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                                        boost::shared_ptr<QDir> default_dir_,
  17                                        const set<int>& sel_paths,
  18                                        SubanalysisWindowRef window,
  19                                        QWidget *parent)
  20   : QMainWindow(parent),
  21     analysis(m),
  22     default_dir(default_dir_),
  23     subanalysis_window(window),
  24     browser(default_dir),
  25     pick_align_menu(tr("Choose Alignment")),
  26     view_align_menu(tr("View Alignment")),
  27     threshold_widget(0),
  28     zoom(0),
  29     alignTB(0)
  30 {
  31   setupActions();
  32   connect(&browser, SIGNAL(basepairsCopied(size_t)),
  33           this, SLOT(showBasePairsCopied(size_t)));
  34   browser.setSequences(analysis->sequences(), analysis->colorMapper());
  35   setSelectedPaths(analysis, sel_paths);
  36   setAlignment(0);
  37   double zoom_level = browser.zoomToSequence();
  38
  39   zoom = new ZoomWidget();
  40   connect(zoom, SIGNAL(valueChanged(double)),
  41           &browser, SLOT(setZoom(double)));
  42   zoom->setValue(zoom_level);
  43   computeMatchLines();
  44   setupMenus();
  45   setupAlignmentMenus();
  46
  47   setCentralWidget(&browser);
  48
  49   // Add a threhold widget set to our current threshold and make it readonly
  50   threshold_widget = new ThresholdWidget;
  51   threshold_widget->setRange(analysis->get_threshold(),analysis->get_window());
  52   threshold_widget->setBasepairThreshold(analysis->get_soft_threshold());
  53   threshold_widget->setReadOnly(true);
  54
  55   alignTB = new QToolBar();
  56   alignTB->addWidget(zoom);
  57   alignTB->addWidget(threshold_widget);
  58   addToolBar(alignTB);
  59
  60   ostringstream message;
  61   message << "Selected " << selected_paths.size() << " paths";
  62   statusBar()->showMessage(message.str().c_str(), 5000);
  63   browser.updatePosition();
  64
  65   updateTitle();
  66 }
  67
  68 void MussaAlignedWindow::setupActions()
  69 {
  70   // more cut-n-paste from MussaWindow
  71   createSubAnalysisAction = new QAction(tr("Add to Subanalysis"), this);
  72   connect(createSubAnalysisAction, SIGNAL(triggered()),
  73           this, SLOT(createSubAnalysis()));
  74
  75   //Save pixel map action
  76   saveBrowserPixmapAction = new QAction(tr("Save to image..."), this);
  77   connect(saveBrowserPixmapAction, (SIGNAL(triggered())),
  78           &browser, SLOT(promptSaveBrowserPixmap()));
  79   saveBrowserPixmapAction->setIcon(QIcon(":/icons/image2.png"));
  80 }
  81
  82 void MussaAlignedWindow::setupMenus()
  83 {
  84   QMenu *newMenu = menuBar()->addMenu(tr("&File"));
  85   newMenu->addAction(saveBrowserPixmapAction);
  86
  87   newMenu = menuBar()->addMenu(tr("&Edit"));
  88   newMenu->addAction(browser.getCopySelectedSequenceAsStringAction());
  89   newMenu->addAction(browser.getCopySelectedSequenceAsFastaAction());
  90   newMenu->addAction(createSubAnalysisAction);
  91
  92   // add some extra features to the context menu
  93   QMenu *popupMenu = browser.getPopupMenu();
  94   if (popupMenu) {
  95     popupMenu->addAction(createSubAnalysisAction);
  96   }
  97 }
  98
  99 void MussaAlignedWindow::setupAlignmentMenus()
 100 {
 101   pick_align_menu.clear();
 102   view_align_menu.clear();
 103   pick_actions.clear();
 104   view_actions.clear();
 105
 106   for(vector<ConservedPath >::iterator pathz_i=selected_paths.begin();
 107       pathz_i != selected_paths.end();
 108       ++pathz_i)
 109   {
 110     ConservedPath::path_type normalized_path = pathz_i->normalizedIndexes();
 111     ostringstream menu_text;
 112     menu_text << pathz_i->window_size << ":";
 113     ConservedPath::iterator element_i = normalized_path.begin();
 114     menu_text << *element_i++;
 115     for (;
 116          element_i != normalized_path.end();
 117          ++element_i)
 118     {
 119       menu_text << ", ";
 120       menu_text << *element_i;
 121     }
 122     int index = pathz_i - selected_paths.begin();
 123     IntAction *pick = new IntAction(QString(menu_text.str().c_str()), index, this);
 124     connect(pick, SIGNAL(triggered(int)), this, SLOT(setAlignment(int)));
 125     pick_actions.push_back(pick);
 126     pick_align_menu.addAction(pick);
