//constructor public Alphabet(IAlphabet alphabet, long id) { if (id < 1) { UpdaterException.check_data_exception(true); } this.id = 0; this.sequence_id = id; this.A = 0; this.C = 0; this.G = 0; this.T = 0; this.Gap = 0; this.ACT = 0; this.AT = 0; this.GA = 0; this.GAT = 0; this.GC = 0; this.GCA = 0; this.GT = 0; this.GTC = 0; this.TC = 0; this.Any = 0; this.has_ambiguity = (alphabet.HasAmbiguity)? 1:0; this.has_gaps = (alphabet.HasGaps)? 1:0; this.has_termination = (alphabet.HasTerminations)? 1:0; this.is_complement_supported = (alphabet.IsComplementSupported)? 1:0; this.dna_name = alphabet.Name; this.alphabet_type_count = alphabet.Count; extract_alphabet_IDs(alphabet); }
public Metadata(GenBankMetadata metadata, long id) { this.id = 0; if (id < 1) { UpdaterException.check_data_exception(true); } this.sequence_id = id; this.primary_accession = metadata.Accession.Primary; foreach (var sec in metadata.Accession.Secondary) { this.secondary_accession += " " + sec; } this.contig = metadata.Contig; this.definition = metadata.Definition; this.keywords = metadata.Keywords; this.prima = metadata.Primary; this.origin = metadata.Origin; this.basecount = metadata.BaseCount; this.dbsource = metadata.DbSource; }
public Comment(string comment, long id) { if (id < 1) { UpdaterException.check_data_exception(true); } this.id = 0; this.value = comment; this.prokaryote_id = id; }
public Qualifier_value(string V, long id) { if (id < 1) { UpdaterException.check_data_exception(true); } this.id = 0; this.qualifier_id = id; this.qualifier_values = V; }
public Qualifier(string K, long id) { if (id < 1) { UpdaterException.check_data_exception(true); } this.id = 0; this.feature_id = id; this.qualifier_key = K; }
public Sequence(ISequence seq, long id) { if (id < 1 || seq.ID.Count() > 40) { UpdaterException.check_data_exception(true); } this.id = 0; this.prokaryote_id = id; this.value = seq.ToString(); this.count = seq.Count; this.genbank_ID = seq.ID; }
public Version(GenBankVersion ver, long id) { if (id < 1 || ver.Accession.Length > 40 || ver.GiNumber.Length > 40 || ver.Version.Length > 2) { UpdaterException.check_data_exception(true); } this.id = 0; this.metadata_id = id; this.accession = ver.Accession; this.compound_accession = ver.CompoundAccession; this.ginumber = ver.GiNumber; this.version = ver.Version; }
//private int sublocation { get; } //private int location_resolver { get; } public Feature(FeatureItem feature, long id) { if (feature == null || id < 1) { UpdaterException.check_data_exception(true); } this.location_operator = (int)feature.Location.Operator + 1; this.location_separator = feature.Location.Separator; this.id = 0; this.metadata_id = id; this.key_type = feature.Key; this.label = feature.Label; this.location_accession = feature.Location.Accession; this.location_end = feature.Location.EndData; this.location_start = feature.Location.StartData; }
public Dblink(CrossReferenceLink dblink, long id) { this.type = (int)dblink.Type + 1; if (id < 1 || this.type < 1 || this.type > 4) { UpdaterException.check_data_exception(true); } this.id = 0; foreach (var s in dblink.Numbers) { this.value += s + "\t"; } this.prokaryote_id = id; }
public Locus(GenBankLocusInfo locus, long id) { this.divisoncode = (int)locus.DivisionCode + 1; this.molecule = (int)locus.MoleculeType + 1; this.strand = (int)locus.Strand + 1; this.strandtopology = (int)locus.StrandTopology + 1; if (id < 1 || this.divisoncode > 20 || this.divisoncode < 1 || this.molecule > 10 || this.molecule < 1 || this.strand > 4 || this.strand < 1 || this.strandtopology > 3 || this.strandtopology < 1 || locus.SequenceType.Length > 40) { UpdaterException.check_data_exception(true); } this.id = 0; this.metadata_id = id; this.date = locus.Date.ToString("yyyy-MM-dd HH:mm:ss"); this.strand_type = locus.SequenceType; }
public Reference(CitationReference reference, long id) { if (id < 1) { UpdaterException.check_data_exception(true); } this.id = 0; this.prokaryote_id = id; this.authors = reference.Authors; this.consortium = reference.Consortiums; this.journal = reference.Journal; this.location = reference.Location; this.medline = reference.Medline; this.pub_med = reference.PubMed; this.remark = reference.Remarks; this.title = reference.Title; }