/// <summary>
/// Initializes a new instance of the <see cref="SequenceTransformerController"/> class.
/// </summary>
public SequenceTransformerController()
{
db = new LibiadaWebEntities();
dnaSequenceRepository = new DnaSequenceRepository(db);
commonSequenceRepository = new CommonSequenceRepository(db);
elementRepository = new ElementRepository(db);
}
/// <summary>
/// Initializes a new instance of the <see cref="LocalCalculationController"/> class.
/// </summary>
public LocalCalculationController()
: base("Local calculation")
{
db = new LibiadaWebEntities();
commonSequenceRepository = new CommonSequenceRepository(db);
characteristicTypeLinkRepository = new CharacteristicTypeLinkRepository(db);
}
public ActionResult Index(long[] matterIds, int characteristicTypeLinkId, int[] characteristicTypeLinkIds, int[] featureIds)
{
return Action(() =>
{
var matterNames = new string[matterIds.Length];
var remoteIds = new string[matterIds.Length];
var subsequencesCharacteristicsNames = new string[characteristicTypeLinkIds.Length];
var calculators = new IFullCalculator[characteristicTypeLinkIds.Length];
var links = new Link[characteristicTypeLinkIds.Length];
var subsequencesCharacteristicsList = new SelectListItem[characteristicTypeLinkIds.Length];
var attributeValues = new List<AttributeValue>();
IEnumerable<SelectListItem> featuresSelectList;
Chain[] chains;
long[] parentSequenceIds;
string sequenceCharacteristicName;
IFullCalculator calculator;
Link link;
using (var db = new LibiadaWebEntities())
{
var featureRepository = new FeatureRepository(db);
featuresSelectList = featureRepository.GetFeaturesById(featureIds).Select(f => new SelectListItem { Value = f.Id.ToString(), Text = f.Name, Selected = true });
var parentSequences = db.DnaSequence.Include(s => s.Matter)
.Where(s => s.NotationId == Aliases.Notation.Nucleotide && 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;
}
var commonSequenceRepository = new CommonSequenceRepository(db);
chains = commonSequenceRepository.GetNucleotideChains(matterIds);
var characteristicTypeLinkRepository = new CharacteristicTypeLinkRepository(db);
sequenceCharacteristicName = characteristicTypeLinkRepository.GetCharacteristicName(characteristicTypeLinkId);
calculator = CalculatorsFactory.CreateFullCalculator(characteristicTypeLinkRepository.GetCharacteristicType(characteristicTypeLinkId).ClassName);
link = characteristicTypeLinkRepository.GetLibiadaLink(characteristicTypeLinkId);
for (int k = 0; k < characteristicTypeLinkIds.Length; k++)
{
links[k] = characteristicTypeLinkRepository.GetLibiadaLink(characteristicTypeLinkIds[k]);
string className = characteristicTypeLinkRepository.GetCharacteristicType(characteristicTypeLinkIds[k]).ClassName;
calculators[k] = CalculatorsFactory.CreateFullCalculator(className);
subsequencesCharacteristicsNames[k] = characteristicTypeLinkRepository.GetCharacteristicName(characteristicTypeLinkIds[k]);
subsequencesCharacteristicsList[k] = new SelectListItem
{
Value = k.ToString(),
Text = subsequencesCharacteristicsNames[k],
Selected = false
};
}
}
var characteristics = SequencesCharacteristicsCalculator.Calculate(chains, calculator, link, characteristicTypeLinkId);
var sequenceData = new SequenceData[parentSequenceIds.Length];
for (int i = 0; i < parentSequenceIds.Length; i++)
{
// all subsequence calculations
var subsequencesData = SubsequencesCharacteristicsCalculator.CalculateSubsequencesCharacteristics(
characteristicTypeLinkIds,
featureIds,
parentSequenceIds[i],
calculators,
links,
attributeValues);
sequenceData[i] = new SequenceData(matterIds[i], matterNames[i], remoteIds[i], characteristics[i], subsequencesData);
}
// sorting organisms by their characteristic
sequenceData = sequenceData.OrderBy(r => r.Characteristic).ToArray();
var resultData = new Dictionary<string, object>
{
{ "result", sequenceData },
{ "subsequencesCharacteristicsNames", subsequencesCharacteristicsNames },
{ "subsequencesCharacteristicsList", subsequencesCharacteristicsList },
{ "sequenceCharacteristicName", sequenceCharacteristicName },
{ "features", featuresSelectList.ToDictionary(f => f.Value) },
{ "attributes", EnumExtensions.ToArray<Attribute>().ToDictionary(a => (byte)a, a => a.GetDisplayValue()) },
{ "attributeValues", attributeValues.Select(sa => new { attribute = sa.AttributeId, value = sa.Value }) }
};
return new Dictionary<string, object>
{
{ "data", JsonConvert.SerializeObject(resultData) }
};
});
}
/// <summary>
/// Initializes a new instance of the <see cref="BuildingsSimilarityController"/> class.
