bool TableRowElement::moveCursor(FormulaCursor& newcursor, FormulaCursor& oldcursor)
{
//TODO: Moving the cursor vertically in the tableelement is a little bit fragile
if ( (newcursor.isHome() && newcursor.direction()==MoveLeft) ||
(newcursor.isEnd() && newcursor.direction()==MoveRight) ) {
return false;
}
int rowpos=parentElement()->positionOfChild(this);
int colpos=(newcursor.position()!=endPosition() ? newcursor.position() : newcursor.position()-1);
if (newcursor.isSelecting()) {
switch(newcursor.direction()) {
case MoveLeft:
newcursor.moveTo(this,newcursor.position()-1);
break;
case MoveRight:
newcursor.moveTo(this,newcursor.position()+1);
break;
case MoveUp:
case MoveDown:
return false;
default:
break;
}
} else {
switch(newcursor.direction()) {
case MoveLeft:
newcursor.setCurrentElement(m_data[newcursor.position()-1]);
newcursor.moveEnd();
break;
case MoveRight:
newcursor.setCurrentElement(m_data[newcursor.position()]);
newcursor.moveHome();
break;
case MoveUp:
if ( rowpos>1 ) {
BasicElement* b=parentElement()->childElements()[rowpos/2-1]->childElements()[colpos];
return newcursor.moveCloseTo(b, oldcursor);
} else {
return false;
}
case MoveDown:
if ( rowpos<endPosition()-1 ) {
BasicElement* b=parentElement()->childElements()[rowpos/2+1]->childElements()[colpos];
return newcursor.moveCloseTo(b, oldcursor);
} else {
return false;
}
default:
break;
}
}
return true;
}
// This avoids the expense of a full fledged delete operation, and avoids a layout that typically results
// from text removal.
bool InsertTextCommand::performTrivialReplace(const String& text, bool selectInsertedText)
{
if (!endingSelection().isRange())
return false;
if (text.contains('\t') || text.contains(' ') || text.contains('\n'))
return false;
Position start = endingSelection().start();
Position end = endingSelection().end();
if (start.node() != end.node() || !start.node()->isTextNode() || isTabSpanTextNode(start.node()))
return false;
replaceTextInNode(static_cast<Text*>(start.node()), start.offset(), end.offset() - start.offset(), text);
Position endPosition(start.node(), start.offset() + text.length());
// We could have inserted a part of composed character sequence,
// so we are basically treating ending selection as a range to avoid validation.
// <http://bugs.webkit.org/show_bug.cgi?id=15781>
Selection forcedEndingSelection;
forcedEndingSelection.setWithoutValidation(start, endPosition);
setEndingSelection(forcedEndingSelection);
if (!selectInsertedText)
setEndingSelection(Selection(endingSelection().visibleEnd()));
return true;
}
vector<Pixel> Line::getPixels() const{
int x1 = mBeginPoint.x;
int x0 = mEndPoint.x;
int y1 = mBeginPoint.y;
int y0 = mEndPoint.y;
int dx = abs(x1-x0), sx = x0<x1 ? 1 : -1;
int dy = -abs(y1-y0), sy = y0<y1 ? 1 : -1;
int err = dx+dy, e2; /* error value e_xy */
vector<Pixel> pixels;
for(;;){ /* loop */
Point position(x0,y0);
Pixel pixel(position,mColor);
pixels.push_back(pixel);
if (x0==x1 && y0==y1) break;
e2 = 2*err;
if (e2 >= dy) { err += dy; x0 += sx; } /* e_xy+e_x > 0 */
if (e2 <= dx) { err += dx; y0 += sy; } /* e_xy+e_y < 0 */
}
for (int i=0;i<pixels.size();i++) {
Point initialPosition = pixels[i].getPosition();
Point endPosition(initialPosition.x+mPositionX,initialPosition.y+mPositionY);
pixels[i].setPosition(endPosition);
}
return pixels;
}
vector<Pixel> ClipDrawable::getPixels() const{
vector<Pixel> pixels;
Point viewPortStart(mPositionX,mPositionY);
Point viewPortEnd(mPositionX+mWidth,mPositionY+mHeight);
Rectangle border(viewPortStart,mWidth,mHeight,Color(255,0,0,0));
vector<Pixel> borderPixel = border.getPixels();
pixels.insert(pixels.end(),borderPixel.begin(),borderPixel.end());
vector<Line> lines = mWorldMap.getLines();
for (int i=0;i<lines.size();i++) {
Line lineInView = CohenShutterlandAlgorithm::getLineInView(scaleLineToView(lines[i]),viewPortStart,viewPortEnd);
vector<Pixel> linePixels = lineInView.getPixels();
pixels.insert(pixels.end(),linePixels.begin(),linePixels.end());
}
for (int i=0;i<pixels.size();i++) {
Point initialPosition = pixels[i].getPosition();
Point endPosition(initialPosition.x+mPositionX,initialPosition.y+mPositionY);
pixels[i].setPosition(endPosition);
}
return pixels;
}
void Segment::rotateAll(vec3 rotation) {
rotate(rotation);
for(int i = 0; i < nextSegments.size(); i++) {
nextSegments[i]->movePosition(vec3(endPosition()));
nextSegments[i]->rotateAll(rotation);
}
}
void PositionInterpolatorTests::testExtremes( TestReporter& reporter )
{
NEW_TEST_FUNCTION( reporter );
PositionInterpolator interpolator;
PositionInterpolatorTester tester( interpolator );
interpolator.disableMC2Conversion();
/**
*
* No data. No correct calculations or assumptions could be made,
* so the position 0, 0 is returned.
