macsimparser.cpp

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#include <qmessagebox.h>
#include <qregexp.h>
#include "macsimparser.h"
#include "trapperdoc.h"
#include "generaldata.h"
#include "readdata.h"
#include "featuredata.h"
#include "qdir.h"
#include <cassert>
#include <iostream>
#include <list>
#include <string>
#include <algorithm>


using namespace std;

MacsimParser::MacsimParser(DbEnv* dbenv, QString projectDir) : 
  env(dbenv), projDir(projectDir), current_doc(0), format_ok(false)
{
  curr_row = 1;
  curr_al_num = 0;
  att_trans["sense"] = "strand";
  att_trans["seq-name"] = "name";
  att_trans["seq-data"] = "trappervector";

//   cerr<<"MacsimParser: NB, due to long names of genomic seq in old files, they are currently being shortened"<<endl;
}


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

  if ( qName == "macsim" ) {
    format_ok = true;
    return true;
    
  }
  else if ( format_ok ) {
    
    return true;
  }
  return false;
  
}

bool MacsimParser::endElement( const QString & namespaceURI, const QString & localName, 
                               const QString & qName)
{
  if ( qName == "alignment" ) {
    curr_al_num++;
    if ( curr_al_num % 100 == 0 ) {
      cerr<<curr_al_num<<" alignments parsed"<<endl;
    }

    curr_row = 1;
    //Delete old doc, if any
    delete current_doc;
    return true;
  }
  else if ( qName == "aln-name") {
    //Contig name
    
    //Create contig data

    QString contigName = curr_data;


    //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 == "sequence") {
    //One ReadData parsed

    QXmlAttributes read_att;

    //Extract ReadData startPos, endPos etc, recalc corresponding feature coordinates
    //This also needs to be done for other features, when they are added

    //strand (group)
    if ( att_map["ReadData"]["strand"].toInt() > -1 ) {
      read_att.append("strand", namespaceURI, localName, "U");
    }
    else {
      read_att.append("strand", namespaceURI, localName, "C");
    }
    
    //name (seq-name)
    read_att.append("name", namespaceURI, localName, att_map["ReadData"]["name"]);
    
    //trappervector (seq-data)
    QString orig_str = att_map["DnaStrData"]["trappervector"].lower();
    
    //Parse out leading and trailing gaps, calculate start and endpos
    int indexleft = orig_str.find( QRegExp("[a-z]") );
    int indexright = orig_str.findRev( QRegExp("[a-z]") );
    assert( indexleft > -1 && indexright > -1 );
    /*
    -----aaatac---
    L = 14
    seqL = 6
    startPos = 5
    endPos = 10
    index = 5
    indexright = 10

    => startPos = indexleft, endPos = indexright
    Feature: endPos = seqL - 1 = indexright - indexleft
    */
    QString seq = orig_str.mid( indexleft, indexright - indexleft + 1 );
    seq.replace('u','t');
    seq.replace('-','*');

    read_att.append("startPos", namespaceURI, localName, QString().number(indexleft));
    read_att.append("endPos", namespaceURI, localName, QString().number(indexright));
    
    //Features, currently only DnaStrData
    QXmlAttributes dna_att;
    dna_att.append("startPos", namespaceURI, localName, "0");
    dna_att.append("endPos", namespaceURI, localName, QString().number(indexright - indexleft) );
    dna_att.append("trappervector", namespaceURI, localName, seq);


    //Create ReadData

    Database::Creator<ReadData> read_creator( current_doc, "ReadData" );
    read_creator.data()->readAttributes( read_att );
    read_creator.data()->setRow(curr_row);
    curr_row++;
    
    db_recno_t new_recno = read_creator.create( false );

    //Create FeatureData

    Database::Creator<DnaStrData> feat_creator( current_doc, "DnaStrData" );
    feat_creator.data()->readAttributes( dna_att );
    feat_creator.data()->setReadRecno( new_recno );
    feat_creator.create(false);

    //Hacking galore: create dummy vals for qual and chromat also
    QXmlAttributes chr_att;
    chr_att.append("startPos", namespaceURI, localName, "0");
    chr_att.append("endPos", namespaceURI, localName, QString().number(indexright - indexleft) );

    Database::Creator<ChromatData> chr_creator( current_doc, "ChromatData" );
    chr_creator.data()->readAttributes( chr_att );
    chr_creator.data()->setReadRecno( new_recno );
    chr_creator.create(false);

    QXmlAttributes qual_att;
    qual_att.append("startPos", namespaceURI, localName, "0");
    qual_att.append("endPos", namespaceURI, localName, QString().number(indexright - indexleft) );
    QString dummyqual;
    for( size_t i = 0; i < static_cast<size_t>(indexright - indexleft + 1); i++ ) {
      dummyqual.append(" 20");
    }
    qual_att.append("trappervector", namespaceURI, localName, dummyqual);

    Database::Creator<QualityData> qual_creator( current_doc, "QualityData" );
    qual_creator.data()->readAttributes( qual_att );
    qual_creator.data()->setReadRecno( new_recno );
    qual_creator.create(false);

    //Tag data
    
    for( size_t i = 0; i < tags.size(); i++ ) {
      assert( tags[i].size() == 5 );
      list<string> type_list = GeneralMaker::listRegistered();
      string type = tags[i][0].ascii();

      if ( find( type_list.begin(), type_list.end(), type ) == type_list.end() ) {
        tags[i][4] = type + " " + tags[i][4];
        type = "TagData";
        
      }
//       cerr<<"type: "<<type<<endl;
      
      
      Database::Creator<TagData> tag_creator( current_doc, type );
      
      QXmlAttributes tag_att;
//       tag_att.append( "startPos", namespaceURI, localName, QString().number( tags[i][1].toInt() - indexleft) );
//       tag_att.append( "endPos", namespaceURI, localName, QString().number( tags[i][2].toInt() - indexleft) );
      tag_att.append( "startPos", namespaceURI, localName, QString().number( tags[i][1].toInt() - 1) );
      tag_att.append( "endPos", namespaceURI, localName, QString().number( tags[i][2].toInt() - 1) );
      tag_att.append( "score", namespaceURI, localName, tags[i][3] );
      tag_att.append( "info", namespaceURI, localName, tags[i][4] );

      tag_creator.data()->readAttributes( tag_att );

      tag_creator.data()->setReadRecno( new_recno );
      tag_creator.create(false);
      
    }
    

    //Clear old data
    att_map.clear();
    tags.clear();
    return true;
    
  }
  else if ( qName == "seq-name" || qName == "group" || qName == "sense" )  {
    //Fill attributes with name, strand, and sequence
//     if ( qName == "seq-name" && curr_data.find('|') != -1 ) {
//       curr_data = curr_data.section('|', 1, 1).section(' ', 0, 0);
//     }
    
    
    att_map["ReadData"][ att_trans[qName] ] = curr_data;

    return true;
  }
  else if ( qName == "seq-data" ) {
    att_map["DnaStrData"][ att_trans[qName] ] = curr_data;
    return true;
  }
  else if ( qName == "ftype" ) {
    vector<QString> tmp;
    tags.push_back(tmp);
    tags[ tags.size() - 1 ].push_back(curr_data);
    
    return true;
  }
  else if ( qName == "fstart" || qName == "fstop" || qName == "fscore" || qName == "fnote" ) {
    tags[ tags.size() - 1 ].push_back(curr_data);
    return true;
  }
  
  return true;
}

bool MacsimParser::characters ( const QString & ch ) 
{
  curr_data = ch;
  return true;
}

QStringList MacsimParser::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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