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>

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	slotEditFindRead ()
void	slotViewToolBar (bool toggle)
void	slotViewStatusBar (bool toggle)
void	slotWindowNewWindow ()
void	slotHelpAbout ()
void	slotHelpManual ()
void	slotStatusHelpMsg (const QString &text)
void	showAssistantErrors (const QString &err)
void	windowMenuAboutToShow ()
void	windowMenuActivated (int id)
void	slotImport ()
void	slotNewImport ()
void	slotChromatImport ()
void	slotMateImport ()
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	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)
void	map_reads_to_docs (str_doc_map &readmap, 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 *	editFindRead
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
QAction *	importAction
QAction *	importNewAction
QAction *	importChromatAction
QAction *	importMateAction
QAction *	importPhdAction
QAction *	exportAction
QAction *	helpAboutApp
QAction *	helpManualApp
QAssistantClient *	assistant
QString	projectDir
DbEnv *	dbenv

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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.

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Member Typedef Documentation

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

Definition at line 77 of file trapper.h.

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Constructor & Destructor Documentation

TrapperApp::TrapperApp (   )

construtor Definition at line 53 of file trapper.cpp. References dbenv, initActions(), initMenuBar(), initStatusBar(), initToolBar(), initView(), pDocList, printer, projectDir, pWorkspace, slotActivatedWindow(), untitledCount, viewStatusBar, and viewToolBar. { qDebug("in TrapperApp::TrapperApp()"); setCaption(tr("Trapper " "0.9" ) ); dbenv = new DbEnv( DB_CXX_NO_EXCEPTIONS ); dbenv->set_cachesize(0, 1000000, 0); 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 ); viewToolBar->setOn(true); viewStatusBar->setOn(true); projectDir = QString::null; // assistant = new QAssistantClient(QDir("/home/erika/lib/qt/bin").absPath(), this); // assistant = new QAssistantClient(QDir("bin/").absPath(), this); // QStringList cmdLst; // cmdLst << "-profile"<<"doc/trapperhelp.adp"; // assistant->setArguments( cmdLst ); // connect( assistant, SIGNAL(error(const QString&)), // this, SLOT(showAssistantErrors(const QString&)) ); connect(pWorkspace, SIGNAL(windowActivated(QWidget*)), this, SLOT(slotActivatedWindow(QWidget*))); }

TrapperApp::~TrapperApp (   )  [virtual]

destructor Definition at line 93 of file trapper.cpp. References dbenv, and printer. { delete printer; dbenv->close(0); }

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Member Function Documentation

QStringList TrapperApp::contigNamesInProjectDir (   )  [private]

Definition at line 1367 of file trapper.cpp. References projectDir. 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; }

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 461 of file trapper.cpp. References TrapperDoc::addView(), pWorkspace, and slotCreateClient(). 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(); }

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 558 of file trapper.cpp. References TrapperDoc::canCloseFrame(), TrapperDoc::firstView(), TrapperView::getDocument(), pDocList, pWorkspace, TrapperDoc::removeView(), and scroll(). { 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::exportToFile (  QString  toXmlFile  )

Definition at line 1309 of file trapper.cpp. References open_docs_not_already_open(), and pDocList. Referenced by slotExport(). { statusBar()->message(tr("Exporting project 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 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); } //Close file outFile<<"</TRAPPER>\n"; outFile.close(); statusBar()->message(tr("Ready.")); }

void TrapperApp::initActions (   )  [private]

