unsigned EstringOp(const short es[], const Seq &sIn, MSA &a) { unsigned uSymbols; unsigned uIndels; EstringCounts(es, &uSymbols, &uIndels); assert(sIn.Length() == uSymbols); unsigned uColCount = uSymbols + uIndels; a.Clear(); a.SetSize(1, uColCount); a.SetSeqName(0, sIn.GetName()); a.SetSeqId(0, sIn.GetId()); unsigned p = 0; unsigned uColIndex = 0; for (;;) { int n = *es++; if (0 == n) break; if (n > 0) for (int i = 0; i < n; ++i) { char c = sIn[p++]; a.SetChar(0, uColIndex++, c); } else for (int i = 0; i < -n; ++i) a.SetChar(0, uColIndex++, '-'); } assert(uColIndex == uColCount); return uColCount; }
void Seq::Copy(const Seq &rhs) { clear(); const unsigned uLength = rhs.Length(); for (unsigned uColIndex = 0; uColIndex < uLength; ++uColIndex) push_back(rhs.at(uColIndex)); const char *ptrName = rhs.GetName(); size_t n = strlen(ptrName) + 1; m_ptrName = new char[n]; strcpy(m_ptrName, ptrName); SetId(rhs.GetId()); }