TrapperDoc Class Reference

TrapperDoc provides a document object for a document-view model. More...

#include <trapperdoc.h>

List of all members.

Public Slots
void	updateAllViews (TrapperView *sender)
Public Member Functions
	TrapperDoc (DbEnv *dbenv)
	~TrapperDoc ()
void	addView (TrapperView *view)
void	removeView (TrapperView *view)
void	changedViewList ()
TrapperView *	firstView ()
bool	isLastView ()
bool	canCloseFrame (TrapperView *pFrame)
void	setModified (bool _m=true)
bool	isModified ()
void	deleteContents ()
bool	newDocument ()
void	closeDocument ()
bool	openDocument (const QString &dirname, const char *format=0)
bool	saveDocument (const QString &filename, const char *format=0)
void	setPathName (const QString &name)
const QString &	pathName () const
void	setTitle (const QString &title)
const QString &	title () const
void	saveExport (ostream &stream)
bool	import (QDomElement &elem)
void	importChromat (const QString &dirname)
void	importMates (const QString &filename)
void	importPhd (const QString &dirname)
std::vector< std::string >	all_readnames ()
void	openDbs ()
void	closeDbs ()
TrDb *	findTrDb (string)
void	changedAlgoList ()
void	addAlgorithm (Algo *)
void	removeAlgorithm (Algo *)
QString	getStatistics ()
Private Attributes
bool	modified
QString	m_title
QString	m_filename
QList< TrapperView > *	pViewList
QList< Algo > *	pAlgoList
TrDbMap	trDbMap
QString	m_contigDir
DbEnv *	dbenv
Friends
class	TrapperView

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Detailed Description

TrapperDoc provides a document object for a document-view model.

The TrapperDoc class provides a document object that can be used in conjunction with the classes TrapperApp and TrapperView to create a document-view model for MDI (Multiple Document Interface) Qt 2.1 applications based on QApplication and QMainWindow as main classes and QWorkspace as MDI manager widget. Thereby, the document object is created by the TrapperApp instance (and kept in a document list) and contains the document structure with the according methods for manipulating the document data by TrapperView objects. Also, TrapperDoc contains the methods for serialization of the document data from and to files.

Author:

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

Version:

KDevelop version 1.1 code generation

Definition at line 56 of file trapperdoc.h.

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Constructor & Destructor Documentation

TrapperDoc::TrapperDoc (  DbEnv *  dbenv  )

Constructor for the fileclass of the application Definition at line 43 of file trapperdoc.cpp. References pAlgoList, pViewList, and setModified(). : dbenv( dbenv_ ) { qDebug("in TrapperDoc::TrapperDoc()"); pViewList = new QList<TrapperView>; // pViewList->setAutoDelete(false); pViewList->setAutoDelete(true); pAlgoList = new QList<Algo>; pAlgoList->setAutoDelete(false); setModified(true ); }

TrapperDoc::~TrapperDoc (   )

Destructor for the fileclass of the application Definition at line 54 of file trapperdoc.cpp. References closeDbs(), pAlgoList, and pViewList. { cerr<<"closing doc"<<endl; delete pViewList; delete pAlgoList; closeDbs(); }

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Member Function Documentation

void TrapperDoc::addAlgorithm (  Algo *   )

adds an algorithm to the document which represents the document contents. Definition at line 68 of file trapperdoc.cpp. References changedAlgoList(), and pAlgoList. Referenced by TrapperView::runAlgo(). { pAlgoList->append(algo); changedAlgoList(); }

void TrapperDoc::addView (  TrapperView *  view  )

adds a view to the document which represents the document contents. Usually this is your main view. Definition at line 62 of file trapperdoc.cpp. References changedViewList(), and pViewList. Referenced by TrapperApp::createClient(). { pViewList->append(view); changedViewList(); }

vector< string > TrapperDoc::all_readnames (   )

