TrapperApp Class Reference

The base class of the application. It sets up the main window and providing a menubar, toolbar and statusbar. For the main view, an instance of class TrapperView is created which creates your view. More...

#include <trapper.h>

Inheritance diagram for TrapperApp:

[legend]Collaboration diagram for TrapperApp:

[legend]List of all members.

Public Types
typedef std::multimap< QString, TrapperDoc * >	str_doc_map
Public Slots
void	slotCreateClient (QString modeView)
void	slotFileQuit ()
Public Member Functions
	TrapperApp ()
virtual	~TrapperApp ()
void	setDbHomeDir (QString dir)
void	setViewModeConfFile (QString filename)
void	openDocumentFile (const char *file=0)
void	exportToFile (QString toXmlFile)
Protected Member Functions
bool	queryExit ()
virtual bool	eventFilter (QObject *object, QEvent *event)
void	createClient (TrapperDoc *doc, QString modeview=QString::null)
Private Slots
void	slotFileNew ()
void	slotFileOpen ()
void	slotFileSave ()
void	slotFileSaveAs ()
void	slotFileClose ()
void	slotFileFlush ()
void	slotFilePrint ()
void	slotEditUndo ()
void	slotEditCut ()
void	slotEditCopy ()
void	slotEditPaste ()
void	slotEditSelectAll ()
void	slotEditSelectBetween ()
void	slotEditSelectBetweenCols ()
void	slotEditFindRead ()
void	slotEditFindTag ()
void	slotViewToolBar (bool toggle)
void	slotViewStatusBar (bool toggle)
void	slotWindowNewWindow ()
void	slotHelpAbout ()
void	slotHelpManual ()
void	slotStatusHelpMsg (const QString &text)
void	windowMenuAboutToShow ()
void	windowMenuActivated (int id)
void	slotImport ()
void	slotNewImport ()
void	slotChromatImport ()
void	slotMateImport ()
void	slotTcImport ()
void	slotPhdImport ()
void	slotExport ()
void	slotZoomIn ()
void	slotZoomInX ()
void	slotZoomInY ()
void	slotZoomOut ()
void	slotZoomOutX ()
void	slotZoomOutY ()
void	slotEnlarge ()
void	slotShrink ()
void	slotShowStatistics ()
void	slotConfigureViewModes ()
void	slotNormalMode ()
void	slotDragMode ()
void	slotViewTimeCourse (bool toggle)
void	slotNormalizeTimeCourse (bool toggle)
void	slotScrollForward ()
void	slotScrollBackwards ()
void	slotClusterWindowChanged (int window_size)
void	slotClusterNumChanged (int num)
void	slotActivatedWindow (QWidget *w)
Private Member Functions
void	initActions ()
void	initMenuBar ()
void	initToolBar ()
void	initStatusBar ()
void	initView ()
void	scroll (int dx, int dy)
void	open_docs_not_already_open (QPtrList< TrapperDoc > &notOpenBefore)
QStringList	contigNamesInProjectDir ()
Private Attributes
QFile	viewmodefile
QPopupMenu *	pFileMenu
QPopupMenu *	pEditMenu
QPopupMenu *	pViewMenu
QPopupMenu *	pHelpMenu
QPopupMenu *	pWindowMenu
QPopupMenu *	pToolsMenu
QToolBar *	fileToolbar
QWorkspace *	pWorkspace
QPrinter *	printer
int	untitledCount
QList< TrapperDoc > *	pDocList
QAction *	fileNew
QAction *	fileOpen
QAction *	fileSave
QAction *	fileSaveAs
QAction *	fileClose
QAction *	filePrint
QAction *	fileQuit
QAction *	fileFlush
QAction *	editUndo
QAction *	editCut
QAction *	editCopy
QAction *	editPaste
QAction *	editSelectAll
QAction *	editSelectBetween
QAction *	editSelectBetweenCols
QAction *	editFindRead
QAction *	editFindTag
QAction *	viewToolBar
QAction *	viewStatusBar
QAction *	zoomInAction
QAction *	zoomInXAction
QAction *	zoomInYAction
QAction *	zoomOutAction
QAction *	zoomOutXAction
QAction *	zoomOutYAction
QAction *	enlargeAction
QAction *	shrinkAction
QAction *	showStatisticsAction
QAction *	configureViewModesAction
QActionGroup *	windowAction
QAction *	windowNewWindow
QAction *	windowTile
QAction *	windowCascade
QActionGroup *	modeActionGroup
QAction *	normalModeAction
QAction *	dragModeAction
QActionGroup *	timecourseActionGroup
QAction *	timecourseAction
QAction *	normalizeAction
QAction *	clusterScrollForwardAction
QAction *	clusterScrollBackwardsAction
QSpinBox *	clusterWindowBox
QSpinBox *	clusterMinNumBox
QAction *	importAction
QAction *	importNewAction
QAction *	importChromatAction
QAction *	importMateAction
QAction *	importTcAction
QAction *	importPhdAction
QAction *	exportAction
QAction *	helpAboutApp
QAction *	helpManualApp
QString	projectDir
DbEnv *	dbenv

---

Detailed Description

The base class of the application. It sets up the main window and providing a menubar, toolbar and statusbar. For the main view, an instance of class TrapperView is created which creates your view.

Author:

Source Framework Automatically Generated by KDevelop, (c) The KDevelop Team.

Version:

KDevelop version 1.3 code generation

Definition at line 56 of file trapper.h.

---

Member Typedef Documentation

typedef std::multimap<QString, TrapperDoc*> TrapperApp::str_doc_map

Definition at line 77 of file trapper.h.

---

Constructor & Destructor Documentation

TrapperApp::TrapperApp

(

)

construtor

Definition at line 63 of file trapper.cpp.

References dbenv, initActions(), initMenuBar(), initStatusBar(), initToolBar(), initView(), pDocList, projectDir, pWorkspace, QAction::setOn(), slotActivatedWindow(), untitledCount, viewStatusBar, and viewToolBar.

{
//   qDebug("in TrapperApp::TrapperApp()");
  setCaption(tr("NGSView " "0.90" ) );
  dbenv = new DbEnv( DB_CXX_NO_EXCEPTIONS );
  
  //Should set these parameters more carefully, got them off the internet...
  //     dbenv->set_cachesize(0, 1000000, 0);
  dbenv->set_cachesize(0, 8388608, 8);
  dbenv->set_lg_regionmax(524288);
  dbenv->set_lg_bsize(2097152);
  
  //     printer = new QPrinter;
  untitledCount=0;
  pDocList = new QList<TrapperDoc>();
  pDocList->setAutoDelete(true);
  
  ///////////////////////////////////////////////////////////////////
  // call inits to invoke all other construction parts
  initView();
  initActions();
  initMenuBar();
  initToolBar();
  initStatusBar();
//   resize( 450, 400 );
  showMaximized();
  
  viewToolBar->setOn(true);
  viewStatusBar->setOn(true);
  
  projectDir = QString::null;
  
  
  connect(pWorkspace, SIGNAL(windowActivated(QWidget*)), this, SLOT(slotActivatedWindow(QWidget*)));
  
  
}

TrapperApp::~TrapperApp

(

)

[virtual]

destructor

Definition at line 101 of file trapper.cpp.

References dbenv.

{
  //    delete printer;
  dbenv->close(0);
}

---

Member Function Documentation

void TrapperApp::setDbHomeDir

(

QString

dir

)

set the directory home for the database environment

Definition at line 1498 of file trapper.cpp.

References QDir::absPath(), QString::ascii(), QMessageBox::critical(), dbenv, QDir::exists(), and projectDir.

Referenced by main().

{
  QDir d(dir);
  if ( d.exists() )
    {
      projectDir = d.absPath();
      int ret;
      /* Open the environment with full transactional support. */
      if ((ret = dbenv->open(projectDir, DB_CREATE |
                             DB_INIT_LOG | DB_INIT_LOCK | DB_INIT_MPOOL | DB_INIT_TXN | DB_RECOVER , 0)) != 0) {
        dbenv->err(ret, "environment open: %s", dir.ascii());
        exit( 1);
      }
//       cerr<<"DB home dir set"<<endl;
    }
  else
    {
      QMessageBox::critical( 0,
                             tr( "Critical Error" ),
                             tr( "Db home dir \"%1\" doesn't exit" ).arg( dir ) );
      
      /* todo: instead of exit, ask for a dir with a dialog */
      exit(1);
    }
  
}

void TrapperApp::setViewModeConfFile

(

QString

filename

)

set the filename for the view modes configuration file

Definition at line 1565 of file trapper.cpp.

References QMessageBox::critical(), TrapperConf::instance(), TrapperConf::loadDom(), QFile::open(), QFile::setName(), and viewmodefile.

Referenced by main().

{
 viewmodefile.setName( filename );
  
  if ( ! viewmodefile.open( IO_ReadWrite ) )
  {
        QMessageBox::critical( 0,
                               tr( "Critical Error" ),
                               tr( "Cannot open configuration file %1" ).arg( filename ) );

        /* todo: instead of exit, ask for a file with a dialog */
        exit(1);
  }

  TrapperConf * conf = TrapperConf::instance();
  Q_CHECK_PTR( conf );
  conf->loadDom( &viewmodefile );
}

void TrapperApp::openDocumentFile

(

const char *

file = 0

)

opens a file specified by commandline option

Definition at line 580 of file trapper.cpp.

References QString::arg(), createClient(), QMessageBox::critical(), dbenv, TrapperDoc::firstView(), TrapperDoc::newDocument(), TrapperDoc::openDocument(), TrapperDoc::pathName(), pDocList, projectDir, QMainWindow::statusBar(), and untitledCount.

Referenced by slotFileNew(), and slotFileOpen().

{
    statusBar()->message(tr("Opening file..."));
//     cerr<<"file: "<<file<<endl<<flush;
    TrapperDoc* doc;
    // check, if document already open. If yes, set the focus to the first view
    for(doc=pDocList->first(); doc > 0; doc=pDocList->next()) {
//       cerr<<"doc->pathName(): "<<doc->pathName()<<endl;
      
      if(doc->pathName() == file) {
        TrapperView* view=doc->firstView();
        view->setFocus();
        return;
      }
    }
    doc = new TrapperDoc(dbenv);
    pDocList->append(doc);
    doc->newDocument();
    // Creates an untitled window if file is 0


    QString fileName;
    if(!file)
    {
      untitledCount+=1;
      fileName=QString(tr("%1/Untitled%2")).arg(projectDir).arg(untitledCount);
//         fileName=QString(tr("%1/Contig13")).arg(projectDir);
    

    }
    else
    {
        fileName = file;
    }

    if(!doc->openDocument(fileName))
    {
        QMessageBox::critical(this, tr("Error !"),tr("Could not open document !"));
        delete doc;
        return;
    }

    // create the window

    //createClient(doc);


    createClient(doc, QString("closeup"));
//     createClient(doc, QString("tagTest"));

    statusBar()->message(tr("Ready."));
}

void TrapperApp::exportToFile

(

QString

toXmlFile

)

Definition at line 1457 of file trapper.cpp.

References QWorkspace::activeWindow(), QString::ascii(), TrapperView::getDocument(), pWorkspace, TrapperDoc::saveExport(), and QMainWindow::statusBar().

Referenced by slotExport().

