inline T &_3dArray<T>::operator()(size_t index0, size_t index1, size_t index2) {
#ifdef FIBER_CHECK_ARRAY_BOUNDS
check_indices(index0, index1, index2);
#endif
return m_storage[index0 + m_extents[0] * index1 +
m_extents[0] * m_extents[1] * index2];
}
inline
void
subview_cube_each2<eT,TB>::operator/= (const Base<eT,T1>& in)
{
arma_extra_debug_sigprint();
Cube<eT>& p = access::rw(subview_cube_each_common<eT>::P);
const unwrap<T1> tmp( in.get_ref() );
const Mat<eT>& A = tmp.M;
subview_cube_each_common<eT>::check_size(A);
const unwrap<TB> U( base_indices.get_ref() );
check_indices(U.M);
const uword p_n_slices = p.n_slices;
const uword p_n_elem_slice = p.n_elem_slice;
const uword* indices_mem = U.M.memptr();
const uword N = U.M.n_elem;
const eT* A_mem = A.memptr();
for(uword i=0; i < N; ++i)
{
const uword slice = indices_mem[i];
arma_debug_check( (slice >= p_n_slices), "each_slice(): index out of bounds" );
arrayops::inplace_div(p.slice_memptr(slice), A_mem, p_n_elem_slice);
}
}
inline const T& _2dArray<T>::operator()(size_t index0, size_t index1) const
{
#ifdef FIBER_CHECK_ARRAY_BOUNDS
check_indices(index0, index1);
#endif
return m_storage[index0 + m_extents[0] * index1];
}
void detect_olaps(output_store* output, SEXP anchor1, SEXP anchor2, SEXP querystarts, SEXP queryends, SEXP subject, SEXP nsubjects, SEXP use_both) {
if (!isInteger(anchor1) || !isInteger(anchor2)) { throw std::runtime_error("anchors must be integer vectors"); }
const int Npairs = LENGTH(anchor1);
if (Npairs != LENGTH(anchor2)) { throw std::runtime_error("anchor vectors must be of equal length"); }
const int* a1ptr=INTEGER(anchor1), *a2ptr=INTEGER(anchor2);
if (!isInteger(querystarts) || !isInteger(queryends)) { throw std::runtime_error("query indices must be integer vectors"); }
const int Nq = LENGTH(querystarts);
if (Nq != LENGTH(queryends)) { throw std::runtime_error("query indices must be of equal length"); }
const int* qsptr=INTEGER(querystarts), *qeptr=INTEGER(queryends);
if (!isInteger(subject)) { throw std::runtime_error("subject indices must be integer"); }
const int Ns = LENGTH(subject);
const int *sjptr=INTEGER(subject);
if (!isInteger(nsubjects) || LENGTH(nsubjects)!=1) { throw std::runtime_error("total number of subjects must be an integer scalar"); }
const int Ns_all = asInteger(nsubjects);
int true_mode_start, true_mode_end;
set_mode_values(use_both, true_mode_start, true_mode_end);
// Checking indices.
check_indices(qsptr, qeptr, Nq, sjptr, Ns, Ns_all);
/* Constructing an output deque */
output->prime(Npairs, Ns_all);
int* latest_pair=(int*)R_alloc(Ns_all, sizeof(int));
for (int checkdex=0; checkdex < Ns_all; ++checkdex) { latest_pair[checkdex] = -1; }
int curpair=0, mode=0, maxmode, curq=0, curindex=0, curs=0;
for (curpair=0; curpair<Npairs; ++curpair) {
maxmode=(a1ptr[curpair]==a2ptr[curpair] ? true_mode_start+1 : true_mode_end); // just check one or the other, if they're the same.
for (mode=true_mode_start; mode<maxmode; ++mode) {
if (mode == 0) {
curq = a1ptr[curpair];
} else {
curq = a2ptr[curpair];
}
if (curq >= Nq || curq < 0 || curq==NA_INTEGER) { throw std::runtime_error("region index out of bounds"); }
for (curindex=qsptr[curq]; curindex<qeptr[curq]; ++curindex) {
curs=sjptr[curindex];
if (latest_pair[curs] < curpair) {
output->acknowledge(curpair, curs);
latest_pair[curs] = curpair;
if (output->quit()) { // If we just want any hit, we go to the next 'curpair'.
goto outofnest; // Ugh. Oh well, cleaner than lots of break's.
