("adbaacbbaaca");
baseChain = new BaseChain("adbaacbbaaca");
}
/// <summary>
/// Extracts nucleotide sequences from database.
/// </summary>
/// <param name="matterIds">
/// The matter ids.
/// </param>
/// <returns>
/// The <see cref="T:Chain[]"/>.
/// </returns>
public Chain[] GetNucleotideChains(long[] matterIds)
{
var chains = new Chain[matterIds.Length];
for (int i = 0; i < matterIds.Length; i++)
{
var matterId = matterIds[i];
var sequenceId = Db.CommonSequence.Single(c => c.MatterId == matterId && c.NotationId == Aliases.Notation.Nucleotide).Id;
chains[i] = ToLibiadaChain(sequenceId);
}
return chains;
}
/// <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;
}
/// <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 void MarkovChainNotCongenericDynamicOneRangTwoTest()
{
// using mock of random generator
IGenerator generator = new MockGenerator();
// rank of markov chain is 2 (each element depends on one previous element)
int markovChainRank = 2;
// heterogeneity is 1 (there are 2 models - for odd and even positions)
int notCongenericRank = 1;
// creating markov chain
// MarkovChainNotCongenericDynamic<Chain, Chain> MarkovChain = new MarkovChainNotCongenericDynamic<Chain, Chain>(markovChainRank, notCongenericRank, generator);
// length of generated sequence
int length = 12;
// teaching markov chain (TeachingMethod.None means there is no preprocessing)
// MarkovChain.Teach(TestChain, TeachingMethod.None);
// Chain Temp = MarkovChain.Generate(length);
/**
* Внутри неоднородной марковской цепи существует n однородных марковских цепей. n - порядок неоднородности цепи
* порядок данных однородных цепей равен порядку неоднородной цепи
* однородные цепи используются по очереди как при обучении так и при генерации.
*
* В данном тесте внутри неоднородной марковской цепи есть 2 однородные цепи.
* Матрицы переходных вероятностей (в скобках указано кол-во входений при обучении) в них такие
*
* 1. Sequence
* first level (unconditional probability)
*
* a| 1/2 (3) |
* b| 1/3 (2) |
* c| 1/6 (1) |
* d| 0 (0) |
*
* second level (conditional probability taking into account 1 previous element)
*
* | a | b | с | d |
* ---|------|------|------|------|
* a |0,3(1)| 0(0) |0,3(1)|0,3(1)|
* ---|------|------|------|------|
* b |0,5(1)|0,5(1)| 0(0) | 0(0) |
* ---|------|------|------|------|
* c | 1(1) | 0(0) | 0(0) | 0(0) |
* ---|------|------|------|------|
* d | 0(0) | 0(0) | 0(0) | 0(0) |
* ---|------|------|------|------|
*
* 2. Sequence
* first level (unconditional probability)
*
* a| 2/5 (2) |
* b| 1/5 (1) |
* c| 1/5 (1) |
* d| 1/5 (1) |
*
* second level (conditional probability taking into account 1 previous element)
*
* | a | b | с | d |
* ---|------|------|------|------|
* a |0,5(1)| 0(0) |0,5(1)| 0(0) |
* ---|------|------|------|------|
* b | 1(1) | 0(0) | 0(0) | 0(0) |
* ---|------|------|------|------|
* c | 0(0) | 1(1) | 0(0) | 0(0) |
* ---|------|------|------|------|
* d | 0(0) | 1(1) | 0(0) | 0(0) |
* ---|------|------|------|------|
*
*
* During teaching pairs are added as folowing
* |-| |-| |-| |-| |-| <>- In second markov chain
* a d b a a c b b a a c a
* |_| |_| |_| |_| |_| |_| <>- In first markov chain
*
*/
// expected result of generation
var result = new Chain(12);
result.Set((ValueString)"b", 0); // 1 chain. вероятность по первому уровню. выпало 0,77 Получаем b
