예제 #1
0
파일: IDMapper.C 프로젝트: BioITer/OpenMS
  void IDMapper::getIDDetails_(const PeptideIdentification & id, DoubleReal & rt_pep, DoubleList & mz_values, IntList & charges, bool use_avg_mass) const
  {
    mz_values.clear();
    charges.clear();

    rt_pep = id.getMetaValue("RT");

    // collect m/z values of pepId
    if (param_.getValue("mz_reference") == "precursor") // use precursor m/z of pepId
    {
      mz_values.push_back(id.getMetaValue("MZ"));
    }

    for (vector<PeptideHit>::const_iterator hit_it = id.getHits().begin();
         hit_it != id.getHits().end(); ++hit_it)
    {
      Int charge = hit_it->getCharge();
      charges.push_back(charge);

      if (param_.getValue("mz_reference") == "peptide") // use mass of each pepHit (assuming H+ adducts)
      {
        DoubleReal mass = use_avg_mass ?
                          hit_it->getSequence().getAverageWeight(Residue::Full, charge) :
                          hit_it->getSequence().getMonoWeight(Residue::Full, charge);

        mz_values.push_back( mass / (DoubleReal) charge);
      }
    }
  }
예제 #2
0
TEST(FastListTest, test)
{
    IntList flist;
    flist.new_node(1);
    IntList::RemovableElementHandler two = flist.new_node(2);
    flist.new_node(3);

    std::list<int> rlist;
    rlist.push_back(1);
    rlist.push_back(2);
    rlist.push_back(3);
    ASSERT_TRUE(compare(flist, rlist));

    // remove 'two'
    two.destroy();
    flist.shrink();
    rlist.remove(2);
    ASSERT_TRUE(compare(flist, rlist));

    two = flist.new_node(2);
    rlist.push_back(2);
    ASSERT_TRUE(compare(flist, rlist));

    for (int i = 10; i < 20; ++i)
    {
        flist.new_node(i);
        rlist.push_back(i);
    }
    ASSERT_TRUE(compare(flist, rlist));

    flist.clear();
    flist.shrink();
    rlist.clear();
    ASSERT_TRUE(flist.empty());
    ASSERT_TRUE(compare(flist, rlist));

    for (int i = 10; i < 30; ++i)
    {
        flist.new_node(i);
        rlist.push_back(i);
    }
    ASSERT_TRUE(compare(flist, rlist));
}
예제 #3
0
/*----------------------------------------------------------------------- */
SEXP
watershed (SEXP x, SEXP _tolerance, SEXP _ext) {
    SEXP res;
    int im, i, j, nx, ny, nz, ext, nprotect = 0;
    double tolerance;

    nx = INTEGER ( GET_DIM(x) )[0];
    ny = INTEGER ( GET_DIM(x) )[1];
    nz = getNumberOfFrames(x,0);
    tolerance = REAL( _tolerance )[0];
    ext = INTEGER( _ext )[0];

    PROTECT ( res = Rf_duplicate(x) );
    nprotect++;
  
    int * index = new int[ nx * ny ];

    for ( im = 0; im < nz; im++ ) {

        double * src = &( REAL(x)[ im * nx * ny ] );
        double * tgt = &( REAL(res)[ im * nx * ny ] );

        /* generate pixel index and negate the image -- filling wells */
        for ( i = 0; i < nx * ny; i++ ) {
	  tgt[ i ] = -src[ i ];
	  index[ i ] = i;
        }
        /* from R includes R_ext/Utils.h */
        /* will resort tgt as well */
        rsort_with_index( tgt, index, nx * ny );
        /* reassign tgt as it was reset above but keep new index */
        for ( i = 0; i < nx * ny; i++ )
            tgt[ i ] = -src[ i ];

        SeedList seeds;  /* indexes of all seed starting points, i.e. lowest values */

        IntList  equals; /* queue of all pixels on the same gray level */
        IntList  nb;     /* seed values of assigned neighbours */
        int ind, indxy, nbseed, x, y, topseed = 0;
        IntList::iterator it;
        TheSeed newseed;
        PointXY pt;
        bool isin;
        /* loop through the sorted index */
        for ( i = 0; i < nx * ny && src[ index[i] ] > BG; ) {
            /* pool a queue of equally lowest values */
            ind = index[ i ];
            equals.push_back( ind );
            for ( i = i + 1; i < nx * ny; ) {
                if ( src[ index[i] ] != src[ ind ] ) break;
                equals.push_back( index[i] );
                i++;
            }
            while ( !equals.empty() ) {
                /* first check through all the pixels if we can assign them to
                 * existing objects, count checked and reset counter on each assigned
                 * -- exit when counter equals queue length */
                for ( j = 0; j < (int) equals.size(); ) {
		  if ((j%1000)==0) R_CheckUserInterrupt();
                    ind = equals.front();
                    equals.pop_front();
                    /* check neighbours:
                     * - if exists one, assign
                     * - if two or more check what should be combined and assign to the steepest
                     * - if none, push back */
                    /* reset j to 0 every time we assign another pixel to restart the loop */
                    nb.clear();
                    pt = pointFromIndex( ind, nx );
                    /* determine which neighbour we have, push them to nb */
                    for ( x = pt.x - ext; x <= pt.x + ext; x++ )
                        for ( y = pt.y - ext; y <= pt.y + ext; y++ ) {
                            if ( x < 0 || y < 0 || x >= nx || y >= ny || (x == pt.x && y == pt.y) ) continue;
                            indxy = x + y * nx;
                            nbseed = (int) tgt[ indxy ];
                            if ( nbseed < 1 ) continue;
                            isin = false;
                            for ( it = nb.begin(); it != nb.end() && !isin; it++ )
                                if ( nbseed == *it ) isin = true;
                            if ( !isin ) nb.push_back( nbseed );
                        }
                    if ( nb.size() == 0 ) {
                        /* push the pixel back and continue with the next one */
                        equals.push_back( ind );
                        j++;
                        continue;
                    }
                    tgt[ ind ] = check_multiple(tgt, src, ind, nb, seeds, tolerance, nx, ny );
                    /* we assigned the pixel, reset j to restart neighbours detection */
                    j = 0;
                }
                /* now we have assigned all that we could */
                if ( !equals.empty() ) {
                    /* create a new seed for one pixel only and go back to assigning neighbours */
                    topseed++;
                    newseed.index = equals.front();
                    newseed.seed = topseed;
                    equals.pop_front();
                    tgt[ newseed.index ] = topseed;
                    seeds.push_back( newseed );
                }
            } // assigning equals
        } // sorted index

        /* now we need to reassign indexes while some seeds could be removed */
        double * finseed = new double[ topseed ];
        for ( i = 0; i < topseed; i++ )
            finseed[ i ] = 0;
        i = 0;
        while ( !seeds.empty() ) {
            newseed = seeds.front();
            seeds.pop_front();
            finseed[ newseed.seed - 1 ] = i + 1;
            i++;
        }
        for ( i = 0; i < nx * ny; i++ ) {
            j = (int) tgt[ i ];
            if ( 0 < j && j <= topseed )
                tgt[ i ] = finseed[ j - 1 ];
        }
        delete[] finseed;

    } // loop through images

    delete[] index;

    UNPROTECT (nprotect);
    return res;
}