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#include "pilercr.h"
static bool CmpAA(const ArrayAln *AA1, const ArrayAln *AA2)
{
return AA1->Pos < AA2->Pos;
}
void AlignArrays(const std::vector<ArrayData *> &ADVec,
std::vector<ArrayAln *> &AAVec)
{
AAVec.clear();
// Create array alignments
const size_t ArrayDataCount = ADVec.size();
for (size_t Index = 0; Index < ArrayDataCount; ++Index)
{
ArrayData &AD = *(ADVec[Index]);
ArrayAln &AA = *new ArrayAln;
AlignArray(AD, AA);
if (AA.Repeats.size() > 0 && AcceptedAA(AA))
AAVec.push_back(&AA);
}
// Sort by position
std::sort(AAVec.begin(), AAVec.end(), CmpAA);
// Check for arrays where we missed some repeats, these got split
// and can be merged.
size_t ArrayIndex = 0;
for (;;)
{
size_t ArrayCount = AAVec.size();
if (ArrayIndex + 1 >= ArrayCount)
break;
bool Merged = MergeAAs(*AAVec[ArrayIndex], *AAVec[ArrayIndex+1]);
if (Merged)
{
// Delete entry from array and continue.
// This allows merger of three or more arrays.
assert(ArrayCount > 1);
for (size_t i = ArrayIndex + 1; i < ArrayCount - 1; ++i)
AAVec[i] = AAVec[i+1];
AAVec.resize(ArrayCount - 1);
}
++ArrayIndex;
}
// Assign ids
size_t ArrayCount = AAVec.size();
int Id = 1;
for (size_t Index = 0; Index < ArrayCount; ++Index)
{
ArrayAln &AA = *(AAVec[Index]);
AA.Id = Id++;
}
}
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