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);
211 connect(saveBrowserPixmapAction, (SIGNAL(triggered())),
212 browser, SLOT(promptSaveBrowserPixmap()));
213 saveBrowserPixmapAction->setIcon(QIcon(":/icons/image2.png"));
215 viewMussaAlignmentAction = new QAction(tr("View sequence alignment"), this);
216 connect(viewMussaAlignmentAction, SIGNAL(triggered()),
217 this, SLOT(viewMussaAlignment() ));
218 viewMussaAlignmentAction->setWhatsThis(tr("Create a zoomed in window "
219 "showing alignment of the seqcomp "
222 whatsThisAction = QWhatsThis::createAction(this);
223 whatsThisAction->setIcon(QIcon(":/icons/help.png"));
228 void MussaWindow::closeEvent(QCloseEvent *event)
230 if(isClearingAnalysisSafe()) {
237 void MussaWindow::setupMainMenu()
239 // we need to run setupActions first
240 assert (closeAction != 0);
242 QMenu *newMenu = menuBar()->addMenu(tr("&File"));
244 newMenu->addAction(newMussaWindowAction);
245 newMenu->addAction(createNewAnalysisAction);
246 newMenu->addAction(loadMupaAction);
247 newMenu->addAction(loadSavedAnalysisAction);
248 newMenu->addAction(saveAnalysisAction);
249 newMenu->addAction(saveAnalysisAsAction);
250 newMenu->addSeparator();
251 newMenu->addAction(loadMotifListAction);
252 newMenu->addAction(saveMotifListAction);
253 newMenu->addSeparator();
254 newMenu->addAction(saveBrowserPixmapAction);
255 newMenu->addSeparator();
256 newMenu->addAction(closeAction);
258 newMenu = menuBar()->addMenu(tr("&Edit"));
259 newMenu->addAction(editMotifsAction);
260 newMenu->addAction(browser->getCopySelectedSequenceAsStringAction());
261 newMenu->addAction(browser->getCopySelectedSequenceAsFastaAction());
262 newMenu->addAction(createSubAnalysisAction);
263 newMenu->addAction(browser->getEditSequencePropertiesAction());
265 newMenu = menuBar()->addMenu(tr("&View"));
266 newMenu->addAction(viewMussaAlignmentAction);
267 newMenu->addAction(showMussaViewToolbarAction);
269 newMenu = menuBar()->addMenu(tr("&Help"));
270 newMenu->addAction(mussaManualAssistantAction);
271 newMenu->addAction(whatsThisAction);
272 newMenu->addSeparator();
273 newMenu->addAction(aboutAction);
275 // add some extra features to the context menu
276 QMenu *popupMenu = browser->getPopupMenu();
278 popupMenu->addAction(viewMussaAlignmentAction);
279 popupMenu->addAction(createSubAnalysisAction);
283 void MussaWindow::setupWidgets()
285 setup_analysis_dialog = new MussaSetupDialog;
286 subanalysis_window.reset(new SubanalysisWindow(analysis));
287 browser = new SequenceBrowserWidget(default_dir);
288 mussaViewTB = new QToolBar("Path Views", this);
289 zoom = new ZoomWidget(mussaViewTB);
290 threshold = new ThresholdWidget(mussaViewTB);
293 void MussaWindow::setupAssistant()
295 #if defined(QT_QTASSISTANT_FOUND)
296 QStringList manualAssistantArgs;
297 manualAssistantArgs = QStringList();
298 manualAssistantArgs << "-profile" << "./doc/manual/mussagl_manual.adp";
299 manualAssistant = new QAssistantClient("assistant", this);
300 manualAssistant->setArguments(manualAssistantArgs);
301 connect(manualAssistant, SIGNAL(error(QString)),
302 this, SLOT(assistantError(QString)));
306 void MussaWindow::about()
309 msg += "Welcome to Multiple Species Sequence Analysis\n";
310 msg += "(c) 2005-2006 California Institute of Technology\n";
311 msg += "Diane Trout, Tristan De Buysscher, Brandon King\n";
313 msg += mussa_version;
316 msg += (char *)glGetString(GL_VERSION);
318 QMessageBox::about(this, tr("About mussa"), msg);
321 void MussaWindow::clear()
323 aligned_windows.clear();
327 void MussaWindow::createNewAnalysis()
330 // ideally we should open a new window if there's an analysis
331 // but this should work for the moment.