{
  statusBar()->message(tr("Exporting contig to file..."));

  //Open file and docs

  ofstream outFile(toXmlFile.ascii());
//   ostream& outFile = cerr;

  outFile<<"<TRAPPER>\n";
//   QPtrList<TrapperDoc> docListNotAlreadyOpen;
//   docListNotAlreadyOpen.setAutoDelete(true);//Will delete docs itself when function exits

//   open_docs_not_already_open( docListNotAlreadyOpen );

  //For each contig, write it to file
  //New deal: just export active window

//   for (TrapperDoc* doc = pDocList->first(); doc != 0; doc = pDocList->next() ) {
//     doc->saveExport(outFile);
//   }
//   for (TrapperDoc* doc = docListNotAlreadyOpen.first(); doc != 0; doc = docListNotAlreadyOpen.next() ) {
//     doc->saveExport(outFile);
//   }

  TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
  if( m ) {
    TrapperDoc* doc = m->getDocument();
    if ( doc ) {
      doc->saveExport(outFile);
    }
  }
  
  //Close file
  outFile<<"</TRAPPER>\n";
  
  outFile.close();
  statusBar()->message(tr("Ready."));
  
}

bool TrapperApp::queryExit

(

)

[protected]

overloaded for Message box on last window exit

Definition at line 633 of file trapper.cpp.

References QMessageBox::information().

{
    int exit=QMessageBox::information(this, tr("Quit..."),
                                      tr("Do your really want to quit?"),
                                      QMessageBox::Ok, QMessageBox::Cancel);

    if (exit==1)
    {}
    else
    {}
    ;

    return (exit==1);
}

bool TrapperApp::eventFilter	(	QObject *	object,
		QEvent *	event
	)			[protected, virtual]

event filter to catch close events for MDI child windows and is installed in createClient() on every child window. Closing a window calls the eventFilter first which removes the view from the connected documents' view list. If the last view is going to be closed, the eventFilter() tests if the document is modified; if yes, it asks the user to save the document. If the document title contains "Untitled", slotFileSaveAs() gets called to get a save name and path.

Definition at line 648 of file trapper.cpp.

References QKeyEvent::accept(), QWorkspace::activateNextWindow(), QWorkspace::activatePrevWindow(), TrapperDoc::canCloseFrame(), TrapperDoc::firstView(), TrapperView::getDocument(), QKeyEvent::ignore(), QKeyEvent::key(), pDocList, pWorkspace, TrapperDoc::removeView(), scroll(), QKeyEvent::state(), and QEvent::type().

{
  if((event->type() == QEvent::Close) && ((TrapperApp*)object!=this) ) {

    QCloseEvent* e = (QCloseEvent*)event;
    TrapperView* pView = (TrapperView*)object;
    TrapperDoc* pDoc = pView->getDocument();
    if(pDoc->canCloseFrame(pView)) {
      pDoc->removeView(pView);
      if( !pDoc->firstView() ) {
        pDocList->remove(pDoc);
      }
      
      e->accept();
      
    }
    else {
      e->ignore();
    }
    return true;
  }
  else if ( (event->type() == QEvent::KeyPress) ) {
    QKeyEvent* e = (QKeyEvent*)event;
    int scrollfactor(10);
    if ( e->state() == Qt::ControlButton )
      scrollfactor *= 10;
    
    if ( e->key() == Qt::Key_Up ) {
      scroll(0, -1*scrollfactor);
      e->accept();
      return true;
    }
    else if ( e->key() == Qt::Key_Down ) {
      scroll(0, 1*scrollfactor);
      e->accept();
      return true;
    }
    else if ( e->key() == Qt::Key_Left ) {
      scroll(-1*scrollfactor, 0);
      e->accept();
      return true;
    }
    else if ( e->key() == Qt::Key_Right ) {
      scroll(1*scrollfactor, 0);
      e->accept();
      return true;
    }
    else if ( e->key() == Qt::Key_Tab ) {
      pWorkspace->activateNextWindow();
      e->accept();
      return true;
    }
    else if ( e->key() == Qt::Key_Backtab ) {
      pWorkspace->activatePrevWindow();
      e->accept();
      return true;
    }
    
    e->ignore();
  }
  
  
  return QWidget::eventFilter( object, event );    // standard event processing
}

void TrapperApp::createClient	(	TrapperDoc *	doc,
		QString	modeview = QString::null
	)			[protected]

creates a new child window. The document that will be connected to it has to be created before and the instances filled, with e.g. openDocument(). Then call createClient() to get a new MDI child window.

See also:

TrapperDoc::addView

TrapperDoc::openDocument

Parameters:

doc

pointer to the document instance that the view will be connected to.

Definition at line 550 of file trapper.cpp.

References TrapperDoc::addView(), pWorkspace, slotCreateClient(), QMainWindow::statusBar(), and QWorkspace::windowList().

Referenced by openDocumentFile(), slotCreateClient(), and slotWindowNewWindow().

{
  
  TrapperView* w = new TrapperView(doc, pWorkspace, modeView, modeView);
  w->installEventFilter(this);
  doc->addView(w);
  connect( w, SIGNAL( message( const QString& ) ), statusBar(), SLOT( message( const QString& ) ) );
  
  //The following line doesn't do anything as far as I can tell...?
  connect( w, SIGNAL( createView( QString ) ), this, SLOT( slotCreateClient( QString ) ) );
  if ( pWorkspace->windowList().isEmpty() ) // show the very first window in maximized mode
    w->showMaximized();
  else
    w->show();
}

void TrapperApp::slotCreateClient

(

QString

modeView

)

[slot]

Definition at line 566 of file trapper.cpp.

References QWorkspace::activeWindow(), createClient(), TrapperView::getDocument(), pWorkspace, and QMainWindow::statusBar().

Referenced by createClient().

{
  cerr<<"I suspect I never get called...???"<<endl;
    statusBar()->message(tr("Opening new view ..."));

    TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
    if( m )
    {
        TrapperDoc* doc = m->getDocument();
        createClient( doc, modeView );
    }
    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotFileQuit

(

)

[slot]

exits the application

Definition at line 834 of file trapper.cpp.

References pDocList, and QMainWindow::statusBar().

Referenced by initActions().

{
    statusBar()->message(tr("Exiting application..."));

    for(TrapperDoc * doc=pDocList->first(); doc > 0; doc=pDocList->next())
    {
        delete doc;
    }


    ///////////////////////////////////////////////////////////////////
    // exits the Application
    //  if(doc->isModified())
    //  {
    //    if(queryExit())
    //    {
    //      qApp->quit();
    //    }
    //    else
    //    {
    //
    //    };
    //  }
    //  else
    //  {
    qApp->quit();


    //    TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
    // if( m )
    // {
    //    TrapperDoc* doc = m->getDocument();
    //    delete doc;
    //  }
    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotFileNew

(

)

[private, slot]

generate a new document in the actual view

Definition at line 717 of file trapper.cpp.

References openDocumentFile(), and QMainWindow::statusBar().

Referenced by initActions().

{
  statusBar()->message(tr("Creating new file..."));
  
  openDocumentFile();
  
  statusBar()->message(tr("Ready."));
}

void TrapperApp::slotFileOpen

(

)

[private, slot]

open a document

Definition at line 726 of file trapper.cpp.

References QMessageBox::critical(), QFileDialog::getExistingDirectory(), QString::isEmpty(), openDocumentFile(), projectDir, and QMainWindow::statusBar().

Referenced by initActions().

{
  statusBar()->message(tr("Opening file..."));
  
  QString dirName = QFileDialog::getExistingDirectory(projectDir,this,"contig dir selection","Choose contig dir");
  if (!dirName.isEmpty())
    {
      QDir d(dirName), projdir(projectDir);
      
      if ( !d.cdUp() || d!= projdir ) {
        QMessageBox::critical(this, tr("Error !"),tr("Contig directory must be a subdirectory of project directory!"));

      }
      else {
//         cerr << "opening contig dir=" << dirName<<endl;
        openDocumentFile(dirName);
      }
    }
  statusBar()->message(tr("Ready."));
}

void TrapperApp::slotFileSave

(

)

[private, slot]

save a document

Definition at line 748 of file trapper.cpp.

References QWorkspace::activeWindow(), QString::contains(), QMessageBox::critical(), TrapperView::getDocument(), TrapperDoc::pathName(), pWorkspace, TrapperDoc::saveDocument(), slotFileSaveAs(), QMainWindow::statusBar(), and TrapperDoc::title().

Referenced by initActions().

{
    statusBar()->message(tr("Saving file..."));

    TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
    if( m )
    {
        TrapperDoc* doc = m->getDocument();
        if(doc->title().contains(tr("Untitled")))
            slotFileSaveAs();
        else
            if(!doc->saveDocument(doc->pathName()))
                QMessageBox::critical (this, tr("I/O Error !"), tr("Could not save the current document !"));
    }

    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotFileSaveAs

(

)

[private, slot]

save a document under a different filename

Definition at line 766 of file trapper.cpp.

References QWorkspace::activeWindow(), TrapperDoc::changedViewList(), QMessageBox::critical(), QFileDialog::getSaveFileName(), QString::isEmpty(), pWorkspace, TrapperDoc::saveDocument(), and QMainWindow::statusBar().

Referenced by slotFileSave().

{
    statusBar()->message(tr("Saving file under new filename..."));
    QString fn = QFileDialog::getSaveFileName(0, 0, this);
    if (!fn.isEmpty())
    {
        TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
        if( m )
        {
            TrapperDoc* doc = m->getDocument();
            if(!doc->saveDocument(fn))
            {
                QMessageBox::critical (this, tr("I/O Error !"), tr("Could not save the current document !"));
                return;
            }
            doc->changedViewList();
        }
    }
    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotFileClose

(

)

[private, slot]

close the actual file

Definition at line 806 of file trapper.cpp.

References QWorkspace::activeWindow(), TrapperDoc::closeDocument(), TrapperView::getDocument(), pWorkspace, and QMainWindow::statusBar().

Referenced by initActions().

{
  cerr<<"Hello slotFileClose() "<<endl;
 
  statusBar()->message(tr("Closing file..."));
  
  TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
  if( m )
    {
      TrapperDoc* doc=m->getDocument();
      doc->closeDocument();
    }
  
  statusBar()->message(tr("Ready."));
  cerr<<"Bye slotFileClose() "<<endl;
}

void TrapperApp::slotFileFlush

(

)

[private, slot]

Flushes dbs

Definition at line 786 of file trapper.cpp.

References GeneralMaker::listRegistered(), pDocList, and QMainWindow::statusBar().

{
  statusBar()->message(tr("Flushing database caches..."));
  
  for(TrapperDoc * doc=pDocList->first(); doc!= 0; doc=pDocList->next())
    {
      cerr<<"doc->pathName(): "<<doc->pathName()<<endl;
      list<string> type_list = GeneralMaker::listRegistered();
      for( list<string>::iterator it = type_list.begin(); it != type_list.end(); ++it ) {
        TrDb* db = doc->findTrDb( *it );
        if ( db ) {
          cerr<<"Syncing "<<*it<<endl;
          db->sync();
          
        }
      }
    }
  statusBar()->message(tr("Ready."));  
}

void TrapperApp::slotFilePrint

(

)

[private, slot]

print the actual file

Definition at line 823 of file trapper.cpp.

References QWorkspace::activeWindow(), TrapperView::print(), printer, pWorkspace, and QMainWindow::statusBar().

Referenced by initActions().