result.Set((ValueString)"a", 1); // 2 chain. вероятность по второму уровню. выпало 0.15 Получаем a
result.Set((ValueString)"c", 2); // 1 chain. вероятность по второму уровню. выпало 0.96 Получаем с
result.Set((ValueString)"b", 3); // 2 chain. вероятность по второму уровню. выпало 0.61 Получаем b
result.Set((ValueString)"a", 4); // 1 chain. вероятность по второму уровню. выпало 0.15 Получаем a
result.Set((ValueString)"c", 5); // 2 chain. вероятность по второму уровню. выпало 0.85 Получаем c
result.Set((ValueString)"a", 6); // 1 chain. вероятность по второму уровню. выпало 0.67 Получаем a
result.Set((ValueString)"c", 7); // 2 chain. вероятность по второму уровню. выпало 0.51 Получаем c
result.Set((ValueString)"a", 8); // 1 chain. вероятность по второму уровню. выпало 0.71 Получаем a
result.Set((ValueString)"a", 9); // 2 chain. вероятность по второму уровню. выпало 0.2 Получаем a
result.Set((ValueString)"c", 10); // 1 chain. вероятность по второму уровню. выпало 0.77 Получаем с
result.Set((ValueString)"b", 11); // 2 chain. вероятность по второму уровню. выпало 0.15 Получаем b
}
/// <summary>
/// Extracts sequences from database.
/// </summary>
/// <param name="matterIds">
/// The matter ids.
/// </param>
/// <param name="notationIds">
/// The notation ids.
/// </param>
/// <param name="languageIds">
/// The language ids.
/// </param>
/// <param name="translatorIds">
/// The translator ids.
/// </param>
/// <returns>
/// The <see cref="T:Chain[][]"/>.
/// </returns>
public Chain[][] GetChains(long[] matterIds, int[] notationIds, int[] languageIds, int?[] translatorIds)
{
var chains = new Chain[matterIds.Length][];
var notationsRepository = new NotationRepository(Db);
for (int i = 0; i < matterIds.Length; i++)
{
var matterId = matterIds[i];
chains[i] = new Chain[notationIds.Length];
for (int j = 0; j < notationIds.Length; j++)
{
Notation notation = notationsRepository.Notations.Single(n => n.Id == notationIds[j]);
long sequenceId;
if (notation.Nature == Nature.Literature)
{
int languageId = languageIds[j];
int? translatorId = translatorIds[j];
sequenceId = Db.LiteratureSequence.Single(l =>
l.MatterId == matterId && l.NotationId == notation.Id
&& l.LanguageId == languageId
&& ((translatorId == null && l.TranslatorId == null)
|| (translatorId == l.TranslatorId))).Id;
}
else
{
sequenceId = Db.CommonSequence.Single(c => c.MatterId == matterId && c.NotationId == notation.Id).Id;
}
chains[i][j] = ToLibiadaChain(sequenceId);
}
}
return chains;
}
public void MarkovChainNotCongenericZeroRankTwoTest()
{
// using mock of random generator
IGenerator generator = new MockGenerator();
// rank of markov chain is 2 (each element depends on one previous element)
const int MarkovChainRank = 2;
// heterogeneity is 1 (there are 2 models - for odd and even positions)
const int NoCongenericRank = 0;
// creating markov chain
var markovChain = new MarkovChainNotCongenericStatic(MarkovChainRank, NoCongenericRank, generator);
// length of generated sequence
const int Length = 30;
// teaching markov chain (TeachingMethod.None means there is no preprocessing)
markovChain.Teach(secondTestChain, TeachingMethod.Cycle);
var temp = markovChain.Generate(Length);
/*
* 1. Sequence a a a a a a b a a a b a
* first level (unconditional probability)
*