Helper function for importing Definition at line 636 of file trapperdoc.cpp. References Database::SecondaryIterator< T >::answer(), Database::SecondaryIterator< T >::first(), ReadData::name(), and Database::SecondaryIterator< T >::next(). Referenced by importChromat(), importMates(), and importPhd(). { vector<string> names; Database::SecondaryIterator<ReadData> name_it( "name", this, "ReadData" ); assert(name_it.first() == 0); string name; do { name = name_it.answer()->name().c_str(); names.push_back(name);//Have to use c_str() due to some straaange bug... }while( name_it.next() == 0 ); return names; }

bool TrapperDoc::canCloseFrame (  TrapperView *  pFrame  )

This method gets called when the user is about to close a frame window. It checks, if more than one view is connected to the document (then the frame can be closed), if pFrame is the last view and the document is modified, the user gets asked if he wants to save the document. Definition at line 232 of file trapperdoc.cpp. References isLastView(), isModified(), pathName(), saveDocument(), and title(). Referenced by TrapperApp::eventFilter(). { if(!isLastView()) return true; bool ret=false; if(isModified()) { QString saveName; switch(QMessageBox::information(pFrame, title(), tr("The current file has been modified.\n" "Do you want to save it?"),QMessageBox::Yes, QMessageBox::No, QMessageBox::Cancel )) { case QMessageBox::Yes: if(title().contains(tr("Untitled"))) { saveName=QFileDialog::getSaveFileName(0, 0, pFrame); if(saveName.isEmpty()) return false; } else saveName=pathName(); if(!saveDocument(saveName)) { switch(QMessageBox::critical(pFrame, tr("I/O Error !"), tr("Could not save the current document !\n" "Close anyway ?"),QMessageBox::Yes ,QMessageBox::No)) { case QMessageBox::Yes: ret=true; case QMessageBox::No: ret=false; } } else ret=true; break; case QMessageBox::No: ret=true; break; case QMessageBox::Cancel: default: ret=false; break; } } else ret=true; return ret; }

void TrapperDoc::changedAlgoList (   )

gets called if a algorithm is removed or added Definition at line 115 of file trapperdoc.cpp. Referenced by addAlgorithm(), and removeAlgorithm(). { }

void TrapperDoc::changedViewList (   )

gets called if a view is removed or added Definition at line 94 of file trapperdoc.cpp. References m_title, TrapperView::mode(), and pViewList. Referenced by addView(), removeView(), TrapperApp::slotFileSaveAs(), and TrapperView::slotSwitchToMode(). { TrapperView *w; if((int)pViewList->count() == 1) { w=pViewList->first(); QString mode = w->mode(); w->setCaption(QString(m_title+" mode=%2").arg(mode)); } else { int i; for( i=1,w=pViewList->first(); w!=0; i++, w=pViewList->next()) { QString mode = w->mode(); w->setCaption(QString(m_title+" :%1 mode=%2").arg(i).arg(mode)); } } }

void TrapperDoc::closeDbs (   )

Definition at line 705 of file trapperdoc.cpp. References trDbMap. Referenced by ~TrapperDoc(). { TrDbMap::iterator it; it = trDbMap.begin(); while (it != trDbMap.end()) { Q_CHECK_PTR( it->second ); it->second->close(); delete it->second; ++it; } trDbMap.clear(); }

void TrapperDoc::closeDocument (   )

closes the acutal document Definition at line 154 of file trapperdoc.cpp. References isLastView(), and pViewList. Referenced by TrapperApp::slotFileClose(). { cerr<<"closeDocument()"<<endl; TrapperView *w; if(!isLastView()) { for(w=pViewList->first(); w!=0; w=pViewList->next()) { if(!w->close()) break; } } if(isLastView()) { w = pViewList->first(); w->close(); } }

void TrapperDoc::deleteContents (   )

deletes the document's contents Definition at line 224 of file trapperdoc.cpp. Referenced by removeAlgorithm(), and removeView(). { ///////////////////////////////////////////////// // TODO: Add implementation to delete the document contents ///////////////////////////////////////////////// }