*
*/
CHECK( !tester.getPosition( 1000 ).isValid(), reporter );
InterpolationHintConsumer& pathConsumer = interpolator;
pathConsumer.prepareNewData( 1000 );
MC2Coordinate checkPosition( 1337, 1337 );
static const int MPSToCmPS = 100;
pathConsumer.addDataPoint( checkPosition, 10 * MPSToCmPS );
pathConsumer.finalizeNewData();
/**
* Only single point, should return point itself.
*/
CHECK( tester.getPosition( 0 ) == checkPosition, reporter );
CHECK( tester.getPosition( 1000 ) == checkPosition, reporter );
CHECK( tester.getPosition( 2000 ) == checkPosition, reporter );
/**
* Two points, test outside scope on both sides of the interval.
* Should be clamped to endpoints.
*/
MC2Coordinate endPosition( 1338, 1338 );
pathConsumer.addDataPoint( endPosition, 10 * MPSToCmPS );
pathConsumer.finalizeNewData();
/**
* Seconds to millisecond conversion unit.
*/
static const int sToMs = 1000;
CHECK( tester.getPosition( 0 ) == checkPosition,
reporter );
CHECK( tester.getPosition( 500000 * sToMs ) == endPosition,
reporter );
}
void DocumentMarkerControllerTest::markNodeContentsWithComposition(Node* node)
{
// Force layoutObjects to be created; TextIterator, which is used in
// DocumentMarkerControllerTest::addMarker(), needs them.
document().updateStyleAndLayout();
auto range = EphemeralRange::rangeOfContents(*node);
markerController().addCompositionMarker(range.startPosition(), range.endPosition(), Color::black, false, Color::black);
}
void Segment::getEndEffectors(vector<vec3> &endEffectors) {
int segs = nextSegments.size();
if(segs == 0)
endEffectors.push_back(vec3(endPosition()));
for(int i = 0; i < segs; i++) {
nextSegments[i]->getEndEffectors(endEffectors);
}
}
void DocumentMarkerControllerTest::markNodeContents(PassRefPtrWillBeRawPtr<Node> node)
{
// Force layoutObjects to be created; TextIterator, which is used in
// DocumentMarkerControllerTest::addMarker(), needs them.
