diff --git a/test/gtest/IndividualTest.cpp b/test/gtest/IndividualTest.cpp
index 98af55791e74a8961a1f37251209fd5d5246671a..9de91e96d1b78e964cc963e12e5979daa4657499 100644
--- a/test/gtest/IndividualTest.cpp
+++ b/test/gtest/IndividualTest.cpp
@@ -39,13 +39,15 @@
#include <gtest/gtest.h>
-#include "legacy/population/Individual.h"
-#include "macros.h"
-#include "GeneticUnit.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 "ExpSetup.h"
+#include "Strand.h"
using namespace aevol;
@@ -61,17 +63,16 @@ class IndividualTest : public testing::Test
virtual void TearDown(void);
// We have an version of each individual for each fuzzy set flavor
- std::vector<Individual*> indivs1;
- std::vector<Individual*> indivs2;
- std::vector<Individual*> indivs3;
- std::vector<Individual*> indivs4;
+ std::vector<Individual_7*> indivs1;
+ std::vector<Individual_7*> indivs2;
+ std::vector<Individual_7*> indivs3;
+ std::vector<Individual_7*> indivs4;
};
// ===========================================================================
// Public Methods
// ===========================================================================
-void IndividualTest::SetUp(void)
-{
+void IndividualTest::SetUp(void) {
// Build ad-hoc genomes
// (and reverse to test the same things on the lagging strand.):
//
@@ -84,33 +85,30 @@ void IndividualTest::SetUp(void)
// AG = Arbitrary Gene
// Do not modify the sequences !
- // Define a few arbitrary sequences
- char as[5][10] = {
- "0011",
- "11101",
- "110011",
- "11000",
- "000101"
+ // Define arbitrary sequences
+ std::array<std::string, 5> as = {
+ "0011",
+ "11101",
+ "110011",
+ "11000",
+ "000101"
};
// Define an arbitrary gene
- char gene[255];
- sprintf(gene, "%s0011000100110110010001", SHINE_DAL_SEQ);
+ std::string gene = std::string(SHINE_DAL_SEQ) + "0011000100110110010001";
// Define an arbitrary terminator
- char term[TERM_SIZE+1] = "01000001101";
+ std::string term = "01000001101";
// 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
+ std::array<std::string, 2> prom = {
+ "0101010001110110010110", // dist from consensus: 2 => basal level: 0.6
+ "0101011001110010010010" // dist from consensus: 1 => basal level: 0.8
};
-
- // Initialize the experimental setup and fuzzy set factory.
+ // Initialize the experimental setup.
// These are needed in the GeneticUnit constructors.
- ExpSetup* exp_s = new ExpSetup(nullptr);
- FuzzyFactory::fuzzyFactory = new FuzzyFactory();
+ ExpSetup exp_s(nullptr);
MutationParams params_mut;
@@ -135,96 +133,77 @@ void IndividualTest::SetUp(void)
}
#endif
- // We initialize a version of each individual for each fuzzy set
- // implementation
- for (int fuzzyFlavor = 0 ; fuzzyFlavor <= 1 ; ++fuzzyFlavor) {
- // Update fuzzy flavor and fuzzy factory
- exp_s->set_fuzzy_flavor(fuzzyFlavor);
+ // We initialize a version of each individual for each fuzzy set implementation
+ for (FuzzyFlavor fuzzyFlavor : {FuzzyFlavor::VECTOR, FuzzyFlavor::DISCRETE_DOUBLE_TABLE}) {
+ // Update fuzzy factory // TODO<dpa> Still needed/useful?
