/// <summary>
/// Creates literature sequence in database.
/// </summary>
/// <param name="commonSequence">
/// The common sequence.
/// </param>
/// <param name="sequenceStream">
/// The sequence stream.
/// </param>
/// <param name="language">
/// The language id.
/// </param>
/// <param name="original">
/// The original.
/// </param>
/// <param name="translator">
/// The translator id.
/// </param>
/// <param name="dropPunctuation">
/// Flag indicating if punctuation should be removed from text.
/// </param>
public void Create(CommonSequence commonSequence, Stream sequenceStream, Language language, bool original, Translator translator, bool dropPunctuation = false)
{
string stringSequence = FileHelper.ReadSequenceFromStream(sequenceStream);
BaseChain chain;
if (commonSequence.Notation == Notation.Letters)
{
stringSequence = stringSequence.ToUpper();
if (dropPunctuation)
{
stringSequence = new string(stringSequence.Where(c => !char.IsPunctuation(c)).ToArray());
}
chain = new BaseChain(stringSequence);
}
else
{
// file always contains empty string at the end
// TODO: rewrite this, add empty string check at the end or write a normal trim
string[] text = stringSequence.Split(new[] { '\n', '\r', ' ', '\t' }, StringSplitOptions.RemoveEmptyEntries);
chain = new BaseChain(text.Select(e => (ValueString)e).Cast <IBaseObject>().ToList());
}
MatterRepository.CreateOrExtractExistingMatterForSequence(commonSequence);
long[] alphabet = ElementRepository.ToDbElements(chain.Alphabet, commonSequence.Notation, true);
Create(commonSequence, original, language, translator, alphabet, chain.Building);
}
/// <summary>
/// Create data sequence and matter.
/// </summary>
/// <param name="sequence">
/// The common sequence.
/// </param>
/// <param name="sequenceStream">
/// The sequence stream.
/// </param>
/// <param name="precision">
/// Precision of data sequence.
/// </param>
public void Create(CommonSequence sequence, Stream sequenceStream, int precision)
{
string stringSequence = FileHelper.ReadSequenceFromStream(sequenceStream);
string[] text = stringSequence.Split(new[] { '\n', '\r' }, StringSplitOptions.RemoveEmptyEntries);
string[] cleanedSequence = text.Where(t => !t.Equals("\"volume\"") && !string.IsNullOrEmpty(t) && !string.IsNullOrWhiteSpace(t)).ToArray();
var elements = new List <IBaseObject>(cleanedSequence.Length);
for (int i = 0; i < cleanedSequence.Length; i++)
{
string element = cleanedSequence[i];
if (element.Substring(element.Length - 2, 2).Equals(".0"))
{
cleanedSequence[i] = cleanedSequence[i].Substring(0, cleanedSequence[i].Length - 2);
}
int intElement = int.Parse(cleanedSequence[i]);
int multiplier = (int)Math.Pow(10, precision);
intElement /= multiplier;
intElement *= multiplier;
elements.Add(new ValueInt(intElement));
}
var chain = new BaseChain(elements);
MatterRepository.CreateOrExtractExistingMatterForSequence(sequence);
long[] alphabet = ElementRepository.ToDbElements(chain.Alphabet, sequence.Notation, true);
Create(sequence, alphabet, chain.Building);
}
/// <summary>
/// Initializes a new instance of the <see cref="ViewDataHelper"/> class.
/// </summary>
/// <param name="db">
/// The db.
/// </param>
public ViewDataHelper(LibiadaWebEntities db)
{
this.db = db;
matterRepository = new MatterRepository(db);
notationRepository = new NotationRepository(db);
featureRepository = new FeatureRepository(db);
characteristicTypeLinkRepository = new CharacteristicTypeLinkRepository(db);
remoteDbRepository = new RemoteDbRepository(db);
}
/// <summary>
/// The create.
/// </summary>
/// <param name="sequence">
/// The sequence.
/// </param>
/// <param name="sequenceStream">
/// The sequence stream.
/// </param>
/// <exception cref="Exception">
/// Thrown if congeneric tracks count not equals 1 (track is not monophonic).