332 if (not isClearingAnalysisSafe()) return;
334 if (setup_analysis_dialog->exec()) {
335 setAnalysis(setup_analysis_dialog->getMussa());
337 } catch(mussa_error e) {
338 QString msg(e.what());
339 QMessageBox::warning(this, tr("Create New Analysis"), msg);
343 void MussaWindow::createSubAnalysis()
345 list<SequenceLocation> result;
346 SequenceLocationModel& model = subanalysis_window->getModel();
347 browser->copySelectedTracksAsSeqLocation(result);
348 for(list<SequenceLocation>::iterator result_itor = result.begin();
349 result_itor != result.end();
352 model.push_back(*result_itor);
355 if (not subanalysis_window->isVisible()) {
356 subanalysis_window->show();
360 void MussaWindow::saveAnalysis()
362 // if we've got an analysis
363 if (analysis and not analysis->empty()) {
364 // if it doesn't have a name we need to pick one
365 if (analysis->get_analysis_path().empty()) {
368 // if we've got a name, has it changed any?
369 // this doesn't work when a sequence changes something (like its
371 //else if (analysis->is_dirty())
374 } catch (std::exception e) {
375 QMessageBox::critical(this,
376 tr("Mussa Save Error"),
378 QMessageBox::Ok, 0, 0);
385 void MussaWindow::saveAnalysisAs()
387 std::auto_ptr<QFileDialog> dialog(new QFileDialog(this));
388 dialog->setAcceptMode(QFileDialog::AcceptSave);
389 dialog->setFileMode(QFileDialog::AnyFile);
390 dialog->setDirectory(*default_dir);
392 QStringList fileNames;
393 if (not dialog->exec()) {
396 fileNames = dialog->selectedFiles();
398 if (fileNames.size() != 1) {
402 fs::path save_path(fileNames[0].toStdString(), fs::native);
403 // do you want to overwrite?
404 if (fs::exists(save_path) and
405 QMessageBox::question(
407 tr("Overwrite File? -- Mussa"),
408 tr("A file called %1 already exists"
409 "do you want to overwrite it?")
411 tr("&Yes"), tr("&No"),
416 analysis->save(save_path);
417 fs::path normalized_path = (save_path / "..").normalize();
418 default_dir->setPath(normalized_path.native_directory_string().c_str());
419 } catch (std::exception e) {
420 QMessageBox::critical(this,
421 tr("Mussa Save Error"),
423 QMessageBox::Ok, 0, 0);
427 bool MussaWindow::isClearingAnalysisSafe()
429 if (analysis and not analysis->empty() and analysis->is_dirty()) {
430 switch (QMessageBox::question(
432 tr("Save Unsaved Changes -- Mussa"),
433 tr("There are unsaved changes,\ndo you want to save?"),
434 tr("&Yes"), tr("&No"), tr("&Cancel"),
449 throw runtime_error("isClearingAnalysis QMesageBox failure");
452 // if we're here we've been saved and can replace
456 void MussaWindow::editMotifs()
458 if (motif_editor != 0) {
459 motif_editor->hide();
462 motif_editor = new MotifEditor(analysis);
463 connect(motif_editor, SIGNAL(changedMotifs()),
464 this, SLOT(updateAnnotations()));
465 motif_editor->show();
468 void MussaWindow::loadMotifList()
470 QString caption("Mussa Load Motifs");
471 QString filter("Motif list(*.txt *.mtl)");
472 QString path = QFileDialog::getOpenFileName(this,
474 default_dir->absolutePath(),
479 // try to load safely
481 fs::path converted_path(path.toStdString(), fs::native);
482 analysis->load_motifs(converted_path);
483 default_dir->setPath(converted_path.branch_path().native_directory_string().c_str());
484 emit changedMotifs();
485 } catch (std::exception e) {
486 QString msg("Unable to load ");
490 QMessageBox::warning(this, caption, msg);
494 void MussaWindow::saveMotifList()
496 QString caption("Mussa Save Motifs");
497 QString filter("Motif list(*.txt *.mtl)");
498 QString path = QFileDialog::getSaveFileName(this,
500 default_dir->absolutePath(),
505 // try to load safely
507 fs::path converted_path(path.toStdString(), fs::native);
508 if (fs::extension(converted_path).size() == 0) {
509 // no extension, so add one
510 fs::path base_path = converted_path.branch_path();
511 fs::path filename(converted_path.leaf() + ".mtl", fs::native);
512 converted_path = base_path / filename;
514 analysis->save_motifs(converted_path);
515 default_dir->setPath(converted_path.branch_path().native_directory_string().c_str());
516 } catch (std::exception e) {
517 QString msg("Unable to save ");
521 QMessageBox::warning(this, caption, msg);
524 void MussaWindow::loadMupa()
526 QString caption("Load a mussa parameter file");
527 QString filter("Mussa Parameters (*.mupa)");
528 QString mupa_path = QFileDialog::getOpenFileName(
531 default_dir->absolutePath(),
535 if (mupa_path.isNull())
537 // try to load safely
539 // ideally we should open a new window if there's an analysis
540 // but this should work for the moment.
