TrapperParser Class Reference

#include <trapperparser.h>

Inheritance diagram for TrapperParser:

[legend]Collaboration diagram for TrapperParser:

[legend]List of all members.

Public Member Functions
	TrapperParser (DbEnv *dbenv, QString projectDir)
bool	startElement (const QString &namespaceURI, const QString &localName, const QString &qName, const QXmlAttributes &attributes)
bool	endElement (const QString &namespaceURI, const QString &localName, const QString &qName)
Private Member Functions
QStringList	contigNamesInProjectDir ()
Private Attributes
DbEnv *	env
QString	projDir
TrapperDoc *	current_doc
db_recno_t	current_read_recno
bool	format_ok
int	curr_start_row
std::set< db_recno_t >	curr_set

---

Detailed Description

Definition at line 12 of file trapperparser.h.

---

Constructor & Destructor Documentation

TrapperParser::TrapperParser	(	DbEnv *	dbenv,
		QString	projectDir
	)			[inline]

Definition at line 16 of file trapperparser.h.

                                                  : 
    env(dbenv), projDir(projectDir), current_doc(0), format_ok(false) {}

---

Member Function Documentation

bool TrapperParser::startElement	(	const QString &	namespaceURI,
		const QString &	localName,
		const QString &	qName,
		const QXmlAttributes &	attributes
	)

Definition at line 14 of file trapperparser.cpp.

References Database::SecondaryIterator< T >::answer(), QString::ascii(), contigNamesInProjectDir(), curr_set, curr_start_row, current_doc, current_read_recno, env, format_ok, Database::SecondaryIterator< T >::last(), TrapperView::message(), TrapperDoc::openDocument(), optimize_layout(), projDir, ReadData::row(), FeatureData::setReadRecno(), ReadData::setRow(), TrapperView::TrapperDoc, QXmlAttributes::value(), and QMessageBox::warning().

{
//   cerr<<"qName: "<<qName<<endl;
  
  //Three cases:
  if ( qName == "TRAPPER" ) {
    format_ok = true;
    return true;
  }
  else if ( qName == "contig" && format_ok ) {
    /* Basically, all the functionality of TrapperApp::slotImport()
       has moved here. The other two cases below now contains the
       old functionality of TrapperDoc::import(). */

    curr_start_row = 1;
    
    //Use attributes to get name
    QString contigName = attributes.value("name");
    cerr<<"Importing contig "<<contigName<<endl;


    //Some bookkeeping to check if contig is already present
    QStringList contigNamesAlreadyPresent = contigNamesInProjectDir();
    if ( contigNamesAlreadyPresent.contains( contigName ) ) {
      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(0,"",message);
      return false;
    }
    //Create directory for contig
    QString fName = projDir + "/" + contigName;
                

    //Create directories and databases for this contig

    current_doc = new TrapperDoc(env);
    current_doc->openDocument(fName);

    return true;
  }
  else if ( qName == "section" && format_ok ) {
    optimize_layout(curr_start_row, curr_set, current_doc);
    curr_set.clear();

    //Figure out start row
    Database::SecondaryIterator<ReadData>* row_it = new Database::SecondaryIterator<ReadData>( "pos", current_doc, "ReadData" );
    int ret_row = row_it->last();
    ReadData* r_row = (ret_row != DB_NOTFOUND) ? row_it->answer() : 0;
    if ( r_row ) {
      curr_start_row = r_row->row() + 5;
    }
    delete row_it;
    return true;
  }
  else if ( format_ok ) {
//     cerr<<"parsing "<<qName<<endl;
    //Get data name from attributes and put into QString generalDataName
    
    bool no_row(false);

    //Create object factory for this data type
    
    Database::Creator<GeneralData> creator( current_doc, qName.ascii() );

    creator.data()->readAttributes( attributes );
    
    if ( qName != "ReadData" ) {//All other cases are FeatureData and need the corresponding read recno
      
      FeatureData* fdata = dynamic_cast<FeatureData*>(creator.data());
      assert( fdata );
      fdata->setReadRecno( current_read_recno );
      
    }
    else {
      if ( attributes.value("row") == "" ) {
        //Data is readdata and row needs to be figured out
        
        no_row = true;

//         ReadsInRect* readsInRect = new ReadsInRect( current_doc );
        
        
        ReadData* rdata = dynamic_cast<ReadData*>(creator.data());
        assert( rdata );
//         readsInRect->setWindowCoord( rdata->startPos(), curr_start_row,  rdata->endPos() - rdata->startPos() + 1, numeric_limits<TR_DNA>::max() - curr_start_row );

//         int previous_row(curr_start_row);
//         int row(0);
//         int num(0);
//         for ( ReadData * r = readsInRect->first(); r; r = readsInRect->next() ) {
//           num++;
//           if ( r->row() - previous_row > 1 ) {
//             row = previous_row + 1;
//             break;
//           }
//           previous_row = r->row();
//         }
//         delete readsInRect;
//         if ( !row ) {
//           if ( num == 0 ) {
//             row = curr_start_row;
//           }
//           else {
//             row = previous_row + 1;
//           }
//         }
        rdata->setRow( curr_start_row );
      }
    }

    db_recno_t new_recno = creator.create( false );//Should give dna, quality etc same recno as read (as previously)
    if ( qName == "ReadData" ) {

      current_read_recno = new_recno;
      if ( no_row ) {
        curr_set.insert(new_recno);
      }

    }
    return true;
  }
  return false;
}

bool TrapperParser::endElement	(	const QString &	namespaceURI,
		const QString &	localName,
		const QString &	qName
	)

Definition at line 141 of file trapperparser.cpp.

References curr_set, curr_start_row, current_doc, and optimize_layout().

{
  if ( qName == "contig" ) {
    
    optimize_layout(curr_start_row, curr_set, current_doc);
    curr_set.clear();

    //Delete old doc, if any
    delete current_doc;
//     cerr<<"end contig"<<endl;
  }
  return true;
}

QStringList TrapperParser::contigNamesInProjectDir

(

)

[private]

Definition at line 158 of file trapperparser.cpp.

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

Referenced by startElement().

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

---

Member Data Documentation

DbEnv* TrapperParser::env [private]

Definition at line 32 of file trapperparser.h.

Referenced by startElement().

QString TrapperParser::projDir [private]

Definition at line 33 of file trapperparser.h.

Referenced by contigNamesInProjectDir(), and startElement().

TrapperDoc* TrapperParser::current_doc [private]

Definition at line 35 of file trapperparser.h.

Referenced by endElement(), and startElement().

db_recno_t TrapperParser::current_read_recno [private]

Definition at line 36 of file trapperparser.h.

Referenced by startElement().

bool TrapperParser::format_ok [private]

Definition at line 37 of file trapperparser.h.

Referenced by startElement().

int TrapperParser::curr_start_row [private]

Definition at line 38 of file trapperparser.h.

Referenced by endElement(), and startElement().

std::set<db_recno_t> TrapperParser::curr_set [private]

Definition at line 39 of file trapperparser.h.

Referenced by endElement(), and startElement().

---

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

• trapperparser.h
• trapperparser.cpp

---