subsetalgo.cc

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#include "subsetalgo.h"
#include <fstream>
#include "viewparam.h"
#include <cassert>
#include <qstring.h>
#include <qfiledialog.h>
#include <qdir.h>
#include <qfile.h>
#include <qmessagebox.h>
#include "trapperview.h"

using namespace std;

void SubsetAlgo::start()
{
  if ( getMAl()->get_num_seq() == 0 ) {
//     cerr<<"Nothing to be done here! "<<endl;
    return;
  }
  
  ViewParam* param = dynamic_cast<ViewParam*>(my_param);
  assert(param);
  
  QString title = param->view()->getDocument()->title();

  QString currdir = QDir::currentDirPath();
  QString contig = title.section( '/', -2 );
  
  QString header = contig + ".subset.seq";
  QString default_file_name = currdir + '/' + header;
  

  QString filename = QFileDialog::getSaveFileName( default_file_name,
                                            0,
                                            0,
                                           "save seqs file dialog"
                                           "Choose a filename to save sequences under" );
  

  if ( filename.isEmpty() ) return;

  if ( QFile::exists( filename ) &&
       QMessageBox::question(
                             0,
                             tr("Overwrite File? -- Trapper"),
                             tr("A file called %1 already exists."
                                "Do you want to overwrite it?")
                             .arg( filename ),
                             tr("&Yes"), tr("&No"),
                             QString::null, 0, 1 ) ) {
    
    return;
  }
  
  default_file_name = filename + ".qual";

  QString filename_qual = QFileDialog::getSaveFileName( default_file_name,
                                                        0,
                                                        0,
                                                        "save quals file dialog"
                                                        "Choose a filename to save quality values under" );
  

  if ( filename_qual.isEmpty() ) return;

  if ( QFile::exists( filename_qual ) &&
       QMessageBox::question(
                             0,
                             tr("Overwrite File? -- Trapper"),
                             tr("A file called %1 already exists."
                                "Do you want to overwrite it?")
                             .arg( filename_qual ),
                             tr("&Yes"), tr("&No"),
                             QString::null, 0, 1 ) ) {
    
    return;
  }
  
  
  ofstream outFile(filename);
  ofstream outFileQ(filename_qual);
  

  for( size_t i = 0; i < getMAl()->get_num_seq(); i++ ) {
    outFile<<'>'<<getMAl()->get_name(i)<<'\n';
    outFileQ<<'>'<<getMAl()->get_name(i)<<'\n';
    int cnt(0);
    int cntQ(0);
    for( size_t j = 0; j < getMAl()->get_len(i); j++ ) {
      char base = getMAl()->get_base(i, j);
      if (  base == '*' || base == '-' ) {
        continue;
      }
      int qual = getMAl()->get_qual(i, j);
      cnt++;
      cntQ++;
      outFile<<base;
      outFileQ<<qual<<' ';
      if ( cnt % 50 == 0 ) {
        outFile<<'\n';
      }
      if ( cntQ % 15 == 0 ) {
        outFileQ<<'\n';
      }
      
    }
    if ( cnt % 50 != 0 ) {
      outFile<<'\n';
    }
    if ( cntQ % 15 != 0 ) {
      outFileQ<<'\n';
    }
  }

  outFile.close();
  outFileQ.close();
  
  
}

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