+ exp_s.set_fuzzy_flavor(fuzzyFlavor);
- if (FuzzyFactory::fuzzyFactory == NULL) {
- FuzzyFactory::fuzzyFactory = new FuzzyFactory();
- } else {
- delete FuzzyFactory::fuzzyFactory;
- FuzzyFactory::fuzzyFactory = new FuzzyFactory();
- }
+ FuzzyFactory_7* fuzzy_factory = new FuzzyFactory_7(fuzzyFlavor, 16, 300, 16);
// Build indiv1
- // Construct a genome with these arbitrary sequences
- char* genome = new char[1024];
- sprintf(genome, "%s%s%s%s%s%s%s%s%s", as[0], prom[0], as[1], gene, as[2],
- term, as[3], prom[1], as[4]);
-
- Individual* indiv1 = new Individual(
- nullptr, nullptr, nullptr, std::make_shared<MutationParams>(params_mut),
- 1.0, 10, 1000, false, 1, "anon-strain-1", 0);
- indiv1->add_GU(genome, strlen(genome));
- genome = NULL;
+ auto genome1 = as[0] + prom[0] + as[1] + gene + as[2] + term + as[3] + prom[1] + as[4];
+ auto indiv1 = Individual_7::make_from_sequence(1.0, fuzzy_factory, genome1.c_str(), genome1.size());
// Do transcription and translation
- indiv1->do_transcription();
- indiv1->do_translation();
+ indiv1->start_stop_RNA();
+ indiv1->prom_compute_RNA(exp_s);
+ indiv1->start_protein();
+ indiv1->compute_protein();
+ indiv1->translate_protein(exp_s, 1.0);
indivs1.push_back(indiv1);
-
- // Build indiv2
- // Reverse the whole genome
- genome = indiv1->genetic_unit(0).dna()->subsequence(0, 0, LAGGING);
- Individual* indiv2 = new Individual(nullptr, nullptr, nullptr,
- std::make_shared<MutationParams>(params_mut), 1.0,
- 10, 1000, false, 1, "anon-strain-2", 0);
- indiv2->add_GU(genome, strlen(genome));
- genome = NULL;
+ // Build indiv2 (reverse the whole genome of indiv1)
+ auto genome2 = indiv1->annotated_chromosome_->dna_->subseq(indiv1->annotated_chromosome_->dna_->length() - 1,
+ indiv1->annotated_chromosome_->dna_->length(),
+ Strand::LAGGING);
+ auto indiv2 = Individual_7::make_from_sequence(1.0, fuzzy_factory, genome2.c_str(), genome2.size());
// Do transcription and translation
- indiv2->do_transcription();
- indiv2->do_translation();
+ indiv2->start_stop_RNA();
+ indiv2->prom_compute_RNA(exp_s);
+ indiv2->start_protein();
+ indiv2->compute_protein();
+ indiv2->translate_protein(exp_s, 1.0);
indivs2.push_back(indiv2);
-
// Build indiv3
- genome = new char[1024];
- sprintf(genome, "%s%s%s%s%s%s%s", as[0], gene, as[1], term, as[2], prom[1],
- as[3]);
- Individual* indiv3 = new Individual(nullptr, nullptr, nullptr,
- std::make_shared<MutationParams>(params_mut), 1.0,
- 10, 1000, false, 1, "anon-strain-3", 0);
- indiv3->add_GU(genome, strlen(genome));
- genome = NULL;
+ auto genome3 = as[0] + gene + as[1] + term + as[2] + prom[1] + as[3];
+ auto indiv3 = Individual_7::make_from_sequence(1.0, fuzzy_factory, genome3.c_str(), genome3.size());
// Do transcription and translation
- indiv3->do_transcription();
- indiv3->do_translation();
+ indiv3->start_stop_RNA();
+ indiv3->prom_compute_RNA(exp_s);
+ indiv3->start_protein();
+ indiv3->compute_protein();
+ indiv3->translate_protein(exp_s, 1.0);
indivs3.push_back(indiv3);
-
- // Build indiv4
- genome = indiv3->genetic_unit(0).dna()->subsequence(0, 0,
- LAGGING);
- Individual* indiv4 = new Individual(nullptr, nullptr, nullptr,
- std::make_shared<MutationParams>(params_mut), 1.0,
- 10, 1000, false, 1, "anon-strain-4", 0);
- indiv4->add_GU(genome, strlen(genome));
- genome = NULL;
+ // Build indiv4 (reverse the whole genome of indiv3)
+ auto genome4 = indiv3->annotated_chromosome_->dna_->subseq(indiv3->annotated_chromosome_->dna_->length() - 1,
+ indiv3->annotated_chromosome_->dna_->length(),
+ Strand::LAGGING);
+ auto indiv4 = Individual_7::make_from_sequence(1.0, fuzzy_factory, genome4.c_str(), genome4.size());
// Do transcription and translation
- indiv4->do_transcription();
- indiv4->do_translation();
+ indiv4->start_stop_RNA();
+ indiv4->prom_compute_RNA(exp_s);
+ indiv4->start_protein();
+ indiv4->compute_protein();
+ indiv4->translate_protein(exp_s, 1.0);
indivs4.push_back(indiv4);
+
+ delete fuzzy_factory;
}
}
-void IndividualTest::TearDown(void)
-{
- for (int fuzzyFlavor = 0 ; fuzzyFlavor <= 1 ; ++fuzzyFlavor) {
- delete indivs1[fuzzyFlavor];
- delete indivs2[fuzzyFlavor];
- delete indivs3[fuzzyFlavor];
- delete indivs4[fuzzyFlavor];
+void IndividualTest::TearDown() {
+ for (auto indiv : indivs1) {
+ delete indiv;
}
}
@@ -234,142 +213,152 @@ void IndividualTest::TearDown(void)
// experimental setup again because it's only used at transcription and
// translation time.