541 if (not isClearingAnalysisSafe()) return;
543 MussaRef m = Mussa::init();
544 fs::path converted_path(mupa_path.toStdString(), fs::native);
545 connect(m.get(), SIGNAL(progress(const QString&, int, int)),
546 this, SLOT(updateProgress(const QString&, int, int)));
547 m->load_mupa_file(converted_path);
551 // grab the path ignoring the mupa file portion
552 default_dir->setPath(converted_path.branch_path().native_directory_string().c_str());
553 } catch (mussa_load_error e) {
554 QString msg("Unable to load ");
558 QMessageBox::warning(this, "Load Parameter", msg);
560 assert (analysis != 0);
563 void MussaWindow::loadSavedAnalysis()
565 QString caption("Load a previously run analysis");
566 QString muway_dir = QFileDialog::getExistingDirectory(
569 default_dir->absolutePath()
572 if (muway_dir.isNull())
574 // try to safely load
576 // ideally we should open a new window if there's an analysis
577 // but this should work for the moment.
578 if (not isClearingAnalysisSafe()) return;
580 MussaRef m = Mussa::init();
581 fs::path converted_path(muway_dir.toStdString(), fs::native);
582 connect(m.get(), SIGNAL(progress(const QString&, int, int)),
583 this, SLOT(updateProgress(const QString&, int, int)));
584 m->load(converted_path);
585 // only switch mussas if we loaded without error
586 if (analysis->empty()) {
587 // our current window is empty so load and replace.
590 default_dir->setPath(converted_path.branch_path().native_directory_string().c_str());
592 MussaWindow *win = new MussaWindow(m);
594 win->default_dir->setPath(converted_path.branch_path().native_directory_string().c_str());
597 } catch (boost::filesystem::filesystem_error e) {
598 QString msg("Unable to load ");
602 QMessageBox::warning(this, "Load Parameter", msg);
603 } catch (mussa_load_error e) {
604 QString msg("Unable to load ");
608 QMessageBox::warning(this, "Load Parameter", msg);
610 assert (analysis != 0);
613 void MussaWindow::newMussaWindow()
615 MussaWindow *win = new MussaWindow(Mussa::init());
616 win->default_dir = default_dir;
620 void MussaWindow::setSoftThreshold(int value)
622 if (analysis->get_soft_threshold() != value) {
623 threshold->setEnabled( false );
624 analysis->set_soft_threshold(value);
628 threshold->setEnabled( true );
632 void MussaWindow::showMussaToolbar()
634 if (mussaViewTB->isVisible())
640 void MussaWindow::showBasePairsCopied(size_t bp_copied)
642 QString msg("Copied ");
644 num.setNum(bp_copied);
645 msg += num + " base pairs";
646 statusBar()->showMessage(msg, 5000);
650 void MussaWindow::toggleMotifs()
655 void MussaWindow::showManual()
657 #if defined(QT_QTASSISTANT_FOUND)
658 if (manualAssistant) {
659 manualAssistant->openAssistant();
661 QMessageBox::warning(this,
662 tr("Mussa Help Error"),
663 tr("QtAssistant not setup correctly"),
665 QMessageBox::NoButton,
666 QMessageBox::NoButton);
669 QUrl manual_url("http://woldlab.caltech.edu/~king/mussagl_manual/");
670 if (not QDesktopServices::openUrl(manual_url)) {
671 QMessageBox::warning(this,
672 tr("Mussa Help Error"),
673 tr("Unable to launch webbrowser"),
675 QMessageBox::NoButton,
676 QMessageBox::NoButton);
678 #endif //QT_QTASSISTANT_FOUND
681 void MussaWindow::assistantError(QString message)
683 //std::cout << "QAssistantError: " << message.toStdString() << "\n";
684 QMessageBox::warning ( this, "Warning: Mussagl Manual", message,
686 QMessageBox::NoButton);
689 void MussaWindow::NotImplementedBox()
