TrapperDoc Class Reference

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

#include <trapperdoc.h>

Inheritance diagram for TrapperDoc:

[legend]Collaboration diagram for TrapperDoc:

[legend]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)
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	importTimeCourse (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

---

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.

---

Constructor & Destructor Documentation

TrapperDoc::TrapperDoc

(

DbEnv *

dbenv

)

Constructor for the fileclass of the application

Definition at line 44 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 55 of file trapperdoc.cpp.

References closeDbs(), pAlgoList, and pViewList.

{
//   cerr<<"closing doc"<<endl;
  delete pViewList;
  delete pAlgoList;
  closeDbs();
}

---

Member Function Documentation

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 63 of file trapperdoc.cpp.

References changedViewList(), and pViewList.

Referenced by TrapperApp::createClient().

{
    pViewList->append(view);
    changedViewList();
}

void TrapperDoc::removeView

(

TrapperView *

view

)

removes a view from the list of currently connected views

Definition at line 75 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();
}

void TrapperDoc::changedViewList

(

)

gets called if a view is removed or added

Definition at line 95 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));
        }
    }
}

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();
  };

bool TrapperDoc::isLastView

(

)

returns true, if the requested view is the last view of the document

Definition at line 120 of file trapperdoc.cpp.

References pViewList.

Referenced by canCloseFrame(), and closeDocument().

{
    return ((int) pViewList->count() == 1);
}

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 233 of file trapperdoc.cpp.

References QMessageBox::critical(), QFileDialog::getSaveFileName(), QMessageBox::information(), QString::isEmpty(), isLastView(), isModified(), pathName(), saveDocument(), title(), and QObject::tr().

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::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;
  };

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;
  };

void TrapperDoc::deleteContents

(

)

deletes the document's contents

Definition at line 225 of file trapperdoc.cpp.

Referenced by removeAlgorithm(), and removeView().

{
    /////////////////////////////////////////////////
    // TODO: Add implementation to delete the document contents
    /////////////////////////////////////////////////

}

bool TrapperDoc::newDocument

(

)

initializes the document generally

Definition at line 171 of file trapperdoc.cpp.

References modified.

Referenced by TrapperApp::openDocumentFile().

{
    /////////////////////////////////////////////////
    // TODO: Add your document initialization code here
    /////////////////////////////////////////////////
    modified=false;
    return true;
}

void TrapperDoc::closeDocument

(

)

closes the acutal document

Definition at line 155 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();
  }
}

bool TrapperDoc::openDocument

(

const QString &

dirname

)

loads the document by filename and format and emits the updateViews() signal

Definition at line 180 of file trapperdoc.cpp.

References QDir::exists(), m_contigDir, m_title, modified, and openDbs().

Referenced by MacsimParser::endElement(), 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;
}

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

saves the document under filename and format.

Definition at line 206 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::setPathName

(

const QString &

name

)

sets the path to the file connected with the document

Definition at line 134 of file trapperdoc.cpp.

References m_contigDir, m_title, and QObject::name().

{
    m_contigDir=name;
    m_title=QFileInfo(name).fileName();
}

const QString & TrapperDoc::pathName

(

)

const

returns the pathname of the current document file

Definition at line 140 of file trapperdoc.cpp.

References m_contigDir.

Referenced by canCloseFrame(), TrapperApp::open_docs_not_already_open(), TrapperApp::openDocumentFile(), saveExport(), and TrapperApp::slotFileSave().

{
    return m_contigDir;
}

void TrapperDoc::setTitle

(

const QString &

title

)

sets the filename of the document

Definition at line 145 of file trapperdoc.cpp.

References m_title, and title().

{
    m_title=title;
}

const QString & TrapperDoc::title

(

)

const

returns the title of the document

Definition at line 150 of file trapperdoc.cpp.

References m_title.

Referenced by canCloseFrame(), setTitle(), and TrapperApp::slotFileSave().

{
    return m_title;
}

void TrapperDoc::saveExport

(

ostream &

stream

)

exports the document to a stream.

Definition at line 285 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(), QString::section(), Database::SecondaryIterator< T >::set(), FeatureData::setReadRecno(), FeatureData::writeXml(), and ReadData::writeXml().

Referenced by TrapperApp::exportToFile().

{

  //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";
  
}

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 333 of file trapperdoc.cpp.

References Database::Creator< T >::data(), QDomNode::isElement(), QDomNode::isNull(), QDomNode::nextSibling(), QDomNode::nodeName(), GeneralData::readDom(), and QDomNode::toElement().