-TEST_F(IndividualTest, TestIndiv1)
-{
+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 (int fuzzyFlavor = 0 ; fuzzyFlavor <= 1 ; ++fuzzyFlavor) {
- Individual* indiv1 = indivs1[fuzzyFlavor];
+ for (auto fuzzyFlavor = 0 ; fuzzyFlavor <= 1 ; ++fuzzyFlavor) {
+ auto indiv = indivs1[fuzzyFlavor];
// Check genome size
- EXPECT_EQ(109, indiv1->amount_of_dna());
- EXPECT_EQ(109, indiv1->genetic_unit_seq_length(0));
+ EXPECT_EQ(109, indiv->annotated_chromosome_->dna_->length());
- //Â Check RNA list
- std::list<const Rna*> rna_list = indiv1->rna_list();
+ // Check RNA list
+ auto rna_list = indiv->annotated_chromosome_->rnas();
EXPECT_EQ(2, rna_list.size());
- const Rna* rna = rna_list.front();
- EXPECT_EQ(LEADING, rna->strand());
- EXPECT_EQ(4, rna->promoter_pos());
- EXPECT_FLOAT_EQ(0.6, rna->basal_level());
- EXPECT_EQ(50, rna->transcript_length());
+ const auto* rna = rna_list.front();
+ EXPECT_EQ(Strand::LEADING, rna->strand_);
+ EXPECT_EQ(4, rna->prom->pos);
+ EXPECT_FLOAT_EQ(0.6, rna->e);
+ EXPECT_EQ(50, rna->length);
rna = rna_list.back();
- EXPECT_EQ(LEADING, rna->strand());
- EXPECT_EQ(81, rna->promoter_pos());
- EXPECT_FLOAT_EQ(0.8, rna->basal_level());
- EXPECT_EQ(82, rna->transcript_length());
+ EXPECT_EQ(Strand::LEADING, rna->strand_);
+ EXPECT_EQ(81, rna->prom->pos);
+ EXPECT_FLOAT_EQ(0.8, rna->e);
+ EXPECT_EQ(82, rna->length);
// Check protein list
- std::list<Protein*> prot_list = indiv1->protein_list();
- EXPECT_EQ(1, prot_list.size());
- Protein* prot = prot_list.front();
- EXPECT_EQ(LEADING, prot->strand());
- EXPECT_EQ(31, prot->shine_dal_pos());
- EXPECT_EQ(4, prot->length());
- EXPECT_FLOAT_EQ(1.4, prot->concentration());
- EXPECT_EQ(2, prot->rna_list().size());
+ auto prot_list = indiv->annotated_chromosome_->proteins();
+ EXPECT_EQ(2, prot_list.size());
+
+ const auto* prot = prot_list.front();
+ EXPECT_EQ(Strand::LEADING, prot->strand_);
+ EXPECT_EQ(44, prot->protein_start);
+ EXPECT_EQ(4, prot->protein_length);
+ EXPECT_FLOAT_EQ(1.4, prot->e);
+ EXPECT_EQ(true, prot->is_init_);
+ EXPECT_EQ(2, prot->rna_list_.size());
+
+ prot = prot_list.back();
+ EXPECT_EQ(Strand::LEADING, prot->strand_);
+ EXPECT_EQ(44, prot->protein_start);
+ EXPECT_EQ(4, prot->protein_length);
+ EXPECT_FLOAT_EQ(0.6, prot->e);
+ EXPECT_EQ(false, prot->is_init_);
+ EXPECT_EQ(1, prot->rna_list_.size());
}
}
-TEST_F(IndividualTest, TestIndiv2)
-{
- for (int fuzzyFlavor = 0; fuzzyFlavor <= 1; ++fuzzyFlavor) {
- Individual* indiv2 = indivs2[fuzzyFlavor];
+TEST_F(IndividualTest, TestIndiv2) {
+ for (auto fuzzyFlavor = 0 ; fuzzyFlavor <= 1 ; ++fuzzyFlavor) {
+ auto indiv = indivs2[fuzzyFlavor];
// Check genome size
- EXPECT_EQ(109, indiv2->amount_of_dna());
- EXPECT_EQ(109, indiv2->genetic_unit_seq_length(0));
+ EXPECT_EQ(109, indiv->annotated_chromosome_->dna_->length());
- //Â Check RNA list
