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);
}
}
}
IntList ParsedEntity::getIntList()
{
auto pList = getList();
auto list = *pList;
IntList retList = MakeIntList();
for (ParsedEntityPtr pe : list)
{
if (pe->getType() == ParsedEntity::Int)
{
retList->push_back(pe->getInt());
}
}
return retList;
}
bool Init()
{
int nRandom = 0;
for (int i = 0; i < g_nMax; ++i)
{
nRandom = i;
g_nSummary += nRandom;
g_dInts.push_back(nRandom);
g_hmInts.insert(std::make_pair(nRandom, nRandom));
g_hsInts.insert(nRandom);
g_lInts.push_back(nRandom);
g_mInts.insert(std::make_pair(nRandom, nRandom));
g_mmInts.insert(std::make_pair(nRandom, nRandom));
g_msInts.insert(nRandom);
g_sInts.insert(nRandom);
g_vInts.push_back(nRandom);
}
return true;
}
int main()
{
IntList test;
test.push_front(5);
test.push_front(2);
test.push_front(5);
test.push_front(7);
test.push_front(5);
cout << "Should display counting down from five: ";
test.display();
cout << endl;
test.push_back(6);
cout << "Should add zero to the end: ";
test.display();
cout << endl;
//test.insert_sorted(3);
test.select_sort();
cout << "Should be in order now: ";
test.display();
cout << endl;
test.remove_duplicates();
cout << "Should remove all same digits: ";
test.display();
cout << endl;
}
// Given a list of lists of possible cage values:
// [[1,2,3], [3,4,5]]
// Recursively generates tuples of combinations from each of the lists as
// follows:
// [1,3]
// [1,4]
// [1,5]
// [2,3]
// [2,4]
// ... etc
// Each of these is checked against the target sum, and pushed into a result
// vector if they match.
// Note: The algorithm assumes that the list of possibles/candidates are
// ordered. This allows it to bail out early if it detects there's no point
// going further.
static void subsetSum(const std::vector<IntList> &possible_lists,
const std::size_t p_size, IntList &tuple,
unsigned tuple_sum, std::vector<IntList> &subsets,
const unsigned target_sum, unsigned list_idx) {
for (unsigned p = list_idx; p < p_size; ++p) {
for (auto &poss : possible_lists[p]) {
// Optimization for small target sums: if the candidate is bigger than
// the target itself then it can't be valid, neither can any candidate
// after it (ordered).
if (target_sum < static_cast<unsigned>(poss)) {
break;
}
// Can't repeat a value inside a cage
if (std::find(tuple.begin(), tuple.end(), poss) != tuple.end()) {
continue;
}
// Pre-calculate the new tuple values to avoid spurious
// insertions/deletions to the vector.
const auto new_tuple_sum = tuple_sum + poss;
const auto new_tuple_size = tuple.size() + 1;
// If we've added too much then we can bail out (ordered).
if (new_tuple_sum > target_sum) {
break;
}
// If there are fewer spots left in the tuple than there are options for
// the sum to reach the target, bail.
// TODO: This could be more sophisticated (can't have more than one 1, so
// it's more like the N-1 sum that it should be greater than.
if ((p_size - new_tuple_size) > (target_sum - new_tuple_sum)) {
break;
}
if (new_tuple_size == p_size) {
// If we've reached our target size then we can stop searching other
// possiblities from this list (ordered).
if (new_tuple_sum == target_sum) {
tuple.push_back(poss);
subsets.push_back(tuple);
tuple.pop_back();
break;
}
// Else, move on to the next candidate in the list.
