void Window::keyboardUpFunc(unsigned char key, int, int) {
Window& win = currentWindow();
Key k = asciiToKey(key);
win.mKeys.erase(k);
win.keyReleased(k);
}
void Window::keyboardFunc(unsigned char key, int, int) {
Window& win = currentWindow();
Key k = asciiToKey(key);
win.mKeys.insert(k);
win.keyPressed(k);
}
QDesignerPropertySheetExtension *QMdiAreaPropertySheet::currentWindowSheet() const
{
QWidget *cw = currentWindow();
if (cw == 0)
return 0;
return qt_extension<QDesignerPropertySheetExtension*>(core()->extensionManager(), cw);
}
QVariant QMdiAreaPropertySheet::property(int index) const
{
switch (mdiAreaProperty(propertyName(index))) {
case MdiAreaSubWindowName:
if (QWidget *w = currentWindow())
return w->objectName();
return QVariant(QString());
case MdiAreaSubWindowTitle:
if (QWidget *w = currentWindow())
return w->windowTitle();
return QVariant(QString());
case MdiAreaNone:
break;
}
return QDesignerPropertySheet::property(index);
}
void OSXStyle::closeWindow()
{
QWidget *w=currentWindow();
if (w) {
w->close();
}
}
void OSXStyle::minimizeWindow()
{
QWidget *w=currentWindow();
if (w) {
w->showMinimized();
}
}
void Window::passiveMotionFunc(int x, int y) {
Window& win = currentWindow();
win.mPreviousMousePos = win.mMousePos;
win.mMousePos.setX(x);
win.mMousePos.setY(y);
win.mMouseMoved = true;
win.mouseMoved({x, y});
}
void Mac::OSXStyle::zoomWindow() {
QWidget *w=currentWindow();
if (w) {
if (w->isMaximized()) {
w->showNormal();
} else {
w->showMaximized();
}
}
}
bool QMdiAreaPropertySheet::isEnabled(int index) const
{
switch (mdiAreaProperty(propertyName(index))) {
case MdiAreaSubWindowName:
case MdiAreaSubWindowTitle:
return currentWindow() != 0;
case MdiAreaNone:
break;
}
return QDesignerPropertySheet::isEnabled(index);
}
void Window::mouseFunc(int button, int state, int, int) {
Window& win = currentWindow();
MouseButton but = glut2MouseButton(button);
if (state == GLUT_DOWN) {
win.mMouseButtons.insert(but);
win.mousePressed(but);
} else if (state == GLUT_UP) {
win.mMouseButtons.erase(but);
win.mouseReleased(but);
}
}
void Window::displayFunc() {
Window& win = currentWindow();
if (win.mMouseMoved)
win.mMouseForce = win.mMousePos - win.mPreviousMousePos;
else
win.mMouseForce = Vector2i(0, 0);
win.mMouseMoved = false;
win.frame();
glutSwapBuffers();
glutPostRedisplay();
}
void LTaskButton::triggerWindow(){
LWinInfo win = currentWindow();
//Check which state the window is currently in and flip it to the other
LX11::WINDOWSTATE state = LX11::GetWindowState(win.windowID());
if(state == LX11::ACTIVE){
qDebug() << "Minimize Window:" << this->text();
LX11::IconifyWindow(win.windowID());
}else if(state == LX11::VISIBLE){
qDebug() << "Activate Window:" << this->text();
LX11::ActivateWindow(win.windowID());
}else{
qDebug() << "Restore Window:" << this->text();
LX11::RestoreWindow(win.windowID());
}
cWin = LWinInfo(); //clear the current
}
void QMdiAreaPropertySheet::setProperty(int index, const QVariant &value)
{
switch (mdiAreaProperty(propertyName(index))) {
case MdiAreaSubWindowName:
if (QWidget *w = currentWindow())
w->setObjectName(value.toString());
break;
case MdiAreaSubWindowTitle: // Forward to window title of subwindow
if (QDesignerPropertySheetExtension *cws = currentWindowSheet()) {
const int index = cws->indexOf(m_windowTitleProperty);
cws->setProperty(index, value);
cws->setChanged(index, true);
}
break;
default:
QDesignerPropertySheet::setProperty(index, value);
break;
}
}
bool QMdiAreaPropertySheet::isChanged(int index) const
{
bool rc = false;
switch (mdiAreaProperty(propertyName(index))) {
case MdiAreaSubWindowName:
rc = currentWindow() != 0;
break;
case MdiAreaSubWindowTitle:
if (QDesignerPropertySheetExtension *cws = currentWindowSheet()) {
const int index = cws->indexOf(m_windowTitleProperty);
rc = cws->isChanged(index);
}
break;
default:
rc = QDesignerPropertySheet::isChanged(index);
break;
}
return rc;
}
static int append_cluster_connections(std::vector<MEI_event>& insertion_events, ControlState& current_state,
UserDefinedSettings* userSettings) {
// Setup maps for base read names of mates we need to collect. Also setup 'exclude_names' holding
// the original read names (we don't want those, only their mates, which fall inside the event).