initializes all QActions of the application Definition at line 99 of file trapper.cpp. References configureViewModesAction, dragModeAction, editCopy, editCut, editFindRead, editPaste, editSelectAll, editSelectBetween, editUndo, enlargeAction, exportAction, fileClose, fileFlush, fileNew, fileOpen, filePrint, fileQuit, fileSave, fileSaveAs, helpAboutApp, importChromatAction, importMateAction, importNewAction, importPhdAction, modeActionGroup, normalModeAction, pWorkspace, showStatisticsAction, shrinkAction, slotChromatImport(), slotConfigureViewModes(), slotDragMode(), slotEditCopy(), slotEditCut(), slotEditFindRead(), slotEditPaste(), slotEditSelectAll(), slotEditSelectBetween(), slotEditUndo(), slotEnlarge(), slotExport(), slotFileClose(), slotFileFlush(), slotFileNew(), slotFileOpen(), slotFilePrint(), slotFileQuit(), slotFileSave(), slotHelpAbout(), slotMateImport(), slotNewImport(), slotNormalMode(), slotPhdImport(), slotShowStatistics(), slotShrink(), slotViewStatusBar(), slotViewToolBar(), slotWindowNewWindow(), slotZoomIn(), slotZoomInX(), slotZoomInY(), slotZoomOut(), slotZoomOutX(), slotZoomOutY(), 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; 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); 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())); 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())); 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); 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())); 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 333 of file trapper.cpp. References editCopy, editCut, editFindRead, editPaste, editSelectAll, editSelectBetween, editUndo, enlargeAction, exportAction, fileClose, fileOpen, fileQuit, helpAboutApp, importChromatAction, importMateAction, importNewAction, importPhdAction, modeActionGroup, pEditMenu, pFileMenu, pHelpMenu, pToolsMenu, pViewMenu, pWindowMenu, showStatisticsAction, shrinkAction, viewStatusBar, viewToolBar, 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); editFindRead->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); // configureViewModesAction->addTo(pViewMenu); /////////////////////////////////////////////////////////////////// // EDIT YOUR APPLICATION SPECIFIC MENUENTRIES HERE pToolsMenu=new QPopupMenu(); // importAction->addTo(pToolsMenu); importNewAction->addTo(pToolsMenu); importChromatAction->addTo(pToolsMenu); importMateAction->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::initStatusBar (   )  [private]

setup the statusbar Definition at line 444 of file trapper.cpp. Referenced by TrapperApp(). { /////////////////////////////////////////////////////////////////// //STATUSBAR statusBar()->message(tr("Ready.")); }

void TrapperApp::initToolBar (   )  [private]

this creates the toolbars. Change the toobar look and add new toolbars in this function Definition at line 421 of file trapper.cpp. References editSelectAll, fileOpen, fileToolbar, modeActionGroup, 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(); QWhatsThis::whatsThisButton(fileToolbar); }

void TrapperApp::initView (   )  [private]

setup the mainview Definition at line 451 of file trapper.cpp. References pWorkspace. 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::map_reads_to_docs (  str_doc_map &  readmap, QPtrList< TrapperDoc > &  notOpenBefore )  [private]

fills a map wit read names as keys and pointers to docs they're present in as values Definition at line 1256 of file trapper.cpp. References Database::SecondaryIterator< T >::answer(), Database::SecondaryIterator< T >::first(), ReadData::name(), Database::SecondaryIterator< T >::next(), and pDocList. { TrapperDoc* doc; for(doc=pDocList->first(); doc !=0; doc=pDocList->next()) { Database::SecondaryIterator<ReadData> name_it( "name", doc, "ReadData" ); assert(name_it.first() == 0); do { readmap.insert(make_pair(QString(name_it.answer()->name()), doc)); }while( name_it.next() == 0 ); } for(doc=notOpenBefore.first(); doc !=0; doc=notOpenBefore.next()) { Database::SecondaryIterator<ReadData> name_it( "name", doc, "ReadData" ); assert(name_it.first() == 0); do { readmap.insert(make_pair(name_it.answer()->name(), doc)); }while( name_it.next() == 0 ); } }

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 1219 of file trapper.cpp. References contigNamesInProjectDir(), dbenv, TrapperDoc::newDocument(), TrapperDoc::openDocument(), TrapperDoc::pathName(), pDocList, and projectDir. Referenced by exportToFile(), 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 ); } } } }

void TrapperApp::openDocumentFile (  const char *  file = 0  )

opens a file specified by commandline option Definition at line 491 of file trapper.cpp. References createClient(), dbenv, TrapperDoc::firstView(), TrapperDoc::newDocument(), TrapperDoc::openDocument(), TrapperDoc::pathName(), pDocList, projectDir, 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")); statusBar()->message(tr("Ready.")); }

bool TrapperApp::queryExit (   )  [protected]

overloaded for Message box on last window exit Definition at line 543 of file trapper.cpp. { 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); }

