test refactoring

tests/test_proteincode.cpp

@@ -581,6 +581,24 @@ TEST_CASE("proteincode test suite.", "[proteincode]")
   reader.parse(file2);
 
 
+  pappso::AaCode aa_code;
+  aa_code.addAaModification('C',
+                            pappso::AaModification::getInstance("MOD:00397"));
+  pappso::AaStringCodec aa_codec(aa_code);
+
+
+  std::vector<pappso::ProteinIntegerCode> arr_codedProtein;
+
+  for(auto &protein : protein_handler.getProteinArray())
+    {
+      pappso::ProteinSp protein_sp = protein.makeProteinSp();
+
+      qDebug() << protein_sp.get()->getAccession();
+      // pappso::ProteinIntegerCode protein_code(protein_sp, aa_codec, 5);
+
+      arr_codedProtein.push_back({protein_sp, aa_codec, 5});
+    }
+
   SECTION("..:: scan spectrum on fasta file ::..", "[proteincodefasta]")
   {
     // compute spectrum code :
@@ -604,12 +622,6 @@ TEST_CASE("proteincode test suite.", "[proteincode]")
 
 
     // ok spectrum code
-
-    pappso::AaCode aa_code;
-    aa_code.addAaModification('C',
-                              pappso::AaModification::getInstance("MOD:00397"));
-    pappso::AaStringCodec aa_codec(aa_code);
-
     pappso::ProteinSp max_protein;
     double max_score = 0;
 
@@ -630,15 +642,13 @@ TEST_CASE("proteincode test suite.", "[proteincode]")
 
     std::vector<double> convolution_score;
 
-    for(auto &protein : protein_handler.getProteinArray())
+    for(auto &coded_protein : arr_codedProtein)
       {
-        pappso::ProteinSp protein_sp = protein.makeProteinSp();
+        pappso::ProteinSp protein_sp = coded_protein.getProteinSp();
 
         qDebug() << protein_sp.get()->getAccession();
-        pappso::ProteinIntegerCode protein_code(protein_sp, aa_codec, 5);
-
         std::vector<double> vec_score =
-          protein_code.convolution(code_list_from_spectrum);
+          coded_protein.convolution(code_list_from_spectrum);
         auto it_score = std::max_element(vec_score.begin(), vec_score.end());
 
         // double score = std::accumulate(it_score - 2, it_score + 5, 0);
@@ -687,17 +697,11 @@ TEST_CASE("proteincode test suite.", "[proteincode]")
     pappso::FilterPeakDelta filter_peak_delta;
     filter_peak_delta.filter(spectrum);
 
-    pappso::FilterGreatestY(400).filter(spectrum);
+    pappso::FilterGreatestY(500).filter(spectrum);
     std::vector<double> mass_list = spectrum.xValues();
 
 
     // ok spectrum code
-
-    pappso::AaCode aa_code;
-    aa_code.addAaModification('C',
-                              pappso::AaModification::getInstance("MOD:00397"));
-    pappso::AaStringCodec aa_codec(aa_code);
-
     pappso::ProteinSp max_protein;
     double max_score = 0;
 
@@ -718,15 +722,15 @@ TEST_CASE("proteincode test suite.", "[proteincode]")
 
     std::vector<double> convolution_score;
 
-    for(auto &protein : protein_handler.getProteinArray())
-      {
-        pappso::ProteinSp protein_sp = protein.makeProteinSp();
 
-        qDebug() << protein_sp.get()->getAccession();
-        pappso::ProteinIntegerCode protein_code(protein_sp, aa_codec, 5);
+    for(auto &coded_protein : arr_codedProtein)
+      {
+        pappso::ProteinSp protein_sp = coded_protein.getProteinSp();
 
+        // qDebug() << protein_sp.get()->getAccession();
         std::vector<double> vec_score =
-          protein_code.convolution(code_list_from_spectrum);
+          coded_protein.convolution(code_list_from_spectrum);
+
         auto it_score = std::max_element(vec_score.begin(), vec_score.end());
 
         // double score = std::accumulate(it_score - 2, it_score + 5, 0);