1 #include "qui/MussaWindow.hpp"
2 #include "mussa_exceptions.hpp"
6 #include <QApplication>
7 #include <QAssistantClient>
9 #include <QDesktopServices>
11 #include <QFileDialog>
12 #include <QHBoxLayout>
15 #include <QMessageBox>
19 #include <QStringList>
27 #include <boost/filesystem/path.hpp>
28 #include <boost/filesystem/operations.hpp>
29 #include <boost/filesystem/convenience.hpp>
30 namespace fs = boost::filesystem;
31 #include <boost/bind.hpp>
35 static void init_resources() {
36 static bool resources_loaded = false;
37 if (not resources_loaded) {
38 Q_INIT_RESOURCE(icons);
39 resources_loaded = true;
43 MussaWindow::MussaWindow(MussaRef analysis_, QWidget *parent) :
47 setup_analysis_dialog(0),
55 createNewAnalysisAction(0),
56 createSubAnalysisAction(0),
58 loadMotifListAction(0),
60 loadSavedAnalysisAction(0),
61 mussaManualAssistantAction(0),
62 newMussaWindowAction(0),
63 saveMotifListAction(0),
64 showMussaViewToolbarAction(0),
65 toggleMotifsAction(0),
66 saveBrowserPixmapAction(0),
68 viewMussaAlignmentAction(0),
77 setWindowIcon(QIcon(":/icons/mussa.png"));
78 default_dir.reset(new QDir(QDir::home().absolutePath()));
80 setCentralWidget(browser);
81 // well updatePosition isn't quite right as we really just need
83 connect(this, SIGNAL(changedAnnotations()), browser, SLOT(update()));
84 connect(this, SIGNAL(changedMotifs()), this, SLOT(updateAnnotations()));
85 connect(browser, SIGNAL(basepairsCopied(size_t)),
86 this, SLOT(showBasePairsCopied(size_t)));
87 connect(zoom, SIGNAL(valueChanged(double)),
88 browser, SLOT(setZoom(double)));
89 mussaViewTB->addWidget(zoom);
91 // threshold range is set in updateAnalysis
92 connect(threshold, SIGNAL(thresholdChanged(int)),
93 this, SLOT(setSoftThreshold(int)));
94 mussaViewTB->addWidget(threshold);
96 addToolBar(mussaViewTB);
98 statusBar()->showMessage("Welcome to mussa", 2000);
100 // FIXME: we should start refactoring the connect call to updateAnalysis or something
102 connect(analysis.get(), SIGNAL(progress(const QString&, int, int)),
103 this, SLOT(updateProgress(const QString&, int, int)));
104 connect(analysis.get(), SIGNAL(isModified(bool)),
105 this, SLOT(updateAnalysisModified(bool)));
111 void MussaWindow::setAnalysis(MussaRef new_analysis)
113 if (new_analysis != 0) {
114 // only switch mussas if we loaded without error
116 analysis.swap(new_analysis);
122 void MussaWindow::setupActions()
124 // we really don't want to run this more than once.
