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);
}
}
}
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));
}
/*----------------------------------------------------------------------- */
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;
}