/// <summary>
/// Initializes a new instance of the <see cref="SubsequencesSimilarityController"/> class.
/// </summary>
public SubsequencesSimilarityController() : base(TaskType.SubsequencesSimilarity)
{
db = new LibiadaWebEntities();
subsequenceExtractor = new SubsequenceExtractor(db);
characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
sequenceAttributeRepository = new SequenceAttributeRepository(db);
}
public ActionResult Index(long[] matterIds, short[] characteristicLinkIds, Feature[] features)
{
return(CreateTask(() =>
{
var sequencesData = new SequenceData[matterIds.Length];
long[] parentSequenceIds;
var matterNames = new string[matterIds.Length];
var remoteIds = new string[matterIds.Length];
var subsequencesCharacteristicsNames = new string[characteristicLinkIds.Length];
var subsequencesCharacteristicsList = new SelectListItem[characteristicLinkIds.Length];
using (var db = new LibiadaWebEntities())
{
var parentSequences = db.DnaSequence.Include(s => s.Matter)
.Where(s => s.Notation == Notation.Nucleotides && 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;
}
}
FullCharacteristicRepository characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
for (int k = 0; k < characteristicLinkIds.Length; k++)
{
subsequencesCharacteristicsNames[k] = characteristicTypeLinkRepository.GetCharacteristicName(characteristicLinkIds[k]);
subsequencesCharacteristicsList[k] = new SelectListItem
{
Value = k.ToString(),
Text = subsequencesCharacteristicsNames[k],
Selected = false
};
}
// TODO: Maybe AttributesValueCache should be created in the Subsequences calculator
var attributeValuesCache = new AttributeValueCacheManager();
for (int i = 0; i < parentSequenceIds.Length; i++)
{
var subsequencesData = CalculateSubsequencesCharacteristics(characteristicLinkIds, features, parentSequenceIds[i]);
attributeValuesCache.FillAttributeValues(subsequencesData);
sequencesData[i] = new SequenceData(matterIds[i], matterNames[i], remoteIds[i], default, subsequencesData);
/// <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;
}
/// <summary>
/// Initializes a new instance of the <see cref="OrderCalculationController"/> class.
/// </summary>
public OrderCalculationController() : base(TaskType.OrderCalculation)
{
characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
}
public ActionResult Index(
long[] matterIds,
short characteristicLinkId,
short subsequencesCharacteristicLinkId,
Feature[] features,
string maxPercentageDifference,
string[] filters)
{
return(CreateTask(() =>
{
double percentageDifference = double.Parse(maxPercentageDifference, CultureInfo.InvariantCulture) / 100;
var attributeValuesCache = new AttributeValueCacheManager();
var characteristics = new SubsequenceData[matterIds.Length][];
long[] parentSequenceIds;
var matterNames = new string[matterIds.Length];
int mattersCount = matterIds.Length;
Dictionary <string, object> characteristicsTypesData;
using (var db = new LibiadaWebEntities())
{
// Sequences characteristic
var geneticSequenceRepository = new GeneticSequenceRepository(db);
long[] chains = geneticSequenceRepository.GetNucleotideSequenceIds(matterIds);
// Sequences characteristic
matterIds = OrderMatterIds(matterIds, characteristicLinkId, chains);
// Subsequences characteristics
var parentSequences = db.DnaSequence.Include(s => s.Matter)
.Where(s => s.Notation == Notation.Nucleotides && matterIds.Contains(s.MatterId))
.Select(s => new { s.Id, s.MatterId, MatterName = s.Matter.Name })
.ToDictionary(s => s.Id);
parentSequenceIds = parentSequences
.OrderBy(ps => Array.IndexOf(matterIds, ps.Value.MatterId))
.Select(ps => ps.Key)
.ToArray();
for (int n = 0; n < parentSequenceIds.Length; n++)
{
matterNames[n] = parentSequences[parentSequenceIds[n]].MatterName;
}
var viewDataHelper = new ViewDataHelper(db);
characteristicsTypesData = viewDataHelper.GetCharacteristicsData(CharacteristicCategory.Full);
}
FullCharacteristicRepository fullCharacteristicRepository = FullCharacteristicRepository.Instance;
string sequenceCharacteristicName = fullCharacteristicRepository.GetCharacteristicName(characteristicLinkId);
string characteristicName = fullCharacteristicRepository.GetCharacteristicName(subsequencesCharacteristicLinkId);
var characteristicValueSubsequences = new Dictionary <double, List <(int matterIndex, int subsequenceIndex)> >();
// cycle through matters
for (int i = 0; i < mattersCount; i++)
{
SubsequenceData[] subsequencesData = CalculateSubsequencesCharacteristics(
new[] { subsequencesCharacteristicLinkId },
features,
parentSequenceIds[i],
filters);
characteristics[i] = subsequencesData;
attributeValuesCache.FillAttributeValues(subsequencesData);
for (int j = 0; j < subsequencesData.Length; j++)
{
double value = subsequencesData[j].CharacteristicsValues[0];
if (characteristicValueSubsequences.TryGetValue(value, out List <(int matterIndex, int subsequenceIndex)> matterAndSubsequenceIdsList))
{
matterAndSubsequenceIdsList.Add((i, j));
}
/// <summary>
/// Initializes a new instance of the <see cref="CustomSequenceCalculationController"/> class.
/// </summary>
public CustomSequenceCalculationController() : base(TaskType.CustomSequenceCalculation)
{
characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
}
/// <summary>
/// Initializes a new instance of the <see cref="SequencesAlignmentController"/> class.
/// </summary>
public SequencesAlignmentController() : base(TaskType.SequencesAlignment)
{
characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
}
/// <summary>
/// Initializes a new instance of the <see cref="IntervalsCharacteristicsDistributionController"/> class.
/// </summary>
public IntervalsCharacteristicsDistributionController() : base(TaskType.IntervalsCharacteristicsDistribution)
{
characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
}
