qui/MussaAlignedWindow.cpp

   1 #include <list>
   2 #include <vector>
   3 #include <sstream>
   4
   5 #include <QStatusBar>
   6 #include <QString>
   7 #include <QMenuBar>
   8
   9 #include "qui/MussaAlignedWindow.hpp"
  10 #include "alg/sequence.hpp"
  11
  12 #include <iostream>
  13 using namespace std;
  14
  15 MussaAlignedWindow::MussaAlignedWindow(MussaRef m,
  16                                        const set<int>& sel_paths,
  17                                        SubanalysisWindowRef window,
  18                                        QWidget *parent)
  19   : QMainWindow(parent),
  20     analysis(m),
  21     subanalysis_window(window),
  22     pick_align_menu(tr("Choose Alignment")),
  23     view_align_menu(tr("View Alignment")),
  24     threshold_widget(0),
  25     zoom(0),
  26     alignTB(0)
  27 {
  28   setupActions();
  29   browser.setSequences(analysis->sequences(), analysis->colorMapper());
  30   setSelectedPaths(analysis, sel_paths);
  31   setAlignment(0);
  32   double zoom_level = browser.zoomToSequence();
  33
  34   zoom = new ZoomWidget();
  35   connect(zoom, SIGNAL(valueChanged(double)),
  36           &browser, SLOT(setZoom(double)));
  37   zoom->setValue(zoom_level);
  38   computeMatchLines();
  39   setupMenus();
  40   setupAlignmentMenus();
  41
  42   setCentralWidget(&browser);
  43
  44   // Add a threhold widget set to our current threshold and make it readonly
  45   threshold_widget = new ThresholdWidget;
  46   threshold_widget->setRange(analysis->get_threshold(),analysis->get_window());
  47   threshold_widget->setBasepairThreshold(analysis->get_soft_threshold());
  48   threshold_widget->setReadOnly(true);
  49
  50   alignTB = new QToolBar();
  51   alignTB->addWidget(zoom);
  52   alignTB->addWidget(threshold_widget);
  53   addToolBar(alignTB);
  54
  55   ostringstream message;
  56   message << "Selected " << selected_paths.size() << " paths";
  57   statusBar()->showMessage(message.str().c_str(), 5000);
  58   browser.updatePosition();
  59 }
  60
  61 void MussaAlignedWindow::setupActions()
  62 {
  63   // more cut-n-paste from MussaWindow
  64   createSubAnalysisAction = new QAction(tr("Add to Subanalysis"), this);
  65   connect(createSubAnalysisAction, SIGNAL(triggered()),
  66           this, SLOT(createSubAnalysis()));
  67
  68   //Save pixel map action
  69   saveBrowserPixmapAction = new QAction(tr("Save to image..."), this);
  70   connect(saveBrowserPixmapAction, (SIGNAL(triggered())),
  71           &browser, SLOT(promptSaveBrowserPixmap()));
  72   saveBrowserPixmapAction->setIcon(QIcon(":/icons/image2.png"));
  73 }
  74
  75 void MussaAlignedWindow::setupMenus()
  76 {
  77   QMenu *newMenu = menuBar()->addMenu(tr("&File"));
  78   newMenu->addAction(saveBrowserPixmapAction);
  79
  80   newMenu = menuBar()->addMenu(tr("&Edit"));
  81   newMenu->addAction(browser.getCopySelectedSequenceAsFastaAction());
  82   newMenu->addAction(createSubAnalysisAction);
  83
  84   // add some extra features to the context menu
  85   QMenu *popupMenu = browser.getPopupMenu();
  86   if (popupMenu) {
  87     popupMenu->addAction(createSubAnalysisAction);
  88   }
  89 }
  90
  91 void MussaAlignedWindow::setupAlignmentMenus()
  92 {
  93   pick_align_menu.clear();
  94   view_align_menu.clear();
  95   pick_actions.clear();
  96   view_actions.clear();
  97
  98   for(vector<ConservedPath >::iterator pathz_i=selected_paths.begin();
  99       pathz_i != selected_paths.end();
 100       ++pathz_i)
 101   {
 102     ConservedPath::path_type normalized_path = pathz_i->normalizedIndexes();
 103     ostringstream menu_text;
 104     menu_text << pathz_i->window_size << ":";
 105     ConservedPath::iterator element_i = normalized_path.begin();
 106     menu_text << *element_i++;
 107     for (;
 108          element_i != normalized_path.end();
 109          ++element_i)
 110     {
 111       menu_text << ", ";
 112       menu_text << *element_i;
 113     }
 114     int index = pathz_i - selected_paths.begin();
 115     IntAction *pick = new IntAction(QString(menu_text.str().c_str()), index, this);