125 assert (closeAction == 0);
127 // the ever popular about box
128 aboutAction = new QAction(tr("&About"), this);
129 connect(aboutAction, SIGNAL(triggered()), this, SLOT(about()));
130 aboutAction->setIcon(QIcon(":/icons/info.png"));
133 closeAction = new QAction(tr("&Close"), this);
134 closeAction->setStatusTip(tr("Close this window"));
135 connect(closeAction, SIGNAL(triggered()), this, SLOT(close()));
136 closeAction->setIcon(QIcon(":/icons/exit.png"));
138 createNewAnalysisAction = new QAction(tr("Create &New Analysis"), this);
139 connect(createNewAnalysisAction, SIGNAL(triggered()),
140 this, SLOT(createNewAnalysis()));
141 createNewAnalysisAction->setIcon(QIcon(":/icons/filenew.png"));
142 createNewAnalysisAction->setShortcut(Qt::CTRL | Qt::Key_N);
144 createSubAnalysisAction = new QAction(tr("Add to Subanalysis"), this);
145 connect(createSubAnalysisAction, SIGNAL(triggered()),
146 this, SLOT(createSubAnalysis()));
148 saveAnalysisAction = new QAction(tr("&Save Analysis"), this);
149 connect(saveAnalysisAction, SIGNAL(triggered()),
150 this, SLOT(saveAnalysis()));
151 saveAnalysisAction->setIcon(QIcon(":/icons/filesave.png"));
152 saveAnalysisAction->setShortcut(Qt::CTRL | Qt::Key_S);
154 saveAnalysisAsAction = new QAction(tr("Save Analysis &As"), this);
155 connect(saveAnalysisAsAction, SIGNAL(triggered()),
156 this, SLOT(saveAnalysisAs()));
157 saveAnalysisAsAction->setIcon(QIcon(":/icons/filesave.png"));
159 editMotifsAction = new QAction(tr("Edit Motifs"), this);;
160 connect(editMotifsAction, SIGNAL(triggered()), this, SLOT(editMotifs()));
162 loadMotifListAction = new QAction(tr("Open Motif List"), this);
163 connect(loadMotifListAction, SIGNAL(triggered()),
164 this, SLOT(loadMotifList()));
165 loadMotifListAction->setIcon(QIcon(":/icons/fileopen.png"));
167 loadMupaAction = new QAction(tr("Create Analysis from File"), this);
168 connect(loadMupaAction, SIGNAL(triggered()),
169 this, SLOT(loadMupa()));
170 loadMupaAction->setIcon(QIcon(":/icons/fileopen.png"));
172 loadSavedAnalysisAction = new QAction(tr("&Open Existing &Analysis"), this);
173 connect(loadSavedAnalysisAction, SIGNAL(triggered()),
174 this, SLOT(loadSavedAnalysis()));
175 loadSavedAnalysisAction->setIcon(QIcon(":/icons/fileopen.png"));
176 loadSavedAnalysisAction->setShortcut(Qt::CTRL | Qt::Key_O);
178 mussaManualAssistantAction = new QAction(tr("Mussagl Manual..."), this);
179 mussaManualAssistantAction->setIcon(QIcon(":/icons/contents.png"));
180 connect(mussaManualAssistantAction, SIGNAL(triggered()),
181 this, SLOT(showManual()));
183 newMussaWindowAction = new QAction(tr("&New Mussa Window"), this);
184 newMussaWindowAction->setStatusTip("open another mussa window to allow comparing results");
185 connect(newMussaWindowAction, SIGNAL(triggered()),
186 this, SLOT(newMussaWindow()));
187 newMussaWindowAction->setIcon(QIcon(":/icons/window_new.png"));
189 saveMotifListAction = new QAction(tr("Save Motifs"), this);
190 connect(saveMotifListAction, SIGNAL(triggered()),
191 this, SLOT(saveMotifList()));
192 saveMotifListAction->setIcon(QIcon(":/icons/filesave.png"));
194 showMussaViewToolbarAction = new QAction(tr("Show Toolbar"), this);
195 connect(showMussaViewToolbarAction, SIGNAL(triggered()),
196 this, SLOT(showMussaToolbar()));
197 showMussaViewToolbarAction->setCheckable(true);
198 showMussaViewToolbarAction->setChecked(true);
200 toggleMotifsAction = new QAction(tr("Toggle Motifs"), this);
201 connect(toggleMotifsAction, SIGNAL(triggered()),
202 this, SLOT(toggleMotifs()));
203 toggleMotifsAction->setCheckable(true);
204 toggleMotifsAction->setIcon(QIcon(":/icons/motif_icon.png"));
205 toggleMotifsAction->setWhatsThis(tr("Toggle motif annotations on/off\n\n"
206 "You can load motif annotations via "
207 "'File->Load Motif List' menu option."));
