chromatparser.cc

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#include "chromatparser.h"
#include <iostream>
#include <qstring.h>
#include <qtextstream.h>
#include <map>
#include <vector>
#include <cassert>

using namespace std;

ChromatParser::ChromatParser() : inDATA(false), curr_tag_num(-1)
{
  
}

ChromatParser::~ChromatParser()
{

}

bool ChromatParser::startElement(  const QString & namespaceURI, const QString & localName, 
                                   const QString & qName, const QXmlAttributes & atts)
{
  
  if ( qName == "DATA") {
    inDATA = true;
    curr_tag_num = atts.value("tag_number").toInt();
  }
  else if ( qName == "FWO_") {
    FWO_ = atts.value("string");
    //Swap vectors if necessary
    //We want C = 0, A = 1, G = 2, T = 3
    map<char, size_t> fwo_map;
    vector<char> fwo_vec(4);

    fwo_map['C'] = FWO_.find('C');
    fwo_vec[ fwo_map['C'] ] = 'C';
    fwo_map['A'] = FWO_.find('A');
    fwo_vec[ fwo_map['A'] ] = 'A';
    fwo_map['G'] = FWO_.find('G');
    fwo_vec[ fwo_map['G'] ] = 'G';
    fwo_map['T'] = FWO_.find('T');
    fwo_vec[ fwo_map['T'] ] = 'T';
    
    
    if ( fwo_map['C'] != 0 ) {
      (*chromats)[ 0 ].stlVector().swap( (*chromats)[ fwo_map['C'] ].stlVector() );

      fwo_map[ fwo_vec[ 0 ] ] = fwo_map['C'];
      fwo_vec[ fwo_map['C'] ] = fwo_vec[ 0 ];

      fwo_map['C'] = 0;
      fwo_vec[ 0 ] = 'C';
      
    }
    if ( fwo_map['A'] != 1 ) {
      (*chromats)[ 1 ].stlVector().swap( (*chromats)[ fwo_map['A'] ].stlVector() );

      fwo_map[ fwo_vec[ 1 ] ] = fwo_map['A'];
      fwo_vec[ fwo_map['A'] ] = fwo_vec[ 1 ];

      fwo_map['A'] = 1;
      fwo_vec[ 1 ] = 'A';
      
    }
    if ( fwo_map['G'] != 2 ) {
      (*chromats)[ 2 ].stlVector().swap( (*chromats)[ fwo_map['G'] ].stlVector() );

      fwo_map[ fwo_vec[ 2 ] ] = fwo_map['G'];
      fwo_vec[ fwo_map['G'] ] = fwo_vec[ 2 ];

      fwo_map['G'] = 2;
      fwo_vec[ 2 ] = 'G';
      
    }
    if ( fwo_map['T'] != 3 ) {
      (*chromats)[ 3 ].stlVector().swap( (*chromats)[ fwo_map['T'] ].stlVector() );

      fwo_map[ fwo_vec[ 3 ] ] = fwo_map['T'];
      fwo_vec[ fwo_map['T'] ] = fwo_vec[ 3 ];

      fwo_map['T'] = 3;
      fwo_vec[ 3 ] = 'T';
      
    }
    assert( fwo_map['C'] == 0 );
    assert( fwo_map['A'] == 1 );
    assert( fwo_map['G'] == 2 );
    assert( fwo_map['T'] == 3 );
    
    assert( fwo_vec[0] == 'C' );
    assert( fwo_vec[1] == 'A' );
    assert( fwo_vec[2] == 'G' );
    assert( fwo_vec[3] == 'T' );
    
  }
  else if ( inDATA &&               //We're parsing DATA
            qName == "integer16" && //We're parsing data array
            curr_tag_num > 8 &&     //9=C, 10=A, 11=G, 12=T
            curr_tag_num < 13) {

    QString array = atts.value("value");
    QTextStream ts(&array, IO_ReadOnly);
    
    while ( !ts.atEnd()) {
      int val;
      ts>>val;
      (*chromats)[ curr_tag_num - 9 ].stlVector().push_back(val);
    }
    

  }
  
  return true;
}

bool ChromatParser::endElement( const QString & namespaceURI, const QString & localName, 
                                const QString & qName )
{
  if ( qName == "DATA") {
    inDATA = false;
  }
  
  return true;
}

void ChromatParser::set_result_array(vector<TrapperVector<Q_UINT32> >* array)
{
  chromats = array;
  chromats->clear();
  TrapperVector<Q_UINT32> tmp;
  //Four curves
  chromats->push_back(tmp);
  chromats->push_back(tmp);
  chromats->push_back(tmp);
  chromats->push_back(tmp);
  
}

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