TrDb * TrapperDoc::findTrDb (  string   )

Definition at line 687 of file trapperdoc.cpp. References m_contigDir, and trDbMap. Referenced by Database::Creator< T >::Creator(), Database::PrimaryIterator< T >::PrimaryIterator(), Database::SecondaryIterator< T >::SecondaryIterator(), and TrapperApp::slotFileFlush(). { TrDb * trdb = NULL; TrDbMap::iterator it; it = trDbMap.find( generalDataName ); if (it != trDbMap.end()) { trdb = it->second; } else { cerr << "TrDb for generalData type=\"" << generalDataName << "\" and contig=\"" << m_contigDir << "\" not found" << endl; } return trdb; }

TrapperView* TrapperDoc::firstView (   )  [inline]

returns the first view instance Definition at line 75 of file trapperdoc.h. References pViewList. Referenced by TrapperApp::eventFilter(), and TrapperApp::openDocumentFile(). { return pViewList->first(); };

QString TrapperDoc::getStatistics (   )

shows berkeley db statistics about underlying databases Definition at line 720 of file trapperdoc.cpp. References trDbMap. Referenced by TrapperApp::slotShowStatistics(). { QString res; TrDbMap::iterator it; it = trDbMap.begin(); while (it != trDbMap.end()) { Q_CHECK_PTR( it->second ); res += it->second->statistics(); ++it; } return res; }

bool TrapperDoc::import (  QDomElement &  elem  )

imports data from file with filename. I believe QDom holds the entire dom tree in ram. This could be a limiting factor for large xml files. To fix that, this function might be enhanced to use "QXmlReader" to find a record and then letting that record be put in a dom tree. Definition at line 332 of file trapperdoc.cpp. References Database::Creator< T >::create(), Database::Creator< T >::data(), and GeneralData::readDom(). Referenced by TrapperApp::slotImport(). { QDomNode node2 = elem1.firstChild(); while ( !node2.isNull() ) { if ( node2.isElement() ) { QString generalDataName = node2.nodeName(); QDomElement elem2 = node2.toElement(); Database::Creator<GeneralData> creator( this, generalDataName.ascii() ); QDomNode node3 = elem2.firstChild(); while ( !node3.isNull() ) { if ( node3.isElement() && node3.nodeName() == "record" ) { QDomElement elem3 = node3.toElement(); creator.data()->readDom( elem3 ); creator.create( true ); } node3 = node3.nextSibling(); } } node2 = node2.nextSibling(); } return true; }

void TrapperDoc::importChromat (  const QString &  dirname  )

