variable modification API modified

src/pappsomspp/peptide/peptide.cpp

@@ -189,6 +189,24 @@ std::vector< unsigned int > Peptide::getAaPositionList(char aa) const {
 
 }
 
+std::vector< unsigned int > Peptide::getAaPositionList(std::list < char > list_aa) const {
+    std::vector< unsigned int > position_list;
+    unsigned int number = 0;
+    std::vector<Aa>::const_iterator it(_aa_vec.begin());
+    while (it != _aa_vec.end()) {
+      
+	bool found = (std::find(list_aa.begin(), list_aa.end(), it->getLetter()) != list_aa.end());
+        if (found) {
+            position_list.push_back(number);
+	}
+        number++;
+        it++;
+    }
+    //qDebug() << "Aa::getMass() end " << mass;
+    return position_list;
+
+}
+
 AaModificationP Peptide::getInternalNterModification() const {
     std::vector<Aa>::const_iterator it(_aa_vec.begin());
     if (it != _aa_vec.end()) {

src/pappsomspp/peptide/peptide.h

@@ -109,6 +109,7 @@ public:
     };
     unsigned int getNumberOfModification(AaModificationP mod) const;
     std::vector< unsigned int > getAaPositionList(char _aa) const;
+    std::vector< unsigned int > getAaPositionList(std::list < char > list_aa) const;
 
     /* \brief print modification except internal modifications */
     const QString toString() const;

src/pappsomspp/protein/peptidefixedmodificationbuilder.h

@@ -40,6 +40,8 @@ public:
     void setSink (PeptideModificatorInterface * sink) override {
         _sink = sink;
     };
+    void setNter(bool arg1) {_nter_mod=arg1;};
+    void setCter(bool arg1) {_cter_mod=arg1;};
 private :
     PeptideModificatorInterface * _sink=nullptr;
     

src/pappsomspp/protein/peptidevariablemodificationbuilder.cpp

@@ -63,8 +63,8 @@ bool next_combination(const Iterator first, Iterator k, const Iterator last)
     return false;
 }
 
-PeptideVariableModificationBuilder::PeptideVariableModificationBuilder( char aa, AaModificationP mod)
-    :  _aa(aa), _mod(mod)
+PeptideVariableModificationBuilder::PeptideVariableModificationBuilder(AaModificationP mod)
+    :  _mod(mod)
 {
 
 }
@@ -74,17 +74,24 @@ PeptideVariableModificationBuilder::~PeptideVariableModificationBuilder()
 
 }
 
+void PeptideVariableModificationBuilder::addAa(char aa) {
+
+    _aa_modification_list.push_back(aa);
+}
+
 void PeptideVariableModificationBuilder::setPeptideSp(ProteinSp & protein_sp, PeptideSp & peptide_sp_original, unsigned int start) {
-    std::vector< unsigned int > position_list = peptide_sp_original.get()->getAaPositionList(_aa);
+    std::vector< unsigned int > position_list = peptide_sp_original.get()->getAaPositionList(_aa_modification_list);
     //std::string s = "12345";
     //no AA modification :
+    if (_min_number_mod == 0) {
         _sink->setPeptideSp(protein_sp, peptide_sp_original, start);
+    }
 
     unsigned int nb_pos = position_list.size();
     if (nb_pos > 0) {
         //loop to find 1 to n-1 AA modification combinations
         unsigned int comb_size = 1;
-        while (comb_size < nb_pos) {
+        while ((comb_size < nb_pos) && (comb_size <= _max_number_mod)) {
             do
             {
                 // std::cout << std::string(being,begin + comb_size) << std::endl;
@@ -98,6 +105,8 @@ void PeptideVariableModificationBuilder::setPeptideSp(ProteinSp & protein_sp, Pe
             while(next_combination(position_list.begin(),position_list.begin() + comb_size,position_list.end()));
             comb_size++;
         }
+
+        if (nb_pos <= _max_number_mod) {
             //the last combination : all aa are modified :
             Peptide new_peptide(*(peptide_sp_original.get()));
             for (unsigned int i=0; i < nb_pos; i++) {
@@ -106,6 +115,7 @@ void PeptideVariableModificationBuilder::setPeptideSp(ProteinSp & protein_sp, Pe
             PeptideSp new_peptide_sp = new_peptide.makePeptideSp();
             _sink->setPeptideSp(protein_sp, new_peptide_sp, start);
         }
+    }
 
 }
 

src/pappsomspp/protein/peptidevariablemodificationbuilder.h

@@ -35,19 +35,25 @@ namespace pappso {
 class PeptideVariableModificationBuilder: public PeptideModificatorInterface, PeptideSpSinkInterface
 {
 public:
-    PeptideVariableModificationBuilder(char aa, AaModificationP mod);
+    PeptideVariableModificationBuilder(AaModificationP mod);
     ~PeptideVariableModificationBuilder();
     void setPeptideSp(ProteinSp & protein_sp, PeptideSp & peptide_sp_original, unsigned int start) override;
 
+    void addAa(char aa);
+    
+    void setMaxNumberMod(unsigned int max_num) {_max_number_mod = max_num;};
+    void setMinNumberMod(unsigned int min_num) {_min_number_mod = min_num;};
+
     void setSink (PeptideModificatorInterface * sink) override {
         _sink = sink;
     };
 private :
     PeptideModificatorInterface * _sink=nullptr;
 
-    char _aa;
+    std::list < char > _aa_modification_list;
     AaModificationP _mod;
-    unsigned int _level=0;
+    unsigned int _max_number_mod=30000;
+    unsigned int _min_number_mod=0;
 };
 }
 

test/test_protein.cpp

@@ -133,7 +133,8 @@ int main(int argc, char *argv[]) {
     //acc = "MOD:00719";
     AaModificationP met_oxy = AaModification::getInstance("MOD:00719");
 
-    PeptideVariableModificationBuilder var_mod_builder('M', met_oxy);
+    PeptideVariableModificationBuilder var_mod_builder( met_oxy);
+    var_mod_builder.addAa('M');
     var_mod_builder.setSink(&modification_sink);
 
     //  QString accMo = "MOD:00719";
@@ -166,5 +167,9 @@ int main(int argc, char *argv[]) {
     qDebug() << "kinase.eat(protein_sp,semi_tryptic)";
     kinase.eat(protein_sp,semi_tryptic);
 
+
+    qDebug() << endl << "..:: Test enzyme motif ::.." << endl;
+    Enzyme motif_digest("(MAMEE[KR])([^P])");
+    motif_digest.eat(fake,digestion);
     return 0;
 }