document().updateLayout();
auto range = EphemeralRange::rangeOfContents(*node);
markerController().addMarker(range.startPosition(), range.endPosition(), DocumentMarker::Spelling);
}
EphemeralRangeTemplate<Strategy> CharacterIteratorAlgorithm<Strategy>::calculateCharacterSubrange(int offset, int length)
{
advance(offset);
const PositionAlgorithm<Strategy> startPos = startPosition();
if (length > 1)
advance(length - 1);
return EphemeralRangeTemplate<Strategy>(startPos, endPosition());
}
PreviewBoard::PreviewBoard(DockPreviewBoard* dockPreviewBoard, QWidget *parent) : QWidget(parent),
dockPreviewBoard_(dockPreviewBoard)
{
srand ( time(NULL) );
for (int x = 0; x < 19; x++) {
for (int y = 0; y < 19; y++) {
whiteStoneType_[x][y] = rand()%35; // between 0 and 35
board_[x][y] = 0;
}
}
// boards.clear();
// resize(400, 400);
// setMinimumSize ( 200, 200 ); //int minw, int minh
// setMaximumSize ( 600, 600 );
// setSizeIncrement ( 0, 0 );
setMouseTracking (true);
QString boardDir = Resources::path();
origBoardImage = QPixmap(boardDir + "Beige1.png");
QPalette palette;
palette.setBrush(backgroundRole(), QBrush(origBoardImage));
setPalette(palette);
setAutoFillBackground ( true );
//connect(this, SIGNAL(click()), this, SLOT(makeFocus()));
previewBoardMenu = new QMenu("Preview board menu", this);
// boardMenu->setTitle ("Preview board menu");
positionActions_ = new QActionGroup(this);
positionActions_->setExclusive(true);
currentPositionAct = new QAction(tr("&Current board position"), this);
currentPositionAct->setCheckable(true);
nextPositionAct = new QAction(tr("&Board next move"), this);
nextPositionAct->setCheckable(true);
endPositionAct = new QAction(tr("&End position"), this);
endPositionAct->setCheckable(true);
positionActions_->addAction (currentPositionAct);
positionActions_->addAction (nextPositionAct);
positionActions_->addAction (endPositionAct);
previewBoardMenu->addActions(positionActions_->actions());
connect(currentPositionAct, SIGNAL(triggered()), this, SLOT(currentPosition()));
connect(nextPositionAct, SIGNAL(triggered()), this, SLOT(nextPosition()));
connect(endPositionAct, SIGNAL(triggered()), this, SLOT(endPosition()));
}
void check_cutted_frags(CharString frag, std::vector<table_entry*> &links,
map<unsigned long long, string> &chains, unsigned int min_length){
if(length(frag) > min_length){
std::queue<int> l_link;
std::queue<int> r_link;
Pattern<CharString, ShiftOr > pattern(frag);
for(unsigned int i=0; i<links.size(); ++i){
CharString text = links[i]->get_short_read()->get_RNA_seq_sequence();
Finder<CharString> finder(text);
find(finder,pattern);
if(beginPosition(finder) < min_length){
//std::cout << "L link " << i << ::std::endl;
l_link.push(i);
}
if(endPosition(finder) > length(text) - min_length){
//std::cout << "R link" << ::std::endl;
r_link.push(i);
}
}
if(l_link.size() != 0 && r_link.size() != 0){
string head;
assign(head,frag);
for(unsigned int z=0; z<min_length*2 - length(frag);++z){
head.append("A");
}
if(chains.find(fingerprint(head)) == chains.end()){
chains[fingerprint(head)] = toCString(frag);
//std::cerr << "CUT: " << frag << " " << length(frag) << std::endl;
}else{
//std::cerr << "Problem:" << std::endl;
//std::cerr << chains[fingerprint(head)] << std::endl;
//std::cerr << toCString(frag) << std::endl;
}
//::std::cout << toCString(frag) << ::std::endl;
while(!l_link.empty()){
links[l_link.front()]->push_D_link(fingerprint(head));
l_link.pop();
}
while(!r_link.empty()){
links[r_link.front()]->push_A_link(fingerprint(head));
r_link.pop();
}
}
}
}
TEST_F(OsgScreenSpaceQuadRenderTests, InitTest)
{
std::shared_ptr<OsgScreenSpaceQuadRepresentation> quad =
std::make_shared<OsgScreenSpaceQuadRepresentation>("Screen Quad");
viewElement->addComponent(quad);
/// Run the thread
runtime->start();
EXPECT_TRUE(graphicsManager->isInitialized());
EXPECT_TRUE(viewElement->isInitialized());
quad->setSize(100, 100);
boost::this_thread::sleep(boost::posix_time::milliseconds(1000));
auto dimensions = viewElement->getView()->getDimensions();
SurgSim::Math::Vector3d startPosition(0.0, 0.0, 0.0);