* a| 10/12 (0,83333) not more than 0,83333|
* b| 2/12 (0,16667) not more than 1|
*
* second level (conditional probability taking into account 1 previous element)
*
* | a | b |
* ---|------|------|
* a |7/9(7)|2/9(2)|
* ---|------|------|
* b |1,0(1)|0,0(0)|
* ---|------|------|
*/
// expected result of generation
var resultTheory = new Chain(30);
resultTheory[0] = (ValueString)"a"; // "a" 0.77;
resultTheory[1] = (ValueString)"a"; // "a" 0.15;
resultTheory[2] = (ValueString)"b"; // "b" 0.96;
resultTheory[3] = (ValueString)"a"; // "a" 0.61;
resultTheory[4] = (ValueString)"a"; // "a" 0.15;
resultTheory[5] = (ValueString)"b"; // "b" 0.85;
resultTheory[6] = (ValueString)"a"; // "a" 0.67;
resultTheory[7] = (ValueString)"a"; // "a" 0.51;
resultTheory[8] = (ValueString)"a"; // "a" 0.71;
resultTheory[9] = (ValueString)"a"; // "a" 0.2;
resultTheory[10] = (ValueString)"a"; // "a" 0.77;
resultTheory[11] = (ValueString)"a"; // "a" 0.15;
resultTheory[12] = (ValueString)"b"; // "b" 0.96;
resultTheory[13] = (ValueString)"a"; // "a" 0.61;
resultTheory[14] = (ValueString)"a"; // "a" 0.15;
resultTheory[15] = (ValueString)"b"; // "b" 0.85;
resultTheory[16] = (ValueString)"a"; // "a" 0.67;
resultTheory[17] = (ValueString)"a"; // "a" 0.51;
resultTheory[18] = (ValueString)"a"; // "a" 0.71;
resultTheory[19] = (ValueString)"a"; // "a" 0.2;
resultTheory[20] = (ValueString)"a"; // "a" 0.77;
resultTheory[21] = (ValueString)"a"; // "a" 0.15;
resultTheory[22] = (ValueString)"b"; // "b" 0.96;
resultTheory[23] = (ValueString)"a"; // "a" 0.61;
resultTheory[24] = (ValueString)"a"; // "a" 0.15;
resultTheory[25] = (ValueString)"b"; // "b" 0.85;
resultTheory[26] = (ValueString)"a"; // "a" 0.67;
resultTheory[27] = (ValueString)"a"; // "a" 0.51;
resultTheory[28] = (ValueString)"a"; // "a" 0.71;
resultTheory[29] = (ValueString)"a"; // "a" 0.2;
Assert.AreEqual(resultTheory, temp);
}
public ActionResult Index(
int[] transformationLinkIds,
int[] transformationIds,
int iterationsCount,
int[] characteristicTypeLinkIds,
string[] customSequences,
bool localFile,
HttpPostedFileBase[] file)
{
return Action(() =>
{
var db = new LibiadaWebEntities();
var characteristicTypeLinkRepository = new CharacteristicTypeLinkRepository(db);
int sequencesCount = localFile ? Request.Files.Count : customSequences.Length;
var sequences = new string[sequencesCount];
var names = new string[sequencesCount];
for (int i = 0; i < sequencesCount; i++)
{
if (localFile)
{
var sequenceStream = FileHelper.GetFileStream(file[i]);
var fastaSequence = NcbiHelper.GetFastaSequence(sequenceStream);
sequences[i] = fastaSequence.ConvertToString();
names[i] = fastaSequence.ID;
}
else
{
sequences[i] = customSequences[i];
names[i] = "Custom sequence " + (i + 1) + ". Length: " + customSequences[i].Length;
}
}
var characteristics = new double[sequences.Length, characteristicTypeLinkIds.Length];
for (int j = 0; j < sequences.Length; j++)
{
for (int k = 0; k < characteristicTypeLinkIds.Length; k++)
{
var sequence = new Chain(sequences[j]);
for (int l = 0; l < iterationsCount; l++)
{
for (int w = 0; w < transformationIds.Length; w++)
{
if (transformationIds[w] == 1)
{
sequence = DissimilarChainFactory.Create(sequence);
}
else
{
sequence = HighOrderFactory.Create(sequence, (Link)transformationLinkIds[w]);
}
}
}
var link = characteristicTypeLinkRepository.GetLibiadaLink(characteristicTypeLinkIds[k]);
