void test()
{
Segment *nil = NULL;
AATree<Segment*> segs(nil);
Segment *s[10];
for (int i = 0; i < 10; i++)
{
s[i] = new Segment(10, i);
}
segs.insert(0, s[0]);
segs.insert(10, s[1]);
segs.insert(10, s[2]);
segs.insert(30, s[3]);
}
cv::Mat ArmObjSegmentation::convertFlowToMat(GraphType *g, NodeTable& nt, int R, int C)
{
cv::Mat segs(R,C, CV_8UC1, cv::Scalar(0));
for (int r = 0; r < R; ++r)
{
uchar* seg_row = segs.ptr<uchar>(r);
for (int c = 0; c < C; ++c)
{
int idx = nt.find(r,c);
if (idx < 0) continue;
int label = (g->what_segment(idx) == GraphType::SOURCE);
seg_row[c] = label*255;
}
}
return segs;
}
Py::Object TriContourGenerator::contour_to_segs(const Contour& contour)
{
Py::List segs(contour.size());
for (Contour::size_type i = 0; i < contour.size(); ++i) {
const ContourLine& line = contour[i];
npy_intp dims[2] = {static_cast<npy_intp>(line.size()),2};
PyArrayObject* py_line = (PyArrayObject*)PyArray_SimpleNew(
2, dims, PyArray_DOUBLE);
double* p = (double*)PyArray_DATA(py_line);
for (ContourLine::const_iterator it = line.begin(); it != line.end(); ++it) {
*p++ = it->x;
*p++ = it->y;
}
segs[i] = Py::asObject((PyObject*)py_line);
}
return segs;
}
int solution(vector<int> &A) {
// write your code in C++11
int n = A.size();
vector<seg> segs(n);
for (int i = 0; i < n; i++) {
segs[i].left = (long long)i - (long long)A[i];
segs[i].right = (long long)i + (long long)A[i];
}
sort(segs.begin(), segs.end());
int sum = 0;
for (int i = 0; i < n - 1; i++) {
int b = search(segs, segs[i].right, i + 1, n - 1);
sum += b - i - 1;
if (sum > 10000000) {
return -1;
}
}
return sum;
}
void
SpectrogramData::updateData()
{
m_.clear();
size_t id1 = std::distance( spectra_->x().begin(), std::lower_bound( spectra_->x().begin(), spectra_->x().end(), xlimits_.first ) );
size_t id2 = std::distance( spectra_->x().begin(), std::lower_bound( spectra_->x().begin(), spectra_->x().end(), xlimits_.second ) );
size1_ = std::min( m_.size1(), id2 - id1 + 1 );
double z_max = std::numeric_limits<double>::lowest();
size_t id = 0;
for ( auto& ms: *spectra_ ) {
double x = spectra_->x()[ id++ ];
if ( xlimits_.first <= x && x <= xlimits_.second ) {
size_t ix = dx(x);
adcontrols::segment_wrapper< const adcontrols::MassSpectrum > segs( *ms );
for ( auto& seg: segs ) {
for ( size_t i = 0; i < seg.size(); ++i ) {
double m = seg.getMass( i );
if ( ylimits_.first < m && m < ylimits_.second ) {
size_t iy = dy(m);
m_( ix, iy ) += seg.getIntensity( i );
z_max = std::max( z_max, m_( ix, iy ) );
}
}
}
}
}
setInterval( Qt::XAxis, QwtInterval( spectra_->x_left(), spectra_->x_right() ) ); // time (sec -> min)
setInterval( Qt::YAxis, QwtInterval( spectra_->lower_mass(), spectra_->upper_mass() ) ); // m/z
#if 0 // normaize
m_ /= ( z_max / 1000.0 );
setInterval( Qt::ZAxis, QwtInterval( 0.0, 1000 ) );
#else
setInterval( Qt::ZAxis, QwtInterval( 0.0, z_max ) );
#endif
}
static void
cpMarchCellHard(
cpFloat t, cpFloat a, cpFloat b, cpFloat c, cpFloat d,
cpFloat x0, cpFloat x1, cpFloat y0, cpFloat y1,
cpMarchSegmentFunc segment, void *segment_data
){
// midpoints
cpFloat xm = cpflerp(x0, x1, 0.5f);
cpFloat ym = cpflerp(y0, y1, 0.5f);
switch((a>t)<<0 | (b>t)<<1 | (c>t)<<2 | (d>t)<<3){
case 0x1: segs(cpv(x0, ym), cpv(xm, ym), cpv(xm, y0), segment, segment_data); break;
case 0x2: segs(cpv(xm, y0), cpv(xm, ym), cpv(x1, ym), segment, segment_data); break;
case 0x3: seg(cpv(x0, ym), cpv(x1, ym), segment, segment_data); break;
case 0x4: segs(cpv(xm, y1), cpv(xm, ym), cpv(x0, ym), segment, segment_data); break;
case 0x5: seg(cpv(xm, y1), cpv(xm, y0), segment, segment_data); break;
case 0x6: segs(cpv(xm, y0), cpv(xm, ym), cpv(x0, ym), segment, segment_data);
segs(cpv(xm, y1), cpv(xm, ym), cpv(x1, ym), segment, segment_data); break;
case 0x7: segs(cpv(xm, y1), cpv(xm, ym), cpv(x1, ym), segment, segment_data); break;
case 0x8: segs(cpv(x1, ym), cpv(xm, ym), cpv(xm, y1), segment, segment_data); break;
case 0x9: segs(cpv(x1, ym), cpv(xm, ym), cpv(xm, y0), segment, segment_data);
segs(cpv(x0, ym), cpv(xm, ym), cpv(xm, y1), segment, segment_data); break;
case 0xA: seg(cpv(xm, y0), cpv(xm, y1), segment, segment_data); break;
case 0xB: segs(cpv(x0, ym), cpv(xm, ym), cpv(xm, y1), segment, segment_data); break;
case 0xC: seg(cpv(x1, ym), cpv(x0, ym), segment, segment_data); break;
case 0xD: segs(cpv(x1, ym), cpv(xm, ym), cpv(xm, y0), segment, segment_data); break;
case 0xE: segs(cpv(xm, y0), cpv(xm, ym), cpv(x0, ym), segment, segment_data); break;
default: break; // 0x0 and 0xF
}
}
void CAlnVec::CreateConsensus(vector<string>& consens) const
{
bool isNucleotide = GetBioseqHandle(0).IsNucleotide();
const int numBases = isNucleotide ? 4 : 26;
int base_count[26]; // must be a compile-time constant for some compilers
// determine what the number of segments required for a gapped consensus
// segment is. this must be rounded to be at least 50%.