{
    statusBar()->message(tr("Printing..."));

    TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
    if ( m )
        m->print( printer );

    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotEditUndo

(

)

[private, slot]

reverts the last editing action

Definition at line 871 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, QMainWindow::statusBar(), and TrapperView::undo().

Referenced by initActions().

{
    statusBar()->message(tr("Reverting last move..."));

    TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
    if ( m )   m->undo();

    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotEditCut

(

)

[private, slot]

put the marked text/object into the clipboard and remove it from the document

Definition at line 881 of file trapper.cpp.

References QWorkspace::activeWindow(), TrapperView::cut(), pWorkspace, and QMainWindow::statusBar().

Referenced by initActions().

{
    statusBar()->message(tr("Cutting selection..."));

    TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
    if ( m ) m->cut();

    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotEditCopy

(

)

[private, slot]

put the marked text/object into the clipboard

Definition at line 891 of file trapper.cpp.

References QWorkspace::activeWindow(), TrapperView::copy(), pWorkspace, and QMainWindow::statusBar().

Referenced by initActions().

{
    statusBar()->message(tr("Copying selection to clipboard..."));

    TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
    if ( m )  m->copy();

    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotEditPaste

(

)

[private, slot]

paste the clipboard into the document

Definition at line 901 of file trapper.cpp.

References QWorkspace::activeWindow(), TrapperView::paste(), pWorkspace, and QMainWindow::statusBar().

Referenced by initActions().

{
    statusBar()->message(tr("Inserting clipboard contents..."));

    TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
    if ( m )   m->paste();
    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotEditSelectAll

(

)

[private, slot]

Selects all reads

Definition at line 910 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, TrapperView::selectAll(), and QMainWindow::statusBar().

Referenced by initActions().

{
    statusBar()->message(tr("Selecting all reads..."));

    TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
    if ( m )   m->selectAll();
    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotEditSelectBetween

(

)

[private, slot]

Selects all reads between two rows

Definition at line 919 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, TrapperView::selectBetween(), and QMainWindow::statusBar().

Referenced by initActions().

{
    statusBar()->message(tr("Selecting all reads between rows..."));

    TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
    if ( m )   m->selectBetween();
    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotEditSelectBetweenCols

(

)

[private, slot]

Selects all reads between two cols

Definition at line 928 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, TrapperView::selectBetweenCols(), and QMainWindow::statusBar().

Referenced by initActions().

{
    statusBar()->message(tr("Selecting all reads between cols..."));

    TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
    if ( m )   m->selectBetweenCols();
    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotEditFindRead

(

)

[private, slot]

Finds a specific read

Definition at line 937 of file trapper.cpp.

References QWorkspace::activeWindow(), TrapperView::findRead(), pWorkspace, and QMainWindow::statusBar().

Referenced by initActions().

{
    statusBar()->message(tr("Finding read..."));

    TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
    if ( m )   m->findRead();
    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotEditFindTag

(

)

[private, slot]

Finds a specific tag

Definition at line 946 of file trapper.cpp.

References QWorkspace::activeWindow(), TrapperView::findTag(), pWorkspace, and QMainWindow::statusBar().

Referenced by initActions().

{
    statusBar()->message(tr("Finding tag..."));

    TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
    if ( m )   m->findTag();
    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotViewToolBar

(

bool

toggle

)

[private, slot]

toggle the toolbar

Definition at line 955 of file trapper.cpp.

References fileToolbar, and QMainWindow::statusBar().

Referenced by initActions().

{
    statusBar()->message(tr("Toggle toolbar..."));
    ///////////////////////////////////////////////////////////////////
    // turn Toolbar on or off
    if (toggle== false)
    {
        fileToolbar->hide();
    }
    else
    {
        fileToolbar->show();
    };
    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotViewStatusBar

(

bool

toggle

)

[private, slot]

toggle the statusbar

Definition at line 971 of file trapper.cpp.

References QMainWindow::statusBar().

Referenced by initActions().

{
    statusBar()->message(tr("Toggle statusbar..."));
    ///////////////////////////////////////////////////////////////////
    //turn Statusbar on or off

    if (toggle == false)
    {
        statusBar()->hide();
    }
    else
    {
        statusBar()->show();
    }
    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotWindowNewWindow

(

)

[private, slot]

creates a new view for the current document

Definition at line 988 of file trapper.cpp.

References QWorkspace::activeWindow(), createClient(), TrapperView::getDocument(), pWorkspace, and QMainWindow::statusBar().

Referenced by initActions().

{
    statusBar()->message(tr("Opening new document view..."));

    TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
    if ( m )
    {
        TrapperDoc* doc = m->getDocument();
        createClient(doc);
    }
    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotHelpAbout

(

)

[private, slot]

shows an about dlg

Definition at line 1001 of file trapper.cpp.

References QMessageBox::about().

Referenced by initActions().

{
  QMessageBox::about(this,tr("About..."),
                     tr("NGSView\nVersion 1.0"
                        "\n(c) 2003 - 2009 by Erik Arner, Martti Tammi, and Erik Sjölund"));
}

void TrapperApp::slotHelpManual

(

)

[private, slot]

shows the online help

Definition at line 1008 of file trapper.cpp.

References QMessageBox::about().

{
  QMessageBox::about(this,tr("Help"),
                     tr("Please see documentation included with DNPTrapper release or at http://dnptrapper.sourceforge.net"));
  
}

void TrapperApp::slotStatusHelpMsg

(

const QString &

text

)

[private, slot]

change the status message of the whole statusbar temporary

Definition at line 1015 of file trapper.cpp.

References QMainWindow::statusBar().

{
    ///////////////////////////////////////////////////////////////////
    // change status message of whole statusbar temporary (text, msec)
    statusBar()->message(text, 2000);
}

void TrapperApp::windowMenuAboutToShow

(

)

[private, slot]

gets called when the window menu is activated; recreates the window menu with all opened window titles.

Definition at line 1022 of file trapper.cpp.

References QWorkspace::activeWindow(), QAction::addTo(), QPopupMenu::clear(), QPopupMenu::insertItem(), QPopupMenu::insertSeparator(), pWindowMenu, pWorkspace, QPopupMenu::setItemChecked(), QPopupMenu::setItemParameter(), windowAction, windowCascade, QWorkspace::windowList(), windowMenuActivated(), windowNewWindow, and windowTile.

Referenced by initMenuBar().

{
    pWindowMenu->clear();
    windowNewWindow->addTo(pWindowMenu);
    windowCascade->addTo(pWindowMenu);
    windowTile->addTo(pWindowMenu);

    if ( pWorkspace->windowList().isEmpty() )
    {
        windowAction->setEnabled(false);
    }
    else
    {
        windowAction->setEnabled(true);
    }

    pWindowMenu->insertSeparator();

    QWidgetList windows = pWorkspace->windowList();
    for ( int i = 0; i < int(windows.count()); ++i )
    {
        int id = pWindowMenu->insertItem(QString("&%1 ").arg(i+1)+windows.at(i)->caption(), this, SLOT( windowMenuActivated( int ) ) );
        pWindowMenu->setItemParameter( id, i );
        pWindowMenu->setItemChecked( id, pWorkspace->activeWindow() == windows.at(i) );
    }
}

void TrapperApp::windowMenuActivated

(

int

id

)

[private, slot]

activates the MDI child widget when it gets selected from the window menu.

Definition at line 1049 of file trapper.cpp.

References pWorkspace, QWidget::setFocus(), and QWorkspace::windowList().

Referenced by windowMenuAboutToShow().

{
    QWidget* w = pWorkspace->windowList().at( id );
    if ( w )
        w->setFocus();
}

void TrapperApp::slotImport

(

)

[private, slot]

imports data

Definition at line 1134 of file trapper.cpp.

References QString::arg(), contigNamesInProjectDir(), dbenv, QDomDocument::documentElement(), QFileDialog::getOpenFileName(), TrapperDoc::import(), QString::isEmpty(), TrapperDoc::openDocument(), projectDir, QDomDocument::setContent(), QMainWindow::statusBar(), and QMessageBox::warning().

{
  statusBar()->message(tr("Importing data from an xml file..."));
  QString fn = QFileDialog::getOpenFileName(0, 0, this,"import from file dialog","Choose your xml file to import from");
  if (!fn.isEmpty()) {
    QFile f( fn );
    if ( !f.open( IO_ReadOnly ) ) {
      QMessageBox::warning(this,"","couldn't read file");
    }
    
    QDomDocument domDoc("Trapper");
    if ( !domDoc.setContent( &f ) ) {
      f.close();
      QMessageBox::warning(this,"","couldn't read xml");
      return;
    }
    f.close();
    
    QDomElement docElem = domDoc.documentElement();
    
    for( QDomNode node1 = docElem.firstChild(); !node1.isNull() ; node1 = node1.nextSibling()) {
      if ( node1.isElement() && node1.nodeName() == "contig" ) {
          QDomElement elem1 = node1.toElement();
          
          Q_ASSERT((elem1.hasAttribute("name")));
          QString contigName = elem1.attribute( "name");
          
          
          bool found = false;
          /*
            TrapperDoc * doc;      
            for(doc=pDocList->first(); doc > 0; doc=pDocList->next())
            {
            
            if(doc->pathName()==contigName)
            { found = true; }
            }
            
          */
          
          QStringList contigNamesAlreadyPresent = contigNamesInProjectDir();
          if ( contigNamesAlreadyPresent.contains( contigName ) ) {
            found = true;
          }
          if ( found ) {
            QString message;
            message = QString("The contig name \"%1\" was specified in the import file, but that contig is already present in the project dir. Skipping this one").arg(contigName);
            QMessageBox::warning(this,"",message);
            continue;
          }
          QString fName = projectDir + "/" + contigName;
          TrapperDoc *  tdoc = new TrapperDoc(dbenv);
          tdoc->openDocument(fName);
          tdoc->import( elem1 );
          delete tdoc;
          tdoc = NULL;
          cerr << "reached after"<<endl;
          
      }
      //        node1 = node1.nextSibling();
    }
    
    /*
      TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
      if( m )
      {
      TrapperDoc* doc = m->getDocument();
      if(!doc->import(fn))
      {
      QMessageBox::critical (this, tr("I/O Error !"), tr("Could not import !"));
      return;
      }
      }
    */
    
  }
  statusBar()->message(tr("Ready."));
}

void TrapperApp::slotNewImport

(

)

[private, slot]

imports data

Definition at line 1213 of file trapper.cpp.

References dbenv, QFileDialog::getOpenFileName(), QString::isEmpty(), QXmlSimpleReader::parse(), QXmlSimpleReader::parseContinue(), projectDir, QMainWindow::statusBar(), and QMessageBox::warning().

Referenced by initActions().

{
  statusBar()->message(tr("Importing data from an xml file..."));
  QString fn = QFileDialog::getOpenFileName(0, 0, this,"import from file dialog","Choose trapper xml or macsim file to import from");
  if (!fn.isEmpty()) {
    QFile f( fn );
    if ( !f.open( IO_ReadOnly ) ) {
        QMessageBox::warning(this,"","couldn't open file");
        return;
    }
    QXmlDefaultHandler* handler;
    
    
    
    if ( fn.endsWith("macsim")) {
      handler = new MacsimParser(dbenv, projectDir);
    }
    else {
      handler = new TrapperParser(dbenv, projectDir);
    }

    
//     QXmlInputSource source( &f );
//     ChunkedXMLInputSource source( &f );
    QXmlInputSource* source = new ChunkedXMLInputSource( &f );
    QXmlSimpleReader reader;
    reader.setContentHandler( handler );
    
    
//     if (!reader.parse(source) ) {
//       QMessageBox::warning(this,"","couldn't read file");
//       return;
//     }
    int num_chunks(0);
    reader.parse( source, true );
    while ( reader.parseContinue() ) {
      num_chunks++;
//       cerr<<num_chunks<<" parsed"<<endl;
    }
    delete source;
    
  }
  statusBar()->message(tr("Ready."));
}

void TrapperApp::slotChromatImport

(

)

[private, slot]

imports chromat data

Definition at line 1258 of file trapper.cpp.