209 //Save pixel map action
210 saveBrowserPixmapAction = new QAction(tr("Save to image..."), this);
212 connect(saveBrowserPixmapAction, (SIGNAL(triggered())),
213 browser, SLOT(promptSaveBrowserPixmap()));
214 saveBrowserPixmapAction->setIcon(QIcon(":/icons/image2.png"));
217 viewMussaAlignmentAction = new QAction(tr("View sequence alignment"), this);
218 connect(viewMussaAlignmentAction, SIGNAL(triggered()),
219 this, SLOT(viewMussaAlignment() ));
220 viewMussaAlignmentAction->setWhatsThis(tr("Create a zoomed in window "
221 "showing alignment of the seqcomp "
224 whatsThisAction = QWhatsThis::createAction(this);
225 whatsThisAction->setIcon(QIcon(":/icons/help.png"));
230 void MussaWindow::closeEvent(QCloseEvent *event)
232 if(isClearingAnalysisSafe()) {
239 void MussaWindow::setupMainMenu()
241 // we need to run setupActions first
242 assert (closeAction != 0);
244 QMenu *newMenu = menuBar()->addMenu(tr("&File"));
246 newMenu->addAction(newMussaWindowAction);
247 newMenu->addAction(createNewAnalysisAction);
248 newMenu->addAction(loadMupaAction);
249 newMenu->addAction(loadSavedAnalysisAction);
250 newMenu->addAction(saveAnalysisAction);
251 newMenu->addAction(saveAnalysisAsAction);
252 newMenu->addSeparator();
253 newMenu->addAction(loadMotifListAction);
254 newMenu->addAction(saveMotifListAction);
255 newMenu->addSeparator();
256 newMenu->addAction(saveBrowserPixmapAction);
257 newMenu->addSeparator();
258 newMenu->addAction(closeAction);
260 newMenu = menuBar()->addMenu(tr("&Edit"));
261 newMenu->addAction(editMotifsAction);
262 if (browser) newMenu->addAction(browser->getCopySelectedSequenceAsStringAction());
263 if (browser) newMenu->addAction(browser->getCopySelectedSequenceAsFastaAction());
264 newMenu->addAction(createSubAnalysisAction);
265 if (browser) newMenu->addAction(browser->getEditSequencePropertiesAction());
267 newMenu = menuBar()->addMenu(tr("&View"));
268 newMenu->addAction(viewMussaAlignmentAction);
269 newMenu->addAction(showMussaViewToolbarAction);
271 newMenu = menuBar()->addMenu(tr("&Help"));
272 newMenu->addAction(mussaManualAssistantAction);
273 newMenu->addAction(whatsThisAction);
274 newMenu->addSeparator();
275 newMenu->addAction(aboutAction);
277 // add some extra features to the context menu
279 QMenu *popupMenu = browser->getPopupMenu();
281 popupMenu->addAction(viewMussaAlignmentAction);
282 popupMenu->addAction(createSubAnalysisAction);
287 void MussaWindow::setupWidgets()
289 setup_analysis_dialog = new MussaSetupDialog;
290 subanalysis_window.reset(new SubanalysisWindow(analysis));
291 browser = new SequenceBrowserWidget(default_dir);
292 mussaViewTB = new QToolBar("Path Views", this);
293 zoom = new ZoomWidget(mussaViewTB);
294 threshold = new ThresholdWidget(mussaViewTB);
297 void MussaWindow::setupAssistant()
299 #if defined(QT_QTASSISTANT_FOUND)
300 QStringList manualAssistantArgs;
301 manualAssistantArgs = QStringList();
302 manualAssistantArgs << "-profile" << "./doc/manual/mussagl_manual.adp";
303 manualAssistant = new QAssistantClient("assistant", this);
304 manualAssistant->setArguments(manualAssistantArgs);
305 connect(manualAssistant, SIGNAL(error(QString)),
306 this, SLOT(assistantError(QString)));
310 void MussaWindow::about()
313 msg += "Welcome to Multiple Species Sequence Analysis\n";
314 msg += "(c) 2005-2006 California Institute of Technology\n";
315 msg += "Diane Trout, Tristan De Buysscher, Brandon King\n";
317 msg += mussa_version;
323 msg += (char *)glGetString(GL_VERSION);
325 QMessageBox::about(this, tr("About mussa"), msg);
328 void MussaWindow::clear()
330 if (motif_editor != 0) {
331 motif_editor->hide();
335 aligned_windows.clear();
339 void MussaWindow::createNewAnalysis()
342 // ideally we should open a new window if there's an analysis
343 // but this should work for the moment.