continue;
}
tuple_sum += poss;
tuple.push_back(poss);
subsetSum(possible_lists, p_size, tuple, tuple_sum, subsets, target_sum,
p + 1);
tuple.pop_back();
tuple_sum -= poss;
}
}
}
/*----------------------------------------------------------------------- */
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;
}
TestList()
{
typedef List<char, DebugAllocator<int> > IntList;
IntList a;
a.push_back('1');
a.push_back('2');
a.push_back('3');
LIST_ASSERT(*a.begin() == '1');
LIST_ASSERT(*++a.begin() == '2');
LIST_ASSERT(*++++a.begin() == '3');
LIST_ASSERT(++++++a.begin() == a.end());
IntList b;
b.push_back('a');
b.push_back('b');
b.push_back('c');
LIST_ASSERT(*b.begin() == 'a');
LIST_ASSERT(*++b.begin() == 'b');
LIST_ASSERT(*++++b.begin() == 'c');
LIST_ASSERT(++++++b.begin() == b.end());
// swap full lists
a.swap(b);
LIST_ASSERT(*a.begin() == 'a');
LIST_ASSERT(*++a.begin() == 'b');
LIST_ASSERT(*++++a.begin() == 'c');
LIST_ASSERT(++++++a.begin() == a.end());
LIST_ASSERT(*b.begin() == '1');
LIST_ASSERT(*++b.begin() == '2');
LIST_ASSERT(*++++b.begin() == '3');
LIST_ASSERT(++++++b.begin() == b.end());
// swap to/from empty list
IntList c;
c.swap(b);
LIST_ASSERT(b.empty());
LIST_ASSERT(*c.begin() == '1');
LIST_ASSERT(*++c.begin() == '2');
LIST_ASSERT(*++++c.begin() == '3');
LIST_ASSERT(++++++c.begin() == c.end());
c.swap(b);
LIST_ASSERT(c.empty());
LIST_ASSERT(*b.begin() == '1');
LIST_ASSERT(*++b.begin() == '2');
LIST_ASSERT(*++++b.begin() == '3');
LIST_ASSERT(++++++b.begin() == b.end());
IntList d;
c.swap(d);
LIST_ASSERT(c.empty());
LIST_ASSERT(d.empty());
c.splice(c.end(), d);
LIST_ASSERT(c.empty());
LIST_ASSERT(d.empty());
// splice full with empty
b.splice(b.end(), c);
LIST_ASSERT(c.empty());
LIST_ASSERT(*b.begin() == '1');
LIST_ASSERT(*++b.begin() == '2');
LIST_ASSERT(*++++b.begin() == '3');
LIST_ASSERT(++++++b.begin() == b.end());
// splice empty with full
c.splice(c.end(), b);
LIST_ASSERT(b.empty());
LIST_ASSERT(*c.begin() == '1');
LIST_ASSERT(*++c.begin() == '2');
LIST_ASSERT(*++++c.begin() == '3');
LIST_ASSERT(++++++c.begin() == c.end());
// splice full with full
c.splice(c.end(), a);
LIST_ASSERT(a.empty());
LIST_ASSERT(*c.begin() == '1');
LIST_ASSERT(*++c.begin() == '2');
LIST_ASSERT(*++++c.begin() == '3');
LIST_ASSERT(*++++++c.begin() == 'a');
LIST_ASSERT(*++++++++c.begin() == 'b');
LIST_ASSERT(*++++++++++c.begin() == 'c');
LIST_ASSERT(++++++++++++c.begin() == c.end());
c.pop_back();
LIST_ASSERT(!c.empty());
c.pop_back();
LIST_ASSERT(!c.empty());
c.pop_back();
LIST_ASSERT(!c.empty());
c.pop_back();
LIST_ASSERT(!c.empty());
c.pop_back();
LIST_ASSERT(!c.empty());
c.pop_back();
LIST_ASSERT(c.empty());
}
int main()
{
IntList temp;
temp.display();
cout << endl;
temp.push_front(5);
temp.display();
cout << endl;
temp.push_front(15);
temp.push_front(45);
temp.display();
cout << endl;
temp.pop_front();
temp.display();
cout << endl;
temp.push_back(32);
temp.display();
cout << endl;
IntList temp2;
temp2.push_back(32);
temp2.display();
cout << endl;
temp2.push_back(45);
temp2.display();
cout << endl;
temp.select_sort();
temp.display();
cout << endl;
IntList temp3;
temp3.select_sort();
temp3.display();
cout << endl;
temp.display();
cout << endl;
temp.insert_sorted(10);
temp.display();
cout << endl;
temp.insert_sorted(33);
temp.display();
cout << endl;
temp.insert_sorted(4);
temp.display();
cout << endl;
temp.insert_sorted(2);
temp.display();
cout << endl;
IntList temp4;
temp4.push_back(249);
temp4.push_back(346);
temp4.push_back(366);
temp4.push_back(374);
temp4.push_back(462);
temp4.push_back(484);
temp4.push_back(600);
temp4.push_back(686);
temp4.push_back(715);
temp4.push_back(799);
temp4.push_back(949);
temp4.display();
cout << endl;
temp4.insert_sorted(800);
temp4.display();
cout << endl;
IntList temp5;
temp5.push_back(249);
temp5.push_back(346);
temp5.push_back(715);
temp5.push_back(799);
temp5.push_back(949);
temp5.push_back(949);
temp5.push_back(366);
temp5.push_back(374);
temp5.push_back(462);
temp5.push_back(462);
temp5.push_back(484);
