movealgo.cpp

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#include "movealgo.h"
#include "algoparam.h"
#include <iostream>
#include "readdata.h"
#include "generaldata.h"
#include <vector>
#include <cassert>
#include "readsinrect.h"
#include <fstream>

using namespace std;

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

  bool allow_overlap(true);

  AlgoMoveParam* param = (AlgoMoveParam*)my_param;//This is so ugly, needs to be fixed!!
  assert(param);
  
  int y_delta = param->get_y_delta();
  int x_delta = param->get_x_delta();

  if ( y_delta == 0 && x_delta == 0) {
    return;
  }
  
  //NB: This should be encapsulated, see TODO list...

  //Have to do it in this ugly way since multiple cursors can't be open simultaneously...

  vector<ReadData> readvec;


  for (set< db_recno_t >::iterator it = selectedReads.begin(); it != selectedReads.end(); it++ ){
    //Have to do it in this ugly way since multiple cursors can't be open simultaneously... FIX THIS!!
    //Also, had to move this sucker here (see above) beacause of some NASTY bug with changing read names...
    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 );
    assert( ret_read == 0 );
    readvec.push_back( *r_test );//Need a copy constructor...
  

    //Check that read does not end up on negative row or negative start index

    if ( (static_cast<int>(r_test->row()) + y_delta) < 0 ||
         (static_cast<int>(r_test->startPos()) + x_delta) < 0 ) {
      param->set_y_delta(0);
      param->set_x_delta(0);
      
      cerr<<"Read will end up on negative row or col, cancelling move "<<endl;
      delete read_it;
      return;
    }
    else {
      delete read_it;
    }

  }
  

  
  for(size_t i = 0; i < readvec.size(); i++ ) {
        
    
    //Check so that new destination isn't on another read. Might cause cursor problem, so watch out...
    
    ReadsInRect* dest_it = new ReadsInRect(pDoc);
    dest_it->setWindowCoord( readvec[i].startPos() + x_delta, readvec[i].row() + y_delta, readvec[i].endPos() - readvec[i].startPos(), 1);
    
    if ( !allow_overlap && dest_it->first() ) {
      //Ooops, read already here...
//       cerr<<"Can't move read to occupied space!"<<endl;
      delete dest_it;
    }
    else {
      delete dest_it;//This is so ugly...
      Database::Creator<ReadData> a_creator(pDoc, "ReadData");
      
      a_creator.data()->setRecno(readvec[i].getRecno());
      a_creator.data()->setRow(readvec[i].row() + y_delta);
      a_creator.data()->setStartPos(readvec[i].startPos() + x_delta);
      a_creator.data()->setEndPos(readvec[i].endPos() + x_delta);
//       a_creator.data()->setName(readvec[i].name());
//       a_creator.data()->setMate(readvec[i].mate());
//       a_creator.data()->setMateLength(readvec[i].mateLength());
//       a_creator.data()->setStrand(readvec[i].strand());
//       a_creator.data()->setBeginGood(readvec[i].beginGood());
//       a_creator.data()->setEndGood(readvec[i].endGood());
//       a_creator.data()->tc_vec.stlVector() = readvec[i].tc_vec.stlVector();
      


      a_creator.create(true);
    }
    
  }
}

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