344 if (not isClearingAnalysisSafe()) return;
346 if (setup_analysis_dialog->exec()) {
347 setAnalysis(setup_analysis_dialog->getMussa());
349 } catch(mussa_error e) {
350 QString msg(e.what());
351 QMessageBox::warning(this, tr("Create New Analysis"), msg);
355 void MussaWindow::createSubAnalysis()
357 list<SequenceLocation> result;
358 SequenceLocationModel& model = subanalysis_window->getModel();
359 browser->copySelectedTracksAsSeqLocation(result);
360 for(list<SequenceLocation>::iterator result_itor = result.begin();
361 result_itor != result.end();
364 model.push_back(*result_itor);
367 if (not subanalysis_window->isVisible()) {
368 subanalysis_window->show();
372 void MussaWindow::saveAnalysis()
374 // if we've got an analysis
375 if (analysis and not analysis->empty()) {
376 // if it doesn't have a name we need to pick one
377 if (analysis->get_analysis_path().empty()) {
380 // if we've got a name, has it changed any?
381 // this doesn't work when a sequence changes something (like its
383 //else if (analysis->is_dirty())
386 } catch (std::exception e) {
387 QMessageBox::critical(this,
388 tr("Mussa Save Error"),
390 QMessageBox::Ok, 0, 0);
397 void MussaWindow::saveAnalysisAs()
399 std::auto_ptr<QFileDialog> dialog(new QFileDialog(this));
400 dialog->setAcceptMode(QFileDialog::AcceptSave);
401 dialog->setFileMode(QFileDialog::AnyFile);
402 dialog->setDirectory(*default_dir);
404 QStringList fileNames;
405 if (not dialog->exec()) {
408 fileNames = dialog->selectedFiles();
410 if (fileNames.size() != 1) {
414 fs::path save_path(fileNames[0].toStdString(), fs::native);
415 // do you want to overwrite?
416 if (fs::exists(save_path) and
417 QMessageBox::question(
419 tr("Overwrite File? -- Mussa"),
420 tr("A file called %1 already exists"
421 "do you want to overwrite it?")
423 tr("&Yes"), tr("&No"),
428 analysis->save(save_path);
429 fs::path normalized_path = (save_path / "..").normalize();
430 default_dir->setPath(normalized_path.native_directory_string().c_str());
431 } catch (std::exception e) {
432 QMessageBox::critical(this,
433 tr("Mussa Save Error"),
435 QMessageBox::Ok, 0, 0);
439 bool MussaWindow::isClearingAnalysisSafe()
441 if (analysis and not analysis->empty() and analysis->is_dirty()) {
442 switch (QMessageBox::question(
444 tr("Save Unsaved Changes -- Mussa"),
445 tr("There are unsaved changes,\ndo you want to save?"),
446 tr("&Yes"), tr("&No"), tr("&Cancel"),
461 throw runtime_error("isClearingAnalysis QMesageBox failure");
464 // if we're here we've been saved and can replace
468 void MussaWindow::editMotifs()
470 if (not motif_editor) {
471 motif_editor = new MotifEditor(analysis);
472 connect(motif_editor, SIGNAL(changedMotifs()),
473 this, SLOT(updateAnnotations()));
475 motif_editor->show();
478 void MussaWindow::loadMotifList()
480 QString caption("Mussa Load Motifs");
481 QString filter("Motif list(*.txt *.mtl)");
482 QString path = QFileDialog::getOpenFileName(this,
484 default_dir->absolutePath(),
489 // try to load safely
491 fs::path converted_path(path.toStdString(), fs::native);
492 analysis->load_motifs(converted_path);
493 default_dir->setPath(converted_path.branch_path().native_directory_string().c_str());
494 emit changedMotifs();
495 } catch (std::exception e) {
496 QString msg("Unable to load ");
500 QMessageBox::warning(this, caption, msg);
504 void MussaWindow::saveMotifList()
506 QString caption("Mussa Save Motifs");
507 QString filter("Motif list(*.txt *.mtl)");
508 QString path = QFileDialog::getSaveFileName(this,
510 default_dir->absolutePath(),
515 // try to load safely
517 fs::path converted_path(path.toStdString(), fs::native);
518 if (fs::extension(converted_path).size() == 0) {
519 // no extension, so add one
520 fs::path base_path = converted_path.branch_path();
521 fs::path filename(converted_path.leaf() + ".mtl", fs::native);
522 converted_path = base_path / filename;
524 analysis->save_motifs(converted_path);
525 default_dir->setPath(converted_path.branch_path().native_directory_string().c_str());
526 } catch (std::exception e) {
527 QString msg("Unable to save ");
531 QMessageBox::warning(this, caption, msg);
534 void MussaWindow::loadMupa()
536 QString caption("Load a mussa parameter file");
537 QString filter("Mussa Parameters (*.mupa)");
538 QString mupa_path = QFileDialog::getOpenFileName(
541 default_dir->absolutePath(),
545 if (mupa_path.isNull())
547 // try to load safely
549 // ideally we should open a new window if there's an analysis
550 // but this should work for the moment.
