void set_untrusted(int val=1) {
flags().Untrusted = val;
}
bool is_untrusted_p() const {
if(reference_p()) {
return flags().Untrusted == 1;
}
return false;
}
bool check_type(object_type type) const {
return reference_p() && flags().obj_type == type;
}
bool in_immix_p() const {
return flags().InImmix == 1;
}
bool is_frozen_p() const {
return flags().Frozen == 1;
}
bool forwarded_p() const {
return flags().Forwarded == 1;
}
int which_mark() const {
return flags().Marked;
}
bool is_private () { return flags().is_private(); }
bool is_protected () { return flags().is_protected(); }
inline timezone get_timezone()
{
return (flags() & uses_local) ? timezone::local : timezone::utc;
}
// Java access flags
bool is_public () { return flags().is_public(); }
inline duration_style get_duration_style()
{
return (flags() & uses_symbol) ? duration_style::symbol : duration_style::prefix;
}
void Curve::intersect(StandardScene *scene, osg::Plane plane, osg::Polytope polytope, osg::Quat quat, bool culling) {
if (!scene) return;
this->m_segments.clear();
osgUtil::PlaneIntersector *picker = new osgUtil::PlaneIntersector(
osgUtil::Intersector::CoordinateFrame::WINDOW, plane, polytope);
osgUtil::IntersectionVisitor iv(picker);
iv.setTraversalMask(StandardScene::NodeMask::Pickable);
scene->screen().camera()->accept(iv);
if (picker->containsIntersections()) {
osgUtil::PlaneIntersector::Intersections &raws(picker->getIntersections());
// Detects and culls occlusion.
if (culling) {
// Rotates polylines to xy-plane.
std::vector<std::vector<bool> > flags(raws.size());
for (size_t i = 0; i < raws.size(); ++i) {
size_t size = raws[i].polyline.size();
flags[i].resize(size, true);
for (size_t j = 0; j < size; ++j) {
raws[i].polyline[j] = quat * raws[i].polyline[j];
raws[i].polyline[j].z() = 0;
}
}
// Sorts knots with respect to x-coordinate.
std::vector<std::pair<real_t, index_t> > knots;
for (size_t i = 0; i < raws.size(); ++i) {
for (size_t j = 0; j < raws[i].polyline.size(); ++j) {
knots.push_back(std::pair<real_t, index_t>(raws[i].polyline[j].x(), index_t(i, j)));
}
}
std::sort(knots.begin(), knots.end(), pred_t());
// Marks occluded knots.
for (size_t i = 0; i < raws.size(); ++i) {
for (size_t j = 0; j < raws[i].polyline.size() - 1; ++j) {
real_t x1 = raws[i].polyline[j].x(), x2 = raws[i].polyline[j + 1].x();
real_t y1 = raws[i].polyline[j].y(), y2 = raws[i].polyline[j + 1].y();
auto beg = std::lower_bound(knots.begin(), knots.end(), std::make_pair(std::min<real_t>(x1, x2), index_t()), pred_t()) + 1;
auto end = std::upper_bound(knots.begin(), knots.end(), std::make_pair(std::max<real_t>(x1, x2), index_t()), pred_t()) - 1;
for (auto iter = beg; iter < end; ++iter) {
real_t x = raws[iter->second.line].polyline[iter->second.knot].x();
real_t y = raws[iter->second.line].polyline[iter->second.knot].y();
real_t det = ((x - x1) * (y2 - y) - (y - y1) * (x2 - x)) * (x2 - x1);
if (det > 0) flags[iter->second.line][iter->second.knot] = false;
}
}
}
// Reconstructs polylines.
std::vector<std::vector<osg::Vec3d> > polylines;
for (size_t i = 0; i < raws.size(); ++i) {
polylines.push_back(std::vector<osg::Vec3d>());
for (size_t j = 0; j < raws[i].polyline.size(); ++j) {
if (flags[i][j]) polylines.back().push_back(raws[i].polyline[j]);
else {
if (polylines.back().size() < 2) polylines.back().clear();
else polylines.push_back(std::vector<osg::Vec3d>());
}
}
if (polylines.back().size() < 2) polylines.pop_back();
}
// Translates to matrix storage.
for (size_t i = 0; i < polylines.size(); ++i) {
size_t size = polylines[i].size();
this->m_segments.push_back(Segment(3, size));
for (size_t j = 0; j < size; ++j) {
this->m_segments.back().col(j) = algo::Util::toVector(polylines[i][j]);
}
this->m_segments.back().row(2).setZero();
}
} else {
// Translates to matrix storage.
