Squashed 'src/cppgoslin/' changes from b14796dc..58837eae

58837eae Merge pull request #16 from lifs-tools/alpine-linux
f5cb5f7f Updated imports
be05b436 Added explicit imports for cstdint and vector
6449f0d8 Merge commit '3892beb34cf318d5e878b565b5f4e802c87858c5'
cb6fcc8e adding more mediator support
3892beb3 adding more trivial mediator names
9329952d Merge commit '48ebc1d373919475f619a0f93852db4efd1e950f'
48ebc1d3 updating grammars
e4cdf628 added lyso galsph glcsph
9ad782e2 Merge commit '37fa28110479dc9e74f8589cc381bebd9e27d01b'
37fa2811 fixed typo in trivial list
8b841231 Merge commit '8c58c13573c8993b48d9f59857b33bbec7cabe88'
8c58c135 adding more HDoHE support
fab15338 more prostaglandins support
3af50808 Merge commit 'cdf1bbf5c3f9495e1bd6a6b7cdf6e4a8246b70f9'
ce56b4b3 adding even more support for oxylipins
cdf1bbf5 adding more support for oxylipins
8e2231d4 added triH
1a161caa Merge commit '93058c0c53af43484158666f7667e412533900dc'
93058c0c updated tri hydro information
fd0bd7f6 bug fixing on recursive function
a54eb4ed added ARA
c66a6549 Merge commit '3759dba1db3f35ecbd676122d2dd6a0cb5142f95'
615bd4b0 updated prostaglandins
3759dba1 updated trivial list
e8a8ce3f Merge commit 'b9cd9277ccb82b64f1bb43b77db6f39468e7f606'
b9cd9277 added more support for oxylipins
649656c6 Merge commit '9946c54034cd8ffea235abfc28b79822690d5795'
9946c540 adding more oxolipins
bd1d4ca4 updated unit tests
09932b8e Merge commit '9437c99f889d4bf246ca7d1e20857ccbb36a3603'
9437c99f updated trivial mediator table
61bdbb5e updated trivial mediators
abcbd041 Merge commit 'd2ba69537010f6720d3ec2426e96c8ed71d69f67'
d2ba6953 added more trivial mediator dbs
f9d048bd added trivial mediator double bond information
ca7df904 Merge commit 'a3af90548efdd6383114521c9e2b7a3cebf68f01'
a3af9054 adding trivial mediator db information

git-subtree-dir: src/cppgoslin
git-subtree-split: 58837eaeeb4e2283f7b7409a647d02a81fa67889

src/cppgoslin/cppgoslin/parser/LipidMapsParserEventHandler.h

@@ -114,6 +114,8 @@ class LipidMapsParserEventHandler : public LipidBaseParserEventHandler {
     void add_carbon_pre_len(TreeNode *node);
     void set_hydro_pre_num(TreeNode *node);
     void new_sphinga_pure(TreeNode *node);
+    void c_type(TreeNode *node);
+    void new_sph(TreeNode *node);
 
 };
 

src/cppgoslin/cppgoslin/parser/Parser.h

@@ -33,7 +33,7 @@ SOFTWARE.
 #include "cppgoslin/parser/ParserClasses.h"
 #include "cppgoslin/domain/Element.h"
 #include "cppgoslin/parser/KnownGrammars.h"
-#include <string>
+#include <cstdint>
 #include <set>
 #include <map>
 #include <vector>

src/cppgoslin/cppgoslin/parser/ParserClasses.h

@@ -28,6 +28,7 @@ SOFTWARE.
 
 
 #include "cppgoslin/domain/StringFunctions.h"
+#include <cstdint>
 #include <string>
 #include <set>
 #include <map>

src/cppgoslin/cppgoslin/parser/Parser_impl.h

@@ -21,6 +21,9 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
 */
+#include <cstdint>
+#include <string>
+#include <vector>
 
 template <class T>
 const uint32_t Parser<T>::SHIFT = 32;

src/cppgoslin/data/goslin/Goslin.g4

@@ -182,7 +182,7 @@ mediator_functions : mediator_mono_functions | mediator_di_functions | mediator_
 mediator_mono_functions: 'H' | 'Oxo' | 'oxo' | 'OXO' | 'keto' | 'Hp' | 'HP' | 'NO2' | 'K' | 'k' | 'hydroxy' | 'd' | 'deoxy' | 'beta' | 'iso';
 mediator_di_functions: 'E' | 'Ep' | 'EP' | 'DH' | 'DiH' | 'diH' | 'dihydro' | 'dh';
 mediator_tri_functions : 'TriH' | 'triH' | 'trihydroxy';
-mediator_full_function : mediator_position_group mediator_func_group_separator mediator_mono_functions | mediator_di_pos mediator_func_group_separator mediator_di_functions | mediator_tri_pos mediator_func_group_separator mediator_tri_functions | mediator_position_group mediator_mono_functions;
+mediator_full_function : mediator_position_group mediator_func_group_separator mediator_mono_functions | mediator_di_pos mediator_func_group_separator mediator_di_functions | mediator_tri_pos mediator_func_group_separator mediator_tri_functions | mediator_position_group mediator_mono_functions | mediator_position_group mediator_mono_functions | mediator_di_pos mediator_di_functions | mediator_tri_pos mediator_tri_functions | mediator_position_group mediator_mono_functions;
 mediator_db_function : mediator_double_bond_positions mediator_func_group_separator mediator_mono_functions;
 mediator_double_bond_positions_full : '(' mediator_double_bond_positions ')';
 mediator_double_bond_positions : mediator_double_bond_position | mediator_double_bond_positions ',' mediator_double_bond_position;