551 if (not isClearingAnalysisSafe()) return;
553 MussaRef m = Mussa::init();
554 fs::path converted_path(mupa_path.toStdString(), fs::native);
555 connect(m.get(), SIGNAL(progress(const QString&, int, int)),
556 this, SLOT(updateProgress(const QString&, int, int)));
557 m->load_mupa_file(converted_path);
561 // grab the path ignoring the mupa file portion
562 default_dir->setPath(converted_path.branch_path().native_directory_string().c_str());
563 } catch (mussa_load_error e) {
564 QString msg("Unable to load ");
568 QMessageBox::warning(this, "Load Parameter", msg);
570 assert (analysis != 0);
573 void MussaWindow::loadSavedAnalysis()
575 QString caption("Load a previously run analysis");
576 QString muway_dir = QFileDialog::getExistingDirectory(
579 default_dir->absolutePath()
582 if (muway_dir.isNull())
584 // try to safely load
586 // ideally we should open a new window if there's an analysis
587 // but this should work for the moment.
588 if (not isClearingAnalysisSafe()) return;
590 MussaRef m = Mussa::init();
591 fs::path converted_path(muway_dir.toStdString(), fs::native);
592 connect(m.get(), SIGNAL(progress(const QString&, int, int)),
593 this, SLOT(updateProgress(const QString&, int, int)));
594 m->load(converted_path);
595 // only switch mussas if we loaded without error
596 if (analysis->empty()) {
597 // our current window is empty so load and replace.
600 default_dir->setPath(converted_path.branch_path().native_directory_string().c_str());
602 MussaWindow *win = new MussaWindow(m);
604 win->default_dir->setPath(converted_path.branch_path().native_directory_string().c_str());
607 } catch (boost::filesystem::filesystem_error e) {
608 QString msg("Unable to load ");
612 QMessageBox::warning(this, "Load Parameter", msg);
613 } catch (mussa_load_error e) {
614 QString msg("Unable to load ");
618 QMessageBox::warning(this, "Load Parameter", msg);
620 assert (analysis != 0);
623 void MussaWindow::newMussaWindow()
625 MussaWindow *win = new MussaWindow(Mussa::init());
626 win->default_dir = default_dir;
630 void MussaWindow::setSoftThreshold(int value)
632 if (analysis->get_soft_threshold() != value) {
633 threshold->setEnabled( false );
634 analysis->set_soft_threshold(value);
638 threshold->setEnabled( true );
642 void MussaWindow::showMussaToolbar()
644 if (mussaViewTB->isVisible())
650 void MussaWindow::showBasePairsCopied(size_t bp_copied)
652 QString msg("Copied ");
654 num.setNum(bp_copied);
655 msg += num + " base pairs";
656 statusBar()->showMessage(msg, 5000);
660 void MussaWindow::toggleMotifs()
665 void MussaWindow::showManual()
667 #if defined(QT_QTASSISTANT_FOUND)
668 if (manualAssistant) {
669 manualAssistant->openAssistant();
671 QMessageBox::warning(this,
672 tr("Mussa Help Error"),
673 tr("QtAssistant not setup correctly"),
675 QMessageBox::NoButton,
676 QMessageBox::NoButton);
679 QUrl manual_url("http://woldlab.caltech.edu/~king/mussagl_manual/");
680 if (not QDesktopServices::openUrl(manual_url)) {
681 QMessageBox::warning(this,
682 tr("Mussa Help Error"),
683 tr("Unable to launch webbrowser"),
685 QMessageBox::NoButton,
686 QMessageBox::NoButton);
688 #endif //QT_QTASSISTANT_FOUND
691 void MussaWindow::assistantError(QString message)
693 //std::cout << "QAssistantError: " << message.toStdString() << "\n";
694 QMessageBox::warning ( this, "Warning: Mussagl Manual", message,
696 QMessageBox::NoButton);
699 void MussaWindow::NotImplementedBox()
