//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;
}
