static void FindSuperFamEdges(FamList &Fams, EdgeList &Edges)
{
const int FamCount = (int) Fams.size();
// Allocate triangular array Related[i][j], value is true
// iff families i and j are related (i.e., there is a local
// alignment between some member of i and some member of j).
const int TriangleSize = (FamCount*(FamCount - 1))/2;
bool *Related = all(bool, TriangleSize);
zero(Related, bool, TriangleSize);
for (PtrFamList p = Fams.begin(); p != Fams.end(); ++p)
{
FamData *Fam = *p;
for (PtrFamData q = Fam->begin(); q != Fam->end(); ++q)
{
FamMemberData &FamMember = *q;
int PileIndex = FamMember.PileIndex;
const PileData &Pile = Piles[PileIndex];
const int FamIndex = Pile.FamIndex;
if (-1 == FamIndex)
continue;
const int ImageCount = Pile.ImageCount;
for (int ImageIndex = 0; ImageIndex < ImageCount; ++ImageIndex)
{
const PileImageData &Image = Pile.Images[ImageIndex];
const int PartnerPileIndex = Image.SIPile;
if (PartnerPileIndex == PileIndex)
continue;
const PileData &PartnerPile = Piles[PartnerPileIndex];
const int PartnerFamIndex = PartnerPile.FamIndex;
if (-1 == PartnerFamIndex || PartnerFamIndex == FamIndex)
continue;
const int Index = TriangleSubscript(FamCount, FamIndex, PartnerFamIndex);
assert(Index >- 0 && Index < TriangleSize);
Related[Index] = true;
}
}
}
Edges.clear();
for (int i = 0; i < FamCount; ++i)
for (int j = i + 1; j < FamCount; ++j)
{
const int Index = TriangleSubscript(FamCount, i, j);
if (Related[Index])
{
// Log("R %d %d\n", i, j);
EdgeData Edge;
Edge.Node1 = i;
Edge.Node2 = j;
Edge.Rev = false;
Edges.push_back(Edge);
}
}
}
static void FindGlobalEdges(EdgeList &Edges, int MaxImageCount)
{
Edges.clear();
PILE_INDEX_TYPE *Partners = all(PILE_INDEX_TYPE, MaxImageCount);
bool *PartnersRev = all(bool, MaxImageCount);
for (int PileIndex = 0; PileIndex < PileCount; ++PileIndex)
{
PileData &Pile = Piles[PileIndex];
int PartnerCount;
if (g_paramSingleHitCoverage)
PartnerCount = FindGlobalEdgesPileSingle(Pile, PileIndex, Partners, PartnersRev);
else
PartnerCount = FindGlobalEdgesPileMulti(Pile, PileIndex, Partners, PartnersRev);
AddEdges(Edges, PileIndex, Partners, PartnersRev, PartnerCount);
}
freemem(Partners);
freemem(PartnersRev);
}
