/// <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);
}
/// <summary>
/// Retrieves attributes values of given subsequences from database.
/// </summary>
/// <param name="subsequenceIds">
/// Ids of subsequences which attributes values are to be retrieved.
/// </param>
/// <returns>
/// Dictionary containing subsequences ids as keys and attributes values as values.
/// </returns>
private Dictionary <long, AttributeValue[]> GetSubsequencesAttributesValues(long[] subsequenceIds)
{
using (var db = new LibiadaWebEntities())
{
var sequenceAttributeRepository = new SequenceAttributeRepository(db);
return(sequenceAttributeRepository.GetAttributes(subsequenceIds));
}
}
/// <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>
/// <exception cref="Exception">
/// thrown if length of sequence from database
/// is not equal to the length of downloaded sequence.
/// </exception>
public SubsequenceImporter(List <FeatureItem> features, long sequenceId)
{
this.features = features;
this.sequenceId = sequenceId;
sequenceAttributeRepository = new SequenceAttributeRepository(db);
allNonGenesLeafLocations = features.Where(f => f.Key != gene)
.Select(f => f.Location.GetLeafLocations())
.ToArray();
int parentLength = db.GetSequenceLength(sequenceId);
int sourceLength = features[0].Location.LocationEnd;
positionsMap = new bool[parentLength];
if (parentLength != sourceLength)
{
throw new Exception($"Local and loaded sequence length are not equal. Local length: {parentLength}, loaded length: {sourceLength}");
}
}