Imports chromatogram data Definition at line 364 of file trapperdoc.cpp. References all_readnames(), Database::SecondaryIterator< T >::answer(), ChromatData::cagt_vec, GeneralData::copy(), Database::Creator< T >::create(), Database::Creator< T >::data(), GeneralData::getRecno(), Database::SecondaryIterator< T >::key(), Database::SecondaryIterator< T >::set(), ChromatParser::set_result_array(), ReadData::setName(), FeatureData::setReadRecno(), and ReadData::strand(). { //Get all readnames vector<string> names = all_readnames(); //Parse files for( size_t i = 0; i < names.size(); i++ ) { vector<TrapperVector<Q_UINT32> > chromat_array; ChromatParser handler; handler.set_result_array( &chromat_array ); QFile xmlFile( dirname + '/' + names[i] + ".xml" ); QXmlInputSource source( &xmlFile ); QXmlSimpleReader reader; reader.setContentHandler( &handler ); if ( !reader.parse( source ) ) { cerr<<"Error, couldn't find chromatogram for "<<names[i]<<endl; continue; } //First, find recno of read Database::SecondaryIterator<ReadData> name_it( "name", this, "ReadData" ); name_it.key()->setName( names[i] ); if ( name_it.set() != 0 ) { cerr<<"Error, couldn't find "<<names[i]<<" in db"<<endl; continue; } //Second, find corresponding chromat feature data Database::SecondaryIterator<ChromatData>* chr_it = new Database::SecondaryIterator<ChromatData>( "readRecno", this, "ChromatData" ); chr_it->key()->setReadRecno( name_it.answer()->getRecno() ); if ( chr_it->set() != 0 ) { cerr<<"Error, couldn't find recno "<<name_it.answer()->getRecno()<<" of read "<<names[i]<<endl; delete chr_it; continue; } //Create new data Database::Creator<ChromatData> creator( this, "ChromatData" ); creator.data()->copy(chr_it->answer()); // creator.data()->setStartPos( chr_it->answer()->startPos() ); // creator.data()->setEndPos( chr_it->answer()->endPos() ); // creator.data()->setReadRecno( name_it.answer()->getRecno() ); creator.data()->cagt_vec.clear(); if ( name_it.answer()->strand() == "C" ) { creator.data()->cagt_vec.push_back(TrapperVector<Q_UINT32>()); creator.data()->cagt_vec.push_back(TrapperVector<Q_UINT32>()); creator.data()->cagt_vec.push_back(TrapperVector<Q_UINT32>()); creator.data()->cagt_vec.push_back(TrapperVector<Q_UINT32>()); //Revcomp, must reverse the chromat and switch curves A->T, G->C // creator.data()->cagt_vec[0].stlVector().clear(); // creator.data()->cagt_vec[0].stlVector().insert(creator.data()->cagt_vec[0].stlVector().begin(), // chromat_array[3].stlVector().rbegin(), chromat_array[3].stlVector().rend()); // creator.data()->cagt_vec[1].stlVector().clear(); // creator.data()->cagt_vec[1].stlVector().insert(creator.data()->cagt_vec[1].stlVector().begin(), // chromat_array[2].stlVector().rbegin(), chromat_array[2].stlVector().rend()); // creator.data()->cagt_vec[2].stlVector().clear(); // creator.data()->cagt_vec[2].stlVector().insert(creator.data()->cagt_vec[2].stlVector().begin(), // chromat_array[1].stlVector().rbegin(), chromat_array[1].stlVector().rend()); // creator.data()->cagt_vec[3].stlVector().clear(); // creator.data()->cagt_vec[3].stlVector().insert(creator.data()->cagt_vec[3].stlVector().begin(), // chromat_array[0].stlVector().rbegin(), chromat_array[0].stlVector().rend()); creator.data()->cagt_vec[0].stlVector().clear(); creator.data()->cagt_vec[0].stlVector().insert(creator.data()->cagt_vec[0].stlVector().begin(), chromat_array[2].stlVector().rbegin(), chromat_array[2].stlVector().rend()); creator.data()->cagt_vec[1].stlVector().clear(); creator.data()->cagt_vec[1].stlVector().insert(creator.data()->cagt_vec[1].stlVector().begin(), chromat_array[3].stlVector().rbegin(), chromat_array[3].stlVector().rend()); creator.data()->cagt_vec[2].stlVector().clear(); creator.data()->cagt_vec[2].stlVector().insert(creator.data()->cagt_vec[2].stlVector().begin(), chromat_array[0].stlVector().rbegin(), chromat_array[0].stlVector().rend()); creator.data()->cagt_vec[3].stlVector().clear(); creator.data()->cagt_vec[3].stlVector().insert(creator.data()->cagt_vec[3].stlVector().begin(), chromat_array[1].stlVector().rbegin(), chromat_array[1].stlVector().rend()); } else { // creator.data()->cagt_vec.push_back(chromat_array[0]); // creator.data()->cagt_vec.push_back(chromat_array[1]); // creator.data()->cagt_vec.push_back(chromat_array[2]); // creator.data()->cagt_vec.push_back(chromat_array[3]); creator.data()->cagt_vec = chromat_array; } delete chr_it; creator.create(true); } }

void TrapperDoc::importMates (  const QString &  filename  )