std::map<std::string, size_t> fwd_name_links, rev_name_links, exclude_names;
std::string tmp_basename;
for (size_t i = 0; i < insertion_events.size(); i++) {
MEI_event event = insertion_events.at(i);
for (size_t j = 0; j < event.fwd_cluster_bp.associated_reads.size(); j++) {
tmp_basename = base_read_name(event.fwd_cluster_bp.associated_reads.at(j).name);
fwd_name_links.insert(std::make_pair(tmp_basename, i));
exclude_names.insert(std::make_pair(event.fwd_cluster_bp.associated_reads.at(j).name, i));
}
for (size_t j = 0; j < event.rev_cluster_bp.associated_reads.size(); j++) {
tmp_basename = base_read_name(event.rev_cluster_bp.associated_reads.at(j).name);
rev_name_links.insert(std::make_pair(tmp_basename, i));
exclude_names.insert(std::make_pair(event.rev_cluster_bp.associated_reads.at(j).name, i));
}
}
// Loop over whole genome to find mates of discordant reads near DD breakpoints.
g_genome.reset();
MEI_data mei_data;
int result;
// Make dummy BED-records spanning the whole genome.
std::vector<BED> dummy_beds;
for (unsigned index = 0; index < g_ChrNameAndSizeAndIndex.size(); index++) {
BED OneBedRecord;
OneBedRecord.ChrName = g_ChrNameAndSizeAndIndex[index].ChrName;
OneBedRecord.Start = 1;
OneBedRecord.End = g_ChrNameAndSizeAndIndex[index].ChrSize;
dummy_beds.push_back(OneBedRecord);
}
// Loop over BED-regions.
for (unsigned bed_index = 0; bed_index < dummy_beds.size(); bed_index++) {
std::string Bed_ChrName = dummy_beds[bed_index].ChrName;
unsigned Bed_start = dummy_beds[bed_index].Start;
unsigned Bed_end = dummy_beds[bed_index].End;
const Chromosome* currentChromosome = g_genome.getChr(Bed_ChrName);
if (currentChromosome == NULL) {
return 1;
}
LOG_INFO(*logStream << time_log() << "Discordant read collection for current window: " << Bed_ChrName <<
", " << Bed_start << "--" << Bed_end << std::endl);
CurrentChrMask.resize(currentChromosome->getCompSize());
for (unsigned int i = 0; i < currentChromosome->getCompSize(); i++) {
CurrentChrMask[i] = 'N';
}
userSettings->getRegion()->SetRegion(Bed_ChrName, Bed_start, Bed_end);
LoopingSearchWindow currentWindow( userSettings->getRegion(), currentChromosome, WINDOW_SIZE, Bed_start, Bed_end );
// loop over one bed region
do {
result = load_discordant_reads(mei_data, current_state.bams_to_parse, currentChromosome->getName(),
currentWindow, userSettings);
if (result) {
// something went wrong loading the reads, return error code.
return result;
}
std::map<std::string, size_t>::iterator name_match;
size_t disc_read_count = mei_data.discordant_reads.size();
for (size_t i = 0; i < disc_read_count; i++) {
// Determine event and strand for which mate is evidence.