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

scroll active view Definition at line 1426 of file trapper.cpp. References pWorkspace. Referenced by eventFilter(). { TrapperView* m = (TrapperView*) pWorkspace->activeWindow(); if ( m ) m->scrollBy(dx, dy); }

void TrapperApp::setDbHomeDir (  QString  dir  )

set the directory home for the database environment Definition at line 1340 of file trapper.cpp. References dbenv, 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 1407 of file trapper.cpp. References TrapperConf::instance(), TrapperConf::loadDom(), 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::showAssistantErrors (  const QString &  err  )  [private, slot]

Displays error message if assistant isn't working properly Definition at line 909 of file trapper.cpp. { // QMessageBox::critical( this, "Assistant Error", err ); }

void TrapperApp::slotActivatedWindow (  QWidget *  w  )  [private, slot]

active window Definition at line 1448 of file trapper.cpp. References dragModeAction, and TrapperView::setDragMode(). Referenced by TrapperApp(). { TrapperView* m = (TrapperView*) w; if ( m ) m->setDragMode(dragModeAction->isOn()); }

void TrapperApp::slotChromatImport (   )  [private, slot]

imports chromat data Definition at line 1133 of file trapper.cpp. References open_docs_not_already_open(), pDocList, and projectDir. 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::slotConfigureViewModes (   )  [private, slot]

configure view modes Definition at line 1398 of file trapper.cpp. Referenced by initActions(). { ShowModesDlg * dlg = new ShowModesDlg( this, QString::null ); if ( dlg->exec() == QDialog::Accepted ) {} }

void TrapperApp::slotCreateClient (  QString  modeView  )  [slot]

Definition at line 477 of file trapper.cpp. References createClient(), TrapperView::getDocument(), and pWorkspace. 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::slotDragMode (   )  [private, slot]

drag mode Definition at line 1441 of file trapper.cpp. References pWorkspace, and TrapperView::setDragMode(). Referenced by initActions(). { TrapperView* m = (TrapperView*) pWorkspace->activeWindow(); if ( m ) m->setDragMode(true); }

void TrapperApp::slotEditCopy (   )  [private, slot]

put the marked text/object into the clipboard Definition at line 801 of file trapper.cpp. References TrapperView::copy(), and pWorkspace. 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::slotEditCut (   )  [private, slot]

put the marked text/object into the clipboard and remove it from the document Definition at line 791 of file trapper.cpp. References TrapperView::cut(), and pWorkspace. Referenced by initActions(). { statusBar()->message(tr("Cutting selection...")); TrapperView* m = (TrapperView*) pWorkspace->activeWindow(); if ( m ) m->cut(); statusBar()->message(tr("Ready.")); }

void TrapperApp::slotEditFindRead (   )  [private, slot]

Finds a specific read Definition at line 838 of file trapper.cpp. References TrapperView::findRead(), and pWorkspace. Referenced by initActions(). { statusBar()->message(tr("Finding read...")); TrapperView* m = (TrapperView*) pWorkspace->activeWindow(); if ( m ) m->findRead(); statusBar()->message(tr("Ready.")); }

void TrapperApp::slotEditPaste (   )  [private, slot]

paste the clipboard into the document Definition at line 811 of file trapper.cpp. References TrapperView::paste(), and pWorkspace. 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 820 of file trapper.cpp. References pWorkspace, and TrapperView::selectAll(). 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 829 of file trapper.cpp. References pWorkspace, and TrapperView::selectBetween(). 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::slotEditUndo (   )  [private, slot]

reverts the last editing action Definition at line 781 of file trapper.cpp. References pWorkspace, 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::slotEnlarge (   )  [private, slot]