Imports mate pair data Definition at line 569 of file trapperdoc.cpp. References all_readnames(), Database::SecondaryIterator< T >::answer(), GeneralData::copy(), Database::Creator< T >::create(), Database::Creator< T >::data(), Database::SecondaryIterator< T >::key(), MateParser::parse_line(), Database::SecondaryIterator< T >::set(), MateParser::set_file(), ReadData::setMate(), ReadData::setMateLength(), and ReadData::setName(). { //Get all readnames vector<string> names = all_readnames(); //Parse file MateParser parser; parser.set_file(filename); string read_name, mate_name; size_t mate_length; while( parser.parse_line( read_name, mate_name, mate_length ) ) { //For each read: //Add mate data //NB, assumes that the same read name is present only once in each contig, might need to fix this Database::Creator<ReadData> creator( this, "ReadData" ); //First, find recno of read with name read_name Database::SecondaryIterator<ReadData>* name_it = new Database::SecondaryIterator<ReadData>( "name", this, "ReadData" ); name_it->key()->setName( read_name ); if ( name_it->set() != 0 ) { delete name_it; continue; } creator.data()->copy( name_it->answer() ); creator.data()->setMate( mate_name ); creator.data()->setMateLength( mate_length ); delete name_it; creator.create(true); //Same for mate //First, find recno of read with name mate_name name_it = new Database::SecondaryIterator<ReadData>( "name", this, "ReadData" ); name_it->key()->setName( mate_name ); if ( name_it->set() != 0 ) { delete name_it; continue; } creator.data()->copy( name_it->answer() ); creator.data()->setMate( read_name ); creator.data()->setMateLength( mate_length ); delete name_it; creator.create(true); } }

void TrapperDoc::importPhd (  const QString &  dirname  )

Imports phd data Definition at line 468 of file trapperdoc.cpp. References all_readnames(), Database::SecondaryIterator< T >::answer(), ChromatData::cagt_vec, GeneralData::copy(), Database::Creator< T >::create(), Database::Creator< T >::data(), DnaStrData::dnaVector, FeatureData::endPos(), ChromatData::gap_vec, GeneralData::getRecno(), Database::SecondaryIterator< T >::key(), PhdParser::parse(), ChromatData::phd_vec, Database::SecondaryIterator< T >::set(), ReadData::setName(), FeatureData::setReadRecno(), TrapperVector< T >::size(), TrapperVector< T >::stlVector(), and ReadData::strand(). { //Get all readnames vector<string> names = all_readnames(); //Parse files for( size_t i = 0; i < names.size(); i++ ) { TrapperVector<Q_UINT32> phd_array; PhdParser parser(dirname + '/' + names[i] + ".phd.1"); phd_array = parser.parse(); if ( phd_array.size() == 0 ) { cerr<<"Error, couldn't find phd file for "<<names[i]<<endl; continue; } //First, find recno of read Database::SecondaryIterator<ReadData> name_it( "name", this, "ReadData" ); name_it.key()->setName( names[i] ); if ( name_it.set() != 0 ) { cerr<<"Error, couldn't find "<<names[i]<<" in db"<<endl; continue; } //Second, find corresponding chromat feature data Database::SecondaryIterator<ChromatData>* chr_it = new Database::SecondaryIterator<ChromatData>( "readRecno", this, "ChromatData" ); chr_it->key()->setReadRecno( name_it.answer()->getRecno() ); if ( chr_it->set() != 0 ) { cerr<<"Error, couldn't find recno "<<name_it.answer()->getRecno()<<" of read "<<names[i]<<endl; delete chr_it; continue; } if ( chr_it->answer()->cagt_vec[0].stlVector().size() == 0 ) { cerr<<"Chromat file for "<<names[i]<<" not imported, skipping phd file"<<endl; delete chr_it; continue; } //Create new data Database::Creator<ChromatData> creator( this, "ChromatData" ); creator.data()->copy(chr_it->answer()); if ( name_it.answer()->strand() == "C" ) { creator.data()->phd_vec.stlVector().clear(); creator.data()->phd_vec.stlVector().insert(creator.data()->phd_vec.stlVector().begin(), phd_array.stlVector().rbegin(), phd_array.stlVector().rend()); for( size_t i = 0; i < creator.data()->phd_vec.stlVector().size(); i++ ) { creator.data()->phd_vec.stlVector()[i] = creator.data()->cagt_vec[0].stlVector().size() - 1 - creator.data()->phd_vec.stlVector()[i]; } } else { creator.data()->phd_vec = phd_array; } delete chr_it; //TEMPORARY FIX OF THE GAP PROBLEM!!! Database::SecondaryIterator<DnaStrData>* dna_it = new Database::SecondaryIterator<DnaStrData>( "readRecno", this, "DnaStrData" ); dna_it->key()->setReadRecno( name_it.answer()->getRecno() ); if ( dna_it->set() != 0 ) { cerr<<"Error, couldn't find recno "<<name_it.answer()->getRecno()<<" of read "<<names[i]<<endl; delete dna_it; continue; } creator.data()->gap_vec.stlVector().clear(); size_t numgap(0); for( size_t i = 0; i < dna_it->answer()->dnaVector.size(); i++ ) { if (dna_it->answer()->dnaVector.stlVector()[i] == '*' ) { numgap++; } creator.data()->gap_vec.stlVector().push_back(numgap); } if ( creator.data()->gap_vec.stlVector().size() != creator.data()->endPos() + 1) { cerr<<"creator.data()->gap_vec.stlVector().size(): "<< creator.data()->gap_vec.stlVector().size()<<endl; cerr<<"creator.data()->endPos(): "<<creator.data()->endPos()<<endl; } assert( creator.data()->gap_vec.stlVector().size() == creator.data()->endPos() + 1 ); delete dna_it; //END FIX!!! creator.create(true); } }