- std::list<const Rna*> rna_list = indiv2->rna_list();
+ // Check RNA list
+ auto rna_list = indiv->annotated_chromosome_->rnas();
EXPECT_EQ(2, rna_list.size());
- const Rna* rna = rna_list.front();
- EXPECT_EQ(LAGGING, rna->strand());
- EXPECT_EQ(104, rna->promoter_pos());
- EXPECT_FLOAT_EQ(0.6, rna->basal_level());
- EXPECT_EQ(50, rna->transcript_length());
+ const auto* rna = rna_list.front();
+ EXPECT_EQ(Strand::LAGGING, rna->strand_);
+ EXPECT_EQ(104, rna->prom->pos);
+ EXPECT_FLOAT_EQ(0.6, rna->e);
+ EXPECT_EQ(50, rna->length);
rna = rna_list.back();
- EXPECT_EQ(LAGGING, rna->strand());
- EXPECT_EQ(27, rna->promoter_pos());
- EXPECT_FLOAT_EQ(0.8, rna->basal_level());
- EXPECT_EQ(82, rna->transcript_length());
+ EXPECT_EQ(Strand::LAGGING, rna->strand_);
+ EXPECT_EQ(27, rna->prom->pos);
+ EXPECT_FLOAT_EQ(0.8, rna->e);
+ EXPECT_EQ(82, rna->length);
// Check protein list
- std::list<Protein*> prot_list = indiv2->protein_list();
- EXPECT_EQ(1, prot_list.size());
- Protein* prot = prot_list.front();
- EXPECT_EQ(LAGGING, prot->strand());
- EXPECT_EQ(77, prot->shine_dal_pos());
- EXPECT_EQ(4, prot->length());
- EXPECT_FLOAT_EQ(1.4, prot->concentration());
- EXPECT_EQ(2, prot->rna_list().size());
+ auto prot_list = indiv->annotated_chromosome_->proteins();
+ EXPECT_EQ(2, prot_list.size());
+
+ const auto* prot = prot_list.front();
+ EXPECT_EQ(Strand::LAGGING, prot->strand_);
+ EXPECT_EQ(64, prot->protein_start);
+ EXPECT_EQ(4, prot->protein_length);
+ EXPECT_FLOAT_EQ(1.4, prot->e);
+ EXPECT_EQ(true, prot->is_init_);
+ EXPECT_EQ(2, prot->rna_list_.size());
+
+ prot = prot_list.back();
+ EXPECT_EQ(Strand::LAGGING, prot->strand_);
+ EXPECT_EQ(64, prot->protein_start);
+ EXPECT_EQ(4, prot->protein_length);
+ EXPECT_FLOAT_EQ(0.6, prot->e);
+ EXPECT_EQ(false, prot->is_init_);
+ EXPECT_EQ(1, prot->rna_list_.size());
}
}
-TEST_F(IndividualTest, TestIndiv3)
-{
- for (int fuzzyFlavor = 0 ; fuzzyFlavor <= 1 ; ++fuzzyFlavor) {
- Individual* indiv3 = indivs3[fuzzyFlavor];
+TEST_F(IndividualTest, TestIndiv3) {
+ for (auto fuzzyFlavor = 0 ; fuzzyFlavor <= 1 ; ++fuzzyFlavor) {
+ auto indiv = indivs3[fuzzyFlavor];
+
// Check genome size
- EXPECT_EQ(81, indiv3->amount_of_dna());
- EXPECT_EQ(81, indiv3->genetic_unit_seq_length(0));
+ EXPECT_EQ(81, indiv->annotated_chromosome_->dna_->length());
- //Â Check RNA list
- std::list<const Rna*> rna_list = indiv3->rna_list();
+ // Check RNA list
+ auto rna_list = indiv->annotated_chromosome_->rnas();
EXPECT_EQ(1, rna_list.size());
- const Rna* rna = rna_list.front();
- EXPECT_EQ(LEADING, rna->strand());
- EXPECT_EQ(54, rna->promoter_pos());
- EXPECT_FLOAT_EQ(0.8, rna->basal_level());
- EXPECT_EQ(42, rna->transcript_length());
+ const auto* rna = rna_list.front();
+ EXPECT_EQ(Strand::LEADING, rna->strand_);
+ EXPECT_EQ(54, rna->prom->pos);
