/// <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]));
}
private static CdnaCoordinateMap[] ReadCdnaMaps(ExtendedBinaryReader reader)
{
int numItems = reader.ReadOptInt32();
var items = new CdnaCoordinateMap[numItems];
for (int i = 0; i < numItems; i++)
{
items[i] = CdnaCoordinateMap.Read(reader);
}
return(items);
}
private static string ConvertGenomicPosToCodingPos(int breakendPosition, CdnaCoordinateMap cdnaCoordinateMap,
bool onReverseStrand, int compDnaCodingStart, int compDnaCodingEnd)
{
int cDnaPos;
if (onReverseStrand)
{
cDnaPos = cdnaCoordinateMap.CdnaStart - breakendPosition + cdnaCoordinateMap.GenomicEnd;
}
else
{
cDnaPos = cdnaCoordinateMap.CdnaEnd + breakendPosition - cdnaCoordinateMap.GenomicEnd;
}
if (cDnaPos > compDnaCodingEnd)
{
return("*" + (cDnaPos - compDnaCodingEnd));
}
if (cDnaPos < compDnaCodingStart)
{
return((cDnaPos - compDnaCodingStart).ToString());
}
return((cDnaPos - compDnaCodingStart + 1).ToString());
}