minimum peptide number bug fixed

src/CMakeLists.txt

@@ -29,8 +29,8 @@ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5
 
 #sudo apt-get install libpappsomspp-dev
 #FIND_PACKAGE( Pappsomspp REQUIRED )
-# SET (PAPPSOMSPP_DIR  "/home/olivier/eclipse/git/pappsomspp")
- SET (PAPPSOMSPP_DIR  "/home/langella/developpement/git/pappsomspp")
+ SET (PAPPSOMSPP_DIR  "/home/olivier/eclipse/git/pappsomspp")
+# SET (PAPPSOMSPP_DIR  "/home/langella/developpement/git/pappsomspp")
  SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
  SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt4.so")
 

src/core/proteinmatch.cpp

@@ -42,48 +42,42 @@ ProteinMatch::~ProteinMatch()
 }
 
 void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
+     qDebug() <<"ProteinMatch::updateAutomaticFilters begin " ;
     _proxy_valid = false;
-    unsigned int _number_of_valid_peptides =0;
-    std::map<const pappso::MsRunId*, unsigned int> _count_per_msrun;
+    unsigned int number_of_valid_peptides =0;
     bool cross_sample = automatic_filter_parameters.getFilterCrossSamplePeptideNumber();
-    std::set<QString> sequence_li_list;
 
-    for (auto & p_peptide_match : _peptide_match_list) {
-        p_peptide_match->updateAutomaticFilters(automatic_filter_parameters);
-        //count valid and checked peptides :
-        if (p_peptide_match->isValidAndChecked()) {
-            QString sequence_li(p_peptide_match->getPeptideXtpSp().get()->toAbsoluteString());
-            std::set<QString>::iterator it_sequence = sequence_li_list.find(sequence_li);
-            if (it_sequence ==  sequence_li_list.end()) {
-                //if this sequence was not already counted
-                sequence_li_list.insert(sequence_li);
-                if (cross_sample) {
-                    _number_of_valid_peptides++;
-                }
-                else {
-                    std::pair<std::map<const pappso::MsRunId*, unsigned int>::iterator,bool> ret = _count_per_msrun.insert(std::pair<const pappso::MsRunId*, unsigned int>(p_peptide_match->getMsRunIdSp().get(),0));
-                    ret.first->second +=1;
-                }
-            }
+    if (cross_sample) {
+        for (auto & p_peptide_match : _peptide_match_list) {
+            p_peptide_match->updateAutomaticFilters(automatic_filter_parameters);
         }
+        number_of_valid_peptides= countValidAndCheckedPeptide(nullptr);
     }
-
-
-    for (auto && pair_msrun_count : _count_per_msrun) {
-        if (pair_msrun_count.second > _number_of_valid_peptides) {
-            _number_of_valid_peptides  = pair_msrun_count.second;
+    else {
+        std::set<const pappso::MsRunId *> msrun_set;
+        for (auto & p_peptide_match : _peptide_match_list) {
+            p_peptide_match->updateAutomaticFilters(automatic_filter_parameters);
+            if (p_peptide_match->isValidAndChecked()) {
+                msrun_set.insert(p_peptide_match->getMsRunIdSp().get());
+            }
+        }
+        for (const pappso::MsRunId * p_msrun : msrun_set) {
+            unsigned int count = countValidAndCheckedPeptide(p_msrun);
+            if (count > number_of_valid_peptides) {
+                number_of_valid_peptides = count;
+            }
         }
     }
-    //update protein evalue ?
 
 
-    if (_number_of_valid_peptides < automatic_filter_parameters.getFilterMinimumPeptidePerMatch()) {
+    if (number_of_valid_peptides < automatic_filter_parameters.getFilterMinimumPeptidePerMatch()) {
     }
     else {
         if (_evalue <= automatic_filter_parameters.getFilterProteinEvalue()) {
             _proxy_valid = true;
         }
     }
+    qDebug() <<"ProteinMatch::updateAutomaticFilters end " << number_of_valid_peptides ;
 }
 
 const ProteinXtpSp & ProteinMatch::getProteinXtpSp() const {
@@ -174,6 +168,27 @@ size_t ProteinMatch::countUniqueSequence()const {
     return sequence_list.size();
 }
 
+unsigned int ProteinMatch::countValidAndCheckedPeptide(const pappso::MsRunId * p_msrun_id) const {
+    std::set<QString> sequence_list;
+    for (auto & p_peptide_match : _peptide_match_list) {
+        if (p_peptide_match->isValidAndChecked()) {
+            if(p_msrun_id != nullptr) {
+                //within sample
+                if (p_peptide_match->getMsRunIdSp().get() == p_msrun_id) {
+                    sequence_list.insert(p_peptide_match->getPeptideXtpSp().get()->getSequenceLi());
+                }
+            }
+            else {
+                //overall samples
+                sequence_list.insert(p_peptide_match->getPeptideXtpSp().get()->getSequenceLi());
+            }
+        }
+    }
+    qDebug() <<"ProteinMatch::countValidAndCheckedPeptide end " << sequence_list.size();
+    return sequence_list.size();
+}
+
+
 unsigned int ProteinMatch::countValidAndCheckedPeptideMassCharge(const pappso::MsRunIdSp & sp_msrun_id) const {
     std::set<QString> sequence_list;
     for (auto & p_peptide_match : _peptide_match_list) {

src/core/proteinmatch.h

@@ -104,6 +104,7 @@ protected :
     void setGroupInstance(GroupStore & group_store);
 
 private :
+    unsigned int countValidAndCheckedPeptide(const pappso::MsRunId * p_msrun_id) const;
     unsigned int countValidAndCheckedPeptideMassCharge(const pappso::MsRunIdSp & sp_msrun_id) const;
 
 private: