/// <summary>
/// reads the transcript from the binary reader
/// </summary>
public static Transcript Read(ExtendedBinaryReader reader, Gene[] cacheGenes, SimpleInterval[] cacheIntrons,
SimpleInterval[] cacheMirnas, string[] cachePeptideSeqs)
{
// transcript
var referenceIndex = reader.ReadUInt16();
var start = reader.ReadOptInt32();
var end = reader.ReadOptInt32();
var id = CompactId.Read(reader);
// gene
var geneIndex = reader.ReadOptInt32();
var gene = cacheGenes[geneIndex];
// encoded data
var encoded = new EncodedTranscriptData(reader.ReadUInt16(), reader.ReadByte());
// exons & introns
var introns = encoded.HasIntrons ? ReadIndices(reader, cacheIntrons) : null;
var cdnaMaps = encoded.HasCdnaMaps ? ReadCdnaMaps(reader) : null;
// protein function predictions
int siftIndex = encoded.HasSift ? reader.ReadOptInt32() : -1;
int polyphenIndex = encoded.HasPolyPhen ? reader.ReadOptInt32() : -1;
// translation
var translation = encoded.HasTranslation ? Translation.Read(reader, cachePeptideSeqs) : null;
// attributes
var mirnas = encoded.HasMirnas ? ReadIndices(reader, cacheMirnas) : null;
return(new Transcript(referenceIndex, start, end, id, encoded.Version, translation, encoded.BioType,
gene, TranscriptUtilities.GetTotalExonLength(cdnaMaps), encoded.StartExonPhase, encoded.IsCanonical,
introns, mirnas, cdnaMaps, siftIndex, polyphenIndex, encoded.TranscriptSource));
}
/// <summary>
/// constructor
/// </summary>
public Translation(CdnaCoordinateMap codingRegion, CompactId proteinId, byte proteinVersion, string peptideSeq)
{
CodingRegion = codingRegion;
ProteinId = proteinId;
ProteinVersion = proteinVersion;
PeptideSeq = peptideSeq;
}
/// <summary>
/// reads the translation from the binary writer
/// </summary>
public static Translation Read(ExtendedBinaryReader reader, string[] peptideSeqs)
{
var codingRegion = CdnaCoordinateMap.Read(reader);
var proteinId = CompactId.Read(reader);
var proteinVersion = reader.ReadByte();
var peptideIndex = reader.ReadOptInt32();
return(new Translation(codingRegion, proteinId, proteinVersion, peptideSeqs[peptideIndex]));
}
/// <summary>
/// constructor
/// </summary>
public Gene(ushort referenceIndex, int start, int end, bool onReverseStrand, string symbol, int hgncId,
CompactId entrezGeneId, CompactId ensemblId, int mimNumber) : base(referenceIndex, start, end)
{
OnReverseStrand = onReverseStrand;
Symbol = symbol;
_hgncId = hgncId;
EntrezGeneId = entrezGeneId;
EnsemblId = ensemblId;
_mimNumber = mimNumber;
}
/// <summary>
/// reads the regulatory element data from the binary reader
/// </summary>
public static RegulatoryElement Read(ExtendedBinaryReader reader)
{
var referenceIndex = reader.ReadUInt16();
int start = reader.ReadOptInt32();
int end = reader.ReadOptInt32();
var type = (RegulatoryElementType)reader.ReadByte();
var id = CompactId.Read(reader);
return(new RegulatoryElement(referenceIndex, start, end, id, type));
}
/// <summary>
/// reads the gene data from the binary reader
/// </summary>
public static Gene Read(ExtendedBinaryReader reader)
{
ushort referenceIndex = reader.ReadUInt16();
int start = reader.ReadOptInt32();
int end = reader.ReadOptInt32();
bool onReverseStrand = reader.ReadBoolean();
string symbol = reader.ReadAsciiString();
int hgncId = reader.ReadOptInt32();
var entrezId = CompactId.Read(reader);
var ensemblId = CompactId.Read(reader);
int mimNumber = reader.ReadOptInt32();
return(new Gene(referenceIndex, start, end, onReverseStrand, symbol, hgncId, entrezId, ensemblId, mimNumber));
}
/// <summary>
/// constructor
/// </summary>
public Transcript(ushort referenceIndex, int start, int end, CompactId id, byte version,
Translation translation, BioType bioType, Gene gene, int totalExonLength, byte startExonPhase,
bool isCanonical, SimpleInterval[] introns, SimpleInterval[] microRnas, CdnaCoordinateMap[] cdnaMaps,
int siftIndex, int polyPhenIndex, TranscriptDataSource transcriptSource) : base(referenceIndex, start, end)
{
Id = id;
Version = version;
Translation = translation;
BioType = bioType;
Gene = gene;
TotalExonLength = totalExonLength;
StartExonPhase = startExonPhase;
IsCanonical = isCanonical;
Introns = introns;
MicroRnas = microRnas;
CdnaMaps = cdnaMaps;
SiftIndex = siftIndex;
PolyPhenIndex = polyPhenIndex;
TranscriptSource = transcriptSource;
TotalExonLength = TranscriptUtilities.GetTotalExonLength(cdnaMaps);
}
/// <summary>
/// constructor
/// </summary>
public RegulatoryElement(ushort referenceIndex, int start, int end, CompactId id, RegulatoryElementType type)
: base(referenceIndex, start, end)
{
Id = id;
Type = type;
}