}
}
}
}
outofnest:
output->postprocess();
}
return;
}
inline const T &_4dArray<T>::operator()(size_t index0, size_t index1,
size_t index2, size_t index3) const {
#ifdef FIBER_CHECK_ARRAY_BOUNDS
check_indices(index0, index1, index2, index3);
#endif
return m_storage[index0 + m_extents[0] * index1 +
m_extents[0] * m_extents[1] * index2 +
m_extents[0] * m_extents[1] * m_extents[2] * index3];
}
inline
void
subview_each2<parent,mode,TB>::operator= (const Base<eT,T1>& in)
{
arma_extra_debug_sigprint();
parent& p = access::rw(subview_each_common<parent,mode>::p);
const unwrap_check<T1> tmp( in.get_ref(), (*this).get_mat_ref() );
const Mat<eT>& A = tmp.M;
subview_each_common<parent,mode>::check_size(A);
const unwrap_check_mixed<TB> U( base_indices.get_ref(), (*this).get_mat_ref() );
check_indices(U.M);
const eT* A_mem = A.memptr();
const uword p_n_rows = p.n_rows;
const uword p_n_cols = p.n_cols;
const uword* indices_mem = U.M.memptr();
const uword N = U.M.n_elem;
if(mode == 0) // each column
{
for(uword i=0; i < N; ++i)
{
const uword col = indices_mem[i];
arma_debug_check( (col > p_n_cols), "each_col(): index out of bounds" );
arrayops::copy( p.colptr(col), A_mem, p_n_rows );
}
}
else // each row
{
for(uword i=0; i < N; ++i)
{
const uword row = indices_mem[i];
arma_debug_check( (row > p_n_rows), "each_row(): index out of bounds" );
for(uword col=0; col < p_n_cols; ++col)
{
p.at(row,col) = A_mem[col];
}
}
}
}
SEXP expand_pair_links(SEXP anchor1, SEXP anchor2, SEXP querystarts1, SEXP queryends1, SEXP subject1, SEXP nsubjects1,
SEXP querystarts2, SEXP queryends2, SEXP subject2, SEXP nsubjects2, SEXP sameness, SEXP use_both) try {
if (!isInteger(anchor1) || !isInteger(anchor2)) { throw std::runtime_error("anchors must be integer vectors"); }
const int Npairs = LENGTH(anchor1);
if (Npairs != LENGTH(anchor2)) { throw std::runtime_error("anchor vectors must be of equal length"); }
const int* a1ptr=INTEGER(anchor1), *a2ptr=INTEGER(anchor2);
if (!isInteger(querystarts1) || !isInteger(queryends1)) { throw std::runtime_error("query indices (1) must be integer vectors"); }
const int Nq = LENGTH(querystarts1);
if (Nq != LENGTH(queryends1)) { throw std::runtime_error("query indices (1) must be of equal length"); }
const int* qsptr1=INTEGER(querystarts1), *qeptr1=INTEGER(queryends1);
if (!isInteger(subject1)) { throw std::runtime_error("subject indices (1) must be integer"); }
const int Ns1 = LENGTH(subject1);
const int *sjptr1=INTEGER(subject1);
if (!isInteger(querystarts2) || !isInteger(queryends2)) { throw std::runtime_error("query indices (2) must be integer vectors"); }
if (Nq != LENGTH(querystarts2) || Nq != LENGTH(queryends2)) { throw std::runtime_error("query indices (2) must be of equal length"); }
const int* qsptr2=INTEGER(querystarts2), *qeptr2=INTEGER(queryends2);
if (!isInteger(subject2)) { throw std::runtime_error("subject indices (2) must be integer"); }
const int Ns2 = LENGTH(subject2);
const int *sjptr2=INTEGER(subject2);
if (!isInteger(nsubjects1) || LENGTH(nsubjects1)!=1) { throw std::runtime_error("total number of subjects (1) must be an integer scalar"); }
const int Ns_all1 = asInteger(nsubjects1);
if (!isInteger(nsubjects2) || LENGTH(nsubjects2)!=1) { throw std::runtime_error("total number of subjects (2) must be an integer scalar"); }
const int Ns_all2 = asInteger(nsubjects2);
int true_mode_start, true_mode_end;
set_mode_values(use_both, true_mode_start, true_mode_end);
if (!isLogical(sameness) || LENGTH(sameness)!=1) { throw std::runtime_error("same region indicator should be a logical scalar"); }
const bool is_same=asLogical(sameness);
if (is_same) { true_mode_end=true_mode_start+1; } // No point examining the flipped ones.