 127     IntAction *view = new IntAction(QString(menu_text.str().c_str()), index, this);
 128     connect(view, SIGNAL(triggered(int)), this, SLOT(toggleViewAlignment(int)));
 129     view->setCheckable(true);
 130     view->setChecked(true);
 131     view_actions.push_back(view);
 132     view_align_menu.addAction(view);
 133   }
 134
 135   menuBar()->addMenu(&pick_align_menu);
 136   menuBar()->addMenu(&view_align_menu);
 137 }
 138
 139
 140 void MussaAlignedWindow::setSelectedPaths(MussaRef m, const set<int>& sel_paths)
 141 {
 142   // sets are sorted
 143   set<int>::iterator sel_i = sel_paths.begin();
 144   list<ConservedPath>::const_iterator path_i = m->paths().refined_pathz.begin();
 145   list<ConservedPath>::const_iterator path_end = m->paths().refined_pathz.end();
 146   size_t path_size = m->paths().refined_pathz.size();
 147   size_t pathid=0;
 148
 149   selected_paths.reserve(sel_paths.size());
 150   view_paths.reserve(sel_paths.size());
 151   while (pathid != path_size and sel_i != sel_paths.end())
 152   {
 153     assert (*sel_i >= 0);
 154     size_t sel_pathid = (size_t)(*sel_i);
 155     if (pathid == sel_pathid) {
 156       selected_paths.push_back(*path_i);
 157       view_paths.push_back(true);
 158       ++pathid;
 159       ++path_i;
 160       ++sel_i;
 161     } else if (pathid < sel_pathid) {
 162       ++pathid;
 163       ++path_i;
 164     } else if (pathid > sel_pathid) {
 165       ++sel_i;
 166     }
 167   }
 168 }
 169
 170 // FIXME: this is a cut-n-paste from MussaWindow, perhaps they should be refactored to
 171 // some shared place
 172 void MussaAlignedWindow::createSubAnalysis()
 173 {
 174   list<SequenceLocation> result;
 175   SequenceLocationModel& model = subanalysis_window->getModel();
 176   browser.copySelectedTracksAsSeqLocation(result);
 177   for(list<SequenceLocation>::iterator result_itor = result.begin();
 178       result_itor != result.end();
 179       ++result_itor)
 180   {
 181     model.push_back(*result_itor);
 182   }
 183
 184   if (not subanalysis_window->isVisible()) {
 185     subanalysis_window->show();
 186   }
 187 }
 188
 189 void MussaAlignedWindow::setAlignment(int alignment_index)
 190 {
 191   if (selected_paths.size() > 0) {
 192     browser.centerOnPath(selected_paths[alignment_index].normalizedIndexes());
 193   }
 194 }
 195
 196 void MussaAlignedWindow::showBasePairsCopied(size_t bp_copied)
 197 {
 198   QString msg("Copied ");
 199   QString num;
 200   num.setNum(bp_copied);
 201   msg += num + " base pairs";
 202   statusBar()->showMessage(msg, 5000);
 203 }
 204
 205 void MussaAlignedWindow::toggleViewAlignment(int alignment_index)
 206 {
 207   view_paths[alignment_index]= not view_paths[alignment_index];
 208   // perhaps it'd be better if we could erase specific sets
 209   // of matches instead of erasing them all and recomputing them all
 210   // but this is easier
 211   computeMatchLines();
 212 }
 213
 214 void MussaAlignedWindow::update()
 215 {
 216   browser.update();
 217 }
 218
 219 void MussaAlignedWindow::updateTitle()
 220 {
 221   std::string title("Sequence View: ");
 222   if (analysis) {
 223     title += analysis->get_title();
 224   }
 225   setWindowTitle(title.c_str());
 226 }
 227
 228 void MussaAlignedWindow::computeMatchLines()
 229 {
 230   browser.clear_links();
 231
 232   // filter out conserved paths
 233   list<ConservedPath> filtered_paths;
 234   vector<ConservedPath>::iterator path_i = selected_paths.begin();
 235   list<ConservedPath::path_type> result;
 236   list<vector<bool> > reversed;
 237
 238   for(vector<ConservedPath>::size_type count = 0;
 239       count != selected_paths.size();
 240       ++count, ++path_i)
 241   {
 242     if (view_paths[count])
 243       filtered_paths.push_back(*path_i);
 244   }
 245   analysis->createLocalAlignment(filtered_paths.begin(),
 246                                  filtered_paths.end(),
 247                                  result,
 248                                  reversed);
 249
 250   list<ConservedPath::path_type>::const_iterator result_i = result.begin();
 251   list<vector<bool> >::const_iterator reversed_i = reversed.begin();
 252   for(int i = 0; i != result.size(); ++i, ++result_i, ++reversed_i)
 253   {
 254     // make 1 base long links
 255     browser.link(*result_i, *reversed_i, 1);
 256   }
 257 }