References QPtrList::first(), QFileDialog::getExistingDirectory(), QString::isEmpty(), QPtrList::next(), open_docs_not_already_open(), pDocList, projectDir, QPtrList::setAutoDelete(), and QMainWindow::statusBar().

Referenced by initActions().

{
  statusBar()->message(tr("Importing chromatogram data..."));
  
  QString chromatDirName = QFileDialog::getExistingDirectory(projectDir,this,"chromat dir selection","Choose chromatogram directory");

  if (chromatDirName.isEmpty()) {
    return;
  }

  //First, open all contigs (docs)
  
  QPtrList<TrapperDoc> docListNotAlreadyOpen;
  docListNotAlreadyOpen.setAutoDelete(true);//Will delete docs itself when function exits

  open_docs_not_already_open( docListNotAlreadyOpen );

  for (TrapperDoc* doc = pDocList->first(); doc != 0; doc = pDocList->next() ) {
    doc->importChromat(chromatDirName);
  }
  for (TrapperDoc* doc = docListNotAlreadyOpen.first(); doc != 0; doc = docListNotAlreadyOpen.next() ) {
    doc->importChromat(chromatDirName);
  }

  //Close all docs that weren't already open - happens automatically with QPtrList
  
  statusBar()->message(tr("Ready."));
}

void TrapperApp::slotMateImport

(

)

[private, slot]

imports mate data

Definition at line 1287 of file trapper.cpp.

References QPtrList::first(), QFileDialog::getOpenFileName(), QString::isEmpty(), QPtrList::next(), open_docs_not_already_open(), pDocList, QPtrList::setAutoDelete(), and QMainWindow::statusBar().

Referenced by initActions().

{
  statusBar()->message(tr("Importing mate data..."));
  
  QString matefile = QFileDialog::getOpenFileName(0, 0, this,"import from file dialog","Choose your mate pair file to import from");

  if (matefile.isEmpty()) {
    return;
  }

  //First, open all contigs (docs)
  
  QPtrList<TrapperDoc> docListNotAlreadyOpen;
  docListNotAlreadyOpen.setAutoDelete(true);//Will delete docs itself when function exits

  open_docs_not_already_open( docListNotAlreadyOpen );

  for (TrapperDoc* doc = pDocList->first(); doc != 0; doc = pDocList->next() ) {
    doc->importMates(matefile);
  }
  for (TrapperDoc* doc = docListNotAlreadyOpen.first(); doc != 0; doc = docListNotAlreadyOpen.next() ) {
    doc->importMates(matefile);
  }

  
  statusBar()->message(tr("Ready."));
}

void TrapperApp::slotTcImport

(

)

[private, slot]

imports time course data

Definition at line 1315 of file trapper.cpp.

References QWorkspace::activeWindow(), TrapperView::getDocument(), QFileDialog::getOpenFileName(), TrapperDoc::importTimeCourse(), QString::isEmpty(), pWorkspace, and QMainWindow::statusBar().

Referenced by initActions().

{
  statusBar()->message(tr("Importing time course data..."));
  
  QString tcfile = QFileDialog::getOpenFileName(0, 0, this,"import from file dialog","Choose your time course file to import from");

  if (tcfile.isEmpty()) {
    return;
  }

  //TC data is imported separately for each document
  TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
  if( m ) {
    TrapperDoc* doc = m->getDocument();
    if ( doc ) {
      doc->importTimeCourse(tcfile);        
    }
  }
  
  statusBar()->message(tr("Ready."));
  
}

void TrapperApp::slotPhdImport

(

)

[private, slot]

imports phd data

Definition at line 1338 of file trapper.cpp.

References QPtrList::first(), QFileDialog::getExistingDirectory(), QString::isEmpty(), QPtrList::next(), open_docs_not_already_open(), pDocList, projectDir, QPtrList::setAutoDelete(), and QMainWindow::statusBar().

Referenced by initActions().

{
  statusBar()->message(tr("Importing phd data..."));
  
  QString phdDirName = QFileDialog::getExistingDirectory(projectDir,this,"phd dir selection","Choose phd directory");

  if (phdDirName.isEmpty()) {
    return;
  }

  //First, open all contigs (docs)
  
  QPtrList<TrapperDoc> docListNotAlreadyOpen;
  docListNotAlreadyOpen.setAutoDelete(true);//Will delete docs itself when function exits

  open_docs_not_already_open( docListNotAlreadyOpen );

  for (TrapperDoc* doc = pDocList->first(); doc != 0; doc = pDocList->next() ) {
    doc->importPhd(phdDirName);
  }
  for (TrapperDoc* doc = docListNotAlreadyOpen.first(); doc != 0; doc = docListNotAlreadyOpen.next() ) {
    doc->importPhd(phdDirName);
  }

  //Close all docs that weren't already open - happens automatically with QPtrList
  
  statusBar()->message(tr("Ready."));
}

void TrapperApp::slotExport

(

)

[private, slot]

exports data

Definition at line 1430 of file trapper.cpp.

References QFile::exists(), exportToFile(), QFileDialog::getSaveFileName(), QString::isEmpty(), QMessageBox::question(), and QMainWindow::statusBar().

Referenced by initActions().

{
    statusBar()->message(tr("Exporting data to an xml file..."));
    QString fn = QFileDialog::getSaveFileName(0, "Trapper Xml (*.xml)", this,
                                              "export to file dialog",
                                              "Choose a filename to save the export data under");
    if (fn.isEmpty())
    {
        return;
    }
    if (  QFile::exists( fn ) &&
          QMessageBox::question(
                                0,
                                tr("Overwrite File? -- Trapper"),
                                tr("A file called %1 already exists."
                                   "Do you want to overwrite it?")
                                .arg( fn ),
                                tr("&Yes"), tr("&No"),
                                QString::null, 0, 1 ) ) {
      
      return;
    }
    
    exportToFile(fn);
    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotZoomIn

(

)

[private, slot]

zooms in

Definition at line 1056 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, and TrapperView::zoomIn().

Referenced by initActions().

{
    TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
    if( m )
    {
        m->zoomIn();
//         m->updateContents();
    }
}

void TrapperApp::slotZoomInX

(

)

[private, slot]

zooms in X

Definition at line 1066 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, and TrapperView::zoomInX().

Referenced by initActions().

{
    TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
    if( m )
    {
        m->zoomInX();
//         m->updateContents();
    }
}

void TrapperApp::slotZoomInY

(

)

[private, slot]

zooms in Y

Definition at line 1076 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, and TrapperView::zoomInY().

Referenced by initActions().

{
    TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
    if( m )
    {
        m->zoomInY();
//         m->updateContents();
    }
}

void TrapperApp::slotZoomOut

(

)

[private, slot]

zooms out

Definition at line 1086 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, and TrapperView::zoomOut().

Referenced by initActions().

{
    TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
    if( m )
    {
        m->zoomOut();
//         m->updateContents();
    }
}

void TrapperApp::slotZoomOutX

(

)

[private, slot]

zooms out X

Definition at line 1096 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, and TrapperView::zoomOutX().

Referenced by initActions().

{
    TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
    if( m )
    {
        m->zoomOutX();
//         m->updateContents();
    }
}

void TrapperApp::slotZoomOutY

(

)

[private, slot]

zooms out Y

Definition at line 1106 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, and TrapperView::zoomOutY().

Referenced by initActions().

{
    TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
    if( m )
    {
        m->zoomOutY();
//         m->updateContents();
    }
}

void TrapperApp::slotEnlarge

(

)

[private, slot]

Enlarges view

Definition at line 1116 of file trapper.cpp.

References QWorkspace::activeWindow(), TrapperView::enlarge(), and pWorkspace.

Referenced by initActions().

{
    TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
    if( m )
    {
        m->enlarge();
    }
}

void TrapperApp::slotShrink

(

)

[private, slot]

Shrinks view

Definition at line 1125 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, and TrapperView::shrink().

Referenced by initActions().

{
    TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
    if( m )
    {
        m->shrink();
    }
}

void TrapperApp::slotShowStatistics

(

)

[private, slot]

show statistics

Definition at line 1536 of file trapper.cpp.

References QWorkspace::activeWindow(), TrapperView::getDocument(), TrapperDoc::getStatistics(), pWorkspace, QTextEdit::setReadOnly(), QTextEdit::setText(), and QMainWindow::statusBar().

Referenced by initActions().

{
    statusBar()->message(tr("Opening statistics window ..."));

    TrapperView* m = (TrapperView*)pWorkspace->activeWindow();
    if( m )
    {
        TrapperDoc* doc = m->getDocument();
        if ( doc )
        {
            QString statisticsText = doc->getStatistics();
            QTextEdit * statView = new QTextEdit( );
            statView->setReadOnly( true );
            statView->setText( statisticsText );
            statView->show();
        }
    }
    statusBar()->message(tr("Ready."));
}

void TrapperApp::slotConfigureViewModes

(

)

[private, slot]

configure view modes

Definition at line 1556 of file trapper.cpp.

References QDialog::exec().

Referenced by initActions().

{
   ShowModesDlg * dlg = new ShowModesDlg( this, QString::null );

   if ( dlg->exec() == QDialog::Accepted )
   {}
}

void TrapperApp::slotNormalMode

(

)

[private, slot]

normal pointer mode

Definition at line 1590 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, and TrapperView::setDragMode().

Referenced by initActions().

{
  
  TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
  if ( m )   m->setDragMode(false);
  
}

void TrapperApp::slotDragMode

(

)

[private, slot]

drag mode

Definition at line 1599 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, and TrapperView::setDragMode().

Referenced by initActions().

{
  TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
  if ( m )   m->setDragMode(true);
  
}

void TrapperApp::slotViewTimeCourse

(

bool

toggle

)

[private, slot]

time course visualization

Definition at line 1619 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, and TrapperView::setViewTimeCourse().

Referenced by initActions().

{
  TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
  if ( m )   m->setViewTimeCourse(toggle);
  
}

void TrapperApp::slotNormalizeTimeCourse

(

bool

toggle

)

[private, slot]

normalize time course

Definition at line 1626 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, and TrapperView::setNormalizeTimeCourse().

Referenced by initActions().

{
  TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
  if ( m )   m->setNormalizeTimeCourse(toggle);

}

void TrapperApp::slotScrollForward

(

)

[private, slot]

scroll to next cluster

Definition at line 1633 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, and TrapperView::scrollToNextCluster().

Referenced by initActions().

{
  TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
  if ( m )   m->scrollToNextCluster(true);
  
}

void TrapperApp::slotScrollBackwards

(

)

[private, slot]

scroll to previous cluster

Definition at line 1640 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, and TrapperView::scrollToNextCluster().

Referenced by initActions().