string className = characteristicTypeLinkRepository.GetCharacteristicType(characteristicTypeLinkIds[k]).ClassName;
var calculator = CalculatorsFactory.CreateFullCalculator(className);
characteristics[j, k] = calculator.Calculate(sequence, link);
}
}
var characteristicNames = characteristicTypeLinkIds.Select(c => characteristicTypeLinkRepository.GetCharacteristicName(c)).ToArray();
var characteristicsList = new SelectListItem[characteristicTypeLinkIds.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 < transformationIds.Length; i++)
{
var link = ((Link)transformationLinkIds[i]).GetDisplayValue();
transformations.Add(i, transformationIds[i] == 1 ? "dissimilar" : "higher order " + link);
}
var result = new Dictionary<string, object>
{
{ "characteristics", characteristics },
{ "characteristicNames", characteristicNames },
{ "characteristicsList", characteristicsList },
{ "transformationsList", transformations },
{ "iterationsCount", iterationsCount }
};
return new Dictionary<string, object>
{
{ "data", JsonConvert.SerializeObject(result) }
};
});
}
public void Initialization()
{
testChain = new Chain("adbaacbbaaca");
}
public ActionResult Index(
long[] matterIds,
int[] characteristicTypeLinkIds,
int? languageId,
int? translatorId,
int notationId,
int length,
int step,
bool delta,
bool fourier,
bool growingWindow,
bool autocorrelation)
{
return Action(() =>
{
var characteristicNames = new string[characteristicTypeLinkIds.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 List<IFullCalculator>();
var links = new List<Link>();
matterIds = matterIds.OrderBy(m => m).ToArray();
var matters = db.Matter.Where(m => matterIds.Contains(m.Id)).ToDictionary(m => m.Id);
for (int k = 0; k < matterIds.Length; k++)
{
long matterId = matterIds[k];
Nature nature = db.Matter.Single(m => m.Id == matterId).Nature;
long sequenceId;
switch (nature)
{
case Nature.Literature:
sequenceId = db.LiteratureSequence.Single(l => l.MatterId == matterId
&& l.NotationId == notationId
&& l.LanguageId == languageId
&& l.TranslatorId == translatorId).Id;
break;
default:
var id = notationId;
sequenceId = db.CommonSequence.Single(c => c.MatterId == matterId
&& c.NotationId == id).Id;
break;
}
chains[k] = commonSequenceRepository.ToLibiadaChain(sequenceId);
}
foreach (int characteristicTypeLinkId in characteristicTypeLinkIds)
{
string className = characteristicTypeLinkRepository.GetCharacteristicType(characteristicTypeLinkId).ClassName;
calculators.Add(CalculatorsFactory.CreateFullCalculator(className));
links.Add(characteristicTypeLinkRepository.GetLibiadaLink(characteristicTypeLinkId));
}
for (int i = 0; i < chains.Length; i++)
{
CutRule cutRule = growingWindow
? (CutRule)new CutRuleWithFixedStart(chains[i].GetLength(), step)
: new SimpleCutRule(chains[i].GetLength(), step, length);
CutRuleIterator iter = cutRule.GetIterator();
List<Chain> fragments = new List<Chain>();
partNames[i] = new List<string>();
starts[i] = new List<int>();
lengthes[i] = new List<int>();
while (iter.Next())
{
var fragment = new Chain(iter.GetEndPosition() - iter.GetStartPosition());
for (int k = 0; iter.GetStartPosition() + k < iter.GetEndPosition(); k++)
{
fragment.Set(chains[i][iter.GetStartPosition() + k], k);
}
fragments.Add(fragment);
partNames[i].Add(fragment.ToString());
