Swap M and T in setting up CTL reactions (Ising).

diff --git a/ss.cpp b/ss.cpp
index c96e4f4..0fc519c 100644 (file)
--- a/ss.cpp
+++ b/ss.cpp
@@ -397,7 +397,7 @@ void importEpitope(RunParameters_SS &r, Species_parray &species, Rxn_parray &rea
     }
 
     for (size_t i = 0; i != r.num_CTL_clones; ++i) {
-        CTLSpecies* T = new CTLSpecies("E",r.init_CTL_numT[i]);
+        CTLSpecies* M = new CTLSpecies("E",r.init_CTL_numM[i]);
 
         std::ifstream input(r.epitopefiles[i].c_str());   // <infile>.ep
         if (!input) { perror((std::string("ERROR in importEpitope: ") + r.epitopeInfile).c_str()); exit(1); }
@@ -405,8 +405,8 @@ void importEpitope(RunParameters_SS &r, Species_parray &species, Rxn_parray &rea
         std::string readStr;
         while (std::getline(input,readStr)) {
 
-            T->num_ep += 1;
-            T->epitopes.push_back(EpitopeRecognizer());
+            M->num_ep += 1;
+            M->epitopes.push_back(EpitopeRecognizer());
 
             std::string word;
             unsigned int site;
@@ -425,7 +425,7 @@ void importEpitope(RunParameters_SS &r, Species_parray &species, Rxn_parray &rea
             aff = strtodouble(word);
             printf("%.6e ",aff);
 
-            T->affinity.push_back(aff);
+            M->affinity.push_back(aff);
 
             // next entries are WT sites
             while (readStrStrm >> word) {
@@ -437,7 +437,7 @@ void importEpitope(RunParameters_SS &r, Species_parray &species, Rxn_parray &rea
                     break;
             }
             //r.eWT.push_back(tmpEp);
-            T->epitopes.back().epitopeWT = tmpEp;
+            M->epitopes.back().epitopeWT = tmpEp;
 
             tmpEp.clear();  // reset temp epitope
             readStrStrm.str("");  readStrStrm.clear();  // reset stream
@@ -454,7 +454,7 @@ void importEpitope(RunParameters_SS &r, Species_parray &species, Rxn_parray &rea
                     break;
             }
             //r.eMut.push_back(tmpEp);
-            T->epitopes.back().epitopeMut = tmpEp;
+            M->epitopes.back().epitopeMut = tmpEp;
 
             //r.numEpitopes++;
 
@@ -462,15 +462,15 @@ void importEpitope(RunParameters_SS &r, Species_parray &species, Rxn_parray &rea
 
         }
 
-        species.push_back(T);   // effector
+        species.push_back(M);   // memory
 
-        CTLSpecies* N = new CTLSpecies(*T);     // naive
+        CTLSpecies* N = new CTLSpecies(*M);     // naive
         N->name = "N";  N->count = r.init_CTL_numN[i];
         species.push_back(N);
 
-        CTLSpecies* M = new CTLSpecies(*T);     // memory
-        M->name = "M";  M->count = r.init_CTL_numM[i];
-        species.push_back(M);
+        CTLSpecies* T = new CTLSpecies(*M);     // effector
+        T->name = "T";  T->count = r.init_CTL_numT[i];
+        species.push_back(T);
 
         print_spec.push_back(T);
         print_spec.push_back(N);