for (size_t i = 0; i < raws.size(); ++i) {
size_t size = raws[i].polyline.size();
this->m_segments.push_back(Segment(3, size));
for (size_t j = 0; j < size; ++j) {
this->m_segments.back().col(j) = algo::Util::toVector(quat * raws[i].polyline[j]);
}
this->m_segments.back().row(2).setZero();
}
}
}
}
void IWnd_stc::UpdateStyle()
{
bool flag =
param.nlang == tempp.nlang &&
param.nsize == tempp.nsize &&
(param.flags.get(FLAG_FOLD) == tempp.flags.get(FLAG_FOLD)) &&
(param.flags.get(FLAG_SYNTAX) == tempp.flags.get(FLAG_SYNTAX))
;
param=tempp;
if(flag)
{
_DoUpdateStyle();
return;
}
BitFlags& flags(param.flags);
StcLangInfo& lf(StcManager::current().langs[param.nlang]);
wxFont fontNr (param.nsize, wxMODERN, wxNORMAL, wxNORMAL,false,str2wx(param.sface));
for (int Nr = 0; Nr < wxSTC_STYLE_LASTPREDEFINED; Nr++)
{
StyleSetFont (Nr, fontNr);
}
if(!flags.get(FLAG_FOLD))
{
ClearDocumentStyle();
}
StyleClearAll();
SetLexer (lf.lexer);
SetMarginType (StcManager::LINE_NR_ID, wxSTC_MARGIN_NUMBER);
StyleSetForeground (wxSTC_STYLE_LINENUMBER, wxColour (wxT("DARK GREY")));
StyleSetBackground (wxSTC_STYLE_LINENUMBER, *wxWHITE);
SetMarginWidth (StcManager::LINE_NR_ID, 0);
// set common styles
StyleSetForeground (wxSTC_STYLE_DEFAULT, wxColour (wxT("DARK GREY")));
StyleSetForeground (wxSTC_STYLE_INDENTGUIDE, wxColour (wxT("DARK GREY")));
SetMarginType(StcManager::DIVIDER_ID, wxSTC_MARGIN_SYMBOL);
SetMarginMask(StcManager::DIVIDER_ID, wxSTC_MASK_FOLDERS);
SetMarginWidth (StcManager::DIVIDER_ID, 0);
SetMarginSensitive (StcManager::DIVIDER_ID, false);
// folding
SetMarginType (StcManager::FOLDING_ID, wxSTC_MARGIN_SYMBOL);
SetMarginMask (StcManager::FOLDING_ID, wxSTC_MASK_FOLDERS);
StyleSetBackground (StcManager::FOLDING_ID, *wxWHITE);
SetMarginWidth (StcManager::FOLDING_ID, 0);
SetMarginSensitive (StcManager::FOLDING_ID, false);
if (flags.get(FLAG_FOLD))
{
SetMarginWidth (StcManager::FOLDING_ID,StcManager::FOLDING_MARGIN);
SetMarginSensitive (StcManager::FOLDING_ID, true);
SetPropertyEx ("fold", true);
SetPropertyEx ("fold.comment",true);
SetPropertyEx ("fold.compact",true);
SetPropertyEx ("fold.preprocessor",true);
SetPropertyEx ("fold.html", true);
SetPropertyEx ("fold.html.preprocessor",true);
SetPropertyEx ("fold.comment.python", true);
SetPropertyEx ("fold.quotes.python", true);
}
else
{
SetMarginWidth (StcManager::DIVIDER_ID, StcManager::FOLDING_MARGIN);
}
SetFoldFlags (wxSTC_FOLDFLAG_LINEBEFORE_CONTRACTED| wxSTC_FOLDFLAG_LINEAFTER_CONTRACTED);
if (flags.get(FLAG_SYNTAX))
{
int keywordnr = 0;
for(StcLangInfo::map_type::iterator it=lf.mapStyles.begin();it!=lf.mapStyles.end();++it)
{
int Nr=(*it).first;
StcLangInfo::StyleWords& s((*it).second);
StcStyleInfo& curType(StcManager::current().style[s.id]);
wxFont font (param.nsize, wxMODERN, wxNORMAL, wxNORMAL, false,str2wx(curType.fontname));
StyleSetFont (Nr, font);
if (curType.foreground!=wxEmptyString)
{
StyleSetForeground (Nr, wxColour (curType.foreground.c_str()));
}
if (curType.background!=wxEmptyString)
{
StyleSetBackground (Nr, wxColour (curType.background.c_str()));
}
StyleSetBold (Nr, curType.fontstyle.get(StcManager::STYLE_BOLD));
StyleSetItalic (Nr, curType.fontstyle.get(StcManager::STYLE_ITALIC));
StyleSetUnderline (Nr, curType.fontstyle.get(StcManager::STYLE_UNDERL));
StyleSetVisible (Nr, !curType.fontstyle.get(StcManager::STYLE_HIDDEN));
//StyleSetCase (Nr, curType.lettercase);
if (s.words!="")
{
SetKeyWords (keywordnr, str2wx(s.words));
keywordnr += 1;
}
}
}
_DoUpdateStyle();
Colourise(0,this->GetLastPosition());
}
gc_zone zone() const {
return flags().zone;
}
bool is_static () { return flags().is_static(); }
unsigned int age() const {
return flags().age;
}
bool is_final () { return flags().is_final(); }
bool marked_p(unsigned int which) const {
return flags().Marked == which;
}
bool is_volatile () { return flags().is_volatile(); }
bool pinned_p() const {
return flags().Pinned == 1;
}
bool is_transient () { return flags().is_transient(); }
bool remembered_p() const {
return flags().Remember == 1;
}
bool KWidget::hasContent()
{
return !(flags() & QGraphicsItem::ItemHasNoContents);
}
bool is_tainted_p() const {
if(reference_p()) {
return flags().Tainted == 1;
}
return false;
}
inline bool isContainer(int node) const { return flags(node) & Directory; }
object_type type_id() const {
return flags().obj_type;
}
inline bool isCompressed(int node) const { return flags(node) & Compressed; }
int main(int argc, char* argv[])
{
if(argc < 3)
{
std::cout
<< "Error: no se especificaron suficientes archivos de entrada."
