public ActionResult Index(IEnumerable <long> matterIds, string transformType)
{
Notation notation = transformType.Equals("toAmino") ? Notation.AminoAcids : Notation.Triplets;
foreach (var matterId in matterIds)
{
var sequenceId = db.CommonSequence.Single(c => c.MatterId == matterId && c.Notation == Notation.Nucleotides).Id;
Chain sourceChain = commonSequenceRepository.GetLibiadaChain(sequenceId);
BaseChain transformedChain = transformType.Equals("toAmino")
? DnaTransformer.EncodeAmino(sourceChain)
: DnaTransformer.EncodeTriplets(sourceChain);
var result = new DnaSequence
{
MatterId = matterId,
Notation = notation
};
long[] alphabet = elementRepository.ToDbElements(transformedChain.Alphabet, notation, false);
dnaSequenceRepository.Insert(result, alphabet, transformedChain.Building);
}
return(RedirectToAction("Index", "CommonSequences"));
}
public ActionResult Index(long matterId,
Notation notation,
Language?language,
Translator?translator,
PauseTreatment?pauseTreatment,
bool?sequentialTransfer,
int scrambling)
{
Matter matter = Cache.GetInstance().Matters.Single(m => m.Id == matterId);
long sequenceId;
switch (matter.Nature)
{
case Nature.Literature:
sequenceId = db.LiteratureSequence.Single(l => l.MatterId == matterId &&
l.Notation == notation &&
l.Language == language &&
l.Translator == translator).Id;
break;
case Nature.Music:
sequenceId = db.MusicSequence.Single(m => m.MatterId == matterId &&
m.Notation == notation &&
m.PauseTreatment == pauseTreatment &&
m.SequentialTransfer == sequentialTransfer).Id;
break;
default:
sequenceId = db.CommonSequence.Single(c => c.MatterId == matterId && c.Notation == notation).Id;
break;
}
BaseChain chain = sequenceRepository.GetLibiadaBaseChain(sequenceId);
for (int i = 0; i < scrambling; i++)
{
int firstIndex = randomGenerator.Next(chain.Length);
int secondIndex = randomGenerator.Next(chain.Length);
IBaseObject firstElement = chain[firstIndex];
IBaseObject secondElement = chain[secondIndex];
chain[firstIndex] = secondElement;
chain[secondIndex] = firstElement;
}
var resultMatter = new Matter
{
Nature = matter.Nature,
Name = $"{matter.Name} {scrambling} mixes"
};
MatterRepository matterRepository = new MatterRepository(db);
matterRepository.SaveToDatabase(resultMatter);
var result = new CommonSequence
{
Notation = notation,
MatterId = resultMatter.Id
};
long[] alphabet = elementRepository.ToDbElements(chain.Alphabet, notation, false);
switch (matter.Nature)
{
case Nature.Genetic:
DnaSequence dnaSequence = db.DnaSequence.Single(c => c.Id == sequenceId);
dnaSequenceRepository.Create(result, dnaSequence.Partial, alphabet, chain.Building);
break;
case Nature.Music:
musicSequenceRepository.Create(result, alphabet, chain.Building);
break;
case Nature.Literature:
LiteratureSequence sequence = db.LiteratureSequence.Single(c => c.Id == sequenceId);
literatureSequenceRepository.Create(result, sequence.Original, sequence.Language, sequence.Translator, alphabet, chain.Building);
break;
case Nature.MeasurementData:
dataSequenceRepository.Create(result, alphabet, chain.Building);
break;
default:
throw new InvalidEnumArgumentException(nameof(matter.Nature), (int)matter.Nature, typeof(Nature));
}
return(RedirectToAction("Index", "Matters"));
}
/// <summary>
/// The index.
/// </summary>
/// <returns>
/// The <see cref="ActionResult"/>.
/// </returns>
public ActionResult Index()
{
using (var db = new LibiadaWebEntities())
{
var matterRepository = new MatterRepository(db);
var dnaSequenceRepository = new GeneticSequenceRepository(db);
var commonSequenceRepository = new CommonSequenceRepository(db);
var elementRepository = new ElementRepository(db);
var matterIds = new long[] { 1332, 1333, 1339, 1330, 1337, 1342, 1331, 1338, 1340, 1943, 1945, 1334 };
DnaSequence[] sequences = db.DnaSequence.Include(d => d.Matter).Where(d => matterIds.Contains(d.MatterId)).ToArray();
for (int i = 0; i < sequences.Length; i++)
{
var newMatter = new Matter
{
Name = $"{sequences[i].Matter.Name} Cleaned of IS110",
Description = sequences[i].Matter.Description,
Nature = sequences[i].Matter.Nature,
Group = sequences[i].Matter.Group,
SequenceType = sequences[i].Matter.SequenceType
};
var newSequence = new CommonSequence
{
Notation = sequences[i].Notation,
Matter = newMatter,
Description = sequences[i].Description,
RemoteDb = sequences[i].RemoteDb,
RemoteId = sequences[i].RemoteId
};
var chain = commonSequenceRepository.GetLibiadaChain(sequences[i].Id);
matterRepository.CreateOrExtractExistingMatterForSequence(newSequence);
dnaSequenceRepository.Create(newSequence, false, elementRepository.ToDbElements(chain.Alphabet, Notation.Nucleotides, false), chain.Building);
var sequenceId = sequences[i].Id;
var subsequences = db.Subsequence.Include(s => s.Position).Include(s => s.SequenceAttribute).Where(s => s.SequenceId == sequenceId).ToList();
var subsequenceIds = subsequences.Select(s => s.Id);
var subsequencesIdsToRemove = db.SequenceAttribute
.Where(sa => subsequenceIds.Contains(sa.SequenceId) && sa.Value.Contains("IS110"))
.Select(sa => sa.SequenceId)
.Distinct()
.ToArray();
subsequences.RemoveAll(s => subsequencesIdsToRemove.Contains(s.Id));
var newSubsequences = new Subsequence[subsequences.Count];
var newSequenceAttributes = new List <SequenceAttribute>();
var newPositions = new List <Position>();
for (int j = 0; j < subsequences.Count; j++)
{
newSubsequences[j] = new Subsequence
{
Id = db.GetNewElementId(),
Feature = subsequences[j].Feature,
SequenceId = newSequence.Id,
Start = subsequences[j].Start,
Length = subsequences[j].Length,
RemoteId = subsequences[j].RemoteId,
Partial = subsequences[j].Partial
};
foreach (SequenceAttribute subsequenceAttribute in subsequences[j].SequenceAttribute.ToArray())
{
newSequenceAttributes.Add(new SequenceAttribute
{
SequenceId = newSubsequences[j].Id,
Attribute = subsequenceAttribute.Attribute,
Value = subsequenceAttribute.Value
});
}
foreach (Position position in subsequences[j].Position.ToArray())
{
newPositions.Add(new Position
{
SubsequenceId = newSubsequences[j].Id,
Length = position.Length,
Start = position.Start
});
}
}
db.Subsequence.AddRange(newSubsequences);
db.SequenceAttribute.AddRange(newSequenceAttributes);
db.Position.AddRange(newPositions);
db.SaveChanges();
}
}
return(View());
}