701 QMessageBox::warning(this, QObject::tr("mussa"), QObject::tr("Not implemented yet"));
704 void MussaWindow::viewMussaAlignment()
706 const set<int>& selected_paths = browser->selectedPaths();
707 if (selected_paths.size() == 0 ) {
708 QMessageBox::warning(this,
709 QObject::tr("mussa"),
710 QObject::tr("you should probably select some paths "
713 MussaAlignedWindowRef ma_win(
714 new MussaAlignedWindow(analysis, default_dir, selected_paths, subanalysis_window)
717 aligned_windows.push_back(ma_win);
718 connect(this, SIGNAL(changedAnnotations()),
719 aligned_windows.back().get(), SLOT(update()));
720 aligned_windows.back()->show();
724 void MussaWindow::updateAnalysis()
726 const Mussa::vector_sequence_type& seqs = analysis->sequences();
727 browser->setSequences(seqs, analysis->colorMapper());
728 assert(browser->sequences().size() == analysis->size());
730 // setRange eventually emits something that causes updateLinks to be called
731 // but it's possible for us to not have had a chance to set out sequences
733 threshold->setRange(analysis->get_threshold(),analysis->get_window());
736 zoom->setValue(browser->zoom());
739 void MussaWindow::updateAnnotations()
741 // motifs were changed in the sequences by
742 // Mussa::update_sequences_motifs
743 emit changedAnnotations();
747 void MussaWindow::updateLinks()
749 if(browser->sequences().size() == 0) {
750 // we don't have any sequences load so we have no business setting links
754 browser->clear_links();
755 bool reversed = false;
756 const NwayPaths& nway = analysis->paths();
758 typedef list<ConservedPath> conserved_paths;
759 typedef conserved_paths::const_iterator const_conserved_paths_itor;
760 for(const_conserved_paths_itor path_itor = nway.refined_pathz.begin();
761 path_itor != nway.refined_pathz.end();
764 // since we were drawing to the start of a window, and opengl lines
765 // are centered around the two connecting points our lines were slightly
766 // offset. the idea of window_offset is to adjust them to the
767 // right for forward compliment or left for reverse compliment
768 // FIXME: figure out how to unit test these computations
769 //GLfloat window_offset = (path_itor->window_size)/2.0;
771 size_t track_len = path_itor->track_indexes.size();
772 vector<int> normalized_path;
773 normalized_path.reserve(track_len);
774 vector<bool> rc_flags(false, track_len);
775 for (size_t track_i=0; track_i != track_len; ++track_i)
777 int x = path_itor->track_indexes[track_i];
778 // at some point when we modify the pathz data structure to keep
779 // track of the score we can put grab the depth here.
781 // are we reverse complimented?
789 normalized_path.push_back(x);
790 rc_flags.push_back(reversed);
792 browser->link(normalized_path, rc_flags, path_itor->window_size);
798 MussaWindow::updateProgress(const QString& description, int current, int max)
801 if (current == max) {
802 if (progress_dialog != 0) {
803 progress_dialog->hide();
804 delete progress_dialog;
808 // if we're starting, create the dialog
809 if (progress_dialog == 0) {
810 QString cancel("Cancel");
811 progress_dialog = new QProgressDialog(description, cancel, current, max, this);
812 progress_dialog->show();
814 // just update the dialog
815 progress_dialog->setValue(current);
818 qApp->processEvents();
821 void MussaWindow::updateAnalysisModified(bool is_modified)
823 setWindowModified(is_modified);
826 void MussaWindow::updateTitle()
829 QString title(analysis->get_title().c_str());
831 setWindowTitle(title);