Bugfix for sort_by_probs issue from #65

Author: Michal Startek

src/IsoSpec++/cwrapper.cpp

@@ -295,6 +295,12 @@ void* setupFixedEnvelope(double* masses, double* probs, size_t size, bool mass_s
     return reinterpret_cast<void*>(ret);
 }
 
+void* setupFixedEnvelopeWithConfs(double* masses, double* probs, int* confs, size_t size, int allDim, bool mass_sorted, bool prob_sorted, double total_prob)
+{
+    FixedEnvelope* ret = new FixedEnvelope(masses, probs, confs, size, allDim, mass_sorted, prob_sorted, total_prob);
+    return reinterpret_cast<void*>(ret);
+}
+
 void deleteFixedEnvelope(void* t, bool release_everything)
 {
     FixedEnvelope* tt = reinterpret_cast<FixedEnvelope*>(t);

src/IsoSpec++/cwrapper.h

@@ -138,6 +138,7 @@ ISOSPEC_C_API void array_mul(double* array, size_t N, double what);
 ISOSPEC_C_API void array_fma(double* array, size_t N, double mul, double add);
 
 ISOSPEC_C_API void* setupFixedEnvelope(double* masses, double* probs, size_t size, bool mass_sorted, bool prob_sorted, double total_prob);
+ISOSPEC_C_API void* setupFixedEnvelopeWithConfs(double* masses, double* probs, int* confs, size_t size, int allDim, bool mass_sorted, bool prob_sorted, double total_prob);
 ISOSPEC_C_API void* copyFixedEnvelope(void* other);
 ISOSPEC_C_API void deleteFixedEnvelope(void* tabulator, bool releaseEverything);
 

src/IsoSpec++/fixedEnvelopes.cpp

@@ -56,6 +56,19 @@ _probs(in_probs),
 _confs(nullptr),
 _confs_no(in_confs_no),
 allDim(0),
+allDimSizeofInt(0),
+sorted_by_mass(masses_sorted),
+sorted_by_prob(probs_sorted),
+total_prob(_total_prob)
+{}
+
+FixedEnvelope::FixedEnvelope(double* in_masses, double* in_probs, int* in_confs, size_t in_confs_no, int _allDim, bool masses_sorted, bool probs_sorted, double _total_prob) :
+_masses(in_masses),
+_probs(in_probs),
+_confs(in_confs),
+_confs_no(in_confs_no),
+allDim(_allDim),
+allDimSizeofInt(_allDim * sizeof(int)),
 sorted_by_mass(masses_sorted),
 sorted_by_prob(probs_sorted),
 total_prob(_total_prob)

src/IsoSpec++/fixedEnvelopes.h

@@ -71,6 +71,7 @@ class ISOSPEC_EXPORT_SYMBOL FixedEnvelope {
     FixedEnvelope(FixedEnvelope&& other);
 
     FixedEnvelope(double* masses, double* probs, size_t confs_no, bool masses_sorted = false, bool probs_sorted = false, double _total_prob = NAN);
+    FixedEnvelope(double* masses, double* probs, int* confs, size_t confs_no, int _allDim, bool masses_sorted = false, bool probs_sorted = false, double _total_prob = NAN);
 
     virtual ~FixedEnvelope()
     {

src/IsoSpecPy/IsoSpecPy.py

@@ -376,7 +376,10 @@ def wrap(typename, what, attrname, mult = 1):
             raise RuntimeError("Invalid arguments for IsoDistribution constructor")
 
     def _get_cobject(self):
-        return isoFFI.clib.setupFixedEnvelope(self.masses, self.probs, len(self.masses), self.mass_sorted, self.prob_sorted, self._total_prob)
+        if hasattr(self, 'raw_confs') and self.raw_confs is not None:
+            return isoFFI.clib.setupFixedEnvelopeWithConfs(self.masses, self.probs, self.raw_confs, len(self.masses), self.sum_isotope_numbers, self.mass_sorted, self.prob_sorted, self._total_prob)
+        else:
+            return isoFFI.clib.setupFixedEnvelope(self.masses, self.probs, len(self.masses), self.mass_sorted, self.prob_sorted, self._total_prob)
 
     def copy(self):
         x = self._get_cobject()

src/IsoSpecPy/isoFFI.py

@@ -110,6 +110,7 @@ def __init__(self):
                             double bin_middle);
 
         void* setupFixedEnvelope(double* masses, double* probs, size_t size, bool mass_sorted, bool prob_sorted, double total_prob);
+        void* setupFixedEnvelopeWithConfs(double* masses, double* probs, int* confs, size_t size, int allDim, bool mass_sorted, bool prob_sorted, double total_prob);
         void* copyFixedEnvelope(void* other);
         void deleteFixedEnvelope(void* tabulator, bool releaseEverything);