SurgSim::Math::Vector3d endPosition(dimensions[0], dimensions[1], 0.0);
SurgSim::Math::Vector2d startSize(0.0, 0.0);
SurgSim::Math::Vector2d endSize(200, 200);
int numSteps = 100;
for (int i = 0; i < numSteps; ++i)
{
/// Calculate t in [0.0, 1.0]
double t = static_cast<double>(i) / numSteps;
RigidTransform3d currentPose = SurgSim::Testing::interpolatePose(
Vector3d::Identity(), Vector3d::Identity(),
startPosition, endPosition, t);
quad->setLocalPose(currentPose);
SurgSim::Math::Vector2d size = SurgSim::Testing::interpolate(startSize, endSize, t);
quad->setSize(size.x(), size.y());
boost::this_thread::sleep(boost::posix_time::milliseconds(1000 / numSteps));
}
}
bool TableRowElement::setCursorTo(FormulaCursor& cursor, QPointF point)
{
if (cursor.isSelecting()) {
if (m_data.isEmpty() || point.x()<0.0) {
cursor.setCurrentElement(this);
cursor.setPosition(0);
return true;
}
//check if the point is behind all child elements
if (point.x() >= width()) {
cursor.setCurrentElement(this);
cursor.setPosition(endPosition());
return true;
}
}
int i=0;
qreal x=0.0;
TableElement* parentTable = static_cast<TableElement*>( parentElement() );
for (; i<m_data.count()-1; ++i) {
//Find the child element the point is in
x+=parentTable->columnWidth( i );
if (x>=point.x()) {
break;
}
}
if (cursor.isSelecting()) {
//we don't need to change current element because we are already in this element
if (cursor.mark()<=i) {
cursor.setPosition(i+1);
}
else {
cursor.setPosition(i);
}
return true;
} else {
point-=m_data[i]->origin();
return m_data[i]->setCursorTo(cursor,point);
}
}
void linking_refinement(::std::vector<table_entry*> & links, map<unsigned long long, string> & chains, unsigned int len,
::std::map<unsigned long long, unsigned long long> & mapping){
for(unsigned int i=0; i<links.size(); ++i){
//Linkato solo a dx
if(links[i]->size_D_link() == 0 && links[i]->size_A_link() != 0){
//::std::cout << "D link" << ::std::endl;
CharString p = ::seqan::prefix(links[i]->get_short_read()->get_RNA_seq_sequence(),len);
Pattern<CharString, ShiftOr > pattern(p);
::std::map<unsigned long long, string>::iterator chain_it;
::std::set<unsigned long long> modif_chains;
for(chain_it = chains.begin(); chain_it != chains.end(); ++chain_it){
CharString text = chain_it->second;
Finder<CharString> finder(text);
if(modif_chains.find(chain_it->first) == modif_chains.end() && find(finder,pattern)){
links[i]->push_D_link(chain_it->first);
if(chain_it->second.length()- endPosition(finder) > len){
//::std::cout << "D " << (i+1) << " " << beginPosition(finder) << ::std::endl;
CharString pre = ::seqan::prefix(chain_it->second, beginPosition(finder) + len);
string str_pre = ::seqan::toCString(pre);
CharString suf = ::seqan::suffix(chain_it->second, beginPosition(finder) + len);
string str_suf = ::seqan::toCString(suf);
//::std::cout << chain_it->second << " - " << chain_it->second.length() << ::std::endl;
//Sono sicuro che sia > len dato che la estraggo da un prefisso
//di lunghezza len...
chains[chain_it->first] = str_pre;
//::std::cout << str_pre << " - " << str_pre.length() << ::std::endl;
modif_chains.insert(chain_it->first);
//...ma il suffissopotrebbe essere piu' corto di len
string head;
if(str_suf.length() >= len){
head = ::seqan::toCString(::seqan::prefix(suf,len));
chains[fingerprint(head)] = str_suf;
mapping[fingerprint(head)] = fingerprint(head);
}else{
head = str_suf;
for(unsigned int z=0; z<len-str_suf.length();++z){
head.append("A");
}
chains[fingerprint(head)] = str_suf;
mapping[fingerprint(head)] = fingerprint(head);
}
//::std::cout << str_suf << " - " << str_suf.length() << ::std::endl << ::std::endl;
modif_chains.insert(fingerprint(head));
for(unsigned int z=0; z<links.size();++z){
for(int k=0; k<links[z]->size_D_link();++k){
if(links[z]->at_D_link(k) == chain_it->first){
links[z]->at_D_link(k) = fingerprint(head);
}
}
}
//Aggiungere un link tra le due catene create
CharString l_part = chains[chain_it->first];
string new_link = ::seqan::toCString(::seqan::suffix(l_part,length(l_part) - len));
unsigned long long f_l = fingerprint(new_link);
new_link.append(head);