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 365 of file trapperdoc.cpp.

References all_readnames(), Database::SecondaryIterator< T >::answer(), ChromatData::cagt_vec, GeneralData::copy(), Database::Creator< T >::create(), Database::Creator< T >::data(), Database::SecondaryIterator< T >::key(), QXmlSimpleReader::parse(), ReadMetaData::readRecno, Database::SecondaryIterator< T >::set(), ChromatParser::set_result_array(), ReadMetaData::setName(), FeatureData::setReadRecno(), and ReadMetaData::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;
//     }

    Database::SecondaryIterator<ReadMetaData> name_it( "name", this, "ReadMetaData" );
    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()->readRecno() );
    
    if ( chr_it->set() != 0 ) {
      cerr<<"Error, couldn't find recno "<<name_it.answer()->readRecno()<<" 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()->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[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 = chromat_array;
    }
    
    delete chr_it;
    
    creator.create(true);
  }


}

void TrapperDoc::importMates

(

const QString &

filename

)

Imports mate pair data

Definition at line 561 of file trapperdoc.cpp.

References Database::SecondaryIterator< T >::answer(), Database::SecondaryIterator< T >::key(), MateParser::parse_line(), Database::SecondaryIterator< T >::set(), MateParser::set_file(), and ReadMetaData::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<ReadMetaData> creator( this, "ReadMetaData" );
    
    //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;
//     }
    Database::SecondaryIterator<ReadMetaData>* name_it =
      new Database::SecondaryIterator<ReadMetaData>( "name", this, "ReadMetaData" );
    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;
//     }
    name_it = new Database::SecondaryIterator<ReadMetaData>( "name", this, "ReadMetaData" );
    name_it->key()->setName( read_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::importTimeCourse

(

const QString &

filename

)

Imports time course data

Definition at line 642 of file trapperdoc.cpp.

References Database::SecondaryIterator< T >::answer(), Database::SecondaryIterator< T >::key(), TcParser::parse_line(), Database::SecondaryIterator< T >::set(), TcParser::set_file(), and ReadMetaData::setName().

Referenced by TrapperApp::slotTcImport().

{
  //Get all readnames
  
//   vector<string> names = all_readnames();
  
  //Parse file
  TcParser parser;
  parser.set_file(filename);
  
  string read_name;
  vector<double> time_course;

  while( parser.parse_line( read_name, time_course ) ) {


    //For each read:
    
    //Add tc data
    //NB, assumes that the same read name is present only once in each contig, might need to fix this


    Database::Creator<ReadMetaData> creator( this, "ReadMetaData" );
    
    //First, find recno of read with name read_name
    Database::SecondaryIterator<ReadMetaData>* name_it =
      new Database::SecondaryIterator<ReadMetaData>( "name", this, "ReadMetaData" );
    name_it->key()->setName( read_name );
    if ( name_it->set() != 0 ) {
      time_course.clear();
      delete name_it;
      continue;
    }
    
    creator.data()->copy( name_it->answer() );
    
    creator.data()->tc_vec.stlVector() = time_course;
//     cerr<<"\nName: "<<read_name<<endl;
//     for( size_t i = 0; i < creator.data()->tc_vec.stlVector().size(); i++ ) {
//       cerr<<creator.data()->tc_vec.stlVector()[i]<<" ";
//     }
//     cerr<<endl;
    delete name_it;
//     for( size_t i = 0; i < creator.data()->tc_vec.stlVector().size(); i++ ) {
//       cerr<<creator.data()->tc_vec.stlVector()[i]<<" ";
//     }
//     cerr<<endl;
    
    creator.create(true);
    time_course.clear();
  }
  
}

void TrapperDoc::importPhd

(

const QString &

dirname

)

Imports phd data

Definition at line 458 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, Database::SecondaryIterator< T >::key(), PhdParser::parse(), ChromatData::phd_vec, ReadMetaData::readRecno, Database::SecondaryIterator< T >::set(), ReadMetaData::setName(), FeatureData::setReadRecno(), TrapperVector< T >::size(), TrapperVector< T >::stlVector(), and ReadMetaData::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;
//     }

    Database::SecondaryIterator<ReadMetaData> name_it( "name", this, "ReadMetaData" );
    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()->readRecno() );
    
    if ( chr_it->set() != 0 ) {
      cerr<<"Error, couldn't find recno "<<name_it.answer()->readRecno()<<" 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()->readRecno() );
    
    if ( dna_it->set() != 0 ) {
      cerr<<"Error, couldn't find recno "<<name_it.answer()->readRecno()<<" 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);
    }

    
    assert( creator.data()->gap_vec.stlVector().size() == static_cast<size_t>(creator.data()->endPos() + 1) );
    delete dna_it;
    
    //END FIX!!!
    
    creator.create(true);
    
  }
  

}

vector< string > TrapperDoc::all_readnames

(

)

Helper function for importing

Definition at line 697 of file trapperdoc.cpp.