691 QMessageBox::warning(this, QObject::tr("mussa"), QObject::tr("Not implemented yet"));
694 void MussaWindow::viewMussaAlignment()
696 const set<int>& selected_paths = browser->selectedPaths();
697 if (selected_paths.size() == 0 ) {
698 QMessageBox::warning(this,
699 QObject::tr("mussa"),
700 QObject::tr("you should probably select some paths "
703 MussaAlignedWindowRef ma_win(
704 new MussaAlignedWindow(analysis, default_dir, selected_paths, subanalysis_window)
707 aligned_windows.push_back(ma_win);
708 connect(this, SIGNAL(changedAnnotations()),
709 aligned_windows.back().get(), SLOT(update()));
710 aligned_windows.back()->show();
714 void MussaWindow::updateAnalysis()
716 const Mussa::vector_sequence_type& seqs = analysis->sequences();
717 browser->setSequences(seqs, analysis->colorMapper());
718 assert(browser->sequences().size() == analysis->size());
720 // setRange eventually emits something that causes updateLinks to be called
721 // but it's possible for us to not have had a chance to set out sequences
723 threshold->setRange(analysis->get_threshold(),analysis->get_window());
726 zoom->setValue(browser->zoom());
729 void MussaWindow::updateAnnotations()
731 // motifs were changed in the sequences by
732 // Mussa::update_sequences_motifs
733 emit changedAnnotations();
737 void MussaWindow::updateLinks()
739 if(browser->sequences().size() == 0) {
740 // we don't have any sequences load so we have no business setting links
744 browser->clear_links();
745 bool reversed = false;
746 const NwayPaths& nway = analysis->paths();
748 typedef list<ConservedPath> conserved_paths;
749 typedef conserved_paths::const_iterator const_conserved_paths_itor;
750 for(const_conserved_paths_itor path_itor = nway.refined_pathz.begin();
751 path_itor != nway.refined_pathz.end();
754 // since we were drawing to the start of a window, and opengl lines
755 // are centered around the two connecting points our lines were slightly
756 // offset. the idea of window_offset is to adjust them to the
757 // right for forward compliment or left for reverse compliment
758 // FIXME: figure out how to unit test these computations
759 //GLfloat window_offset = (path_itor->window_size)/2.0;
761 size_t track_len = path_itor->track_indexes.size();
762 vector<int> normalized_path;
763 normalized_path.reserve(track_len);
764 vector<bool> rc_flags(false, track_len);
765 for (size_t track_i=0; track_i != track_len; ++track_i)
767 int x = path_itor->track_indexes[track_i];
768 // at some point when we modify the pathz data structure to keep
769 // track of the score we can put grab the depth here.
771 // are we reverse complimented?
779 normalized_path.push_back(x);
780 rc_flags.push_back(reversed);
782 browser->link(normalized_path, rc_flags, path_itor->window_size);
788 MussaWindow::updateProgress(const QString& description, int current, int max)
791 if (current == max) {
792 if (progress_dialog != 0) {
793 progress_dialog->hide();
794 delete progress_dialog;
798 // if we're starting, create the dialog
799 if (progress_dialog == 0) {
800 QString cancel("Cancel");
801 progress_dialog = new QProgressDialog(description, cancel, current, max, this);
802 progress_dialog->show();
804 // just update the dialog
805 progress_dialog->setValue(current);
808 qApp->processEvents();
811 void MussaWindow::updateAnalysisModified(bool is_modified)
813 setWindowModified(is_modified);
816 void MussaWindow::updateTitle()
819 QString title(analysis->get_title().c_str());
821 setWindowTitle(title);