bool TrapperDoc::isLastView (   )

returns true, if the requested view is the last view of the document Definition at line 119 of file trapperdoc.cpp. References pViewList. Referenced by canCloseFrame(), and closeDocument(). { return ((int) pViewList->count() == 1); }

bool TrapperDoc::isModified (   )  [inline]

returns if the document is modified or not. Use this to determine if your document needs saving by the user on closing. Definition at line 92 of file trapperdoc.h. References modified. Referenced by canCloseFrame(). { return modified; };

bool TrapperDoc::newDocument (   )

initializes the document generally Definition at line 170 of file trapperdoc.cpp. References modified. Referenced by TrapperApp::open_docs_not_already_open(), and TrapperApp::openDocumentFile(). { ///////////////////////////////////////////////// // TODO: Add your document initialization code here ///////////////////////////////////////////////// modified=false; return true; }

void TrapperDoc::openDbs (   )

Definition at line 654 of file trapperdoc.cpp. References dbenv, GeneralData::getIndexMap(), GeneralMaker::listRegistered(), m_contigDir, GeneralMaker::newData(), TrDb::open(), and trDbMap. Referenced by openDocument(). { list<string> alist = GeneralMaker::listRegistered(); for ( list<string>::iterator it = alist.begin(); it != alist.end(); ++it ) { GeneralData * data = GeneralMaker::newData( *it ); if ( data ) { QString directoryName( m_contigDir ); directoryName += "/"; directoryName += it->c_str() ; QDir dir; dir.mkdir( directoryName , true ); TrDb * trdb = new TrDb( dbenv, directoryName.ascii() , data->getIndexMap() ); trDbMap.insert( make_pair( it->c_str(), trdb ) ); // cerr << "trDbMap.insert( make_pair( it->c_str(), trdb ) ) ******* " // << it->c_str() << " ***************** " // << directoryName.ascii() << endl; delete data; trdb->open(); // cerr<<"trdb->primaryDb(): "<<trdb->primaryDb()<<endl; } } }

