/// <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()); }