/// <summary>
/// writes the translation to the binary writer
/// </summary>
public void Write(ExtendedBinaryWriter writer, int peptideIndex)
{
CodingRegion.Write(writer);
ProteinId.Write(writer);
writer.Write(ProteinVersion);
writer.WriteOpt(peptideIndex);
}
/// <summary>
/// writes the regulatory element data to the binary writer
/// </summary>
public void Write(ExtendedBinaryWriter writer)
{
writer.Write(ReferenceIndex);
writer.WriteOpt(Start);
writer.WriteOpt(End);
writer.Write((byte)Type);
Id.Write(writer);
}
/// <summary>
/// writes the transcript to the binary writer
/// </summary>
public void Write(ExtendedBinaryWriter writer, Dictionary <Gene, int> geneIndices,
Dictionary <SimpleInterval, int> intronIndices, Dictionary <SimpleInterval, int> microRnaIndices,
Dictionary <string, int> peptideIndices)
{
// transcript
writer.Write(ReferenceIndex);
writer.WriteOpt(Start);
writer.WriteOpt(End);
Id.Write(writer);
// gene
writer.WriteOpt(GetIndex(Gene, geneIndices));
// encoded data
var encoded = new EncodedTranscriptData(BioType, Version, TranscriptSource, IsCanonical, SiftIndex != -1,
PolyPhenIndex != -1, MicroRnas != null, Introns != null, CdnaMaps != null, Translation != null,
StartExonPhase);
encoded.Write(writer);
// exons & introns
if (encoded.HasIntrons)
{
WriteIndices(writer, Introns, intronIndices);
}
if (encoded.HasCdnaMaps)
{
WriteCdnaMaps(writer);
}
// protein function predictions
if (encoded.HasSift)
{
writer.WriteOpt(SiftIndex);
}
if (encoded.HasPolyPhen)
{
writer.WriteOpt(PolyPhenIndex);
}
// translation
if (encoded.HasTranslation)
{
// ReSharper disable once PossibleNullReferenceException
var peptideIndex = GetIndex(Translation.PeptideSeq, peptideIndices);
Translation.Write(writer, peptideIndex);
}
// attributes
if (encoded.HasMirnas)
{
WriteIndices(writer, MicroRnas, microRnaIndices);
}
}
/// <summary>
/// writes the gene data to the binary writer
/// </summary>
public void Write(ExtendedBinaryWriter writer)
{
writer.Write(ReferenceIndex);
writer.WriteOpt(Start);
writer.WriteOpt(End);
writer.Write(OnReverseStrand);
writer.WriteOptAscii(Symbol);
writer.WriteOpt(_hgncId);
// ReSharper disable ImpureMethodCallOnReadonlyValueField
EntrezGeneId.Write(writer);
EnsemblId.Write(writer);
// ReSharper restore ImpureMethodCallOnReadonlyValueField
writer.WriteOpt(_mimNumber);
}
