#include <list>
+#include <vector>
#include <sstream>
-#include <QVBoxLayout>
+#include <QStatusBar>
+#include <QString>
+#include <QMenuBar>
#include "qui/MussaAlignedWindow.hpp"
+#include "alg/sequence.hpp"
-
+#include <iostream>
using namespace std;
-MussaAlignedWindow::MussaAlignedWindow(Mussa& m,
- const set<int>& sel_paths,
+MussaAlignedWindow::MussaAlignedWindow(MussaRef m,
+ boost::shared_ptr<QDir> default_dir_,
+ const set<int>& sel_paths,
+ SubanalysisWindowRef window,
QWidget *parent)
- : QWidget(parent),
- analysis(m)//,
- //selected_paths(sel_paths)
-
+ : QMainWindow(parent),
+ analysis(m),
+ default_dir(default_dir_),
+ subanalysis_window(window),
+ browser(default_dir),
+ pick_align_menu(tr("Choose Alignment")),
+ view_align_menu(tr("View Alignment")),
+ threshold_widget(0),
+ zoom(0),
+ alignTB(0)
{
- browser.setSequences(analysis.sequences(), analysis.colorMapper());
- setSelectedPaths(m, sel_paths);
+ setupActions();
+ connect(&browser, SIGNAL(basepairsCopied(size_t)),
+ this, SLOT(showBasePairsCopied(size_t)));
+ browser.setSequences(analysis->sequences(), analysis->colorMapper());
+ setSelectedPaths(analysis, sel_paths);
setAlignment(0);
+ double zoom_level = browser.zoomToSequence();
- QVBoxLayout *layout = new QVBoxLayout;
- layout->addWidget(&browser);
- layout->addWidget(&status);
- setLayout(layout);
+ zoom = new ZoomWidget();
+ connect(zoom, SIGNAL(valueChanged(double)),
+ &browser, SLOT(setZoom(double)));
+ zoom->setValue(zoom_level);
+
+ // Mouse scroll wheel zooming!
+ connect(&browser, SIGNAL(mouseWheelZoom(double)),
+ zoom, SLOT(setValue(double)));
+
+ computeMatchLines();
+ setupMenus();
+ setupAlignmentMenus();
+
+ setCentralWidget(&browser);
+ // Add a threhold widget set to our current threshold and make it readonly
+ threshold_widget = new ThresholdWidget;
+ threshold_widget->setRange(analysis->get_threshold(),analysis->get_window());
+ threshold_widget->setBasepairThreshold(analysis->get_soft_threshold());
+ threshold_widget->setReadOnly(true);
+
+ alignTB = new QToolBar();
+ alignTB->addWidget(zoom);
+ alignTB->addWidget(threshold_widget);
+ addToolBar(alignTB);
+
ostringstream message;
message << "Selected " << selected_paths.size() << " paths";
- status.showMessage(message.str().c_str(), 5000);
+ statusBar()->showMessage(message.str().c_str(), 5000);
+ browser.updatePosition();
+
+ updateTitle();
+}
+
+void MussaAlignedWindow::setupActions()
+{
+ // more cut-n-paste from MussaWindow
+ createSubAnalysisAction = new QAction(tr("Add to Subanalysis"), this);
+ connect(createSubAnalysisAction, SIGNAL(triggered()),
+ this, SLOT(createSubAnalysis()));
+
+ //Save pixel map action
+ saveBrowserPixmapAction = new QAction(tr("Save to image..."), this);
+ connect(saveBrowserPixmapAction, (SIGNAL(triggered())),
+ &browser, SLOT(promptSaveBrowserPixmap()));
+ saveBrowserPixmapAction->setIcon(QIcon(":/icons/image2.png"));
+}
+
+void MussaAlignedWindow::setupMenus()
+{
+ QMenu *newMenu = menuBar()->addMenu(tr("&File"));
+ newMenu->addAction(saveBrowserPixmapAction);
+
+ newMenu = menuBar()->addMenu(tr("&Edit"));
+ newMenu->addAction(browser.getCopySelectedSequenceAsStringAction());
+ newMenu->addAction(browser.getCopySelectedSequenceAsFastaAction());
+ newMenu->addAction(createSubAnalysisAction);
+
+ // add some extra features to the context menu
+ QMenu *popupMenu = browser.getPopupMenu();
+ if (popupMenu) {
+ popupMenu->addAction(createSubAnalysisAction);
+ }
+}
+
+void MussaAlignedWindow::setupAlignmentMenus()
+{
+ pick_align_menu.clear();
+ view_align_menu.clear();
+ pick_actions.clear();
+ view_actions.clear();
+
+ for(vector<ConservedPath >::iterator pathz_i=selected_paths.begin();
+ pathz_i != selected_paths.end();
+ ++pathz_i)
+ {
+ ConservedPath::path_type normalized_path = pathz_i->normalizedIndexes();
+ ostringstream menu_text;
+ menu_text << pathz_i->window_size << ":";
+ ConservedPath::iterator element_i = normalized_path.begin();
+ menu_text << *element_i++;
+ for (;
+ element_i != normalized_path.end();
+ ++element_i)
+ {
+ menu_text << ", ";
+ menu_text << *element_i;
+ }
+ int index = pathz_i - selected_paths.begin();
