WIP add tests

test/gtest/MiniEukTest.cpp

+// ****************************************************************************
+//
+//          Aevol - An in silico experimental evolution platform
+//
+// ****************************************************************************
+//
+// Copyright: See the AUTHORS file provided with the package or <www.aevol.fr>
+// Web: http://www.aevol.fr/
+// E-mail: See <http://www.aevol.fr/contact/>
+// Original Authors : Guillaume Beslon, Carole Knibbe, David Parsons
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 2 of the License, or
+// (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with this program.  If not, see <http://www.gnu.org/licenses/>.
+//
+//*****************************************************************************
+
+
+
+
+// =================================================================
+//                              Includes
+// =================================================================
+#include <inttypes.h>
+#include <cstring>
+
+#include <list>
+#include <vector>
+#include <memory>
+
+#include <gtest/gtest.h>
+
+#include "DnaFactory.h"
+#include "ExpManager_7.h"
+#include "ExpSetup.h"
+#include "fuzzy/FuzzyFactory_7.h"
+#include "Individual_7.h"
+#include "legacy/biochemistry/Rna.h"
+#include "legacy/biochemistry/Protein.h"
+#include "macros.h"
+#include "MutationParams.h"
+#include "Strand.h"
+
+using namespace aevol;
+
+//############################################################################
+//                                                                           #
+//                         Class IndividualTest                              #
+//                                                                           #
+//############################################################################
+class IndividualTest : public testing::Test
+{
+ protected:
+  virtual void SetUp(void);
+  virtual void TearDown(void);
+
+  // We have an version of each individual for each fuzzy set flavor
+  Individual_7* indiv1;
+};
+
+// ===========================================================================
+//                                 Public Methods
+// ===========================================================================
+void IndividualTest::SetUp(void)
+{
+  // Build ad-hoc genomes
+  // (and reverse to test the same things on the lagging strand.):
+  //
+  // indiv1: LEAD (prom-1 + AS + AG + AS + term)
+  //   size 22+5+28+6+11=72
+  // AS = Arbitrary Sequence
+  // AG = Arbitrary Gene
+  // Do not modify the sequences !
+
+  // Define a few arbitrary sequences
+  char as[5][10] = {
+    "0011",
+    "11101",
+    "110011",
+    "11000",
+    "000101"
+  };
+
+  const char* SHINE_DAL_SEQ = "011011";
+  // const char* SHINE_DAL_SEQ_LAG = "001001";
+  // Define an arbitrary gene
+  char gene[100];
+  sprintf(gene, "%s0011000100110110010001", SHINE_DAL_SEQ);
+
+  // char lag_gene[100];
+  // sprintf(lag_gene, "1100111011001001101110%s", SHINE_DAL_SEQ_LAG);
+
+  // Define an arbitrary terminator
+  char term[TERM_SIZE+1] = "01000001101";
+  // char bad_term_end[TERM_SIZE] = "0100000110";
+  // char bad_term_beg[TERM_SIZE] = "1000001101";
+
+  // Define a few arbitrary promoters
+  // char prom[2][23] = {
+  //   "0101010001110110010110", // dist from consensus: 2 => basal level: 0.6
+  //   "0101011001110010010010"  // dist from consensus: 1 => basal level: 0.8
+  // };
+
+  // char lag_prom[2][23] = {
+  //   "1001011001000111010101", // dist from consensus: 2 => basal level: 0.6
+  //   "1011011011000110010101"  // dist from consensus: 1 => basal level: 0.8
+  // };
+
+
+  char bad_prom[2][23] = {
+    "101010001110110010110", // removed first base : add 0 at end
+    "010101100111001001001"  // removed last base : add 0 at begin
+  };
+
+  //   char bad_lag_prom[2][23] = {
+  //   "001011001000111010101", // removed first base : add 1 at end
+  //   "101101101100011001010"  // removed last base : add 1 at begin
+  // };
+
+
+  // Initialize the experimental setup.