{
  TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
  if ( m )   m->scrollToNextCluster(false);
  
}

void TrapperApp::slotClusterWindowChanged

(

int

window_size

)

[private, slot]

change window size for cluster browsing

Definition at line 1647 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, and TrapperView::setClusterWindow().

Referenced by initToolBar().

{
  TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
  if ( m )   m->setClusterWindow(window_size);
}

void TrapperApp::slotClusterNumChanged

(

int

num

)

[private, slot]

change min read number for cluster browsing

Definition at line 1653 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, and TrapperView::setClusterMinNum().

Referenced by initToolBar().

{
  TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
  if ( m )   m->setClusterMinNum(num);
}

void TrapperApp::slotActivatedWindow

(

QWidget *

w

)

[private, slot]

active window

Definition at line 1606 of file trapper.cpp.

References clusterMinNumBox, clusterWindowBox, dragModeAction, QAction::isOn(), normalizeAction, timecourseAction, and QSpinBox::value().

Referenced by TrapperApp().

{
  TrapperView* m = (TrapperView*) w;
  if ( m ) {
    m->setDragMode(dragModeAction->isOn());
    m->setViewTimeCourse(timecourseAction->isOn());
    m->setNormalizeTimeCourse(normalizeAction->isOn());
    m->setClusterWindow(clusterWindowBox->value());
    m->setClusterMinNum(clusterMinNumBox->value());
  }
  
}

void TrapperApp::initActions

(

)

[private]

initializes all QActions of the application

Definition at line 107 of file trapper.cpp.

References QActionGroup::add(), clusterScrollBackwardsAction, clusterScrollForwardAction, configureViewModesAction, dragModeAction, editCopy, editCut, editFindRead, editFindTag, editPaste, editSelectAll, editSelectBetween, editSelectBetweenCols, editUndo, enlargeAction, exportAction, fileClose, fileFlush, fileNew, fileOpen, filePrint, fileQuit, fileSave, fileSaveAs, helpAboutApp, importChromatAction, importMateAction, importNewAction, importPhdAction, importTcAction, modeActionGroup, normalizeAction, normalModeAction, pWorkspace, QAction::setEnabled(), QAction::setOn(), QAction::setStatusTip(), QAction::setToggleAction(), QAction::setWhatsThis(), showStatisticsAction, shrinkAction, slotChromatImport(), slotConfigureViewModes(), slotDragMode(), slotEditCopy(), slotEditCut(), slotEditFindRead(), slotEditFindTag(), slotEditPaste(), slotEditSelectAll(), slotEditSelectBetween(), slotEditSelectBetweenCols(), slotEditUndo(), slotEnlarge(), slotExport(), slotFileClose(), slotFileNew(), slotFileOpen(), slotFilePrint(), slotFileQuit(), slotFileSave(), slotHelpAbout(), slotMateImport(), slotNewImport(), slotNormalizeTimeCourse(), slotNormalMode(), slotPhdImport(), slotScrollBackwards(), slotScrollForward(), slotShowStatistics(), slotShrink(), slotTcImport(), slotViewStatusBar(), slotViewTimeCourse(), slotViewToolBar(), slotWindowNewWindow(), slotZoomIn(), slotZoomInX(), slotZoomInY(), slotZoomOut(), slotZoomOutX(), slotZoomOutY(), QAccel::stringToKey(), timecourseAction, timecourseActionGroup, viewStatusBar, viewToolBar, windowAction, windowCascade, windowNewWindow, windowTile, zoomInAction, zoomInXAction, zoomInYAction, zoomOutAction, zoomOutXAction, and zoomOutYAction.

Referenced by TrapperApp().

{
    QPixmap openIcon, saveIcon, newIcon, selectAllIcon, zoomPlusIcon, zoomMinusIcon,
      zoomPlusIconX, zoomPlusIconY, zoomMinusIconX, zoomMinusIconY, flushIcon, dragIcon, pointerIcon,
      tcViewIcon, tcNormIcon, leftArrowIcon, rightArrowIcon;

    newIcon = QPixmap(filenew);
    openIcon = QPixmap(fileopen);
    saveIcon = QPixmap(filesave);
    selectAllIcon = QPixmap( editselectall );
    zoomPlusIcon = QPixmap( zoom_in );
    zoomPlusIconX = QPixmap( zoom_in_x );
    zoomPlusIconY = QPixmap( zoom_in_y );
    zoomMinusIcon = QPixmap( zoom_out );
    zoomMinusIconX = QPixmap( zoom_out_x);
    zoomMinusIconY = QPixmap( zoom_out_y);
    flushIcon = QPixmap( dbflush );
    pointerIcon = QPixmap(pointerbutton);
    dragIcon = QPixmap(dragbutton);
    tcViewIcon = QPixmap(tcview);
    tcNormIcon = QPixmap(tcnorm);
    leftArrowIcon = QPixmap(left_arrow);
    rightArrowIcon = QPixmap(right_arrow);


    fileNew = new QAction(tr("New Project"), newIcon, tr("&New"), QAccel::stringToKey(tr("Ctrl+N")), this);
    fileNew->setStatusTip(tr("Creates a new project"));
    fileNew->setWhatsThis(tr("New Project\n\nCreates a new project"));
    connect(fileNew, SIGNAL(activated()), this, SLOT(slotFileNew()));

    fileOpen = new QAction(tr("Open Contig"), openIcon, tr("&Open..."), QAccel::stringToKey(tr("Ctrl+O")), this);
    fileOpen->setStatusTip(tr("Opens an existing contig or creates a new one"));
    fileOpen->setWhatsThis(tr("Open Contig\n\nOpens an existing contig or creates a new one. To create a new contig, simply create a new directory in the file dialog and choose it"));
    connect(fileOpen, SIGNAL(activated()), this, SLOT(slotFileOpen()));

    fileSave = new QAction(tr("Save File"), saveIcon, tr("&Save"), QAccel::stringToKey(tr("Ctrl+S")), this);
    fileSave->setStatusTip(tr("Saves the actual document"));
    fileSave->setWhatsThis(tr("Save File.\n\nSaves the actual document"));
    connect(fileSave, SIGNAL(activated()), this, SLOT(slotFileSave()));

    fileSaveAs = new QAction(tr("Save File As"), tr("Save &as..."), 0, this);
    fileSaveAs->setStatusTip(tr("Saves the actual document under a new filename"));
    fileSaveAs->setWhatsThis(tr("Save As\n\nSaves the actual document under a new filename"));
    connect(fileSaveAs, SIGNAL(activated()), this, SLOT(slotFileSave()));

    fileClose = new QAction(tr("Close Project"), tr("&Close"), QAccel::stringToKey(tr("Ctrl+W")), this);
    fileClose->setStatusTip(tr("Closes the actual project"));
    fileClose->setWhatsThis(tr("Close Project\n\nCloses the actual project"));
    connect(fileClose, SIGNAL(activated()), this, SLOT(slotFileClose()));

    filePrint = new QAction(tr("Print File"), tr("&Print"), QAccel::stringToKey(tr("Ctrl+P")), this);
    filePrint->setStatusTip(tr("Prints out the actual document"));
    filePrint->setWhatsThis(tr("Print File\n\nPrints out the actual document"));
    connect(filePrint, SIGNAL(activated()), this, SLOT(slotFilePrint()));

    fileQuit = new QAction(tr("Exit"), tr("E&xit"), QAccel::stringToKey(tr("Ctrl+Q")), this);
    fileQuit->setStatusTip(tr("Quits the application"));
    fileQuit->setWhatsThis(tr("Exit\n\nQuits the application"));
    connect(fileQuit, SIGNAL(activated()), this, SLOT(slotFileQuit()));

    fileFlush = new QAction(tr("Flush"), flushIcon, tr("&Flush"), QAccel::stringToKey(tr("Ctrl+F")), this);
    fileFlush->setStatusTip(tr("Flushes cached data"));
    fileFlush->setWhatsThis(tr("Flush\n\nFlushes cached data to database"));
//     connect(fileFlush, SIGNAL(activated()), this, SLOT(slotFileFlush()));

    editCut = new QAction(tr("Cut"), tr("Cu&t"), QAccel::stringToKey(tr("Ctrl+X")), this);
    editCut->setStatusTip(tr("Cuts the selected section and puts it to the clipboard"));
    editCut->setWhatsThis(tr("Cut\n\nCuts the selected section and puts it to the clipboard"));
    connect(editCut, SIGNAL(activated()), this, SLOT(slotEditCut()));

    editCopy = new QAction(tr("Copy"), tr("&Copy"), QAccel::stringToKey(tr("Ctrl+C")), this);
    editCopy->setStatusTip(tr("Copies the selected section to the clipboard"));
    editCopy->setWhatsThis(tr("Copy\n\nCopies the selected section to the clipboard"));
    connect(editCopy, SIGNAL(activated()), this, SLOT(slotEditCopy()));

    editUndo = new QAction(tr("Undo last move"), tr("&Undo last move"), QAccel::stringToKey(tr("Ctrl+Z")), this);
    editUndo->setStatusTip(tr("Reverts the last move"));
    editUndo->setWhatsThis(tr("Undo\n\nReverts the last read moving action"));
    connect(editUndo, SIGNAL(activated()), this, SLOT(slotEditUndo()));

    editPaste = new QAction(tr("Paste"), tr("&Paste"), QAccel::stringToKey(tr("Ctrl+V")), this);
    editPaste->setStatusTip(tr("Pastes the clipboard contents to actual position"));
    editPaste->setWhatsThis(tr("Paste\n\nPastes the clipboard contents to actual position"));
    connect(editPaste, SIGNAL(activated()), this, SLOT(slotEditPaste()));

    editSelectAll = new QAction(tr("Select All"), selectAllIcon, tr("Select &All"), QAccel::stringToKey(tr("Ctrl+A")), this);
    editSelectAll->setStatusTip(tr("Selects all reads"));
    editSelectAll->setWhatsThis(tr("Select All\n\nSelects all reads"));
    connect(editSelectAll, SIGNAL(activated()), this, SLOT(slotEditSelectAll()));

    editSelectBetween = new QAction(tr("Select Between rows"), tr("Select &Between rows"), 0, this);
    editSelectBetween->setStatusTip(tr("Selects all reads between two rows"));
    editSelectBetween->setWhatsThis(tr("Select Between rows\n\nSelects all reads between two rows"));
    connect(editSelectBetween, SIGNAL(activated()), this, SLOT(slotEditSelectBetween()));

    editSelectBetweenCols = new QAction(tr("Select Between cols"), tr("Select Between cols"), 0, this);
    editSelectBetweenCols->setStatusTip(tr("Selects all reads between two cols"));
    editSelectBetweenCols->setWhatsThis(tr("Select Between rows\n\nSelects all reads between two cols"));
    connect(editSelectBetweenCols, SIGNAL(activated()), this, SLOT(slotEditSelectBetweenCols()));

    editFindRead = new QAction(tr("Find Read"), tr("Find Read"), 0, this);
    editFindRead->setStatusTip(tr("Selects a specific read"));
    editFindRead->setWhatsThis(tr("Find Read\n\nSelects a specific read"));
    connect(editFindRead, SIGNAL(activated()), this, SLOT(slotEditFindRead()));

    editFindTag = new QAction(tr("Find Tag"), tr("Find Tag"), 0, this);
    editFindTag->setStatusTip(tr("Selects a specific tag"));
    editFindTag->setWhatsThis(tr("Find Tag\n\nSelects a specific tag"));
    connect(editFindTag, SIGNAL(activated()), this, SLOT(slotEditFindTag()));