table_entry* t_new = new table_entry(new_link,f_l,fingerprint(head));
t_new->push_D_link(chain_it->first);
t_new->push_A_link(fingerprint(head));
links.push_back(t_new);
}
}
}
}
//Linkato solo a sx
if(links[i]->size_A_link() == 0 && links[i]->size_D_link() != 0){
//::std::cout << "A link" << ::std::endl;
CharString p = ::seqan::suffix(links[i]->get_short_read()->get_RNA_seq_sequence(),len);
Pattern<CharString, ShiftOr > pattern(p);
::std::map<unsigned long long, string>::iterator chain_it;
::std::set<unsigned long long> modif_chains;
for(chain_it = chains.begin(); chain_it != chains.end(); ++chain_it){
CharString text = chain_it->second;
Finder<CharString> finder(text);
if(modif_chains.find(chain_it->first) == modif_chains.end() && find(finder,pattern)){
//if(find(finder,pattern)){
//::std::cout << "1 - if " << beginPosition(finder) << " " << endPosition(finder) << ::std::endl;
if(beginPosition(finder) == 0){
links[i]->push_A_link(chain_it->first);
}
if(endPosition(finder) > len){
//::std::cout << "A " << (i+1) << " " << beginPosition(finder) << ::std::endl;
CharString pre = ::seqan::prefix(chain_it->second, beginPosition(finder) + len);
string str_pre = ::seqan::toCString(pre);
CharString suf = ::seqan::suffix(chain_it->second, beginPosition(finder) + len);
string str_suf = ::seqan::toCString(suf);
chains[chain_it->first] = str_pre;
//::std::cout << str_pre << " - " << str_pre.length() << ::std::endl;
modif_chains.insert(chain_it->first);
string head;
if(str_suf.length() >= len){
head = ::seqan::toCString(::seqan::prefix(suf,len));
chains[fingerprint(head)] = str_suf;
mapping[fingerprint(head)] = fingerprint(head);
}else{
head = str_suf;
for(unsigned int z=0; z<len-str_suf.length();++z){
head.append("A");
}
chains[fingerprint(head)] = str_suf;
mapping[fingerprint(head)] = fingerprint(head);
}
//::std::cout << str_suf << " - " << str_suf.length() << ::std::endl << ::std::endl;
modif_chains.insert(fingerprint(head));
for(unsigned int z=0; z<links.size();++z){
for(int k=0; k<links[z]->size_D_link();++k){
if(links[z]->at_D_link(k) == chain_it->first){
links[z]->at_D_link(k) = fingerprint(head);
}
}
}
//Aggiungere un link tra le due catene create
CharString l_part = chains[chain_it->first];
string new_link = ::seqan::toCString(::seqan::suffix(l_part,length(l_part) - len));
unsigned long long f_l = fingerprint(new_link);
new_link.append(head);
table_entry* t_new = new table_entry(new_link,f_l,fingerprint(head));
t_new->push_D_link(chain_it->first);
t_new->push_A_link(fingerprint(head));
links.push_back(t_new);
links[i]->push_A_link(fingerprint(head));
}
}
}
}
}
//::std::cout << chains.size() << ::std::endl;
}
iterator& end() const {
iterator it(this, endPosition());
itend = it;
return itend;
}
EphemeralRange PlainTextRange::createRangeFor(const ContainerNode& scope, GetRangeFor getRangeFor) const
{
ASSERT(isNotNull());
size_t docTextPosition = 0;
bool startRangeFound = false;
Position textRunStartPosition;
Position textRunEndPosition;
TextIteratorBehaviorFlags behaviorFlags = TextIteratorEmitsObjectReplacementCharacter;
if (getRangeFor == ForSelection)
behaviorFlags |= TextIteratorEmitsCharactersBetweenAllVisiblePositions;
auto range = EphemeralRange::rangeOfContents(scope);
TextIterator it(range.startPosition(), range.endPosition(), behaviorFlags);
// FIXME: the atEnd() check shouldn't be necessary, workaround for
// <http://bugs.webkit.org/show_bug.cgi?id=6289>.
if (!start() && !length() && it.atEnd())
return EphemeralRange(Position(it.currentContainer(), 0));
Position resultStart = Position(&scope.document(), 0);
Position resultEnd = resultStart;
for (; !it.atEnd(); it.advance()) {
int len = it.length();
textRunStartPosition = it.startPositionInCurrentContainer();
textRunEndPosition = it.endPositionInCurrentContainer();
bool foundStart = start() >= docTextPosition && start() <= docTextPosition + len;
bool foundEnd = end() >= docTextPosition && end() <= docTextPosition + len;
// Fix textRunRange->endPosition(), but only if foundStart || foundEnd, because it is only
// in those cases that textRunRange is used.