+ EXPECT_FLOAT_EQ(0.8, rna->e);
+ EXPECT_EQ(42, rna->length);
// Check protein list
- std::list<Protein*> prot_list = indiv3->protein_list();
+ auto prot_list = indiv->annotated_chromosome_->proteins();
EXPECT_EQ(1, prot_list.size());
- Protein* prot = prot_list.front();
- EXPECT_EQ(LEADING, prot->strand());
- EXPECT_EQ(4, prot->shine_dal_pos());
- EXPECT_EQ(4, prot->length());
- EXPECT_FLOAT_EQ(0.8, prot->concentration());
- EXPECT_EQ(1, prot->rna_list().size());
+
+ const auto* prot = prot_list.front();
+ EXPECT_EQ(Strand::LEADING, prot->strand_);
+ EXPECT_EQ(17, prot->protein_start);
+ EXPECT_EQ(4, prot->protein_length);
+ EXPECT_FLOAT_EQ(0.8, prot->e);
+ EXPECT_EQ(true, prot->is_init_);
+ EXPECT_EQ(1, prot->rna_list_.size());
}
}
-TEST_F(IndividualTest, TestIndiv4)
-{
- for (int fuzzyFlavor = 0 ; fuzzyFlavor <= 1 ; ++fuzzyFlavor) {
- Individual* indiv4 = indivs4[fuzzyFlavor];
+TEST_F(IndividualTest, TestIndiv4) {
+ for (auto fuzzyFlavor = 0 ; fuzzyFlavor <= 1 ; ++fuzzyFlavor) {
+ auto indiv = indivs4[fuzzyFlavor];
+
// Check genome size
- EXPECT_EQ(81, indiv4->amount_of_dna());
- EXPECT_EQ(81, indiv4->genetic_unit_seq_length(0));
+ EXPECT_EQ(81, indiv->annotated_chromosome_->dna_->length());
- //Â Check RNA list
- std::list<const Rna*> rna_list = indiv4->rna_list();
+ // Check RNA list
+ auto rna_list = indiv->annotated_chromosome_->rnas();
EXPECT_EQ(1, rna_list.size());
- const Rna* rna = rna_list.front();
- EXPECT_EQ(LAGGING, rna->strand());
- EXPECT_EQ(26, rna->promoter_pos());
- EXPECT_FLOAT_EQ(0.8, rna->basal_level());
- EXPECT_EQ(42, rna->transcript_length());
+ const auto* rna = rna_list.front();
+ EXPECT_EQ(Strand::LAGGING, rna->strand_);
+ EXPECT_EQ(26, rna->prom->pos);
+ EXPECT_FLOAT_EQ(0.8, rna->e);
+ EXPECT_EQ(42, rna->length);
// Check protein list
- std::list<Protein*> prot_list = indiv4->protein_list();
+ auto prot_list = indiv->annotated_chromosome_->proteins();
EXPECT_EQ(1, prot_list.size());
- Protein* prot = prot_list.front();
- EXPECT_EQ(LAGGING, prot->strand());
- EXPECT_EQ(76, prot->shine_dal_pos());
- EXPECT_EQ(4, prot->length());
- EXPECT_FLOAT_EQ(0.8, prot->concentration());
- EXPECT_EQ(1, prot->rna_list().size());
+
+ const auto* prot = prot_list.front();
+ EXPECT_EQ(Strand::LAGGING, prot->strand_);
+ EXPECT_EQ(63, prot->protein_start);
+ EXPECT_EQ(4, prot->protein_length);
+ EXPECT_FLOAT_EQ(0.8, prot->e);
+ EXPECT_EQ(true, prot->is_init_);
+ EXPECT_EQ(1, prot->rna_list_.size());
}
}
-
-// ===========================================================================
-// Protected Methods
-// ===========================================================================
-
-// ===========================================================================
-// Non inline accessors
-// ===========================================================================