    viewToolBar = new QAction(tr("Toolbar"), tr("Tool&bar"), 0, this, 0, true);
    viewToolBar->setStatusTip(tr("Enables/disables the toolbar"));
    viewToolBar->setWhatsThis(tr("Toolbar\n\nEnables/disables the toolbar"));
    connect(viewToolBar, SIGNAL(toggled(bool)), this, SLOT(slotViewToolBar(bool)));

    viewStatusBar = new QAction(tr("Statusbar"), tr("&Statusbar"), 0, this, 0, true);
    viewStatusBar->setStatusTip(tr("Enables/disables the statusbar"));
    viewStatusBar->setWhatsThis(tr("Statusbar\n\nEnables/disables the statusbar"));
    connect(viewStatusBar, SIGNAL(toggled(bool)), this, SLOT(slotViewStatusBar(bool)));

    windowNewWindow = new QAction(tr("New Wiew"), tr("&New Wiew"), 0, this);
    windowNewWindow->setStatusTip(tr("Opens a new view for the current document"));
    windowNewWindow->setWhatsThis(tr("New Wiew\n\nOpens a new view for the current document"));
    connect(windowNewWindow, SIGNAL(activated()), this, SLOT(slotWindowNewWindow()));

    windowCascade = new QAction(tr("Cascade"), tr("&Cascade"), 0, this);
    windowCascade->setStatusTip(tr("Cascades all windows"));
    windowCascade->setWhatsThis(tr("Cascade\n\nCascades all windows"));
    connect(windowCascade, SIGNAL(activated()), pWorkspace, SLOT(cascade()));

    windowTile = new QAction(tr("Tile"), tr("&Tile"), 0, this);
    windowTile->setStatusTip(tr("Tiles all windows"));
    windowTile->setWhatsThis(tr("Tile\n\nTiles all windows"));
    connect(windowTile, SIGNAL(activated()), pWorkspace, SLOT(tile()));

    windowAction = new QActionGroup(this, 0, false);
    windowAction->add(windowNewWindow);
    windowAction->add(windowCascade);
    windowAction->add(windowTile);
    
    normalModeAction = new QAction(tr("Normal mode"), pointerIcon, tr("Normal mode"), 0, this);
    normalModeAction->setStatusTip(tr("Sets mode to normal"));
    normalModeAction->setWhatsThis(tr("Normal mode\n\nFor selection of reads, normal moving etc"));
    normalModeAction->setToggleAction(true);
    normalModeAction->setOn(true);
    connect(normalModeAction, SIGNAL(activated()), this, SLOT(slotNormalMode()));
    
    dragModeAction = new QAction(tr("Drag mode"), dragIcon, tr("Drag mode"), 0, this);
    dragModeAction->setStatusTip(tr("Sets mode to drag mode"));
    dragModeAction->setWhatsThis(tr("Drag mode\n\nFor moving reads between contigs, and sideways moving"));
    dragModeAction->setToggleAction(true);
    connect(dragModeAction, SIGNAL(activated()), this, SLOT(slotDragMode()));

    modeActionGroup = new QActionGroup(this, 0, true);
    modeActionGroup->add(normalModeAction);
    modeActionGroup->add(dragModeAction);

    timecourseAction = new QAction(tr("View Time Course data"), tcViewIcon, tr("Time Course"), 0, this);
    timecourseAction->setStatusTip(tr("Enables Time Course viewing"));
    timecourseAction->setWhatsThis(tr("Time Course\n\nFor viewing of time course data"));
    timecourseAction->setToggleAction(true);
    timecourseAction->setOn(false);
    connect(timecourseAction, SIGNAL(toggled(bool)), this, SLOT(slotViewTimeCourse(bool)));
    
    normalizeAction = new QAction(tr("View Time Course data normalized"), tcNormIcon, tr("Normalized Time Course"), 0, this);
    normalizeAction->setStatusTip(tr("Normalize Time Course viewing"));
    normalizeAction->setWhatsThis(tr("Normalize Time Course\n\nFor viewing of time course data normalized for each individual read"));
    normalizeAction->setToggleAction(true);
    normalizeAction->setOn(false);
    normalizeAction->setEnabled(false);
    connect(normalizeAction, SIGNAL(toggled(bool)), this, SLOT(slotNormalizeTimeCourse(bool)));
    connect(timecourseAction, SIGNAL(toggled(bool)), normalizeAction, SLOT(setEnabled(bool)));
            
    timecourseActionGroup = new QActionGroup(this, 0, false);
    timecourseActionGroup->add(timecourseAction);
    timecourseActionGroup->add(normalizeAction);

    clusterScrollForwardAction = new QAction(tr("Scroll Right"), rightArrowIcon, tr("Scroll Right"), ALT + Key_Right, this);
    clusterScrollForwardAction->setStatusTip(tr("Scrolls right to next cluster"));
    clusterScrollForwardAction->setWhatsThis(tr("Scrolls right to next cluster"));
    connect(clusterScrollForwardAction, SIGNAL(activated()), this, SLOT(slotScrollForward()));

    clusterScrollBackwardsAction = new QAction(tr("Scroll Left"), leftArrowIcon, tr("Scroll Left"), ALT + Key_Left, this);
    clusterScrollBackwardsAction->setStatusTip(tr("Scrolls left to previous cluster"));
    clusterScrollBackwardsAction->setWhatsThis(tr("Scrolls left to previous cluster"));
    connect(clusterScrollBackwardsAction, SIGNAL(activated()), this, SLOT(slotScrollBackwards()));

//     clusterWindowBox = new QSpinBox(1, numeric_limits<int>::max(), 1, this);
//     clusterWindowBox->setValue(100);
//     connect(clusterWindowBox, SIGNAL(valueChanged(int)), this, SLOT(slotClusterWindowChanged(int)));

//     clusterMinNumBox = new QSpinBox(1, numeric_limits<int>::max(), 1, this);
//     clusterMinNumBox->setValue(10);
//     connect(clusterMinNumBox, SIGNAL(valueChanged(int)), this, SLOT(slotClusterNumChanged(int)));
    
    helpAboutApp = new QAction(tr("About"), tr("&About..."), 0, this);
    helpAboutApp->setStatusTip(tr("About the application"));
    helpAboutApp->setWhatsThis(tr("About\n\nAbout the application"));
    connect(helpAboutApp, SIGNAL(activated()), this, SLOT(slotHelpAbout()));

//     helpManualApp = new QAction(tr("Manual"), tr("&Manual"), 0, this);
//     helpManualApp->setStatusTip(tr("Trapper Manual"));
//     helpManualApp->setWhatsThis(tr("Trapper Manual\n\nManual decribing how to use Trapper"));
//     connect(helpManualApp, SIGNAL(activated()), this, SLOT(slotHelpManual()));

//     importAction = new QAction(tr("Import project"), tr("&Import project"), 0, this);
//     importAction->setStatusTip(tr("Imports project data"));
//     importAction->setWhatsThis(tr("Imports project data"));
//     connect(importAction, SIGNAL(activated()), this, SLOT(slotImport()));

    importNewAction = new QAction(tr("Import project"), tr("&Import project"), 0, this);
    importNewAction->setStatusTip(tr("Imports project data"));
    importNewAction->setWhatsThis(tr("Imports project data"));
    connect(importNewAction, SIGNAL(activated()), this, SLOT(slotNewImport()));

    importChromatAction = new QAction(tr("Import Chromatograms"), tr("Import Chromatograms"), 0, this);
    importChromatAction->setStatusTip(tr("Imports chromatogram data"));
    importChromatAction->setWhatsThis(tr("Imports chromatogram data"));
    connect(importChromatAction, SIGNAL(activated()), this, SLOT(slotChromatImport()));

    importMateAction = new QAction(tr("Import Mate pairs"), tr("Import Mate Pairs"), 0, this);
    importMateAction->setStatusTip(tr("Imports mate pair data"));
    importMateAction->setWhatsThis(tr("Imports mate pair data"));
    connect(importMateAction, SIGNAL(activated()), this, SLOT(slotMateImport()));

    importTcAction = new QAction(tr("Import Time Course Data"), tr("Import Time Course"), 0, this);
    importTcAction->setStatusTip(tr("Imports Time Course Data"));
    importTcAction->setWhatsThis(tr("Imports Time Course Data"));
    connect(importTcAction, SIGNAL(activated()), this, SLOT(slotTcImport()));

    importPhdAction = new QAction(tr("Import phd data"), tr("Import phd data"), 0, this);
    importPhdAction->setStatusTip(tr("Imports phd data"));
    importPhdAction->setWhatsThis(tr("Imports phd data"));
    connect(importPhdAction, SIGNAL(activated()), this, SLOT(slotPhdImport()));

    exportAction = new QAction(tr("Export"), tr("&Export"), 0, this);
    exportAction->setStatusTip(tr("Exports data"));
    exportAction->setWhatsThis(tr("Exports data"));
    connect(exportAction, SIGNAL(activated()), this, SLOT(slotExport()));

    zoomInAction = new QAction(tr("Zoom in"), zoomPlusIcon, tr("Zoom in"), Key_Plus, this);
    zoomInAction->setStatusTip(tr("Zooms in"));
    zoomInAction->setWhatsThis(tr("Zooms in"));
    connect(zoomInAction, SIGNAL(activated()), this, SLOT(slotZoomIn()));

    zoomInXAction = new QAction(tr("Zoom in X"), zoomPlusIconX, tr("Zoom in X"),CTRL + Key_Plus, this);
    zoomInXAction->setStatusTip(tr("Zooms in X"));
    zoomInXAction->setWhatsThis(tr("Zooms in X direction"));
    connect(zoomInXAction, SIGNAL(activated()), this, SLOT(slotZoomInX()));

    zoomInYAction = new QAction(tr("Zoom in Y"), zoomPlusIconY, tr("Zoom in Y"), CTRL + ALT + Key_Plus, this);
    zoomInYAction->setStatusTip(tr("Zooms in Y"));
    zoomInYAction->setWhatsThis(tr("Zooms in Y direction"));
    connect(zoomInYAction, SIGNAL(activated()), this, SLOT(slotZoomInY()));

    zoomOutAction = new QAction(tr("Zoom out"), zoomMinusIcon, tr("&Zoom out"), Key_Minus, this);
    zoomOutAction->setStatusTip(tr("Zooms out"));
    zoomOutAction->setWhatsThis(tr("Zooms out"));
    connect(zoomOutAction, SIGNAL(activated()), this, SLOT(slotZoomOut()));

    zoomOutXAction = new QAction(tr("Zoom out X"), zoomMinusIconX, tr("Zoom out X"), CTRL + Key_Minus, this);
    zoomOutXAction->setStatusTip(tr("Zooms out X"));
    zoomOutXAction->setWhatsThis(tr("Zooms out in X direction"));
    connect(zoomOutXAction, SIGNAL(activated()), this, SLOT(slotZoomOutX()));

    zoomOutYAction = new QAction(tr("Zoom out Y"), zoomMinusIconY, tr("Zoom out Y"), CTRL + ALT + Key_Minus, this);
    zoomOutYAction->setStatusTip(tr("Zooms out Y"));
    zoomOutYAction->setWhatsThis(tr("Zooms out in Y direction"));
    connect(zoomOutYAction, SIGNAL(activated()), this, SLOT(slotZoomOutY()));

    enlargeAction = new QAction(tr("Enlarge"), tr("&Enlarge"), 0, this);
    enlargeAction->setStatusTip(tr("Adds more viewable rows"));
    enlargeAction->setWhatsThis(tr("Enlarges view, so that more rows and columns can be displayed"));
    connect(enlargeAction, SIGNAL(activated()), this, SLOT(slotEnlarge()));

    shrinkAction = new QAction(tr("Shrink"), tr("&Shrink"), 0, this);
    shrinkAction->setStatusTip(tr("Removes viewable rows. Does not affect data."));
    shrinkAction->setWhatsThis(tr("Shrinks view, displaying fewer rows and columns. Does not affect data."));
    connect(shrinkAction, SIGNAL(activated()), this, SLOT(slotShrink()));

    showStatisticsAction = new QAction(tr("Show statistics"), tr("Show statistics"), 0, this);
    showStatisticsAction->setStatusTip(tr("Show statistics about contig"));
    showStatisticsAction->setWhatsThis(tr("Show underlying berkeley db statistics for this contig"));
    connect(showStatisticsAction, SIGNAL(activated()), this, SLOT(slotShowStatistics()));

    configureViewModesAction = new QAction(tr("Configure view modes"), tr("&Configure modes"), 0, this);
    configureViewModesAction->setStatusTip(tr("Configure view modes"));
    configureViewModesAction->setWhatsThis(tr("Configure view modes"));
    connect(configureViewModesAction, SIGNAL(activated()), this, SLOT(slotConfigureViewModes()));

