violent bug reported by Céline Henry on Fasta file export fixed

src/output/exportfastafile.cpp

@@ -26,6 +26,7 @@
  ******************************************************************************/
 
 #include "exportfastafile.h"
+#include <pappsomspp/pappsoexception.h>
 
 ExportFastaFile::ExportFastaFile(QString filename, ExportFastaType type)
 {
@@ -33,10 +34,21 @@ ExportFastaFile::ExportFastaFile(QString filename, ExportFastaType type)
   m_exportType       = type;
 }
 
+ExportFastaFile::~ExportFastaFile()
+{
+  close();
+}
+
+
 void
 ExportFastaFile::write(ProjectSp project_sp)
 {
-
+  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+  if(mp_outputFastaFile == nullptr)
+    {
+      throw pappso::PappsoException(
+        QObject::tr("error : mp_outputFastaFile is null\n"));
+    }
   mp_outputFastaFile->open(QIODevice::WriteOnly);
   QTextStream *p_outputStream = new QTextStream(mp_outputFastaFile);
 
@@ -48,17 +60,23 @@ ExportFastaFile::write(ProjectSp project_sp)
     {
       writeIdentificationGroup(fasta_output, identification);
     }
-
+  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
   mp_outputFastaFile->flush();
-  delete mp_outputFastaFile;
+  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
   mp_outputFastaFile->close();
+  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+  close();
+  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
 }
 
 void
 ExportFastaFile::close()
 {
-  delete mp_outputFastaFile;
-  mp_outputFastaFile = nullptr;
+  if(mp_outputFastaFile != nullptr)
+    {
+      delete mp_outputFastaFile;
+      mp_outputFastaFile = nullptr;
+    }
 }
 
 
@@ -66,7 +84,7 @@ void
 ExportFastaFile::writeIdentificationGroup(
   pappso::FastaOutputStream &fasta_output, IdentificationGroup *p_ident)
 {
-
+  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
   for(const std::pair<unsigned int, GroupingGroupSp> &group_pair :
       p_ident->getGroupStore().getGroupMap())
     {
@@ -79,7 +97,8 @@ ExportFastaFile::writeIdentificationGroup(
       std::vector<const ProteinMatch *> protein_match_list =
         group_pair.second.get()->getProteinMatchList();
 
-      std::sort(protein_match_list.begin(), protein_match_list.end(),
+      std::sort(protein_match_list.begin(),
+                protein_match_list.end(),
                 [](const ProteinMatch *a, const ProteinMatch *b) {
                   return a->getGrpProteinSp().get()->getGroupingId() <
                          b->getGrpProteinSp().get()->getGroupingId();
@@ -115,4 +134,5 @@ ExportFastaFile::writeIdentificationGroup(
           fasta_output.writeProtein(protein);
         }
     }
+  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
 }

src/output/exportfastafile.h

@@ -44,6 +44,7 @@ class ExportFastaFile
 
   public:
   ExportFastaFile(QString filename, ExportFastaType type);
+  virtual ~ExportFastaFile();
   void write(ProjectSp project_sp);
   void close();
 };