trapperparser.cpp

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#include <qmessagebox.h>

#include "trapperparser.h"
#include "trapperdoc.h"
#include "generaldata.h"
#include "featuredata.h"
#include "qdir.h"

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


    //Use attributes to get name
    QString contigName = attributes.value("name");


    //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 ( format_ok ) {
//     cerr<<"parsing "<<qName<<endl;
    //Get data name from attributes and put into QString generalDataName

    //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 );
      
    }
    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;
    }
    return true;
  }
  return false;
}

bool TrapperParser::endElement( const QString & namespaceURI, const QString & localName, 
                                const QString & qName)
{
  if ( qName == "contig" ) {
    //Delete old doc, if any
    delete current_doc;
//     cerr<<"end contig"<<endl;
  }
  return true;
}



QStringList TrapperParser::contigNamesInProjectDir()
{
    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;
}

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