/// </summary>
public BuildingsSimilarityController()
: base("Buildings comparison")
{
db = new LibiadaWebEntities();
sequenceRepository = new CommonSequenceRepository(db);
}
public ActionResult Index(
long[] matterIds,
int[] characteristicTypeLinkIds,
int[] notationIds,
int[] languageIds,
int?[] translatorIds,
bool rotate,
bool complementary,
uint? rotationLength)
{
return Action(() =>
{
var sequencesCharacteristics = new SequenceCharacteristics[matterIds.Length];
var characteristicNames = new string[characteristicTypeLinkIds.Length];
var characteristicsList = new SelectListItem[characteristicTypeLinkIds.Length];
var links = new Link[characteristicTypeLinkIds.Length];
var calculators = new IFullCalculator[characteristicTypeLinkIds.Length];
Dictionary<long, string> mattersNames;
double[][] characteristics;
Chain[][] chains;
using (var db = new LibiadaWebEntities())
{
mattersNames = db.Matter.Where(m => matterIds.Contains(m.Id)).ToDictionary(m => m.Id, m => m.Name);
var commonSequenceRepository = new CommonSequenceRepository(db);
chains = commonSequenceRepository.GetChains(matterIds, notationIds, languageIds, translatorIds);
var characteristicTypeLinkRepository = new CharacteristicTypeLinkRepository(db);
for (int k = 0; k < characteristicTypeLinkIds.Length; k++)
{
links[k] = characteristicTypeLinkRepository.GetLibiadaLink(characteristicTypeLinkIds[k]);
string className = characteristicTypeLinkRepository.GetCharacteristicType(characteristicTypeLinkIds[k]).ClassName;
calculators[k] = CalculatorsFactory.CreateFullCalculator(className);
characteristicNames[k] = characteristicTypeLinkRepository.GetCharacteristicName(characteristicTypeLinkIds[k], notationIds[k]);
characteristicsList[k] = new SelectListItem
{
Value = k.ToString(),
Text = characteristicNames[k],
Selected = false
};
}
}
if (!rotate && !complementary)
{
characteristics = SequencesCharacteristicsCalculator.Calculate(chains, calculators, links, characteristicTypeLinkIds);
}
else
{
characteristics = SequencesCharacteristicsCalculator.Calculate(chains, calculators, links, rotate, complementary, rotationLength);
}
for (int i = 0; i < matterIds.Length; i++)
{
sequencesCharacteristics[i] = new SequenceCharacteristics
{
MatterName = mattersNames[matterIds[i]],
Characteristics = characteristics[i]
};
}
var result = new Dictionary<string, object>
{
{ "characteristics", sequencesCharacteristics },
{ "characteristicNames", characteristicNames },
{ "characteristicsList", characteristicsList }
};
return new Dictionary<string, object>
{
{ "data", JsonConvert.SerializeObject(result) }
};
});
}
/// <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>
/// Initializes a new instance of the <see cref="OrderTransformerController"/> class.
/// </summary>
public OrderTransformerController()
: base("Order transformation")
{
db = new LibiadaWebEntities();
commonSequenceRepository = new CommonSequenceRepository(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();
}
public ActionResult Index(
long[] matterIds,
int[] transformationLinkIds,
int[] transformationIds,
int iterationsCount,
int[] characteristicTypeLinkIds,
int[] notationIds,
int[] languageIds,
int?[] translatorIds)
{
return Action(() =>
{
var db = new LibiadaWebEntities();
var characteristicTypeLinkRepository = new CharacteristicTypeLinkRepository(db);
var commonSequenceRepository = new CommonSequenceRepository(db);
var mattersCharacteristics = new object[matterIds.Length];
matterIds = matterIds.OrderBy(m => m).ToArray();
var matters = db.Matter.Where(m => matterIds.Contains(m.Id)).ToDictionary(m => m.Id);
for (int i = 0; i < matterIds.Length; i++)
{
var matterId = matterIds[i];
var characteristics = new List<double>();
for (int k = 0; k < notationIds.Length; k++)
{
int notationId = notationIds[k];
long sequenceId;
if (matters[matterId].Nature == Nature.Literature)
{
int languageId = languageIds[k];
int? translatorId = translatorIds[k];
sequenceId = db.LiteratureSequence.Single(l => l.MatterId == matterId &&
l.NotationId == notationId
&& l.LanguageId == languageId
&&
((translatorId == null &&
l.TranslatorId == null)
|| (translatorId == l.TranslatorId))).Id;
}
else
{
sequenceId = db.CommonSequence.Single(c => c.MatterId == matterId && c.NotationId == notationId).Id;
}
var sequence = commonSequenceRepository.ToLibiadaChain(sequenceId);
for (int l = 0; l < iterationsCount; l++)
{
for (int j = 0; j < transformationIds.Length; j++)
{
if (transformationIds[j] == 1)
{
sequence = DissimilarChainFactory.Create(sequence);
}
else
{
sequence = HighOrderFactory.Create(sequence, (LibiadaCore.Core.Link)transformationLinkIds[j]);
}
}
}
int characteristicTypeLinkId = characteristicTypeLinkIds[k];
var link = characteristicTypeLinkRepository.GetLibiadaLink(characteristicTypeLinkId);
string className = characteristicTypeLinkRepository.GetCharacteristicType(characteristicTypeLinkId).ClassName;
IFullCalculator calculator = CalculatorsFactory.CreateFullCalculator(className);
characteristics.Add(calculator.Calculate(sequence, link));
}
mattersCharacteristics[i] = new { matterName = matters[matterId].Name, characteristics };
}
var characteristicNames = new string[characteristicTypeLinkIds.Length];
for (int k = 0; k < characteristicTypeLinkIds.Length; k++)
{
characteristicNames[k] = characteristicTypeLinkRepository.GetCharacteristicName(characteristicTypeLinkIds[k], notationIds[k]);
}
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 = ((LibiadaCore.Core.Link)transformationLinkIds[i]).GetDisplayValue();
transformations.Add(i, transformationIds[i] == 1 ? "dissimilar" : "higher order " + link);
}
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) }
};
});
}
/// <summary>
/// Initializes a new instance of the <see cref="SequenceCheckController"/> class.
/// </summary>
public SequenceCheckController()
: base("Sequence check")
{
db = new LibiadaWebEntities();
commonSequenceRepository = new CommonSequenceRepository(db);
}
/// <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);
}
