9 #include "qui/MussaAlignedWindow.hpp"
10 #include "alg/sequence.hpp"
15 MussaAlignedWindow::MussaAlignedWindow(Mussa& m,
16 const set<int>& sel_paths,
18 : QMainWindow(parent),
20 pick_align_menu(tr("Choose Alignment")),
21 view_align_menu(tr("View Alignment")),
26 browser.setSequences(analysis.sequences(), analysis.colorMapper());
27 setSelectedPaths(m, sel_paths);
29 double zoom_level = browser.zoomToSequence();
31 zoom = new ZoomWidget();
32 connect(zoom, SIGNAL(valueChanged(double)),
33 &browser, SLOT(setZoom(double)));
34 zoom->setValue(zoom_level);
37 setupAlignmentMenus();
39 setCentralWidget(&browser);
41 alignTB = new QToolBar();
42 alignTB->addWidget(zoom);
45 ostringstream message;
46 message << "Selected " << selected_paths.size() << " paths";
47 statusBar()->showMessage(message.str().c_str(), 5000);
48 browser.updatePosition();
51 void MussaAlignedWindow::setupActions()
53 //Save pixel map action
54 saveBrowserPixmapAction = new QAction(tr("Save to image..."), this);
55 connect(saveBrowserPixmapAction, (SIGNAL(triggered())),
56 &browser, SLOT(promptSaveBrowserPixmap()));
57 saveBrowserPixmapAction->setIcon(QIcon(":/icons/image2.png"));
60 void MussaAlignedWindow::setupMenus()
62 QMenu *newMenu = menuBar()->addMenu(tr("&File"));
63 newMenu->addAction(saveBrowserPixmapAction);
65 newMenu = menuBar()->addMenu(tr("&Edit"));
66 newMenu->addAction(browser.getCopySelectedSequenceAsFastaAction());
69 void MussaAlignedWindow::setupAlignmentMenus()
71 pick_align_menu.clear();
72 view_align_menu.clear();
76 for(vector<ConservedPath >::iterator pathz_i=selected_paths.begin();
77 pathz_i != selected_paths.end();
80 ConservedPath::path_type normalized_path = pathz_i->normalizedIndexes();
81 ostringstream menu_text;
82 menu_text << pathz_i->window_size << ":";
83 ConservedPath::iterator element_i = normalized_path.begin();
84 menu_text << *element_i++;
86 element_i != normalized_path.end();
90 menu_text << *element_i;
92 int index = pathz_i - selected_paths.begin();
93 IntAction *pick = new IntAction(QString(menu_text.str().c_str()), index, this);
94 connect(pick, SIGNAL(triggered(int)), this, SLOT(setAlignment(int)));
95 pick_actions.push_back(pick);
96 pick_align_menu.addAction(pick);
97 IntAction *view = new IntAction(QString(menu_text.str().c_str()), index, this);
98 connect(view, SIGNAL(triggered(int)), this, SLOT(toggleViewAlignment(int)));
99 view->setCheckable(true);
100 view->setChecked(true);
101 view_actions.push_back(view);
102 view_align_menu.addAction(view);
105 menuBar()->addMenu(&pick_align_menu);
106 menuBar()->addMenu(&view_align_menu);
110 void MussaAlignedWindow::setSelectedPaths(Mussa &m, const set<int>& sel_paths)
113 set<int>::iterator sel_i = sel_paths.begin();
114 list<ConservedPath>::const_iterator path_i = m.paths().refined_pathz.begin();
115 list<ConservedPath>::const_iterator path_end = m.paths().refined_pathz.end();
116 size_t path_size = m.paths().refined_pathz.size();
119 selected_paths.reserve(sel_paths.size());
120 view_paths.reserve(sel_paths.size());
121 while (pathid != path_size and sel_i != sel_paths.end())
123 assert (*sel_i >= 0);
124 size_t sel_pathid = (size_t)(*sel_i);
125 if (pathid == sel_pathid) {
126 selected_paths.push_back(*path_i);
127 view_paths.push_back(true);
131 } else if (pathid < sel_pathid) {
134 } else if (pathid > sel_pathid) {
140 void MussaAlignedWindow::setAlignment(int alignment_index)
142 if (selected_paths.size() > 0) {
143 browser.centerOnPath(selected_paths[alignment_index].normalizedIndexes());
147 void MussaAlignedWindow::toggleViewAlignment(int alignment_index)
149 view_paths[alignment_index]= not view_paths[alignment_index];
150 // perhaps it'd be better if we could erase specific sets
151 // of matches instead of erasing them all and recomputing them all
152 // but this is easier
156 void MussaAlignedWindow::update()
161 void MussaAlignedWindow::computeMatchLines()
163 browser.clear_links();
165 // filter out conserved paths
166 list<ConservedPath> filtered_paths;
167 vector<ConservedPath>::iterator path_i = selected_paths.begin();
168 list<ConservedPath::path_type> result;
169 list<vector<bool> > reversed;
171 for(vector<ConservedPath>::size_type count = 0;
172 count != selected_paths.size();
175 if (view_paths[count])
176 filtered_paths.push_back(*path_i);
178 analysis.createLocalAlignment(filtered_paths.begin(),
179 filtered_paths.end(),
183 list<ConservedPath::path_type>::const_iterator result_i = result.begin();
184 list<vector<bool> >::const_iterator reversed_i = reversed.begin();
185 for(int i = 0; i != result.size(); ++i, ++result_i, ++reversed_i)
187 // make 1 base long links
188 browser.link(*result_i, *reversed_i, 1);