src/cppgoslin/data/goslin/LipidMaps.g4

@@ -122,8 +122,8 @@ hg_threepl: 'SLBPA' | 'PS-NAc' | 'NAPE';
 
 /* sphingolipid rules */
 sl: lsl | dsl;
-lsl: hg_lslc round_open_bracket lcb round_close_bracket | hg_lslc lcb | sphinga;
-dsl: hg_dslc dsl_species | hg_dslc dsl_subspecies;
+lsl: hg_lslc round_open_bracket lcb round_close_bracket | hg_lslc lcb | sphinga | hg_lsl_pure;
+dsl: hg_dslc dsl_species | hg_dslc dsl_subspecies | hg_dslc c_type;
 dsl_species: round_open_bracket lcb round_close_bracket | lcb;
 dsl_subspecies: round_open_bracket lcb_fa_sorted round_close_bracket | lcb_fa_sorted;
 
@@ -140,6 +140,7 @@ sphinga_C_lcb : 'C' sphinga_lcb_len;
 sphinga_lcb_len : number;
 sphinga_bracket_lcb : round_open_bracket lcb round_close_bracket | lcb;
 
+c_type : 'C' carbon | 'C' carbon carbon_db_separator db;
 
 
 hg_dslc: hg_dsl_global | hg_dsl_global headgroup_separator;
@@ -167,9 +168,8 @@ greek : 'alpha' | 'beta' | 'α' | 'β';
 
 
 hg_lslc: hg_lsl | hg_lsl headgroup_separator;
-hg_lsl: 'SPH' | 'Sph' | 'S1P' | 'HexSph' | 'SPC' | 'SPH-P' | 'LysoSM' | 'SIP';
-
-
+hg_lsl_pure : hg_lsl;
+hg_lsl: 'SPH' | 'Sph' | 'S1P' | 'HexSph' | 'SPC' | 'SPH-P' | 'LysoSM' | 'SIP' | 'GlcSph' | 'GalSph';
 
 /* polyketides */
 pk : pk_hg pk_fa;

src/cppgoslin/data/goslin/lipid-list.csv

@@ -181,6 +181,8 @@ LCL,GP,Glycerophosphoglycerophosphoglycerols [GP12],4,3,Lyso;Cardio,C9H18O13P2,M
 LDMPE,GP,Lysodimethylphosphatidylethanolamine,2,1,Lyso,,,,,,,,,
 Lex-GM1,SP,Globoside,2,2,,C57H93N3O42,,,,,,,,
 LHexCer,SP,Hexosylsphingosine,1,1,,C6H12O5,HexSph,,,,,,,
+LGalCer,SP,Hexosylsphingosine,1,1,,C6H12O5,GalSph,,,,,,,
+LGlcCer,SP,Hexosylsphingosine,1,1,,C6H12O5,GlcSph,,,,,,,
 LHex2Cer,SP,Neutral glycosphingolipids [SP05],1,1,,C12H22O10,LDHCer,LDHCER,,,,,,
 LHex3Cer,SP,Neutral glycosphingolipids [SP05],1,1,,C18H32O15,LTHCer,LTHCER,,,,,,
 Linoleic acid,FA,Unsaturated fatty acids [FA0103],0,0,,C18H32O2,,,,,,,,

src/cppgoslin/data/goslin/trivial_mediators.csv

@@ -171,3 +171,8 @@
 16-HDoHE	4,7,10,13,17,19
 17-HDoHE	4,7,10,13,15,19
 20-HDoHE	4,7,10,13,16,18
+7(8)-EpDPE	4,10,13,16,19
+10(11)-EpDPE	4,7,13,16,19
+13(14)-EpDPE	4,7,10,16,19
+16(17)-EpDPE	4,7,10,13,19
+19(20)-EpDPE	4,7,10,13,16

src/cppgoslin/src/parser/GoslinParserEventHandler.cpp

@@ -28,7 +28,7 @@ SOFTWARE.
 #define reg(x, y) BaseParserEventHandler<LipidAdduct*>::registered_events->insert({x, bind(&GoslinParserEventHandler::y, this, placeholders::_1)})
 