+ IntAction *pick = new IntAction(QString(menu_text.str().c_str()), index, this);
+ connect(pick, SIGNAL(triggered(int)), this, SLOT(setAlignment(int)));
+ pick_actions.push_back(pick);
+ pick_align_menu.addAction(pick);
+ IntAction *view = new IntAction(QString(menu_text.str().c_str()), index, this);
+ connect(view, SIGNAL(triggered(int)), this, SLOT(toggleViewAlignment(int)));
+ view->setCheckable(true);
+ view->setChecked(true);
+ view_actions.push_back(view);
+ view_align_menu.addAction(view);
+ }
+
+ menuBar()->addMenu(&pick_align_menu);
+ menuBar()->addMenu(&view_align_menu);
}
-void MussaAlignedWindow::setSelectedPaths(Mussa &m, const set<int>& sel_paths)
+void MussaAlignedWindow::setSelectedPaths(MussaRef m, const set<int>& sel_paths)
{
// sets are sorted
set<int>::iterator sel_i = sel_paths.begin();
- list<ExtendedConservedPath>::const_iterator path_i = m.paths().rpbegin();
- list<ExtendedConservedPath>::const_iterator path_end = m.paths().rpend();
- size_t path_size = m.paths().refined_pathz.size();
+ list<ConservedPath>::const_iterator path_i = m->paths().refined_pathz.begin();
+ list<ConservedPath>::const_iterator path_end = m->paths().refined_pathz.end();
+ size_t path_size = m->paths().refined_pathz.size();
size_t pathid=0;
selected_paths.reserve(sel_paths.size());
+ view_paths.reserve(sel_paths.size());
while (pathid != path_size and sel_i != sel_paths.end())
{
assert (*sel_i >= 0);
size_t sel_pathid = (size_t)(*sel_i);
if (pathid == sel_pathid) {
- cout << "found one " << *path_i << endl;
selected_paths.push_back(*path_i);
+ view_paths.push_back(true);
++pathid;
++path_i;
++sel_i;
}
}
-void MussaAlignedWindow::setAlignment(size_t alignment_index)
+// FIXME: this is a cut-n-paste from MussaWindow, perhaps they should be refactored to
+// some shared place
+void MussaAlignedWindow::createSubAnalysis()
+{
+ list<SequenceLocation> result;
+ SequenceLocationModel& model = subanalysis_window->getModel();
+ browser.copySelectedTracksAsSeqLocation(result);
+ for(list<SequenceLocation>::iterator result_itor = result.begin();
+ result_itor != result.end();
+ ++result_itor)
+ {
+ model.push_back(*result_itor);
+ }
+
+ if (not subanalysis_window->isVisible()) {
+ subanalysis_window->show();
+ }
+}
+
+void MussaAlignedWindow::setAlignment(int alignment_index)
{
if (selected_paths.size() > 0) {
- browser.centerOnPath(selected_paths[alignment_index].track_indexes);
+ browser.centerOnPath(selected_paths[alignment_index].normalizedIndexes());
+ }
+}
+
+void MussaAlignedWindow::showBasePairsCopied(size_t bp_copied)
+{
+ QString msg("Copied ");
+ QString num;
+ num.setNum(bp_copied);
+ msg += num + " base pairs";
+ statusBar()->showMessage(msg, 5000);
+}
+
+void MussaAlignedWindow::toggleViewAlignment(int alignment_index)
+{
+ view_paths[alignment_index]= not view_paths[alignment_index];
+ // perhaps it'd be better if we could erase specific sets
+ // of matches instead of erasing them all and recomputing them all
+ // but this is easier
+ computeMatchLines();
+}
+
+void MussaAlignedWindow::update()
+{
+ browser.update();
+}
+
+void MussaAlignedWindow::updateTitle()
+{
+ std::string title("Sequence View: ");
+ if (analysis) {
+ title += analysis->get_title();
}
+ setWindowTitle(title.c_str());
}
+void MussaAlignedWindow::computeMatchLines()
+{
+ browser.clear_links();
+
+ // filter out conserved paths
+ list<ConservedPath> filtered_paths;
+ vector<ConservedPath>::iterator path_i = selected_paths.begin();
+ list<ConservedPath::path_type> result;
+ list<vector<bool> > reversed;
+
+ for(vector<ConservedPath>::size_type count = 0;
+ count != selected_paths.size();
+ ++count, ++path_i)
+ {
+ if (view_paths[count])
+ filtered_paths.push_back(*path_i);
+ }
+ analysis->createLocalAlignment(filtered_paths.begin(),
+ filtered_paths.end(),
+ result,
+ reversed);
+
+ list<ConservedPath::path_type>::const_iterator result_i = result.begin();
+ list<vector<bool> >::const_iterator reversed_i = reversed.begin();
+ for(int i = 0; i != result.size(); ++i, ++result_i, ++reversed_i)
+ {
+ // make 1 base long links
+ browser.link(*result_i, *reversed_i, 1);
+ }
+}
projects / mussa.git / blobdiff