bool TrapperDoc::openDocument (  const QString &  dirname, const char *  format = 0 )

loads the document by filename and format and emits the updateViews() signal Definition at line 179 of file trapperdoc.cpp. References m_contigDir, m_title, modified, and openDbs(). Referenced by TrapperApp::open_docs_not_already_open(), TrapperApp::openDocumentFile(), TrapperApp::slotImport(), and TrapperParser::startElement(). { cerr<<"openDocument() "<<endl; m_contigDir=dirname; QDir dir( m_contigDir ); if ( !dir.exists() ) { QDir dir2; if ( !dir2.mkdir( m_contigDir, true ) ) { // oops, still doesn't exist cerr << "creating new dir failed, dir name=" << m_contigDir << endl; exit(1); } } ///////////////////////////////////////////////// // TODO: Add your document opening code here ///////////////////////////////////////////////// modified=false; m_title=dirname; openDbs(); return true; }

const QString & TrapperDoc::pathName (   )  const

returns the pathname of the current document file Definition at line 139 of file trapperdoc.cpp. References m_contigDir. Referenced by canCloseFrame(), TrapperApp::open_docs_not_already_open(), TrapperApp::openDocumentFile(), saveExport(), TrapperApp::slotFileFlush(), and TrapperApp::slotFileSave(). { return m_contigDir; }

void TrapperDoc::removeAlgorithm (  Algo *   )

removes an algorithm from the list of currently connected algorithm Definition at line 84 of file trapperdoc.cpp. References changedAlgoList(), deleteContents(), pAlgoList, and pViewList. Referenced by TrapperView::runAlgo(). { pAlgoList->remove (algo); if(!pViewList->isEmpty() || !pAlgoList->isEmpty() ) changedAlgoList(); else deleteContents(); }

void TrapperDoc::removeView (  TrapperView *  view  )

removes a view from the list of currently connected views Definition at line 74 of file trapperdoc.cpp. References changedViewList(), deleteContents(), pAlgoList, and pViewList. Referenced by TrapperApp::eventFilter(). { pViewList->remove (view); if(!pViewList->isEmpty() || !pAlgoList->isEmpty() ) changedViewList(); else deleteContents(); }

bool TrapperDoc::saveDocument (  const QString &  filename, const char *  format = 0 )

saves the document under filename and format. Definition at line 205 of file trapperdoc.cpp. References m_contigDir, m_title, and modified. Referenced by canCloseFrame(), TrapperApp::slotFileSave(), and TrapperApp::slotFileSaveAs(). { /* we are using the berkeley db so changes are automatically changed in the files after the commit of the transaction. Here we might instead have some change of m_contigdir, to move the contig dir to another name to reflect the change of a "sandbox" contig to a regular contig. */ return false; ///////////////////////////////////////////////// // TODO: Add your document saving code here ///////////////////////////////////////////////// modified=false; m_contigDir=filename; m_title=filename; return true; }

void TrapperDoc::saveExport (  ostream &  stream  )

exports the document to a stream. Definition at line 284 of file trapperdoc.cpp. References Database::SecondaryIterator< T >::answer(), Database::PrimaryIterator< T >::answer(), Database::PrimaryIterator< T >::first(), GeneralData::getRecno(), Database::SecondaryIterator< T >::key(), GeneralMaker::listRegistered(), Database::PrimaryIterator< T >::next(), Database::SecondaryIterator< T >::nextdup(), pathName(), Database::SecondaryIterator< T >::set(), FeatureData::setReadRecno(), FeatureData::writeXml(), and ReadData::writeXml(). { //Ugly fix for strange behaviour... int offset(-1); if ( pathName()[pathName().length() -1] == '/' ) { --offset; } stream<<"<contig name=\""<<pathName().section('/', offset)<<"\">\n"; Database::PrimaryIterator<ReadData> iter( this, "ReadData" ); if ( iter.first() == 0 ) { do { //ReadData iter.answer()->writeXml(stream); //FeatureData list<string> alist = GeneralMaker::listRegistered(); for ( list<string>::iterator it = alist.begin(); it != alist.end(); ++it ) { if ( *it == "ReadData") { continue; } Database::SecondaryIterator<FeatureData> f_it( "readRecno", this, *it ); f_it.key()->setReadRecno( iter.answer()->getRecno() ); if ( f_it.set() == 0 ) { do { f_it.answer()->writeXml(stream); }while(f_it.nextdup() == 0); } } //End ReadData stream<<"</ReadData>\n"; }while( iter.next() == 0 ); } stream<<"</contig>\n"; }