<< std::endl;
return 1;
}
std::string filename1 = argv[1];
std::string filename2 = argv[2];
FASTAReader reader1(filename1);
FASTAReader reader2(filename2);
reader1.setDefault(0);
reader2.setDefault(1);
//matriz de sustitucion
int smatrix[]{ 5, -4, -4, -4,
-4, 5, -4, -4,
-4, -4, 5, -4,
-4, -4, -4, 5};
int gap_open = 10;
int gap_extend = 1;
int match = 5;
int mismatch = -4;
#pragma omp parallel
{
int seq_len = DEFAULT_SEQ_LEN;
//container vectors for sequences
Buffer<int16_t> seqs1(seq_len * VSIZE, ALNSIZE);
Buffer<int16_t> seqs2(seq_len * VSIZE, ALNSIZE);
//containers for ids
std::vector<std::string> seqs1_ids(VSIZE);
std::vector<std::string> seqs2_ids(VSIZE);
//legths of sequences
int seqs1_len[VSIZE];
int seqs2_len[VSIZE];
//containter for flags
Buffer<int8_t> flags(seq_len * seq_len * VSIZE, ALNSIZE);
int16_t __attribute((aligned(ALNSIZE))) scores[VSIZE];
int16_t __attribute((aligned(ALNSIZE))) ipos[VSIZE];
int16_t __attribute((aligned(ALNSIZE))) jpos[VSIZE];
//containers for arrays
int16_t inf = gap_open + gap_extend + 1;
//int16_t aF[256 * VSIZE] __attribute((aligned(ALNSIZE))) = {(int16_t)(-inf)};
//int16_t aH[256 * VSIZE] __attribute((aligned(ALNSIZE))) = {0};
int bsize = 128 * VSIZE;
//Buffer<int16_t> E(bsize, ALNSIZE);
Buffer<int16_t> F(bsize, ALNSIZE);
Buffer<int16_t> H(bsize, ALNSIZE);
//int16_t __attribute((aligned(ALNSIZE))) H[128 * VSIZE];
//alignments
char aln1[256];
char aln2[256];
//max sizes
int max_x, max_y;
//alignment start position
int x0, y0;
while(read_seqs(reader1, reader2, &seqs1, &seqs2, seqs1_len, seqs2_len,
&seqs1_ids, &seqs2_ids))
{
max_x = *std::max_element(seqs1_len, seqs1_len + VSIZE) + 1;
max_y = *std::max_element(seqs2_len, seqs2_len + VSIZE) + 1;
//E.clear(-inf);
F.clear(-inf);
H.clear(0);
//flags.clear(0);
smith_waterman(seqs1.data(), seqs2.data(), match, mismatch, gap_open, gap_extend,
flags.data(), scores, ipos, jpos, max_x, max_y, F.data(), H.data());
for(int i = 0; i < VSIZE; i++)
{
//std::cout << scores[i] << std::endl;
//std::cout << ipos[i] << std::endl;
//std::cout << jpos[i] << std::endl;
sw_backtrack(i, flags.data(), seqs1.data(), seqs2.data(), max_x, max_y,
aln1, aln2, ipos[i], jpos[i], x0, y0);
//puts(aln1);
//puts(aln2);
print_alignment (stdout, seqs1_ids, seqs2_ids, scores,
aln1, aln2, strlen(aln1), i);
}
}
}
return 0;
}
bool is_untrusted_p() {
return flags().Untrusted == 1;
}