starts[i].Add(iter.GetStartPosition());
lengthes[i].Add(fragment.GetLength());
}
var fragmentsData = new FragmentData[fragments.Count];
for (int k = 0; k < fragments.Count; k++)
{
var characteristics = new double[calculators.Count];
for (int j = 0; j < calculators.Count; j++)
{
characteristics[j] = calculators[j].Calculate(fragments[k], links[j]);
}
fragmentsData[k] = new FragmentData(characteristics, fragments[k].ToString(), starts[i][k], fragments[k].GetLength());
}
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 { matterName = matters[matterIds[i]].Name, fragmentsData, differenceData, fourierData, autocorrelationData };
}
for (int l = 0; l < characteristicTypeLinkIds.Length; l++)
{
characteristicNames[l] = characteristicTypeLinkRepository.GetCharacteristicType(characteristicTypeLinkIds[l]).Name;
}
var characteristicsList = new SelectListItem[characteristicTypeLinkIds.Length];
for (int k = 0; k < characteristicTypeLinkIds.Length; k++)
{
characteristicNames[k] = characteristicTypeLinkRepository.GetCharacteristicName(characteristicTypeLinkIds[k], notationId);
characteristicsList[k] = new SelectListItem
{
Value = k.ToString(),
Text = characteristicNames[k],
Selected = false
};
}
string notationName = db.Notation.Single(n => n.Id == notationId).Name;
var result = new Dictionary<string, object>
{
{ "characteristics", mattersCharacteristics },
{ "notationName", notationName },
{ "starts", starts },
{ "partNames", partNames },
{ "lengthes", lengthes },
{ "characteristicNames", characteristicNames },
{ "matterIds", matterIds },
{ "characteristicsList", characteristicsList }
};
return new Dictionary<string, object> { { "data", JsonConvert.SerializeObject(result) } };
});
}
/// <summary>
/// The calculate.
/// </summary>
/// <param name="chain">
/// The chain.
/// </param>
/// <returns>
/// The <see cref="bool"/>.
/// </returns>
/// <exception cref="Exception">
/// Thrown if chain doesn't contain fmotives.
/// </exception>
private static bool Calculate(FmotivChain chain)
{
if (chain.FmotivList.Count < 1)
{
throw new Exception("Unable to count note remoteness with no elements in chain!");
}
var noteList = new List<ValueNote>(); // список нот, класса Note, всей цепи фмотивов
foreach (Fmotiv fmotiv in chain.FmotivList)
{
foreach (ValueNote note in fmotiv.TieGathered().PauseTreatment((int)ParamPauseTreatment.Ignore).NoteList)
{
noteList.Add((ValueNote)note.Clone());
}
}
var noteChain = new Chain(noteList.Count);
for (int i = 0; i < noteList.Count; i++)
{
string temp = string.Empty; // строка для временного хранения набора высот
foreach (Pitch pitch in noteList[i].Pitch)
{
temp += Convert.ToString(pitch.MidiNumber);
}
// TODO: переделать нормально чтоб цепочка складывалась из ValueNote, а не как попало
noteChain[i] = new ValueString(temp + " " + Convert.ToString(noteList[i].Duration.Value * 10000000));
}
valR = new AverageRemoteness().Calculate(noteChain, Link.End);
valG = new Depth().Calculate(noteChain, Link.End);
return true;
}
/// <summary>
/// The make new chain.
/// </summary>
/// <returns>
/// The <see cref="Chain"/>.
/// </returns>
public Chain MakeNewChain()
{
var newChain = new Chain(range.Length);
for (int i = 0; i < range.Length; i++)
{
newChain[i] = new ValueInt(range.Data[i].Id);
}
chain = (Chain)newChain.Clone();
return newChain;
}
