reading Xtandem files seems to work!

src/core/identificationgroup.cpp

@@ -54,11 +54,19 @@ ProteinMatch * IdentificationGroup::getProteinMatch(const QString accession) {
     if (accession.isEmpty()) {
         throw pappso::PappsoException(QObject::tr("Error protein match not found : accession is empty"));
     }
-    for (ProteinMatch * p_protein_match : _protein_match_list) {
-        if (p_protein_match->getProteinXtpSp().get()->getAccession() == accession) {
-            return p_protein_match;
+    auto it_cache = _cache_accession_protein_match.find(accession);
+    if (it_cache == _cache_accession_protein_match.end()) {
+        //accession not found in cache
+        for (ProteinMatch * p_protein_match : _protein_match_list) {
+            if (p_protein_match->getProteinXtpSp().get()->getAccession() == accession) {
+                _cache_accession_protein_match.insert(std::pair<QString, ProteinMatch *>(accession, p_protein_match));
+                return p_protein_match;
+            }
         }
     }
+    else {
+        return it_cache->second;
+    }
     return nullptr;
 }
 void IdentificationGroup::addProteinMatch(ProteinMatch * protein_match) {
@@ -66,20 +74,13 @@ void IdentificationGroup::addProteinMatch(ProteinMatch * protein_match) {
     if (accession.isEmpty()) {
         throw pappso::PappsoException(QObject::tr("Error adding protein match : accession is empty"));
     }
-    bool push = true;
-    for (ProteinMatch * p_protein_match : _protein_match_list) {
-        if (p_protein_match == protein_match) {
-            push = false;
-        }
-        else {
-            if(p_protein_match->getProteinXtpSp().get()->getAccession() == accession) {
-                throw pappso::PappsoException(QObject::tr("Error adding protein match : accession %1 already registered").arg(accession));
-            }
-        }
-    }
-    if (push) {
+    auto it_cache = _cache_already_added_protein_match.find(protein_match);
+    if (it_cache == _cache_already_added_protein_match.end()) {
+        //accession not found in cache
+        _cache_already_added_protein_match.insert(protein_match);
         _protein_match_list.push_back(protein_match);
     }
+
 }
 
 bool IdentificationGroup::contains (const MsRun * p_msrun) const {

src/core/identificationgroup.h

@@ -31,6 +31,7 @@
 #ifndef IDENTIFICATIONGROUP_H
 #define IDENTIFICATIONGROUP_H
 
+#include <set>
 
 class Project;
 
@@ -92,6 +93,9 @@ private :
     std::vector<ProteinMatch *> _protein_match_list;
 
     std::vector<MsRunSp> _ms_run_list;
+    
+    std::map<QString, ProteinMatch *> _cache_accession_protein_match;
+    std::set<ProteinMatch *> _cache_already_added_protein_match;
 };
 
 #endif // IDENTIFICATIONGROUP_H