+  // These are needed in the GeneticUnit constructors.
+  ExpSetup* exp_s = new ExpSetup(nullptr);
+  MutationParams params_mut;
+
+
+  // Update fuzzy flavor and fuzzy factory // TODO<dpa> Still needed/useful?
+  FuzzyFlavor fuzzyFlavor = FuzzyFlavor::VECTOR;
+  exp_s->set_fuzzy_flavor(fuzzyFlavor);
+
+  DnaFactory* dna_factory = new DnaFactory(DnaFactory_Policy::LOCAL_GLOBAL_FIT, 48, 1000, 16);
+  FuzzyFactory_7* fuzzy_factory = new FuzzyFactory_7(fuzzyFlavor, 16, 300, 16);
+
+
+
+  // Build indiv1                         LEAD (prom-1 + AS + AG + AS + term)
+  // Construct a genome with these arbitrary sequences
+  char* genome = new char[100];
+  sprintf(genome, "%s%s%s%s%s0",bad_prom[0], as[1], gene, as[2], term);
+
+  indiv1 = new Individual_7(1.0, dna_factory, fuzzy_factory);
+  indiv1->annotated_chromosome_[A]->dna_ = dna_factory->get_dna(strlen(genome));
+  indiv1->annotated_chromosome_[A]->dna_->ann_chrsm_ = indiv1->annotated_chromosome_[A];
+  indiv1->annotated_chromosome_[A]->dna_->dna_factory_ = dna_factory;
+  indiv1->annotated_chromosome_[A]->dna_->set_indiv(genome, strlen(genome), indiv1);
+
+  indiv1->annotated_chromosome_[B]->dna_ = dna_factory->get_dna(strlen(genome));
+  indiv1->annotated_chromosome_[B]->dna_->ann_chrsm_ = indiv1->annotated_chromosome_[B];
+  indiv1->annotated_chromosome_[B]->dna_->dna_factory_ = dna_factory;
+  indiv1->annotated_chromosome_[B]->dna_->set_indiv(genome, strlen(genome), indiv1);
+  genome = nullptr;
+
+  // Do transcription and translation
+  indiv1->start_stop_RNA();
+  indiv1->prom_compute_RNA(*exp_s);
+  indiv1->start_protein();
+  indiv1->compute_protein();
+  indiv1->translate_protein(*exp_s, 1.0);
+
+}
+
+void IndividualTest::TearDown() {
+//  for (auto indiv : indivs1) {
+//    delete indiv;
+//  }
+}
+
+// For each version of each individual constructed with a different
+// fuzzy set implementation, we check that all values are correct.
+// We don't need to change the fuzzy set implementation in the
+// experimental setup again because it's only used at transcription and
+// translation time.
+
+TEST_F(IndividualTest, TestIndiv1) {
+  // Check that we have the right number of promoters, terminators etc
+  // and at the right positions
+  // "right" means those values we have computed by hand
+    for (auto chrsm: {A,B}){
+    // Check genome size
+    EXPECT_EQ(72, indiv1->annotated_chromosome_[chrsm]->dna_->length());
+    EXPECT_EQ(72, indiv1->annotated_chromosome_[chrsm]->length());
+
+    // Check Prom list
+    EXPECT_EQ(0, indiv1->annotated_chromosome_[chrsm]->promoter_list().promoter_count());
+
+    // Check RNA list
+    auto rna_list = indiv1->annotated_chromosome_[chrsm]->rnas();
+    EXPECT_EQ(0, rna_list.size());
+
+    // Check protein list
+    auto prot_list = indiv1->annotated_chromosome_[chrsm]->proteins();
+    EXPECT_EQ(0, prot_list.size());
+    }
+}
+
+
+
+// ===========================================================================
+//                                Protected Methods
+// ===========================================================================
+
+// ===========================================================================
+//                              Non inline accessors
+// ===========================================================================