    
}

void TrapperApp::initMenuBar

(

)

[private]

initMenuBar creates the menu_bar and inserts the menuitems

Definition at line 400 of file trapper.cpp.

References QActionGroup::addTo(), QAction::addTo(), editCopy, editCut, editFindRead, editFindTag, editPaste, editSelectAll, editSelectBetween, editSelectBetweenCols, editUndo, exportAction, fileClose, fileOpen, fileQuit, helpAboutApp, importMateAction, importNewAction, importTcAction, QPopupMenu::insertItem(), QPopupMenu::insertSeparator(), QMainWindow::menuBar(), modeActionGroup, pEditMenu, pFileMenu, pHelpMenu, pToolsMenu, pViewMenu, pWindowMenu, QPopupMenu::setCheckable(), showStatisticsAction, timecourseActionGroup, viewStatusBar, viewToolBar, QMainWindow::whatsThis(), windowMenuAboutToShow(), zoomInAction, zoomInXAction, zoomInYAction, zoomOutAction, zoomOutXAction, and zoomOutYAction.

Referenced by TrapperApp().

{
    ///////////////////////////////////////////////////////////////////
    // MENUBAR

    ///////////////////////////////////////////////////////////////////
    // menuBar entry pFileMenu
    pFileMenu=new QPopupMenu();
//     fileNew->addTo(pFileMenu);
    fileOpen->addTo(pFileMenu);
    fileClose->addTo(pFileMenu);
//     pFileMenu->insertSeparator();
//     fileFlush->addTo( pFileMenu );//DANGEROUS??
    //    fileSave->addTo(pFileMenu);
    // fileSaveAs->addTo(pFileMenu);
//     pFileMenu->insertSeparator();
//     filePrint->addTo(pFileMenu);
    pFileMenu->insertSeparator();
    fileQuit->addTo(pFileMenu);




    ///////////////////////////////////////////////////////////////////
    // menuBar entry editMenu
    pEditMenu=new QPopupMenu();
    editUndo->addTo(pEditMenu);
//     pEditMenu->insertSeparator();
    editCut->addTo(pEditMenu);
    editCopy->addTo(pEditMenu);
    editPaste->addTo(pEditMenu);
    editSelectAll->addTo(pEditMenu);
    editSelectBetween->addTo(pEditMenu);
    editSelectBetweenCols->addTo(pEditMenu);
    editFindRead->addTo(pEditMenu);
    editFindTag->addTo(pEditMenu);

    ///////////////////////////////////////////////////////////////////
    // menuBar entry viewMenu
    pViewMenu=new QPopupMenu();
    pViewMenu->setCheckable(true);
    viewToolBar->addTo(pViewMenu);
    viewStatusBar->addTo(pViewMenu);

    zoomInAction->addTo(pViewMenu);
    zoomOutAction->addTo(pViewMenu);
    zoomInXAction->addTo(pViewMenu);
    zoomOutXAction->addTo(pViewMenu);
    zoomInYAction->addTo(pViewMenu);
    zoomOutYAction->addTo(pViewMenu);
//     enlargeAction->addTo(pViewMenu);
//     shrinkAction->addTo(pViewMenu);
    showStatisticsAction->addTo(pViewMenu);
    timecourseActionGroup->addTo(pViewMenu);
//     configureViewModesAction->addTo(pViewMenu);

    ///////////////////////////////////////////////////////////////////
    // EDIT YOUR APPLICATION SPECIFIC MENUENTRIES HERE

    pToolsMenu=new QPopupMenu();
//     importAction->addTo(pToolsMenu);
    importNewAction->addTo(pToolsMenu);
//     importChromatAction->addTo(pToolsMenu);
    importMateAction->addTo(pToolsMenu);
    importTcAction->addTo(pToolsMenu);
//     importPhdAction->addTo(pToolsMenu);
    modeActionGroup->addTo(pToolsMenu);
    exportAction->addTo(pToolsMenu);

    ///////////////////////////////////////////////////////////////////
    // menuBar entry windowMenu
    pWindowMenu = new QPopupMenu(this);
    pWindowMenu->setCheckable(true);
    connect(pWindowMenu, SIGNAL(aboutToShow()), this, SLOT(windowMenuAboutToShow()));

    ///////////////////////////////////////////////////////////////////
    // menuBar entry helpMenu
    pHelpMenu=new QPopupMenu();
//     helpManualApp->addTo(pHelpMenu);
    helpAboutApp->addTo(pHelpMenu);
    pHelpMenu->insertSeparator();
    pHelpMenu->insertItem(tr("What's &This"), this, SLOT(whatsThis()), SHIFT+Key_F1);

    menuBar()->insertItem(tr("&Contig"), pFileMenu);
    menuBar()->insertItem(tr("&Edit"), pEditMenu);
    menuBar()->insertItem(tr("&View"), pViewMenu);
    menuBar()->insertItem(tr("&Window"), pWindowMenu);
    menuBar()->insertItem(tr("&Tools"), pToolsMenu);
    menuBar()->insertItem(tr("&Help"), pHelpMenu);

}

void TrapperApp::initToolBar

(

)

[private]

this creates the toolbars. Change the toobar look and add new toolbars in this function

Definition at line 492 of file trapper.cpp.

References QToolTip::add(), QToolBar::addSeparator(), QActionGroup::addTo(), QAction::addTo(), clusterMinNumBox, clusterScrollBackwardsAction, clusterScrollForwardAction, clusterWindowBox, editSelectAll, fileOpen, fileToolbar, modeActionGroup, QSpinBox::setValue(), slotClusterNumChanged(), slotClusterWindowChanged(), timecourseActionGroup, QWhatsThis::whatsThisButton(), zoomInAction, zoomInXAction, zoomInYAction, zoomOutAction, zoomOutXAction, and zoomOutYAction.

Referenced by TrapperApp().

{
    ///////////////////////////////////////////////////////////////////
    // TOOLBAR
    fileToolbar = new QToolBar(this, "file operations");
//     fileNew->addTo(fileToolbar);
    fileOpen->addTo(fileToolbar);
//     fileFlush->addTo(fileToolbar);DANGEROUS??
//     fileSave->addTo(fileToolbar);
    editSelectAll->addTo(fileToolbar);
    zoomInAction->addTo(fileToolbar);
    zoomOutAction->addTo(fileToolbar);
    zoomInXAction->addTo(fileToolbar);
    zoomOutXAction->addTo(fileToolbar);
    zoomInYAction->addTo(fileToolbar);
    zoomOutYAction->addTo(fileToolbar);
    
    fileToolbar->addSeparator();
    modeActionGroup->addTo(fileToolbar);
    fileToolbar->addSeparator();
    timecourseActionGroup->addTo(fileToolbar);
    fileToolbar->addSeparator();


    clusterWindowBox = new QSpinBox(1, numeric_limits<int>::max(), 1, fileToolbar);
    clusterWindowBox->setValue(100);
    connect(clusterWindowBox, SIGNAL(valueChanged(int)), this, SLOT(slotClusterWindowChanged(int)));
    QToolTip::add(clusterWindowBox, "Window size for cluster scrolling");

    clusterMinNumBox = new QSpinBox(1, numeric_limits<int>::max(), 1, fileToolbar);
    clusterMinNumBox->setValue(10);
    connect(clusterMinNumBox, SIGNAL(valueChanged(int)), this, SLOT(slotClusterNumChanged(int)));
    QToolTip::add(clusterMinNumBox, "Min number of tags in window for cluster scrolling");

    clusterScrollBackwardsAction->addTo(fileToolbar);
    clusterScrollForwardAction->addTo(fileToolbar);
    fileToolbar->addSeparator();

    QWhatsThis::whatsThisButton(fileToolbar);
}

void TrapperApp::initStatusBar

(

)

[private]

setup the statusbar

Definition at line 533 of file trapper.cpp.

References QMainWindow::statusBar().

Referenced by TrapperApp().

{
    ///////////////////////////////////////////////////////////////////
    //STATUSBAR
    statusBar()->message(tr("Ready."));
}

void TrapperApp::initView

(

)

[private]

setup the mainview

Definition at line 540 of file trapper.cpp.

References pWorkspace, and QMainWindow::setCentralWidget().

Referenced by TrapperApp().

{
    ////////////////////////////////////////////////////////////////////
    // set the main widget here
    QVBox* view_back = new QVBox( this );
    view_back->setFrameStyle( QFrame::StyledPanel | QFrame::Sunken );
    pWorkspace = new QWorkspace( view_back );
    setCentralWidget(view_back);
}

void TrapperApp::scroll	(	int	dx,
		int	dy
	)			[private]

scroll active view

Definition at line 1584 of file trapper.cpp.

References QWorkspace::activeWindow(), pWorkspace, and QScrollView::scrollBy().

Referenced by eventFilter().

{
  
  TrapperView* m = (TrapperView*) pWorkspace->activeWindow();
  if ( m )   m->scrollBy(dx, dy);
}

void TrapperApp::open_docs_not_already_open

(

QPtrList< TrapperDoc > &

notOpenBefore

)

[private]

opens contigs that weren't already open and put them in list. User is responsible for deleting docs after use

Definition at line 1367 of file trapper.cpp.

References QPtrList::append(), contigNamesInProjectDir(), QMessageBox::critical(), dbenv, TrapperDoc::pathName(), pDocList, projectDir, and QString::section().

Referenced by slotChromatImport(), slotMateImport(), and slotPhdImport().