temp5.push_back(600);
temp5.push_back(249);
temp5.push_back(686);
temp5.display();
cout << endl;
temp5.select_sort();
temp5.display();
cout << endl;
temp5.remove_duplicates();
temp5.display();
cout << endl;
IntList temp6;
temp6.push_back(667);
temp6.push_back(314);
temp6.push_back(895);
temp6.push_back(63);
temp6.push_back(462);
temp6.display();
cout << endl;
temp6.remove_duplicates();
temp6.display();
cout << endl;
cout << "End" << endl;
}
int main()
{
IntList theList;
IntList theOtherList;
IntList theFinalList;
theList.display();
cout << endl;
theList.push_front(133);
theList.display();
cout << endl;
theList.push_front(250);
theList.display();
cout << endl;
theList.push_front(550);
theList.display();
cout << endl;
theList.pop_front();
theList.display();
cout << endl;
theList.push_back(13);
theList.display();
cout << endl;
theList.select_sort();
theList.display();
cout << endl;
theList.insert_sorted(10);
theList.display();
cout << endl;
theList.insert_sorted(225);
theList.display();
cout << endl;
theList.pop_front();
theList.display();
cout << endl;
theList.pop_front();
theList.display();
cout << endl;
theList.pop_front();
theList.display();
cout << endl;
theList.push_back(45);
theList.display();
cout << endl;
cout << "The other list shit:\n";
theOtherList.insert_sorted(225);
theOtherList.display();
cout << endl;
theOtherList.insert_sorted(12);
theOtherList.display();
cout << endl;
theOtherList.insert_sorted(13);
theOtherList.display();
cout << endl;
theOtherList.insert_sorted(13);
theOtherList.display();
cout << endl;
theOtherList.insert_sorted(12);
theOtherList.display();
cout << endl;
theOtherList.insert_sorted(5000);
theOtherList.display();
cout << endl;
theOtherList.remove_duplicates();
theOtherList.display();
cout << endl;
cout << "The other list shit:\n";
theFinalList.push_front(10);
theFinalList.display();
cout << endl;
theFinalList.push_front(10);
theFinalList.display();
cout << endl;
theFinalList.push_front(30);
theFinalList.display();
cout << endl;
theFinalList.push_front(5);
theFinalList.display();
cout << endl;
theFinalList.push_front(20);
theFinalList.display();
cout << endl;
theFinalList.push_front(10);
theFinalList.display();
cout << endl;
theFinalList.push_back(30);
theFinalList.display();
cout << endl;
theFinalList.remove_duplicates();
theFinalList.display();
cout << endl;
return 0;
}
int main()
{
IntList a;
IntList b;
string divider = string(68, '-');
cout << divider << endl;
// testing push_front function
a.push_front(1);
a.push_front(4);
a.push_front(412);
// tests display
cout << "IntList 1: testing push_front function" << endl;
cout << "(should display 412 4 1): ";
a.display(); cout << endl;
cout << "IntList 2: testing empty list" << endl;
cout << "(should display nothing): ";
b.display(); cout << endl;
cout << divider << endl;
// tests pop_front;
a.pop_front();
cout << "IntList 1: testing pop_front function" << endl;
cout << "(should display 4 1): ";
a.display(); cout << endl;
cout << "IntList 2: testing pop_front on empty" << endl;
cout << "(should do nothing): ";
b.pop_front();
b.display(); cout << endl;
b.push_front(4);
cout << "IntList 2: testing pop_front on 1 element" << endl;
cout << "(should see nothing): ";
b.pop_front();
b.display(); cout << endl;
cout << divider << endl;
a.push_back(3);
a.push_back(213);
a.push_back(61);
// testing select_sort
cout << "IntList 1: testing select_sort function" << endl;
cout << "(should display 1 3 4 61 213): ";
a.select_sort();
a.display(); cout << endl;
cout << "IntList 2: testing empty list" << endl;
b.select_sort();
b.display(); cout << endl;
cout << divider << endl;
// testing insert_sorted()
cout << "IntList 1: testing insert_sorted function" << endl;
cout << "(should display 1 2 3 4 61 213 400): ";
a.insert_sorted(2);
a.insert_sorted(400);
a.display(); cout << endl;
cout << "IntList 2: testing_sorted on empty list" << endl;
cout << "(should display 4): ";
b.insert_sorted(4);
b.display(); cout << endl;
cout << divider << endl;
return 0;
}