// Check indices.
check_indices(qsptr1, qeptr1, Nq, sjptr1, Ns1, Ns_all1);
check_indices(qsptr2, qeptr2, Nq, sjptr2, Ns2, Ns_all2);
// Setting up the set.
typedef std::pair<int, int> link;
std::set<link> currently_active;
std::set<link>::const_iterator itca;
std::deque<link> stored_inactive;
std::deque<int> interactions;
int curpair=0, mode=0, maxmode, curq1=0, curq2=0, curindex1=0, curindex2=0;
for (curpair=0; curpair<Npairs; ++curpair) {
maxmode = (a1ptr[curpair] == a2ptr[curpair] ? true_mode_start+1 : true_mode_end);
// Repeating with switched anchors, if the query sets are not the same.
for (mode=true_mode_start; mode<maxmode; ++mode) {
if (mode==0) {
curq1 = a1ptr[curpair];
curq2 = a2ptr[curpair];
if (curq1 >= Nq || curq1 < 0 || curq1==NA_INTEGER) { throw std::runtime_error("region index (1) out of bounds"); }
if (curq2 >= Nq || curq2 < 0 || curq2==NA_INTEGER) { throw std::runtime_error("region index (2) out of bounds"); }
} else {
curq2 = a1ptr[curpair];
curq1 = a2ptr[curpair];
}
/* Storing all combinations associated with this pair. Avoiding redundant combinations
* for self-linking (we can't use a simple rule like curindex2 < curindex1 to restrict
* the loop, as the second anchor can overlap regions above the first anchor if the
* latter is nested within the former).
*/
for (curindex1=qsptr1[curq1]; curindex1<qeptr1[curq1]; ++curindex1) {
for (curindex2=qsptr2[curq2]; curindex2<qeptr2[curq2]; ++curindex2) {
if (is_same && sjptr1[curindex1] < sjptr2[curindex2]) {
currently_active.insert(link(sjptr2[curindex2], sjptr1[curindex1]));
} else {
currently_active.insert(link(sjptr1[curindex1], sjptr2[curindex2]));
}
}
}
}
// Relieving the set by storing all inactive entries (automatically sorted as well).
for (itca=currently_active.begin(); itca!=currently_active.end(); ++itca) {
stored_inactive.push_back(*itca);
}
interactions.resize(interactions.size() + currently_active.size(), curpair);
currently_active.clear();
}
// Popping back a list of information.
