trapperparser.cpp

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#include <qmessagebox.h>

#include "trapperparser.h"
#include "trapperdoc.h"
#include "generaldata.h"
#include "featuredata.h"
#include "qdir.h"
#include "readsinrect.h"
#include <limits>
#include "optimizelayout.h"

using namespace std;

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