From d8d4560184404b4b0aa1581764ce58f818255999 Mon Sep 17 00:00:00 2001
From: Dariusz Murakowski <murakdar@mit.edu>
Date: Tue, 21 Apr 2015 15:37:56 -0400
Subject: [PATCH] Print virus species sequence when verbose.

---
 pop_ss.h |  4 ++++
 ss.cpp   | 25 +++++++++++++++++++------
 ss.h     |  2 +-
 3 files changed, 24 insertions(+), 7 deletions(-)

diff --git a/pop_ss.h b/pop_ss.h
index 8f35f16..6bacf5e 100644
--- a/pop_ss.h
+++ b/pop_ss.h
@@ -61,6 +61,10 @@ public:
     Species(long c) : count(c), name("") {}
     Species(std::string x) : count(0), name(x) {}
     Species(std::string x, long c) : count(c), name(x) {}
+
+    // necessary otherwise compiler complains 'source type is not polymorphic'
+    // ...should probably have a virtual destructor....
+    virtual void allow_dynamic_cast() {}
 };
 
 class SimpleSpecies : public Species {
diff --git a/ss.cpp b/ss.cpp
index f13069e..094bba7 100644
--- a/ss.cpp
+++ b/ss.cpp
@@ -111,7 +111,7 @@ void run(RunParameters_SS &r, unsigned seed) {
     //double t_end = 1000.0;
     //long max_steps = LONG_MAX;
     //double sample_interval = 1.0;
-    simulate(reactions, species, r.t_end, r.max_steps, r.sample_interval, print_spec);
+    simulate(reactions, species, r.t_end, r.max_steps, r.sample_interval, print_spec, r.useVerbose);
 
     gsl_rng_free(rnd);  //Free up memory from random number generator
 
@@ -147,21 +147,34 @@ void print_species_header(const Species_parray &print_spec)
     std::cout << '\n';
 }
 
-void print_species_traj(double t, const Species_parray &print_spec)
+void print_species_traj(double t, const Species_parray &print_spec, bool verbose)
 {
     std::cout << t;
     for (Species_parray::const_iterator spec = print_spec.begin(),
-            end = print_spec.end();
+                                         end = print_spec.end();
             spec != end; ++spec)
     {
         // TODO: prettier representation
         std::cout << '\t' << (*spec)->count;
+
+        if (verbose) {
+            VirusSpecies *V = dynamic_cast<VirusSpecies*> (*spec);
+            if (V) {
+                virus_map::iterator  it = V->pop.begin(),
+                                    end = V->pop.end();
+                for (; it != end; ++it) {
+                    std::cout << ' ' << it->second
+                              << '(' << it->first.mutated_sites << ')';
+                }
+            }
+        }
+
     }
     std::cout << '\n';
 }
 
 
-void simulate(Rxn_parray &reactions, Species_parray &species, double t_end, long max_steps, double sample_interval, const Species_parray &print_spec)
+void simulate(Rxn_parray &reactions, Species_parray &species, double t_end, long max_steps, double sample_interval, const Species_parray &print_spec, bool verbose)
 {
     long step = 0;
 
@@ -216,13 +229,13 @@ void simulate(Rxn_parray &reactions, Species_parray &species, double t_end, long
         // print copy numbers
         if (t_next_sample <= t) {
             t_next_sample += sample_interval;
-            print_species_traj(t,print_spec);
+            print_species_traj(t,print_spec,verbose);
         }
 
     }
 
     if (t_end == HUGE_VAL)
-        print_species_traj(t,print_spec);
+        print_species_traj(t,print_spec,verbose);
 
 }
 
diff --git a/ss.h b/ss.h
index 8d7f02b..da25a2e 100644
--- a/ss.h
+++ b/ss.h
@@ -238,7 +238,7 @@ public:
 void run(RunParameters_SS &r);
 void importState(RunParameters_SS &r);
 void importEpitope(RunParameters_SS &r, Species_parray &species, Rxn_parray &reactions, VirusSpecies *V, Species_parray &print_spec);
-void simulate(Rxn_parray &reactions, Species_parray &species, double t_end, long max_steps, double sample_interval, const Species_parray &print_spec);
+void simulate(Rxn_parray &reactions, Species_parray &species, double t_end, long max_steps, double sample_interval, const Species_parray &print_spec, bool verbose);
 
 
 #endif
-- 
2.7.4