findmatesalgo.cc

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#include "findmatesalgo.h"
#include "algoparam.h"
#include <iostream>
#include "readdata.h"
#include "generaldata.h"
#include <cassert>
#include <qmessagebox.h>
#include <qinputdialog.h>
#include <limits>
#include "featuredata.h"

using namespace std;

void FindMatesAlgo::start()
{
  if ( selectedReads.empty() ) {
    return;
  }

  int res = QMessageBox::question( 0, "Find mates", "All mates, or mates within an interval?", "All", "Interval", "Cancel", 0, 2 );
  
  size_t min_ = 0;
  size_t max_ = numeric_limits<size_t>::max();

  if( res == 2 ) {
    return;
  }
  else if ( res == 1 ) {
    bool ok;
    int low = QInputDialog::getInteger(
                                       "Find mates", "Lower bound", 0, 0, numeric_limits<int>::max(), 1,
                                       &ok, 0 );
    
    if ( ok ) {
      // user entered something and pressed OK
      min_ = low;
    } else {
      // user pressed Cancel
      return;
    }
    int high = QInputDialog::getInteger(
                                        "Find mates", "Upper bound", numeric_limits<int>::max(), low, numeric_limits<int>::max(), 1,
                                        &ok, 0 );
    
    if ( ok ) {
      // user entered something and pressed OK
      max_ = high;
    } else {
      // user pressed Cancel
      return;
    }
    
  }
  

  set< db_recno_t > selected_temp = selectedReads;
  
  selectedReads.clear();

  for (set< db_recno_t >::iterator it = selected_temp.begin(); it != selected_temp.end(); it++ ){

    //New 090316
    Database::PrimaryIterator<ReadData>* read_it = new Database::PrimaryIterator<ReadData>(pDoc, "ReadData");

    int ret_read = read_it->setFromRecno(*it);
    ReadData* r_test = (ret_read != DB_NOTFOUND) ? read_it->answer() : 0;
    assert( r_test );

    int rstart = read_it->answer()->startPos();
    int rend = read_it->answer()->endPos();
    delete read_it;
    //END New 090316

    Database::SecondaryIterator<ReadMetaData>* read_meta_it = 
      new Database::SecondaryIterator<ReadMetaData>("readRecno", pDoc, "ReadMetaData"); 
    
    read_meta_it->key()->setReadRecno(*it);

    assert( read_meta_it->set() == 0 );
    
    string mate = read_meta_it->answer()->mate();
    delete read_meta_it;

    //Find mate (if any) and get its recno
    
    Database::SecondaryIterator<ReadMetaData>* name_it =
      new Database::SecondaryIterator<ReadMetaData>( "name", pDoc, "ReadMetaData" );
    name_it->key()->setName( mate );

    //New 090316

//     if ( name_it->set() == 0 && 
//          name_it->answer()->mateLength() >= min_ && 
//          name_it->answer()->mateLength() <= max_ ) {
//       selectedReads.insert(*it);
//       selectedReads.insert(name_it->answer()->readRecno());
      
//     }
    if ( name_it->set() == 0 ) {

      
      Database::PrimaryIterator<ReadData>* mate_it = new Database::PrimaryIterator<ReadData>(pDoc, "ReadData");
      ret_read = mate_it->setFromRecno(name_it->answer()->readRecno());
      r_test = (ret_read != DB_NOTFOUND) ? mate_it->answer() : 0;
      assert( r_test );
      
      int mstart = mate_it->answer()->startPos();
      int mend = mate_it->answer()->endPos();
      
      int start = min(rstart, mstart);
      int stop = max(rend, mend);
      
      int len = stop - start + 1;
      
      if ( len >= min_ && len <= max_ ) {
        
        selectedReads.insert(*it);
        selectedReads.insert(name_it->answer()->readRecno());
      }
      
      delete mate_it;
      
    }

    //END New 090316
    
    delete name_it;
//     delete read_it;
    

  }
  
}

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