tmp_basename = base_read_name(mei_data.discordant_reads.at(i)->name);
int event_idx = -1;
char strand = Plus;
name_match = fwd_name_links.find(tmp_basename);
if (name_match != fwd_name_links.end()) {
// Current read referenced by a DD event near bp on fwd strand.
event_idx = (*name_match).second;
} else {
name_match = rev_name_links.find(tmp_basename);
if (name_match != rev_name_links.end()) {
// Current read referenced by a DD event near bp on rev strand.
event_idx = (*name_match).second;
strand = Minus;
}
}
if (event_idx == -1) {
// No match found, this read is not related to an event.
continue;
}
if (exclude_names.find(mei_data.discordant_reads.at(i)->name) != exclude_names.end()) {
// read name in exlude list, this is one of the reads we used for calling
// the breakpoint, skip it!
continue;
}
if (strand == Plus) {
insertion_events.at(event_idx).fwd_mapping_reads.push_back(*(mei_data.discordant_reads.at(i)));
} else {
insertion_events.at(event_idx).rev_mapping_reads.push_back(*(mei_data.discordant_reads.at(i)));
}
}
cleanup_reads(mei_data.discordant_reads);
currentWindow.next();
} while (!currentWindow.finished());
}
return 0;
}
void StackedWindow::popWindow() {
if (StackedWindow *w = currentWindow()) {
w->close();
}
}
void Window::closeFunc() {
currentWindow().mClosed = true;
}
void LTaskButton::closeWindow(){
if(winMenu->isVisible()){ winMenu->hide(); }
LWinInfo win = currentWindow();
LX11::CloseWindow(win.windowID());
cWin = LWinInfo(); //clear the current
}
// This function is based on Pindel's main function. Todo: integrate with pindel's main structure.
int searchMEImain(ControlState& current_state, Genome& genome, UserDefinedSettings* userSettings) {
// Reset genome before traversal.
g_genome.reset();
std::ofstream file_output(userSettings->getMEIOutputFilename().c_str());
MEI_data mei_data;
int result;
std::string CurrentChrName;
std::string PreviousChrName = "";
// Loop over BED-regions defined in control state.
for (unsigned bed_index = 0; bed_index < current_state.IncludeBed.size(); bed_index++) {
std::string Bed_ChrName = current_state.IncludeBed[bed_index].ChrName;
unsigned Bed_start = current_state.IncludeBed[bed_index].Start;
unsigned Bed_end = current_state.IncludeBed[bed_index].End;
const Chromosome* currentChromosome = g_genome.getChr(Bed_ChrName);
if (currentChromosome == NULL) {
std::cout << "There is no " << CurrentChrName << " in the reference file." << std::endl;
return 1;
}
LOG_INFO(*logStream << time_log() << "Dispersed Duplication detection current window: " << Bed_ChrName <<
", " << Bed_start << "--" << Bed_end << std::endl);
CurrentChrMask.resize(currentChromosome->getCompSize());
for (unsigned int i = 0; i < currentChromosome->getCompSize(); i++) {
CurrentChrMask[i] = 'N';
}
userSettings->getRegion()->SetRegion(Bed_ChrName, Bed_start, Bed_end);
LoopingSearchWindow currentWindow( userSettings->getRegion(), currentChromosome, WINDOW_SIZE, Bed_start, Bed_end );
// loop over one bed region
do {
result = load_discordant_reads(mei_data, current_state.bams_to_parse, currentChromosome->getName(),
currentWindow, userSettings);
if (result) {
// something went wrong loading the reads, return error code.
return result;
}
searchMEIBreakpoints(mei_data, current_state.bams_to_parse, currentChromosome, userSettings);
cleanup_reads(mei_data.discordant_reads);
currentWindow.next();
} while (!currentWindow.finished());
}
// Reset genome for subsequent traversals.
g_genome.reset();
std::map<int, std::string> seq_name_dictionary = get_sequence_name_dictionary(current_state);
searchMEI(mei_data, genome, seq_name_dictionary, userSettings, current_state, file_output);
file_output.close();
return 0;
}
void Window::reshapeFunc(int, int) {
currentWindow().resized();
}