Enlarges view Definition at line 1010 of file trapper.cpp. References TrapperView::enlarge(), and pWorkspace. Referenced by initActions(). { TrapperView* m = (TrapperView*)pWorkspace->activeWindow(); if( m ) { m->enlarge(); } }

void TrapperApp::slotExport (   )  [private, slot]

exports data Definition at line 1282 of file trapper.cpp. References exportToFile(). 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::slotFileClose (   )  [private, slot]

close the actual file Definition at line 716 of file trapper.cpp. References TrapperDoc::closeDocument(), TrapperView::getDocument(), and pWorkspace. 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 696 of file trapper.cpp. References TrapperDoc::findTrDb(), GeneralMaker::listRegistered(), TrapperDoc::pathName(), pDocList, and TrDb::sync(). Referenced by initActions(). { 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::slotFileNew (   )  [private, slot]

generate a new document in the actual view Definition at line 627 of file trapper.cpp. References openDocumentFile(). 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 636 of file trapper.cpp. References openDocumentFile(), and projectDir. 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::slotFilePrint (   )  [private, slot]

print the actual file Definition at line 733 of file trapper.cpp. References TrapperView::print(), printer, and pWorkspace. Referenced by initActions(). { statusBar()->message(tr("Printing...")); TrapperView* m = (TrapperView*) pWorkspace->activeWindow(); if ( m ) m->print( printer ); statusBar()->message(tr("Ready.")); }

void TrapperApp::slotFileQuit (   )  [slot]

exits the application Definition at line 744 of file trapper.cpp. References pDocList. 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::slotFileSave (   )  [private, slot]

save a document Definition at line 658 of file trapper.cpp. References TrapperView::getDocument(), TrapperDoc::pathName(), pWorkspace, TrapperDoc::saveDocument(), slotFileSaveAs(), 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 676 of file trapper.cpp. References TrapperDoc::changedViewList(), TrapperView::getDocument(), pWorkspace, and TrapperDoc::saveDocument(). 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::slotHelpAbout (   )  [private, slot]

shows an about dlg Definition at line 893 of file trapper.cpp. Referenced by initActions(). { QMessageBox::about(this,tr("About..."), tr("Trapper\nVersion 0.1" "\n(c) 2003 - 2005 by Erik Arner, Martti Tammi, Erik Sjölund and Staffan Alveteg")); }

void TrapperApp::slotHelpManual (   )  [private, slot]

shows the online help Definition at line 900 of file trapper.cpp. { // if ( !assistant->isOpen() ) { // assistant->openAssistant(); // } }

void TrapperApp::slotImport (   )  [private, slot]

imports data Definition at line 1028 of file trapper.cpp. References contigNamesInProjectDir(), dbenv, TrapperDoc::import(), TrapperDoc::openDocument(), and projectDir. { 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::slotMateImport (   )  [private, slot]

imports mate data Definition at line 1162 of file trapper.cpp. References open_docs_not_already_open(), and pDocList. 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::slotNewImport (   )  [private, slot]

imports data Definition at line 1107 of file trapper.cpp. References dbenv, and projectDir. Referenced by initActions(). { 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 open file"); return; } TrapperParser handler(dbenv, projectDir); QXmlInputSource source( &f ); QXmlSimpleReader reader; reader.setContentHandler( &handler ); if (!reader.parse(source) ) { QMessageBox::warning(this,"","couldn't read file"); return; } } statusBar()->message(tr("Ready.")); }

void TrapperApp::slotNormalMode (   )  [private, slot]

normal pointer mode Definition at line 1432 of file trapper.cpp. References pWorkspace, and TrapperView::setDragMode(). Referenced by initActions(). { TrapperView* m = (TrapperView*) pWorkspace->activeWindow(); if ( m ) m->setDragMode(false); }

void TrapperApp::slotPhdImport (   )  [private, slot]

imports phd data Definition at line 1190 of file trapper.cpp. References open_docs_not_already_open(), pDocList, and projectDir. 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::slotShowStatistics (   )  [private, slot]

show statistics Definition at line 1378 of file trapper.cpp. References TrapperView::getDocument(), TrapperDoc::getStatistics(), and pWorkspace. 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::slotShrink (   )  [private, slot]