 116     connect(pick, SIGNAL(triggered(int)), this, SLOT(setAlignment(int)));
 117     pick_actions.push_back(pick);
 118     pick_align_menu.addAction(pick);
 119     IntAction *view = new IntAction(QString(menu_text.str().c_str()), index, this);
 120     connect(view, SIGNAL(triggered(int)), this, SLOT(toggleViewAlignment(int)));
 121     view->setCheckable(true);
 122     view->setChecked(true);
 123     view_actions.push_back(view);
 124     view_align_menu.addAction(view);
 125   }
 126
 127   menuBar()->addMenu(&pick_align_menu);
 128   menuBar()->addMenu(&view_align_menu);
 129 }
 130
 131
 132 void MussaAlignedWindow::setSelectedPaths(MussaRef m, const set<int>& sel_paths)
 133 {
 134   // sets are sorted
 135   set<int>::iterator sel_i = sel_paths.begin();
 136   list<ConservedPath>::const_iterator path_i = m->paths().refined_pathz.begin();
 137   list<ConservedPath>::const_iterator path_end = m->paths().refined_pathz.end();
 138   size_t path_size = m->paths().refined_pathz.size();
 139   size_t pathid=0;
 140
 141   selected_paths.reserve(sel_paths.size());
 142   view_paths.reserve(sel_paths.size());
 143   while (pathid != path_size and sel_i != sel_paths.end())
 144   {
 145     assert (*sel_i >= 0);
 146     size_t sel_pathid = (size_t)(*sel_i);
 147     if (pathid == sel_pathid) {
 148       selected_paths.push_back(*path_i);
 149       view_paths.push_back(true);
 150       ++pathid;
 151       ++path_i;
 152       ++sel_i;
 153     } else if (pathid < sel_pathid) {
 154       ++pathid;
 155       ++path_i;
 156     } else if (pathid > sel_pathid) {
 157       ++sel_i;
 158     }
 159   }
 160 }
 161
 162 // FIXME: this is a cut-n-paste from MussaWindow, perhaps they should be refactored to
 163 // some shared place
 164 void MussaAlignedWindow::createSubAnalysis()
 165 {
 166   list<SequenceLocation> result;
 167   SequenceLocationModel& model = subanalysis_window->getModel();
 168   browser.copySelectedTracksAsSeqLocation(result);
 169   for(list<SequenceLocation>::iterator result_itor = result.begin();
 170       result_itor != result.end();
 171       ++result_itor)
 172   {
 173     model.push_back(*result_itor);
 174   }
 175
 176   if (not subanalysis_window->isVisible()) {
 177     subanalysis_window->show();
 178   }
 179 }
 180
 181 void MussaAlignedWindow::setAlignment(int alignment_index)
 182 {
 183   if (selected_paths.size() > 0) {
 184     browser.centerOnPath(selected_paths[alignment_index].normalizedIndexes());
 185   }
 186 }
 187
 188 void MussaAlignedWindow::toggleViewAlignment(int alignment_index)
 189 {
 190   view_paths[alignment_index]= not view_paths[alignment_index];
 191   // perhaps it'd be better if we could erase specific sets
 192   // of matches instead of erasing them all and recomputing them all
 193   // but this is easier
 194   computeMatchLines();
 195 }
 196
 197 void MussaAlignedWindow::update()
 198 {
 199   browser.update();
 200 }
 201
 202 void MussaAlignedWindow::computeMatchLines()
 203 {
 204   browser.clear_links();
 205
 206   // filter out conserved paths
 207   list<ConservedPath> filtered_paths;
 208   vector<ConservedPath>::iterator path_i = selected_paths.begin();
 209   list<ConservedPath::path_type> result;
 210   list<vector<bool> > reversed;
 211
 212   for(vector<ConservedPath>::size_type count = 0;
 213       count != selected_paths.size();
 214       ++count, ++path_i)
 215   {
 216     if (view_paths[count])
 217       filtered_paths.push_back(*path_i);
 218   }
 219   analysis->createLocalAlignment(filtered_paths.begin(),
 220                                  filtered_paths.end(),
 221                                  result,
 222                                  reversed);
 223
 224   list<ConservedPath::path_type>::const_iterator result_i = result.begin();
 225   list<vector<bool> >::const_iterator reversed_i = reversed.begin();
 226   for(int i = 0; i != result.size(); ++i, ++result_i, ++reversed_i)
 227   {
 228     // make 1 base long links
 229     browser.link(*result_i, *reversed_i, 1);
 230   }
 231 }