/// <summary>
/// Initializes a new instance of the <see cref="SubsequencesSimilarityController"/> class.
/// </summary>
public SubsequencesSimilarityController()
: base("Subsequences similarity")
{
db = new LibiadaWebEntities();
subsequenceExtractor = new SubsequenceExtractor(db);
characteristicTypeLinkRepository = new CharacteristicTypeLinkRepository(db);
sequenceAttributeRepository = new SequenceAttributeRepository(db);
}
/// <summary>
/// Initializes a new instance of the <see cref="SubsequenceImporter"/> class.
/// </summary>
/// <param name="features">
/// The features.
/// </param>
/// <param name="sequenceId">
/// The sequence id.
/// </param>
public SubsequenceImporter(List<FeatureItem> features, long sequenceId)
{
this.features = features;
this.sequenceId = sequenceId;
featureRepository = new FeatureRepository(db);
sequenceAttributeRepository = new SequenceAttributeRepository(db);
using (var commonSequenceRepository = new CommonSequenceRepository(db))
{
var parentSequence = commonSequenceRepository.ToLibiadaBaseChain(sequenceId);
parentLength = parentSequence.GetLength();
}
gene = featureRepository.GetFeatureById(Aliases.Feature.Gene).Type;
sourceLength = features[0].Location.LocationEnd;
positionsMap = new bool[parentLength];
allNonGenesLeafLocations = features.Where(f => f.Key != gene)
.Select(f => f.Location.GetLeafLocations())
.ToArray();
}
/// <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;
}
}