Shrinks view Definition at line 1019 of file trapper.cpp. References pWorkspace, and TrapperView::shrink(). Referenced by initActions(). { TrapperView* m = (TrapperView*)pWorkspace->activeWindow(); if( m ) { m->shrink(); } }

void TrapperApp::slotStatusHelpMsg (  const QString &  text  )  [private, slot]

change the status message of the whole statusbar temporary Definition at line 915 of file trapper.cpp. { /////////////////////////////////////////////////////////////////// // change status message of whole statusbar temporary (text, msec) statusBar()->message(text, 2000); }

void TrapperApp::slotViewStatusBar (  bool  toggle  )  [private, slot]

toggle the statusbar Definition at line 863 of file trapper.cpp. 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::slotViewToolBar (  bool  toggle  )  [private, slot]

toggle the toolbar Definition at line 847 of file trapper.cpp. References fileToolbar. 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::slotWindowNewWindow (   )  [private, slot]

creates a new view for the current document Definition at line 880 of file trapper.cpp. References createClient(), TrapperView::getDocument(), and pWorkspace. 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::slotZoomIn (   )  [private, slot]

zooms in Definition at line 956 of file trapper.cpp. References pWorkspace, and TrapperView::zoomIn(). Referenced by initActions(). { TrapperView* m = (TrapperView*)pWorkspace->activeWindow(); if( m ) { m->zoomIn(); } }

void TrapperApp::slotZoomInX (   )  [private, slot]

zooms in X Definition at line 965 of file trapper.cpp. References pWorkspace, and TrapperView::zoomInX(). Referenced by initActions(). { TrapperView* m = (TrapperView*)pWorkspace->activeWindow(); if( m ) { m->zoomInX(); } }

void TrapperApp::slotZoomInY (   )  [private, slot]

zooms in Y Definition at line 974 of file trapper.cpp. References pWorkspace, and TrapperView::zoomInY(). Referenced by initActions(). { TrapperView* m = (TrapperView*)pWorkspace->activeWindow(); if( m ) { m->zoomInY(); } }

void TrapperApp::slotZoomOut (   )  [private, slot]

zooms out Definition at line 983 of file trapper.cpp. References pWorkspace, and TrapperView::zoomOut(). Referenced by initActions(). { TrapperView* m = (TrapperView*)pWorkspace->activeWindow(); if( m ) { m->zoomOut(); } }

void TrapperApp::slotZoomOutX (   )  [private, slot]

zooms out X Definition at line 992 of file trapper.cpp. References pWorkspace, and TrapperView::zoomOutX(). Referenced by initActions(). { TrapperView* m = (TrapperView*)pWorkspace->activeWindow(); if( m ) { m->zoomOutX(); } }

void TrapperApp::slotZoomOutY (   )  [private, slot]

zooms out Y Definition at line 1001 of file trapper.cpp. References pWorkspace, and TrapperView::zoomOutY(). Referenced by initActions(). { TrapperView* m = (TrapperView*)pWorkspace->activeWindow(); if( m ) { m->zoomOutY(); } }

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 922 of file trapper.cpp. References pWindowMenu, pWorkspace, windowAction, windowCascade, 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 949 of file trapper.cpp. References pWorkspace. Referenced by windowMenuAboutToShow(). { QWidget* w = pWorkspace->windowList().at( id ); if ( w ) w->setFocus(); }

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Member Data Documentation

QAssistantClient* TrapperApp::assistant [private]

Definition at line 300 of file trapper.h.

QAction* TrapperApp::configureViewModesAction [private]

Definition at line 279 of file trapper.h. Referenced by initActions().

DbEnv* TrapperApp::dbenv [private]

Definition at line 304 of file trapper.h. Referenced by open_docs_not_already_open(), openDocumentFile(), setDbHomeDir(), slotImport(), slotNewImport(), TrapperApp(), and ~TrapperApp().