void TrapperDoc::setModified (  bool  _m = true  )  [inline]

sets the modified flag for the document after a modifying action on the view connected to the document. Definition at line 87 of file trapperdoc.h. References modified. Referenced by TrapperDoc(). { modified=_m; };

void TrapperDoc::setPathName (  const QString &  name  )

sets the path to the file connected with the document Definition at line 133 of file trapperdoc.cpp. References m_contigDir, and m_title. { m_contigDir=name; m_title=QFileInfo(name).fileName(); }

void TrapperDoc::setTitle (  const QString &  title  )

sets the filename of the document Definition at line 144 of file trapperdoc.cpp. References m_title. { m_title=title; }

const QString & TrapperDoc::title (   )  const

returns the title of the document Definition at line 149 of file trapperdoc.cpp. References m_title. Referenced by canCloseFrame(), TrapperApp::slotFileSave(), SubsetAlgo::start(), ReadnamesAlgo::start(), and ConsAlgo::start(). { return m_title; }

void TrapperDoc::updateAllViews (  TrapperView *  sender  )  [slot]

calls repaint() on all views connected to the document object and is called by the view by which the document has been changed. As this view normally repaints itself, it is excluded from the paintEvent. Definition at line 124 of file trapperdoc.cpp. References pViewList, and TrapperView::update(). { TrapperView *w; for(w=pViewList->first(); w!=0; w=pViewList->next()) { w->update(sender); } }

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Friends And Related Function Documentation

friend class TrapperView [friend]

Definition at line 60 of file trapperdoc.h.

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Member Data Documentation

DbEnv* TrapperDoc::dbenv [private]

Definition at line 162 of file trapperdoc.h. Referenced by openDbs().

QString TrapperDoc::m_contigDir [private]

Definition at line 161 of file trapperdoc.h. Referenced by findTrDb(), openDbs(), openDocument(), pathName(), saveDocument(), and setPathName().

QString TrapperDoc::m_filename [private]

Definition at line 156 of file trapperdoc.h.

QString TrapperDoc::m_title [private]

Definition at line 155 of file trapperdoc.h. Referenced by changedViewList(), openDocument(), saveDocument(), setPathName(), setTitle(), and title().

bool TrapperDoc::modified [private]

the modified flag of the current document Definition at line 154 of file trapperdoc.h. Referenced by isModified(), newDocument(), openDocument(), saveDocument(), and setModified().

QList<Algo>* TrapperDoc::pAlgoList [private]

Definition at line 159 of file trapperdoc.h. Referenced by addAlgorithm(), removeAlgorithm(), removeView(), TrapperDoc(), and ~TrapperDoc().

QList<TrapperView>* TrapperDoc::pViewList [private]

the list of the views currently connected to the document Definition at line 158 of file trapperdoc.h. Referenced by addView(), changedViewList(), closeDocument(), firstView(), isLastView(), removeAlgorithm(), removeView(), TrapperDoc(), updateAllViews(), and ~TrapperDoc().

TrDbMap TrapperDoc::trDbMap [private]

Definition at line 160 of file trapperdoc.h. Referenced by closeDbs(), findTrDb(), getStatistics(), and openDbs().

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

• trapperdoc.h
• trapperdoc.cpp

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