References Database::SecondaryIterator< T >::answer(), Database::SecondaryIterator< T >::first(), ReadMetaData::name(), QObject::name(), and Database::SecondaryIterator< T >::next().

Referenced by importChromat(), and importPhd().

{
  vector<string> names;

  Database::SecondaryIterator<ReadMetaData> name_it( "name", this, "ReadMetaData" );
  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;
  
}

void TrapperDoc::openDbs

(

)

Definition at line 715 of file trapperdoc.cpp.

References QString::ascii(), dbenv, GeneralMaker::listRegistered(), m_contigDir, QDir::mkdir(), 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;
        }
    }

}

void TrapperDoc::closeDbs

(

)

Definition at line 766 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();
}

TrDb * TrapperDoc::findTrDb

(

string

)

Definition at line 748 of file trapperdoc.cpp.

References m_contigDir, and trDbMap.

Referenced by Database::Creator< T >::Creator(), Database::PrimaryIterator< T >::PrimaryIterator(), and Database::SecondaryIterator< T >::SecondaryIterator().

{
    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;
}

void TrapperDoc::changedAlgoList

(

)

gets called if a algorithm is removed or added

Definition at line 116 of file trapperdoc.cpp.

Referenced by addAlgorithm(), and removeAlgorithm().

{
}

void TrapperDoc::addAlgorithm

(

Algo *

)

adds an algorithm to the document which represents the document contents.

Definition at line 69 of file trapperdoc.cpp.

References changedAlgoList(), and pAlgoList.

Referenced by TrapperView::runAlgo().

{
    pAlgoList->append(algo);
    changedAlgoList();
}

void TrapperDoc::removeAlgorithm

(

Algo *

)

removes an algorithm from the list of currently connected algorithm

Definition at line 85 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();
}

QString TrapperDoc::getStatistics

(

)

shows berkeley db statistics about underlying databases

Definition at line 781 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;
}

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 125 of file trapperdoc.cpp.

References pViewList, QObject::sender(), and TrapperView::update().

{
    TrapperView *w;
    for(w=pViewList->first(); w!=0; w=pViewList->next())
    {
        w->update(sender);
    }
}

---

Friends And Related Function Documentation

friend class TrapperView [friend]

Definition at line 60 of file trapperdoc.h.

---

Member Data Documentation

bool TrapperDoc::modified [private]

the modified flag of the current document

Definition at line 156 of file trapperdoc.h.

Referenced by isModified(), newDocument(), openDocument(), saveDocument(), and setModified().

QString TrapperDoc::m_title [private]

Definition at line 157 of file trapperdoc.h.

Referenced by changedViewList(), openDocument(), saveDocument(), setPathName(), setTitle(), and title().

QString TrapperDoc::m_filename [private]

Definition at line 158 of file trapperdoc.h.

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

the list of the views currently connected to the document

Definition at line 160 of file trapperdoc.h.

Referenced by addView(), changedViewList(), closeDocument(), firstView(), isLastView(), removeAlgorithm(), removeView(), TrapperDoc(), updateAllViews(), and ~TrapperDoc().

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

Definition at line 161 of file trapperdoc.h.

Referenced by addAlgorithm(), removeAlgorithm(), removeView(), TrapperDoc(), and ~TrapperDoc().

TrDbMap TrapperDoc::trDbMap [private]

Definition at line 162 of file trapperdoc.h.

Referenced by closeDbs(), findTrDb(), getStatistics(), and openDbs().

QString TrapperDoc::m_contigDir [private]

Definition at line 163 of file trapperdoc.h.

Referenced by findTrDb(), openDbs(), openDocument(), pathName(), saveDocument(), and setPathName().

DbEnv* TrapperDoc::dbenv [private]

Definition at line 164 of file trapperdoc.h.

Referenced by openDbs().

---

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

• trapperdoc.h
• trapperdoc.cpp

---