if (foundEnd) {
// FIXME: This is a workaround for the fact that the end of a run
// is often at the wrong position for emitted '\n's or if the
// layoutObject of the current node is a replaced element.
if (len == 1 && (it.characterAt(0) == '\n' || it.isInsideAtomicInlineElement())) {
it.advance();
if (!it.atEnd()) {
textRunEndPosition = it.startPositionInCurrentContainer();
} else {
Position runEnd = nextPositionOf(createVisiblePosition(textRunStartPosition)).deepEquivalent();
if (runEnd.isNotNull())
textRunEndPosition = runEnd;
}
}
}
if (foundStart) {
startRangeFound = true;
if (textRunStartPosition.computeContainerNode()->isTextNode()) {
int offset = start() - docTextPosition;
resultStart = Position(textRunStartPosition.computeContainerNode(), offset + textRunStartPosition.offsetInContainerNode());
} else {
if (start() == docTextPosition)
resultStart = textRunStartPosition;
else
resultStart = textRunEndPosition;
}
}
if (foundEnd) {
if (textRunStartPosition.computeContainerNode()->isTextNode()) {
int offset = end() - docTextPosition;
resultEnd = Position(textRunStartPosition.computeContainerNode(), offset + textRunStartPosition.offsetInContainerNode());
} else {
if (end() == docTextPosition)
resultEnd = textRunStartPosition;
else
resultEnd = textRunEndPosition;
}
docTextPosition += len;
break;
}
docTextPosition += len;
}
if (!startRangeFound)
return EphemeralRange();
if (length() && end() > docTextPosition) { // end() is out of bounds
resultEnd = textRunEndPosition;
}
return EphemeralRange(resultStart.toOffsetInAnchor(), resultEnd.toOffsetInAnchor());
}
void check_overlapping_nodes(::std::vector<table_entry*> & links, map<unsigned long long, string> & chains, int len,
::std::map<unsigned long long, unsigned long long>& mapping, unsigned int min_overlap,
int ov_perc){
::std::map<unsigned long long, string>::iterator chain_it;
::std::map<unsigned long long, string>::iterator chain_it_2;
::std::vector<small_frag> short_blocks;
stack<unsigned int> s;
queue<unsigned long long> q;
for(chain_it = chains.begin(); chain_it != chains.end(); ++chain_it){
for(chain_it_2 = chains.begin(); chain_it_2 != chains.end(); ++chain_it_2){
unsigned int ov = overlappedStringLength(chain_it->second,chain_it_2->second);
if(chain_it != chain_it_2 && ov < (ov_perc*chain_it->second.length())/100 &&
(ov_perc*ov < chain_it_2->second.length())/100 && ov > min_overlap){
bool new_node = false;
CharString pat_text=prefix(chain_it_2->second,ov);
//::std::cout << chain_it->second << ::std::endl;
//::std::cout << chain_it_2->second << ::std::endl;
//::std::cout << ov << ::std::endl;
Pattern<CharString, ShiftAnd> pattern(pat_text);
for(unsigned int i=0; i<links.size();++i){
CharString link_read = links[i]->get_short_read()->get_RNA_seq_sequence();
Finder<CharString> finder(link_read);
if(find(finder,pattern) && (
prefix(link_read,beginPosition(finder)) == infix(chain_it->second,chain_it->second.length()-ov-beginPosition(finder),chain_it->second.length()-ov) ||
suffix(link_read,length(link_read) - endPosition(finder)) == infix(chain_it_2->second,ov,ov+endPosition(finder)))){
//::std::cout << link_read << ::std::endl;
//::std::cout << prefix(link_read,beginPosition(finder)) << ::std::endl;
//::std::cout << infix(chain_it->second,chain_it->second.length()-ov-beginPosition(finder),chain_it->second.length()-ov) << ::std::endl;
//::std::cout << suffix(link_read,length(link_read) - endPosition(finder)) << ::std::endl;
//::std::cout << infix(chain_it_2->second,ov,ov+endPosition(finder)) << ::std::endl;
new_node = true;
}
}
if(new_node){
small_frag f;
f.frag_links.D_chain = chain_it->first;
f.frag_links.A_chain = chain_it_2->first;
f.frag = prefix(chain_it_2->second,ov);
short_blocks.push_back(f);