{

  TrapperDoc* doc;
  set<QString> alreadyOpen;
  
  for(doc=pDocList->first(); doc !=0; doc=pDocList->next()) {
    
    alreadyOpen.insert(doc->pathName().section('/', -2));
  }
  

  QStringList contigs = contigNamesInProjectDir();
  
  for ( QStringList::Iterator it = contigs.begin(); it != contigs.end(); ++it ) {
    
    
    if ( *it != "." && *it != ".." && alreadyOpen.find( *it ) == alreadyOpen.end() ) {
      
      
      TrapperDoc* tdoc = new TrapperDoc(dbenv);
      tdoc->newDocument();
      if ( !tdoc->openDocument(projectDir + "/" + *it ) ) {
        QMessageBox::critical(this, tr("Error !"),tr("Could not open document!"));
        delete tdoc;
      }
      else {
        notOpenBefore.append( tdoc );
      }
      
    }
    

  }
  
}

QStringList TrapperApp::contigNamesInProjectDir

(

)

[private]

Definition at line 1525 of file trapper.cpp.

References QDir::entryList(), QDir::exists(), projectDir, QDir::setFilter(), and QDir::setSorting().

Referenced by open_docs_not_already_open(), and slotImport().

{
    QString contigName;
    QDir d( projectDir );
    Q_ASSERT( d.exists() );
    d.setFilter( QDir::Dirs | QDir::NoSymLinks );
    d.setSorting( QDir::Name );
    QStringList slist = d.entryList();
    return slist;
}

---

Member Data Documentation

QFile TrapperApp::viewmodefile [private]

fills a map wit read names as keys and pointers to docs they're present in as values

Definition at line 233 of file trapper.h.

Referenced by setViewModeConfFile().

QPopupMenu* TrapperApp::pFileMenu [private]

file_menu contains all items of the menubar entry "File"

Definition at line 241 of file trapper.h.

Referenced by initMenuBar().

QPopupMenu* TrapperApp::pEditMenu [private]

edit_menu contains all items of the menubar entry "Edit"

Definition at line 243 of file trapper.h.

Referenced by initMenuBar().

QPopupMenu* TrapperApp::pViewMenu [private]

view_menu contains all items of the menubar entry "View"

Definition at line 245 of file trapper.h.

Referenced by initMenuBar().

QPopupMenu* TrapperApp::pHelpMenu [private]

view_menu contains all items of the menubar entry "Help"

Definition at line 247 of file trapper.h.

Referenced by initMenuBar().

QPopupMenu* TrapperApp::pWindowMenu [private]

the window menu

Definition at line 249 of file trapper.h.

Referenced by initMenuBar(), and windowMenuAboutToShow().

QPopupMenu* TrapperApp::pToolsMenu [private]

the tools menu

Definition at line 251 of file trapper.h.

Referenced by initMenuBar().

QToolBar* TrapperApp::fileToolbar [private]

Definition at line 253 of file trapper.h.

Referenced by initToolBar(), and slotViewToolBar().

QWorkspace* TrapperApp::pWorkspace [private]

pWorkspace is the MDI frame widget that handles MDI child widgets. Inititalized in initView()

Definition at line 258 of file trapper.h.

Referenced by createClient(), eventFilter(), exportToFile(), initActions(), initView(), scroll(), slotClusterNumChanged(), slotClusterWindowChanged(), slotCreateClient(), slotDragMode(), slotEditCopy(), slotEditCut(), slotEditFindRead(), slotEditFindTag(), slotEditPaste(), slotEditSelectAll(), slotEditSelectBetween(), slotEditSelectBetweenCols(), slotEditUndo(), slotEnlarge(), slotFileClose(), slotFilePrint(), slotFileSave(), slotFileSaveAs(), slotNormalizeTimeCourse(), slotNormalMode(), slotScrollBackwards(), slotScrollForward(), slotShowStatistics(), slotShrink(), slotTcImport(), slotViewTimeCourse(), slotWindowNewWindow(), slotZoomIn(), slotZoomInX(), slotZoomInY(), slotZoomOut(), slotZoomOutX(), slotZoomOutY(), TrapperApp(), windowMenuAboutToShow(), and windowMenuActivated().

QPrinter* TrapperApp::printer [private]

the printer instance

Definition at line 260 of file trapper.h.

Referenced by slotFilePrint().

int TrapperApp::untitledCount [private]

a counter that gets increased each time the user creates a new document with "File"->"New"

Definition at line 262 of file trapper.h.

Referenced by openDocumentFile(), and TrapperApp().

QList<TrapperDoc>* TrapperApp::pDocList [private]

a list of all open documents. If the last window of a document gets closed, the installed eventFilter removes this document from the list. The document list is checked for modified documents when the user is about to close the application.

Definition at line 266 of file trapper.h.

Referenced by eventFilter(), open_docs_not_already_open(), openDocumentFile(), slotChromatImport(), slotFileFlush(), slotFileQuit(), slotMateImport(), slotPhdImport(), and TrapperApp().

QAction* TrapperApp::fileNew [private]

Definition at line 268 of file trapper.h.

Referenced by initActions().

QAction* TrapperApp::fileOpen [private]

Definition at line 269 of file trapper.h.

Referenced by initActions(), initMenuBar(), and initToolBar().

QAction* TrapperApp::fileSave [private]

Definition at line 270 of file trapper.h.

Referenced by initActions().

QAction* TrapperApp::fileSaveAs [private]

Definition at line 271 of file trapper.h.

Referenced by initActions().

QAction* TrapperApp::fileClose [private]

Definition at line 272 of file trapper.h.

Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::filePrint [private]

Definition at line 273 of file trapper.h.

Referenced by initActions().

QAction* TrapperApp::fileQuit [private]

Definition at line 274 of file trapper.h.

Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::fileFlush [private]

Definition at line 275 of file trapper.h.

Referenced by initActions().

QAction* TrapperApp::editUndo [private]

Definition at line 277 of file trapper.h.

Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::editCut [private]

Definition at line 278 of file trapper.h.

Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::editCopy [private]

Definition at line 279 of file trapper.h.

Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::editPaste [private]

Definition at line 280 of file trapper.h.

Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::editSelectAll [private]

Definition at line 281 of file trapper.h.

Referenced by initActions(), initMenuBar(), and initToolBar().

QAction* TrapperApp::editSelectBetween [private]

Definition at line 282 of file trapper.h.

Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::editSelectBetweenCols [private]

Definition at line 283 of file trapper.h.

Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::editFindRead [private]

Definition at line 284 of file trapper.h.

Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::editFindTag [private]

Definition at line 285 of file trapper.h.

Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::viewToolBar [private]

Definition at line 287 of file trapper.h.

Referenced by initActions(), initMenuBar(), and TrapperApp().

QAction* TrapperApp::viewStatusBar [private]

Definition at line 288 of file trapper.h.

Referenced by initActions(), initMenuBar(), and TrapperApp().

QAction* TrapperApp::zoomInAction [private]

Definition at line 289 of file trapper.h.

Referenced by initActions(), initMenuBar(), and initToolBar().

QAction* TrapperApp::zoomInXAction [private]

Definition at line 290 of file trapper.h.

Referenced by initActions(), initMenuBar(), and initToolBar().

QAction* TrapperApp::zoomInYAction [private]

Definition at line 291 of file trapper.h.

Referenced by initActions(), initMenuBar(), and initToolBar().

QAction* TrapperApp::zoomOutAction [private]

Definition at line 292 of file trapper.h.

Referenced by initActions(), initMenuBar(), and initToolBar().

QAction* TrapperApp::zoomOutXAction [private]

Definition at line 293 of file trapper.h.

Referenced by initActions(), initMenuBar(), and initToolBar().

QAction* TrapperApp::zoomOutYAction [private]

Definition at line 294 of file trapper.h.

Referenced by initActions(), initMenuBar(), and initToolBar().

QAction* TrapperApp::enlargeAction [private]

Definition at line 295 of file trapper.h.

Referenced by initActions().

QAction* TrapperApp::shrinkAction [private]

Definition at line 296 of file trapper.h.

Referenced by initActions().

QAction* TrapperApp::showStatisticsAction [private]

Definition at line 297 of file trapper.h.

Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::configureViewModesAction [private]

Definition at line 298 of file trapper.h.

Referenced by initActions().

QActionGroup* TrapperApp::windowAction [private]

Definition at line 300 of file trapper.h.

Referenced by initActions(), and windowMenuAboutToShow().

QAction* TrapperApp::windowNewWindow [private]

Definition at line 301 of file trapper.h.

Referenced by initActions(), and windowMenuAboutToShow().

QAction* TrapperApp::windowTile [private]

Definition at line 302 of file trapper.h.

Referenced by initActions(), and windowMenuAboutToShow().

QAction* TrapperApp::windowCascade [private]

Definition at line 303 of file trapper.h.

Referenced by initActions(), and windowMenuAboutToShow().

QActionGroup* TrapperApp::modeActionGroup [private]

Definition at line 305 of file trapper.h.

Referenced by initActions(), initMenuBar(), and initToolBar().

QAction* TrapperApp::normalModeAction [private]

Definition at line 306 of file trapper.h.

Referenced by initActions().

QAction* TrapperApp::dragModeAction [private]

Definition at line 307 of file trapper.h.

Referenced by initActions(), and slotActivatedWindow().

QActionGroup* TrapperApp::timecourseActionGroup [private]

Definition at line 309 of file trapper.h.

Referenced by initActions(), initMenuBar(), and initToolBar().

QAction* TrapperApp::timecourseAction [private]

Definition at line 310 of file trapper.h.

Referenced by initActions(), and slotActivatedWindow().

QAction* TrapperApp::normalizeAction [private]

Definition at line 311 of file trapper.h.

Referenced by initActions(), and slotActivatedWindow().

QAction* TrapperApp::clusterScrollForwardAction [private]

Definition at line 313 of file trapper.h.

Referenced by initActions(), and initToolBar().

QAction* TrapperApp::clusterScrollBackwardsAction [private]

Definition at line 314 of file trapper.h.

Referenced by initActions(), and initToolBar().

QSpinBox* TrapperApp::clusterWindowBox [private]

Definition at line 315 of file trapper.h.

Referenced by initToolBar(), and slotActivatedWindow().

QSpinBox* TrapperApp::clusterMinNumBox [private]

Definition at line 316 of file trapper.h.

Referenced by initToolBar(), and slotActivatedWindow().

QAction* TrapperApp::importAction [private]

Definition at line 319 of file trapper.h.

QAction* TrapperApp::importNewAction [private]

Definition at line 320 of file trapper.h.

Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::importChromatAction [private]

Definition at line 321 of file trapper.h.

Referenced by initActions().

QAction* TrapperApp::importMateAction [private]

Definition at line 322 of file trapper.h.

Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::importTcAction [private]

Definition at line 323 of file trapper.h.

Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::importPhdAction [private]

Definition at line 324 of file trapper.h.

Referenced by initActions().

QAction* TrapperApp::exportAction [private]

Definition at line 325 of file trapper.h.

Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::helpAboutApp [private]

Definition at line 326 of file trapper.h.

Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::helpManualApp [private]

Definition at line 327 of file trapper.h.

QString TrapperApp::projectDir [private]

Definition at line 331 of file trapper.h.

Referenced by contigNamesInProjectDir(), open_docs_not_already_open(), openDocumentFile(), setDbHomeDir(), slotChromatImport(), slotFileOpen(), slotImport(), slotNewImport(), slotPhdImport(), and TrapperApp().

DbEnv* TrapperApp::dbenv [private]

Definition at line 333 of file trapper.h.

Referenced by open_docs_not_already_open(), openDocumentFile(), setDbHomeDir(), slotImport(), slotNewImport(), TrapperApp(), and ~TrapperApp().

---

The documentation for this class was generated from the following files:

• trapper.h
• trapper.cpp

---