SEXP output=PROTECT(allocVector(VECSXP, 3));
try {
const int total_entries=interactions.size();
SET_VECTOR_ELT(output, 0, allocVector(INTSXP, total_entries));
int * oiptr=INTEGER(VECTOR_ELT(output, 0));
SET_VECTOR_ELT(output, 1, allocVector(INTSXP, total_entries));
int * os1ptr=INTEGER(VECTOR_ELT(output, 1));
SET_VECTOR_ELT(output, 2, allocVector(INTSXP, total_entries));
int * os2ptr=INTEGER(VECTOR_ELT(output, 2));
std::copy(interactions.begin(), interactions.end(), oiptr);
for (int curdex=0; curdex < total_entries; ++curdex) {
os1ptr[curdex]=stored_inactive[curdex].first;
os2ptr[curdex]=stored_inactive[curdex].second;
}
} catch (std::exception& e) {
UNPROTECT(1);
throw;
}
UNPROTECT(1);
return output;
} catch (std::exception& e) {
return mkString(e.what());
}
void detect_paired_olaps(output_store* output, SEXP anchor1, SEXP anchor2,
SEXP querystarts, SEXP queryends, SEXP subject,
SEXP next_anchor_start1, SEXP next_anchor_end1, SEXP next_id1,
SEXP next_anchor_start2, SEXP next_anchor_end2, SEXP next_id2,
SEXP num_next_pairs, SEXP use_both) {
if (!isInteger(anchor1) || !isInteger(anchor2)) { throw std::runtime_error("anchors must be integer vectors"); }
const int Npairs = LENGTH(anchor1);
if (Npairs != LENGTH(anchor2)) { throw std::runtime_error("anchor vectors must be of equal length"); }
const int* a1ptr=INTEGER(anchor1), *a2ptr=INTEGER(anchor2);
if (!isInteger(querystarts) || !isInteger(queryends)) { throw std::runtime_error("query indices must be integer vectors"); }
const int Nq = LENGTH(querystarts);
if (Nq != LENGTH(queryends)) { throw std::runtime_error("query indices must be of equal length"); }
const int* qsptr=INTEGER(querystarts), *qeptr=INTEGER(queryends);
if (!isInteger(subject)) { throw std::runtime_error("subject indices must be integer"); }
const int Ns = LENGTH(subject);
const int *sjptr=INTEGER(subject);
if (!isInteger(next_anchor_start1) || !isInteger(next_anchor_end1)) { throw std::runtime_error("next indices (1) must be integer vectors"); }
const int Nas=LENGTH(next_anchor_start1);
if (Nas != LENGTH(next_anchor_end1)) { throw std::runtime_error("next indices (1) must be of equal length"); }
const int* nasptr1=INTEGER(next_anchor_start1), *naeptr1=INTEGER(next_anchor_end1);
if (!isInteger(next_id1)) { throw std::runtime_error("next ID indices (1) must be integer"); }
const int *niptr1=INTEGER(next_id1);
if (!isInteger(next_anchor_start2) || !isInteger(next_anchor_end2)) { throw std::runtime_error("next indices (2) must be integer vectors"); }
if (Nas != LENGTH(next_anchor_start2) || Nas != LENGTH(next_anchor_end2)) { throw std::runtime_error("next indices (2) must be of equal length"); }
const int* nasptr2=INTEGER(next_anchor_start2), *naeptr2=INTEGER(next_anchor_end2);
if (!isInteger(next_id2)) { throw std::runtime_error("next ID indices (2) must be integer"); }
const int *niptr2=INTEGER(next_id2);
if (!isInteger(num_next_pairs) || LENGTH(num_next_pairs)!=1) { throw std::runtime_error("total number of next pairs must be an integer scalar"); }
const int Nnp = asInteger(num_next_pairs);
if (LENGTH(next_id1)!=Nnp || LENGTH(next_id2)!=Nnp) { throw std::runtime_error("number of next IDs is not equal to specified number of pairs"); }
int true_mode_start, true_mode_end;
set_mode_values(use_both, true_mode_start, true_mode_end);
// Check indices.
check_indices(qsptr, qeptr, Nq, sjptr, Ns, Nas);
check_indices(nasptr1, naeptr1, Nas, niptr1, Nnp, Nnp);
check_indices(nasptr2, naeptr2, Nas, niptr2, Nnp, Nnp);
// Setting up logging arrays.
