fasta files can be writed by groups or subgroups

src/output/exportfastafile.cpp

@@ -26,19 +26,19 @@
  ******************************************************************************/
 
 #include "exportfastafile.h"
-#include <pappsomspp/fasta/fastaoutputstream.h>
 
 ExportFastaFile::ExportFastaFile(QString filename, ExportFastaType type)
 {
-  p_outputFastaFile = new QFile(filename);
+  mp_outputFastaFile = new QFile(filename);
+  m_exportType       = type;
 }
 
 void
 ExportFastaFile::write(ProjectSp project_sp)
 {
 
-  p_outputFastaFile->open(QIODevice::WriteOnly);
-  QTextStream *p_outputStream = new QTextStream(p_outputFastaFile);
+  mp_outputFastaFile->open(QIODevice::WriteOnly);
+  QTextStream *p_outputStream = new QTextStream(mp_outputFastaFile);
 
 
   pappso::FastaOutputStream fasta_output(*p_outputStream);
@@ -46,29 +46,74 @@ ExportFastaFile::write(ProjectSp project_sp)
   for(IdentificationGroup *identification :
       project_sp.get()->getIdentificationGroupList())
     {
-      for(ProteinMatch *protein_match : identification->getProteinMatchList())
-        {
-          if(protein_match->getValidationState() >= ValidationState::grouped)
-            {
-              pappso::Protein protein(
-                QString("%1 %2")
-                  .arg(protein_match->getProteinXtpSp().get()->getAccession())
-                  .arg(
-                    protein_match->getProteinXtpSp().get()->getDescription()),
-                protein_match->getProteinXtpSp().get()->getSequence());
-              fasta_output.writeProtein(protein);
-            }
-        }
+      writeIdentificationGroup(fasta_output, identification);
     }
 
-  p_outputStream->flush();
-  delete p_outputStream;
-  p_outputFastaFile->close();
+  mp_outputFastaFile->flush();
+  delete mp_outputFastaFile;
+  mp_outputFastaFile->close();
 }
 
 void
 ExportFastaFile::close()
 {
-  delete p_outputFastaFile;
-  p_outputFastaFile = nullptr;
+  delete mp_outputFastaFile;
+  mp_outputFastaFile = nullptr;
+}
+
+
+void
+ExportFastaFile::writeIdentificationGroup(
+  pappso::FastaOutputStream &fasta_output, IdentificationGroup *p_ident)
+{
+
+  for(const std::pair<unsigned int, GroupingGroupSp> &group_pair :
+      p_ident->getGroupStore().getGroupMap())
+    {
+      unsigned int protein_rank        = 0;
+      unsigned int group_number        = 0;
+      unsigned int subgroup_number     = 0;
+      unsigned int old_group_number    = 0;
+      unsigned int old_subgroup_number = 0;
+
+      std::vector<const ProteinMatch *> protein_match_list =
+        group_pair.second.get()->getProteinMatchList();
+
+      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();
+                });
+
+      for(auto &protein_match : protein_match_list)
+        {
+          pappso::GrpProtein *p_grp_protein =
+            protein_match->getGrpProteinSp().get();
+          ProteinXtp *p_protein = protein_match->getProteinXtpSp().get();
+
+          group_number    = p_grp_protein->getGroupNumber();
+          subgroup_number = p_grp_protein->getSubGroupNumber();
+
+          if((m_exportType == ExportFastaType::oneBySubgroup) &&
+             (group_number == old_group_number) &&
+             (subgroup_number == old_subgroup_number) &&
+             (p_grp_protein->getRank() > 1))
+            continue;
+
+          if((m_exportType == ExportFastaType::oneByGroup) &&
+             (group_number == old_group_number) && (subgroup_number > 1))
+            continue;
+
+          old_group_number    = group_number;
+          old_subgroup_number = subgroup_number;
+
+          pappso::Protein protein(QString("%1|%2 %3")
+                                    .arg(p_grp_protein->getGroupingId())
+                                    .arg(p_protein->getAccession())
+                                    .arg(p_protein->getDescription()),
+                                  p_protein->getSequence());
+          fasta_output.writeProtein(protein);
+        }
+    }
 }

src/output/exportfastafile.h

@@ -30,11 +30,16 @@
 #include <QString>
 #include "../utils/types.h"
 #include "../core/project.h"
+#include <pappsomspp/fasta/fastaoutputstream.h>
 
 class ExportFastaFile
 {
   private:
-  QFile *p_outputFastaFile = nullptr;
+  QFile *mp_outputFastaFile = nullptr;
+  ExportFastaType m_exportType;
+
+  private:
+  void writeIdentificationGroup(pappso::FastaOutputStream & fasta_output,IdentificationGroup *p_ident);
 
   public:
   ExportFastaFile(QString filename, ExportFastaType type);