}
}else{
if(chain_it != chain_it_2 && ov>=(ov_perc*chain_it->second.length())/100){
//::std::cout << "Chain_it sub-node of Chain_it_2" << ::std::endl;
//::std::cout << "Chain_it " << chain_it->second << ::std::endl;
//::std::cout << "Chain_it_2 " << chain_it_2->second << ::std::endl;
//::std::cout << ov << ::std::endl;
q.push(chain_it->first);
}else{
if(chain_it != chain_it_2 && ov>=(ov_perc*chain_it_2->second.length())/100){
//::std::cout << "Chain_it_2 sub-node of Chain_it" << ::std::endl;
//::std::cout << "Chain_it " << chain_it->second << ::std::endl;
//::std::cout << "Chain_it_2 " <<chain_it_2->second << ::std::endl;
//::std::cout << ov << ::std::endl;
q.push(chain_it_2->first);
}
}
}
}
}
for(unsigned int i=0; i<short_blocks.size(); ++i){
bool sub_seq = false;
for(unsigned int k=0; k<short_blocks.size(); ++k){
if(short_blocks[i].frag == short_blocks[k].frag && i<k){
links_pair erased_links;
erased_links.D_chain = short_blocks[i].frag_links.D_chain;
erased_links.A_chain = short_blocks[i].frag_links.A_chain;
short_blocks[k].other_links.push_back(erased_links);
sub_seq = true;
}
if(i!=k && (::seqan::length(short_blocks[i].frag)) < (::seqan::length(short_blocks[k].frag))){
Finder<CharString> finder(short_blocks[k].frag);
Pattern<CharString, ShiftAnd> pattern(short_blocks[i].frag);
if(find(finder,pattern)){
links_pair erased_links;
erased_links.D_chain = short_blocks[i].frag_links.D_chain;
erased_links.A_chain = short_blocks[i].frag_links.A_chain;
//::std::cout << i << k << " - " << beginPosition(finder) << " " << endPosition(finder) << ::std::endl;
short_blocks[k].other_links.push_back(erased_links);
sub_seq = true;
}
}
}
if(sub_seq){
s.push(i);
}
}
while(!s.empty()){
short_blocks.erase(short_blocks.begin()+s.top());
s.pop();
}
while(!q.empty()){
chains.erase(q.front());
q.pop();
}
for(unsigned int i=0; i<short_blocks.size(); ++i){
//::std::cout << short_blocks[i].frag << " " << length(short_blocks[i].frag) << ::std::endl;
string ch = "";
for(unsigned int z = 0; z<len-length(short_blocks[i].frag); ++z){
ch.append("A");
}
ch.append(toCString(short_blocks[i].frag));
//if(chains.find(fingerprint(ch)) == chains.end()){//Start_If_5
//chains[fingerprint(ch)] = ::seqan::toCString(short_blocks[i].frag);
//::std::cout << ::seqan::toCString(short_blocks[i].frag) <<" "<< length(short_blocks[i].frag)<<::std::endl;
//mapping[fingerprint(ch)] = fingerprint(ch);
//Add the first link
string first_half;
assign(first_half,prefix(chains[short_blocks[i].frag_links.D_chain],len));
string new_link_1 = first_half;
new_link_1.append(ch);
table_entry* link_1 = new table_entry(new_link_1,fingerprint(first_half),fingerprint(ch));
link_1->push_D_link(short_blocks[i].frag_links.D_chain);
link_1->push_A_link(short_blocks[i].frag_links.A_chain);
links.push_back(link_1);
/*
//Add the second link
string second_half;
assign(second_half,prefix(chains[short_blocks[i].frag_links.A_chain],len));
string new_link_2 = ch;
new_link_2.append(second_half);
table_entry* link_2 = new table_entry(new_link_2,fingerprint(ch),fingerprint(second_half));
link_2->push_D_link(short_blocks[i].frag_links.D_chain);
link_2->push_A_link(short_blocks[i].frag_links.A_chain);
links.push_back(link_2);
*/
//::std::cout<<links[short_blocks[i].frag_links.D_chain]->get_short_read()->get_RNA_seq_sequence()<<::std::endl;
//::std::cout<<links[short_blocks[i].frag_links.A_chain]->get_short_read()->get_RNA_seq_sequence()<<::std::endl;
for(unsigned int j=0; j<short_blocks[i].other_links.size(); ++j){//Start_For_6
string second_half;
assign(first_half,prefix(chains[short_blocks[i].other_links[j].D_chain],len));
string new_link_2 = second_half;
new_link_2.append(ch);