output->prime(Npairs, Nnp);
int* latest_pair_A=(int*)R_alloc(Nnp, sizeof(int));
int* latest_pair_B=(int*)R_alloc(Nnp, sizeof(int));
bool* is_complete_A=(bool*)R_alloc(Nnp, sizeof(bool));
bool* is_complete_B=(bool*)R_alloc(Nnp, sizeof(bool));
for (int checkdex=0; checkdex < Nnp; ++checkdex) {
latest_pair_A[checkdex] = latest_pair_B[checkdex] = -1;
is_complete_A[checkdex] = is_complete_B[checkdex] = true;
}
int curpair=0, mode=0, maxmode, curq1=0, curq2=0,
curindex=0, cur_subreg=0, cur_nextanch=0, cur_nextid;
int * latest_pair;
bool * is_complete;
for (curpair=0; curpair<Npairs; ++curpair) {
maxmode = (a1ptr[curpair] == a2ptr[curpair] ? true_mode_start+1 : true_mode_end);
/* Checking whether the first and second anchor overlaps anything in the opposing query sets.
* Doing this twice; first and second anchors to the first and second query sets (A, mode=0), then
* the first and second anchors to the second and first query sets (B, mode=1).
*/
for (mode=true_mode_start; mode<maxmode; ++mode) {
if (mode==0) {
curq1 = a1ptr[curpair];
curq2 = a2ptr[curpair];
if (curq1 >= Nq || curq1 < 0 || curq1==NA_INTEGER) { throw std::runtime_error("region index (1) out of bounds"); }
if (curq2 >= Nq || curq2 < 0 || curq2==NA_INTEGER) { throw std::runtime_error("region index (2) out of bounds"); }
latest_pair = latest_pair_A;
is_complete = is_complete_A;
} else {
curq2 = a1ptr[curpair];
curq1 = a2ptr[curpair];
latest_pair = latest_pair_B;
is_complete = is_complete_B;
}
for (curindex=qsptr[curq1]; curindex<qeptr[curq1]; ++curindex) {
cur_subreg=sjptr[curindex];
for (cur_nextanch=nasptr1[cur_subreg]; cur_nextanch<naeptr1[cur_subreg]; ++cur_nextanch) {
cur_nextid=niptr1[cur_nextanch];
/* An overlap with element 'checkdex' has already been added from the "A" cycle, if
* is_complete[checkdex]=true and latest_pair[checkdex] is at the current query index.
* Otherwise, updating latest_pair if it hasn't already been updated - setting
* latest_pair to the query index to indicate that the first anchor region is overlapped,
* but also setting is_complete to false to indicate that the overlap is not complete.
*/
if (mode!=0 && latest_pair_A[cur_nextid] == curpair && is_complete_A[cur_nextid]) { continue; }
if (latest_pair[cur_nextid] < curpair) {
latest_pair[cur_nextid] = curpair;
is_complete[cur_nextid] = false;
}
}
}
for (curindex=qsptr[curq2]; curindex<qeptr[curq2]; ++curindex) {
cur_subreg=sjptr[curindex];
for (cur_nextanch=nasptr2[cur_subreg]; cur_nextanch<naeptr2[cur_subreg]; ++cur_nextanch) {
cur_nextid=niptr2[cur_nextanch];
/* Again, checking if overlap has already been added from the "A" cycle. Otherwise, we only add
* an overlap if anchor region 1 was overlapped by 'cur_nextid', as indicated by latest_pair
* (and is_complete is false, to avoid re-adding something that was added in this cycle).
*/
if (mode!=0 && latest_pair_A[cur_nextid] == curpair && is_complete_A[cur_nextid]) { continue; }
if (latest_pair[cur_nextid] == curpair && !is_complete[cur_nextid]) {
output->acknowledge(curpair, cur_nextid);
is_complete[cur_nextid] = true;
if (output->quit()) { // If we just want any hit, we go to the next 'curpair'.
goto outofnest;
}
}
}
}
}
outofnest:
output->postprocess();
}
return;
}