QAction* TrapperApp::dragModeAction [private]

Definition at line 288 of file trapper.h. Referenced by initActions(), and slotActivatedWindow().

QAction* TrapperApp::editCopy [private]

Definition at line 262 of file trapper.h. Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::editCut [private]

Definition at line 261 of file trapper.h. Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::editFindRead [private]

Definition at line 266 of file trapper.h. Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::editPaste [private]

Definition at line 263 of file trapper.h. Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::editSelectAll [private]

Definition at line 264 of file trapper.h. Referenced by initActions(), initMenuBar(), and initToolBar().

QAction* TrapperApp::editSelectBetween [private]

Definition at line 265 of file trapper.h. Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::editUndo [private]

Definition at line 260 of file trapper.h. Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::enlargeAction [private]

Definition at line 276 of file trapper.h. Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::exportAction [private]

Definition at line 295 of file trapper.h. Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::fileClose [private]

Definition at line 255 of file trapper.h. Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::fileFlush [private]

Definition at line 258 of file trapper.h. Referenced by initActions().

QAction* TrapperApp::fileNew [private]

Definition at line 251 of file trapper.h. Referenced by initActions().

QAction* TrapperApp::fileOpen [private]

Definition at line 252 of file trapper.h. Referenced by initActions(), initMenuBar(), and initToolBar().

QAction* TrapperApp::filePrint [private]

Definition at line 256 of file trapper.h. Referenced by initActions().

QAction* TrapperApp::fileQuit [private]

Definition at line 257 of file trapper.h. Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::fileSave [private]

Definition at line 253 of file trapper.h. Referenced by initActions().

QAction* TrapperApp::fileSaveAs [private]

Definition at line 254 of file trapper.h. Referenced by initActions().

QToolBar* TrapperApp::fileToolbar [private]

Definition at line 236 of file trapper.h. Referenced by initToolBar(), and slotViewToolBar().

QAction* TrapperApp::helpAboutApp [private]

Definition at line 296 of file trapper.h. Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::helpManualApp [private]

Definition at line 297 of file trapper.h.

QAction* TrapperApp::importAction [private]

Definition at line 290 of file trapper.h.

QAction* TrapperApp::importChromatAction [private]

Definition at line 292 of file trapper.h. Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::importMateAction [private]

Definition at line 293 of file trapper.h. Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::importNewAction [private]

Definition at line 291 of file trapper.h. Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::importPhdAction [private]

Definition at line 294 of file trapper.h. Referenced by initActions(), and initMenuBar().

QActionGroup* TrapperApp::modeActionGroup [private]

Definition at line 286 of file trapper.h. Referenced by initActions(), initMenuBar(), and initToolBar().

QAction* TrapperApp::normalModeAction [private]

Definition at line 287 of file trapper.h. Referenced by initActions().

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 249 of file trapper.h. Referenced by eventFilter(), exportToFile(), map_reads_to_docs(), open_docs_not_already_open(), openDocumentFile(), slotChromatImport(), slotFileFlush(), slotFileQuit(), slotMateImport(), slotPhdImport(), and TrapperApp().

QPopupMenu* TrapperApp::pEditMenu [private]

edit_menu contains all items of the menubar entry "Edit" Definition at line 226 of file trapper.h. Referenced by initMenuBar().

QPopupMenu* TrapperApp::pFileMenu [private]

file_menu contains all items of the menubar entry "File" Definition at line 224 of file trapper.h. Referenced by initMenuBar().

QPopupMenu* TrapperApp::pHelpMenu [private]

view_menu contains all items of the menubar entry "Help" Definition at line 230 of file trapper.h. Referenced by initMenuBar().

QPrinter* TrapperApp::printer [private]

the printer instance Definition at line 243 of file trapper.h. Referenced by slotFilePrint(), TrapperApp(), and ~TrapperApp().

QString TrapperApp::projectDir [private]

Definition at line 302 of file trapper.h. Referenced by contigNamesInProjectDir(), open_docs_not_already_open(), openDocumentFile(), setDbHomeDir(), slotChromatImport(), slotFileOpen(), slotImport(), slotNewImport(), slotPhdImport(), and TrapperApp().

