added check for same number of double bonds and double bond positions

lifs-tools · May 20, 2020 · 675865b · 675865b
1 parent 8054025
commit 675865b
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Showing 3 changed files with 27 additions and 4 deletions.
diff --git a/cppgoslin/domain/FattyAcid.cpp b/cppgoslin/domain/FattyAcid.cpp
@@ -26,7 +26,6 @@ SOFTWARE.
 
 #include "FattyAcid.h"
 
-
 FattyAcid::FattyAcid(string _name, int _num_carbon, int _num_double_bonds, int _num_hydroxyl, LipidFaBondType _lipid_FA_bond_type, bool _lcb, int _position, map<int, string> *_double_bond_positions){
     name = _name;
     position = _position;
@@ -36,6 +35,9 @@ FattyAcid::FattyAcid(string _name, int _num_carbon, int _num_double_bonds, int _
     lipid_FA_bond_type = _lipid_FA_bond_type;
     lcb = _lcb;
     if (_double_bond_positions != NULL){
+        if (num_double_bonds != (int)_double_bond_positions->size()) {
+            throw ConstraintViolationException("Isomeric FattyAcid must receive double bond positions for all double bonds! Got " + std::to_string(num_double_bonds) + " double bonds and " + std::to_string(_double_bond_positions->size()) + " positions.");
+        }
         for (auto kv : *_double_bond_positions){
             double_bond_positions.insert({kv.first, kv.second});
         }
@@ -110,6 +112,10 @@ string FattyAcid::to_string(bool special_case){
     if (special_case && lipid_suffix.length() > 0) s << "O-";
     s << num_carbon << ":" << num_double_bonds;
 
+    if (double_bond_positions.size() > 0 && num_double_bonds != (int)double_bond_positions.size()) {
+        throw ConstraintViolationException("Isomeric FattyAcid must receive double bond positions for all double bonds! Got " + std::to_string(num_double_bonds) + " double bonds and " + std::to_string(double_bond_positions.size()) + " positions.");
+    }
+
     if (double_bond_positions.size()){
         stringstream db;
         db << "(";

diff --git a/cppgoslin/parser/GoslinParserEventHandler.cpp b/cppgoslin/parser/GoslinParserEventHandler.cpp
@@ -127,7 +127,7 @@ void GoslinParserEventHandler::set_isomeric_level(TreeNode* node){
 
 void GoslinParserEventHandler::add_db_position(TreeNode* node){
     if (current_fa != NULL){
-       current_fa->double_bond_positions.insert({db_position, db_cistrans});
+        current_fa->double_bond_positions.insert({db_position, db_cistrans});
     }
 }
 

diff --git a/cppgoslin/tests/ParserTest.cpp b/cppgoslin/tests/ParserTest.cpp
@@ -105,7 +105,6 @@ int main(int argc, char** argv){
 
 
 
-
     // check lipid maps and swiss lipids parser with illegal lipid name
     string failLipidSL = "TG(16::1_18:1_24:0)";
     try {
@@ -157,6 +156,7 @@ int main(int argc, char** argv){
     assert (lipid->get_sum_formula() == "C42H83NO4");
     assert (abs(lipid->get_mass() - 665.632209) < 1e-3);
     delete lipid;
+
 
 
     lipid = lipid_maps_parser.parse("Cer(d18:1(4E)/24:0(2OH))");
@@ -194,13 +194,15 @@ int main(int argc, char** argv){
     assert (lipid->get_lipid_string() == "PG 22:1(5Z)/12:0");
     delete lipid;
 
+
     lipid_name = "PG(22:1/12:0)";
     lipid = swiss_lipids_parser.parse(lipid_name);
     assert (lipid);
     assert (lipid->lipid->info.level == STRUCTURAL_SUBSPECIES);
     assert (lipid->get_lipid_string() == "PG 22:1/12:0");
     delete lipid;
 
+
     lipid_name = "PG(22:1_12:0)";
     lipid = swiss_lipids_parser.parse(lipid_name);
     assert (lipid);
@@ -231,7 +233,22 @@ int main(int argc, char** argv){
         lipid = lipid_parser.parse(lipid_name);
         assert (false);
     }
-    catch(LipidException &e){ }
+    catch(LipidException &e){
+    }
+
+
+
+    lipid_name = "PA 19:2(12E)/12:0";
+    lipid = lipid_parser.parse(lipid_name);
+    try {
+        string l = lipid->get_lipid_string();
+        assert (false);
+        assert(l == "foo");
+    }
+    catch(LipidException &e){
+        delete lipid;
+    }
+