/// </exception>
public void Create(CommonSequence sequence, Stream sequenceStream)
{
string stringSequence = FileHelper.ReadSequenceFromStream(sequenceStream);
var doc = new XmlDocument();
doc.LoadXml(stringSequence);
var parser = new MusicXmlParser();
parser.Execute(doc);
ScoreTrack tempTrack = parser.ScoreModel;
if (tempTrack.CongenericScoreTracks.Count != 1)
{
throw new Exception("Track contains more then one or zero congeneric score tracks (parts).");
}
MatterRepository.CreateOrExtractExistingMatterForSequence(sequence);
BaseChain notesSequence = ConvertCongenericScoreTrackToNotesBaseChain(tempTrack.CongenericScoreTracks[0]);
long[] notesAlphabet = ElementRepository.GetOrCreateNotesInDb(notesSequence.Alphabet);
sequence.Notation = Notation.Notes;
Create(sequence, notesAlphabet, notesSequence.Building);
BaseChain measuresSequence = ConvertCongenericScoreTrackToMeasuresBaseChain(tempTrack.CongenericScoreTracks[0]);
long[] measuresAlphabet = MeasureRepository.GetOrCreateMeasuresInDb(measuresSequence.Alphabet);
sequence.Notation = Notation.Measures;
sequence.Id = default;
Create(sequence, measuresAlphabet, measuresSequence.Building);
sequence.Notation = Notation.FormalMotifs;
var pauseTreatments = EnumExtensions.ToArray <PauseTreatment>().Where(pt => pt != PauseTreatment.NotApplicable);
foreach (PauseTreatment pauseTreatment in pauseTreatments)
{
BaseChain fmotifsSequence = ConvertCongenericScoreTrackToFormalMotifsBaseChain(tempTrack.CongenericScoreTracks[0], pauseTreatment, false);
long[] fmotifsAlphabet = FmotifRepository.GetOrCreateFmotifsInDb(fmotifsSequence.Alphabet);
sequence.Id = default;
Create(sequence, fmotifsAlphabet, fmotifsSequence.Building, pauseTreatment, false);
fmotifsSequence = ConvertCongenericScoreTrackToFormalMotifsBaseChain(tempTrack.CongenericScoreTracks[0], pauseTreatment, true);
fmotifsAlphabet = FmotifRepository.GetOrCreateFmotifsInDb(fmotifsSequence.Alphabet);
sequence.Id = default;
Create(sequence, fmotifsAlphabet, fmotifsSequence.Building, pauseTreatment, true);
}
}
/// <summary>
/// The create DNA sequence.
/// </summary>
/// <param name="sequence">
/// The common sequence.
/// </param>
/// <param name="fastaSequence">
/// Sequence as <see cref="ISequence"/>>.
/// </param>
/// <param name="partial">
/// The partial.
/// </param>
/// <exception cref="Exception">
/// Thrown if at least one element of new sequence is missing in db
/// or if sequence is empty or invalid.
/// </exception>
public void Create(CommonSequence sequence, ISequence fastaSequence, bool partial)
{
if (fastaSequence.ID.Contains("Resource temporarily unavailable"))
{
throw new Exception("Sequence is empty or invalid (probably ncbi is not responding).");
}
string stringSequence = fastaSequence.ConvertToString().ToUpper();
var chain = new BaseChain(stringSequence);
if (!ElementRepository.ElementsInDb(chain.Alphabet, sequence.Notation))
{
throw new Exception("At least one element of new sequence is invalid (not A, C, T, G or U).");
}
MatterRepository.CreateOrExtractExistingMatterForSequence(sequence);
long[] alphabet = ElementRepository.ToDbElements(chain.Alphabet, sequence.Notation, false);
Create(sequence, partial, alphabet, chain.Building);
}
/// <summary>
/// Initializes a new instance of the <see cref="SequenceImporter"/> class.
/// </summary>
/// <param name="db">
/// The db.
/// </param>
protected SequenceImporter(LibiadaWebEntities db)
{
Db = db;
MatterRepository = new MatterRepository(db);
ElementRepository = new ElementRepository(db);
}
/// <summary>
/// Initializes a new instance of the <see cref="SequenceImporter"/> class.
/// </summary>
/// <param name="db">
/// The db.
/// </param>
protected SequenceImporter(LibiadaWebEntities db)
{
Db = db;
MatterRepository = new MatterRepository(db);
ElementRepository = new ElementRepository(db);
}