QPopupMenu* TrapperApp::pToolsMenu [private]

the tools menu Definition at line 234 of file trapper.h. Referenced by initMenuBar().

QPopupMenu* TrapperApp::pViewMenu [private]

view_menu contains all items of the menubar entry "View" Definition at line 228 of file trapper.h. Referenced by initMenuBar().

QPopupMenu* TrapperApp::pWindowMenu [private]

the window menu Definition at line 232 of file trapper.h. Referenced by initMenuBar(), and windowMenuAboutToShow().

QWorkspace* TrapperApp::pWorkspace [private]

pWorkspace is the MDI frame widget that handles MDI child widgets. Inititalized in initView() Definition at line 241 of file trapper.h. Referenced by createClient(), eventFilter(), initActions(), initView(), scroll(), slotCreateClient(), slotDragMode(), slotEditCopy(), slotEditCut(), slotEditFindRead(), slotEditPaste(), slotEditSelectAll(), slotEditSelectBetween(), slotEditUndo(), slotEnlarge(), slotFileClose(), slotFilePrint(), slotFileSave(), slotFileSaveAs(), slotNormalMode(), slotShowStatistics(), slotShrink(), slotWindowNewWindow(), slotZoomIn(), slotZoomInX(), slotZoomInY(), slotZoomOut(), slotZoomOutX(), slotZoomOutY(), TrapperApp(), windowMenuAboutToShow(), and windowMenuActivated().

QAction* TrapperApp::showStatisticsAction [private]

Definition at line 278 of file trapper.h. Referenced by initActions(), and initMenuBar().

QAction* TrapperApp::shrinkAction [private]

Definition at line 277 of file trapper.h. Referenced by initActions(), and initMenuBar().

int TrapperApp::untitledCount [private]

a counter that gets increased each time the user creates a new document with "File"->"New" Definition at line 245 of file trapper.h. Referenced by openDocumentFile(), and TrapperApp().

QFile TrapperApp::viewmodefile [private]

Definition at line 216 of file trapper.h. Referenced by setViewModeConfFile().

QAction* TrapperApp::viewStatusBar [private]

Definition at line 269 of file trapper.h. Referenced by initActions(), initMenuBar(), and TrapperApp().

QAction* TrapperApp::viewToolBar [private]

Definition at line 268 of file trapper.h. Referenced by initActions(), initMenuBar(), and TrapperApp().

QActionGroup* TrapperApp::windowAction [private]

Definition at line 281 of file trapper.h. Referenced by initActions(), and windowMenuAboutToShow().

QAction* TrapperApp::windowCascade [private]

Definition at line 284 of file trapper.h. Referenced by initActions(), and windowMenuAboutToShow().

QAction* TrapperApp::windowNewWindow [private]

Definition at line 282 of file trapper.h. Referenced by initActions(), and windowMenuAboutToShow().

QAction* TrapperApp::windowTile [private]

Definition at line 283 of file trapper.h. Referenced by initActions(), and windowMenuAboutToShow().

QAction* TrapperApp::zoomInAction [private]

Definition at line 270 of file trapper.h. Referenced by initActions(), initMenuBar(), and initToolBar().

QAction* TrapperApp::zoomInXAction [private]

Definition at line 271 of file trapper.h. Referenced by initActions(), initMenuBar(), and initToolBar().

QAction* TrapperApp::zoomInYAction [private]

Definition at line 272 of file trapper.h. Referenced by initActions(), initMenuBar(), and initToolBar().

QAction* TrapperApp::zoomOutAction [private]

Definition at line 273 of file trapper.h. Referenced by initActions(), initMenuBar(), and initToolBar().

QAction* TrapperApp::zoomOutXAction [private]

Definition at line 274 of file trapper.h. Referenced by initActions(), initMenuBar(), and initToolBar().

QAction* TrapperApp::zoomOutYAction [private]

Definition at line 275 of file trapper.h. Referenced by initActions(), initMenuBar(), and initToolBar().

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

• trapper.h
• trapper.cpp

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