void C_NNcluster2d::mergeClusters() {
C_cluster2d_elements::iterator it,jt;
int N0 = cluster.size();
int NM=0;
for ( it=cluster.begin() ; it != cluster.end(); it++ ) {
if (it != cluster.begin()) {
jt = it;
jt--;
int i = (*it).first;
int j = (*jt).first;
bool morethan1 = cluster[j].N>1;
bool thin = cluster[j].std[0]<dx[0];
bool close = (cluster[i].low[0]-cluster[j].high[0])<2*dx[0];
close = close & (fabs(cluster[i].mean[1]-cluster[j].mean[1])<dx[0]);
if (thin&close&morethan1) {
// int ix=cluster[i].inp[0]; why inp?
// int jx=cluster[j].inp[0];
// connect(ix,jx);
connect(i,j);
NM++;
cerr << "merge " << NM << endl;
}
}
}
cluster.clear();
makeClusters();
NC = cluster.size();
printf(" mergeCluster merged %d of %d clusters leaving NC %d\n",NM,N0,NC);
}
// full constructor
C_NNcluster2d::C_NNcluster2d(const vector<vector<double> > & x1,const vector<vector<double> > & wx1
, const vector<int> & ip1
, const double fx1[2] , const string & tn1, const string & sn1, const string & cn1) {
typeName = tn1;
setName = sn1;
contigName = cn1;
Nmin=1;
Smin[0]=-1;
Smin[1]=-1;
NC=0;
cluster.clear();
fx[0]=fx1[0]; // neighborhood scale
fx[1]=fx1[1];
x=x1;
wx=wx1;
ip=ip1;
N=x.size();
dx[0]=0;
dx[1]=0;
for (int i=0; i<N; i++) {
wx[i][0]*=fx[0];
wx[i][1]*=fx[1];
if ( wx[i][0]>dx[0] ) { dx[0]=wx[i][0]; }
if ( wx[i][1]>dx[1] ) { dx[1]=wx[i][1]; }
}
init();
makeConnections();
makeClusters();
}
//------------------------------------------------------------------------------
// merge near clusters
//------------------------------------------------------------------------------
void C_NNcluster1d::mergeClusters() {
C_cluster1d_elements::iterator it,jt;
int N0 = cluster.size();
int NM=0;
for ( it=cluster.begin() ; it != cluster.end(); it++ ) {
if (it != cluster.begin()) {
jt = it;
jt--;
int i = (*it).first;
int j = (*jt).first;
bool morethan1 = cluster[j].N>1;
bool thin = cluster[j].std<dx;
bool close = (cluster[i].low-cluster[j].high)<(dx);
close = close & (fabs(cluster[i].mean-cluster[j].mean)<(2*dx));
if (thin&close&morethan1) {
int ix=cluster[i].inp[0];
int jx=cluster[j].inp[0];
connect(ix,jx);
NM++;
}
}
}
cluster.clear();
makeClusters();
NC = cluster.size();
printf(" mergeCluster merged %d of %d clusters leaving NC %d\n",NM,N0,NC);
}
// constructor w/o label
C_NNcluster1d::C_NNcluster1d(const vector<double> & x1, const double DX) {
NC=0;
cluster.clear();
dx=DX; // neighborhood scale
x=x1;
N=x.size();
init();
Nmin=1;
Smin=0;
makeConnections();
makeClusters();
}
// full constructor
C_NNcluster1d::C_NNcluster1d(const vector<double> & x1, const double DX
, const string & tn1, const string & sn1, const string & cn1) {
typeName = tn1;
setName = sn1;
contigName = cn1;
NC=0;
cluster.clear();
dx=DX; // neighborhood scale
x=x1;
N=x.size();
init();
Nmin=1;
Smin=0;
makeConnections();
makeClusters();
}
void SeqSwapper::swapSequences()
{
int numNormal = m_cd->GetNumRows();
LOG_POST("Clustering");
vector< vector<int> * > clusters;
makeClusters(m_clusteringThreshold, clusters);
vector< pair<int, int> > replacementPairs;
set<int> structures;
LOG_POST("Clustering is done (made " << clusters.size() << " clusters)");
LOG_POST("Find replacements by BLAST in each cluster");
for (int i = 0; i < clusters.size(); i++)
{
vector<int>* cluster = clusters[i];
if (cluster) {
findReplacements(*cluster, replacementPairs, structures);
delete cluster;
}
}
LOG_POST("Done with BLAST in each cluster");
set<int> usedPendings;
vector<int> selectedNormalRows;
int newMaster = -1;
for (int p = 0; p < replacementPairs.size(); p++)
{
//debug
CRef< CSeq_id > seqId;
m_ac.GetSeqIDForRow(replacementPairs[p].first, seqId);
string nid = seqId->AsFastaString();
m_ac.GetSeqIDForRow(replacementPairs[p].second, seqId);
string pid = seqId->AsFastaString();
LOG_POST("replacing "<<nid<<" with "<<pid);
//take care of master replacement
if (replacementPairs[p].first == 0)
newMaster = replacementPairs[p].second - numNormal;
else
{
selectedNormalRows.push_back(replacementPairs[p].first);
usedPendings.insert(replacementPairs[p].second - numNormal);
}
}
m_cd->EraseTheseRows(selectedNormalRows);
if (structures.size() > 0)
{
LOG_POST("Adding "<<structures.size()<<" structures");
for (set<int>::iterator sit = structures.begin(); sit != structures.end(); sit++)
usedPendings.insert(*sit - numNormal);
}
if (newMaster >= 0)
promotePendingRows(usedPendings, &newMaster);
else
promotePendingRows(usedPendings);
//findStructuralPendings(structures);
if (newMaster > 0)
{
ReMasterCdWithoutUnifiedBlocks(m_cd, newMaster, true);
vector<int> rows;
rows.push_back(newMaster);
m_cd->EraseTheseRows(rows);
}
m_cd->ResetPending();
m_cd->EraseSequences();
}