table_entry* link_2 = new table_entry(new_link_2,fingerprint(second_half),fingerprint(ch));
link_2->push_D_link(short_blocks[i].other_links[j].D_chain);
link_2->push_A_link(short_blocks[i].other_links[j].A_chain);
links.push_back(link_1);
}//End_For_6
//}//End_If_5
}
}
PassRefPtrWillBeRawPtr<Range> PlainTextRange::createRangeFor(const ContainerNode& scope, GetRangeFor getRangeFor) const
{
ASSERT(isNotNull());
RefPtrWillBeRawPtr<Range> resultRange = scope.document().createRange();
size_t docTextPosition = 0;
bool startRangeFound = false;
Position textRunStartPosition;
Position textRunEndPosition;
TextIteratorBehaviorFlags behaviorFlags = TextIteratorEmitsObjectReplacementCharacter;
if (getRangeFor == ForSelection)
behaviorFlags |= TextIteratorEmitsCharactersBetweenAllVisiblePositions;
auto range = rangeOfContents(const_cast<ContainerNode*>(&scope));
TextIterator it(range->startPosition(), range->endPosition(), behaviorFlags);
// FIXME: the atEnd() check shouldn't be necessary, workaround for <http://bugs.webkit.org/show_bug.cgi?id=6289>.
if (!start() && !length() && it.atEnd()) {
resultRange->setStart(it.currentContainer(), 0, ASSERT_NO_EXCEPTION);
resultRange->setEnd(it.currentContainer(), 0, ASSERT_NO_EXCEPTION);
return resultRange.release();
}
for (; !it.atEnd(); it.advance()) {
int len = it.length();
textRunStartPosition = it.startPositionInCurrentContainer();
textRunEndPosition = it.endPositionInCurrentContainer();
bool foundStart = start() >= docTextPosition && start() <= docTextPosition + len;
bool foundEnd = end() >= docTextPosition && end() <= docTextPosition + len;
// Fix textRunRange->endPosition(), but only if foundStart || foundEnd, because it is only
// in those cases that textRunRange is used.
if (foundEnd) {
// FIXME: This is a workaround for the fact that the end of a run
// is often at the wrong position for emitted '\n's or if the
// renderer of the current node is a replaced element.
if (len == 1 && (it.characterAt(0) == '\n' || it.isInsideReplacedElement())) {
it.advance();
if (!it.atEnd()) {
textRunEndPosition = it.startPositionInCurrentContainer();
} else {
Position runEnd = VisiblePosition(textRunStartPosition).next().deepEquivalent();
if (runEnd.isNotNull())
textRunEndPosition = createLegacyEditingPosition(runEnd.containerNode(), runEnd.computeOffsetInContainerNode());
}
}
}
if (foundStart) {
startRangeFound = true;
if (textRunStartPosition.containerNode()->isTextNode()) {
int offset = start() - docTextPosition;
resultRange->setStart(textRunStartPosition.containerNode(), offset + textRunStartPosition.offsetInContainerNode(), IGNORE_EXCEPTION);
} else {
if (start() == docTextPosition)
resultRange->setStart(textRunStartPosition.containerNode(), textRunStartPosition.offsetInContainerNode(), IGNORE_EXCEPTION);
else
resultRange->setStart(textRunEndPosition.containerNode(), textRunEndPosition.offsetInContainerNode(), IGNORE_EXCEPTION);
}
}
if (foundEnd) {
if (textRunStartPosition.containerNode()->isTextNode()) {
int offset = end() - docTextPosition;
resultRange->setEnd(textRunStartPosition.containerNode(), offset + textRunStartPosition.offsetInContainerNode(), IGNORE_EXCEPTION);
} else {
if (end() == docTextPosition)
resultRange->setEnd(textRunStartPosition.containerNode(), textRunStartPosition.offsetInContainerNode(), IGNORE_EXCEPTION);
else
resultRange->setEnd(textRunEndPosition.containerNode(), textRunEndPosition.offsetInContainerNode(), IGNORE_EXCEPTION);
}
docTextPosition += len;
break;
}
docTextPosition += len;
}
if (!startRangeFound)
return nullptr;
if (length() && end() > docTextPosition) { // end() is out of bounds
resultRange->setEnd(textRunEndPosition.containerNode(), textRunEndPosition.offsetInContainerNode(), IGNORE_EXCEPTION);
}
return resultRange.release();
}