int gap_seg_thresh = m_NumRows - m_NumRows / 2;
for (size_t j = 0; j < (size_t)m_NumSegs; ++j) {
// evaluate for gap / no gap
int gap_count = 0;
for (size_t i = 0; i < (size_t)m_NumRows; ++i) {
if (m_Starts[ j*m_NumRows + i ] == -1) {
++gap_count;
}
}
// check to make sure that this seg is not a consensus
// gap seg
if ( gap_count > gap_seg_thresh )
continue;
// the base threshold for being considered unique is at least
// 70% of the available sequences
int base_thresh =
((m_NumRows - gap_count) * 7 + 5) / 10;
{
// we will build a segment with enough bases to match
consens[j].resize(m_Lens[j]);
// retrieve all sequences for this segment
vector<string> segs(m_NumRows);
RetrieveSegmentSequences(j, segs);
TransposeSequences(segs);
typedef multimap<int, unsigned char, greater<int> > TRevMap;
//
// evaluate for a consensus
//
for (size_t i = 0; i < m_Lens[j]; ++i) {
if (isNucleotide) {
CollectNucleotideFrequences(segs[i], base_count, numBases);
} else {
CollectProteinFrequences(segs[i], base_count, numBases);
}
// we create a sorted list (in descending order) of
// frequencies of appearance to base
// the frequency is "global" for this position: that is,
// if 40% of the sequences are gapped, the highest frequency
// any base can have is 0.6
TRevMap rev_map;
for (int k = 0; k < numBases; ++k) {
// this gets around a potentially tricky idiosyncrasy
// in some implementations of multimap. depending on
// the library, the key may be const (or not)
TRevMap::value_type p(base_count[k], isNucleotide ? (1<<k) : k);
rev_map.insert(p);
}
// now, the first element here contains the best frequency
// we scan for the appropriate bases
if (rev_map.count(rev_map.begin()->first) == 1 &&
rev_map.begin()->first >= base_thresh) {
consens[j][i] = isNucleotide ?
ToIupac(rev_map.begin()->second) :
(rev_map.begin()->second+'A');
} else {
// now we need to make some guesses based on IUPACna
// notation
int count;
unsigned char c = 0x00;
int freq = 0;
TRevMap::iterator curr = rev_map.begin();
TRevMap::iterator prev = rev_map.begin();
for (count = 0;
curr != rev_map.end() &&
(freq < base_thresh || prev->first == curr->first);
++curr, ++count) {
prev = curr;
freq += curr->first;
if (isNucleotide) {
c |= curr->second;
} else {
unsigned char cur_char = curr->second+'A';
switch (c) {
case 0x00:
c = cur_char;
break;
case 'N': case 'D':
c = (cur_char == 'N' || cur_char == 'N') ? 'B' : 'X';
break;
case 'Q': case 'E':
c = (cur_char == 'Q' || cur_char == 'E') ? 'Z' : 'X';
break;
case 'I': case 'L':
c = (cur_char == 'I' || cur_char == 'L') ? 'J' : 'X';
break;
default:
c = 'X';
}
}
}
//
// catchall
//
if (count > 2) {
consens[j][i] = isNucleotide ? 'N' : 'X';
} else {
consens[j][i] = isNucleotide ? ToIupac(c) : c;
}
}
}
}
}
}
static int three_register_execute(UM_machine machine,
Um_instruction instruction)
{
unsigned op = Bitpack_getu(instruction, BITS_PER_OP_CODE, 28);
unsigned A = Bitpack_getu(instruction, BITS_PER_REG_NUM, 6);
unsigned B = Bitpack_getu(instruction, BITS_PER_REG_NUM, 3);
unsigned C = Bitpack_getu(instruction, BITS_PER_REG_NUM, 0);
switch(op){
case 0: //
movc(machine, A, B, C);
return 1;
case 1:
segl(machine, A, B, C);
return 1;
case 2:
segs(machine, A, B, C);
return 1;
case 3:
add(machine, A, B, C);
return 1;
case 4:
mult(machine, A, B, C);
return 1;
case 5:
divi(machine, A, B, C);
return 1;
case 6:
nand(machine, A, B, C);
return 1;
case 7:
return 0;
case 8:
map(machine, B, C);
return 1;
case 9:
unmap(machine, C);
return 1;
case 10:
out(machine, C);
return 1;
case 11:
in(machine, C);
return 1;
case 12:
loadp(machine, B, C);
return 1;
default:
return 0;
}
}