 
-const map<string, int> GoslinParserEventHandler::mediator_FA{{"H", 17}, {"O", 18}, {"E", 20}, {"Do", 22}};
+const map<string, int> GoslinParserEventHandler::mediator_FA{{"H", 17}, {"O", 18}, {"E", 20}, {"Do", 22}, {"D", 22}};
 const map<string, int> GoslinParserEventHandler::mediator_DB{{"M", 1}, {"D", 2}, {"Tr", 3}, {"T", 4}, {"P", 5}, {"H", 6}};
 
 

src/cppgoslin/src/parser/LipidMapsParserEventHandler.cpp

@@ -68,6 +68,8 @@ LipidMapsParserEventHandler::LipidMapsParserEventHandler() : LipidBaseParserEven
     reg("lcb_post_event", clean_lcb);
     reg("fa_pre_event", new_fa);
     reg("fa_post_event", append_fa);
+    reg("c_type_pre_event", c_type);
+    reg("c_type_post_event", append_fa);
     reg("glyco_struct_pre_event", add_glyco);
     reg("db_single_position_pre_event", set_isomeric_level);
     reg("db_single_position_post_event", add_db_position);
@@ -95,6 +97,7 @@ LipidMapsParserEventHandler::LipidMapsParserEventHandler() : LipidBaseParserEven
     reg("isotope_element_pre_event", set_heavy_element);
     reg("isotope_number_pre_event", set_heavy_number);
     reg("sphinga_pre_event", new_sphinga);
+    reg("hg_lsl_pure_pre_event", new_sph);
     reg("sphinga_phospho_pre_event", add_phospho);
     reg("sphinga_suffix_pre_event", sphinga_db_set);
     reg("sphinga_lcb_len_pre_event", add_carbon_pre_len);
@@ -166,41 +169,70 @@ void LipidMapsParserEventHandler::add_additional_modifier(TreeNode* node){
 
 
 void LipidMapsParserEventHandler::add_carbon_pre_len(TreeNode* node){
-        lcb_carbon_pre_set = node->get_int();
+    lcb_carbon_pre_set = node->get_int();
 }
 
 void LipidMapsParserEventHandler::sphinga_db_set(TreeNode* node){
-        sphinga_suffix = node->get_text();
-        
-        if (sphinga_suffix == "anine") lcb_db_pre_set = 0;
-        else if (sphinga_suffix == "osine") lcb_db_pre_set = 1;
-        else if (sphinga_suffix == "adienine") lcb_db_pre_set = 2;
+    sphinga_suffix = node->get_text();
+
+    if (sphinga_suffix == "anine") lcb_db_pre_set = 0;
+    else if (sphinga_suffix == "osine") lcb_db_pre_set = 1;
+    else if (sphinga_suffix == "adienine") lcb_db_pre_set = 2;
 }
-        
-        
-        
-        
+
+
+
+
 void LipidMapsParserEventHandler::new_sphinga(TreeNode* node){
-        head_group = "SPB";
+    head_group = "SPB";
 }
-
-
-
-void LipidMapsParserEventHandler::new_sphinga_pure(TreeNode* node){
+
+
+void LipidMapsParserEventHandler::c_type(TreeNode* node){
+    if (head_group == "Cer"){
+        new_sphinga_pure(node);
+    }
+    else {
         sphinga_pure = true;
         lcb_hydro_pre_set.push_back(KnownFunctionalGroups::get_functional_group("OH"));
+        lcb_hydro_pre_set[0]->position = 3;
+        new_lcb(node);
+    }
+    clean_lcb(node);
+    new_fa(node);
+}
+
+
+void LipidMapsParserEventHandler::new_sph(TreeNode* node){
+    if (to_lower(head_group) == "sph"){
+        new_sphinga_pure(node);
+    }
+    else {
+        sphinga_pure = true;
         lcb_hydro_pre_set.push_back(KnownFunctionalGroups::get_functional_group("OH"));
-        lcb_hydro_pre_set[0]->position = 1;
-        lcb_hydro_pre_set[1]->position = 3;
+        lcb_hydro_pre_set[0]->position = 3;
         new_lcb(node);
+    }
+    clean_lcb(node);
 }
-
-
-
+
+
+
+void LipidMapsParserEventHandler::new_sphinga_pure(TreeNode* node){
+    sphinga_pure = true;
+    lcb_hydro_pre_set.push_back(KnownFunctionalGroups::get_functional_group("OH"));
+    lcb_hydro_pre_set.push_back(KnownFunctionalGroups::get_functional_group("OH"));
+    lcb_hydro_pre_set[0]->position = 1;
+    lcb_hydro_pre_set[1]->position = 3;
+    new_lcb(node);
+}
+
+
+
 void LipidMapsParserEventHandler::set_hydro_pre_num(TreeNode* node){
-        lcb_hydro_pre_set.push_back(KnownFunctionalGroups::get_functional_group("OH"));
-        lcb_hydro_pre_set.back()->position = 4;
-        sphinga_prefix = node->get_text();
+    lcb_hydro_pre_set.push_back(KnownFunctionalGroups::get_functional_group("OH"));
+    lcb_hydro_pre_set.back()->position = 4;
+    sphinga_prefix = node->get_text();
 }