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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/CONCEPT/classTest.h>
#include <BALLTestConfig.h>
///////////////////////////
#include <BALL/KERNEL/nucleicAcid.h>
#include <BALL/KERNEL/nucleotide.h>
#include <BALL/CONCEPT/textPersistenceManager.h>
///////////////////////////
START_TEST(NucleicAcid)
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
using namespace BALL;
String filename;
NucleicAcid* r;
CHECK(NucleicAcid() throw())
r = new NucleicAcid;
TEST_NOT_EQUAL(r, 0)
RESULT
CHECK(~NucleicAcid() throw())
delete r;
RESULT
CHECK(NucleicAcid(const NucleicAcid& nucleic_acid, bool deep = true) throw())
NucleicAcid* na1 = new NucleicAcid;
na1->setName("testname");
Nucleotide a("a");
na1->insert(a);
NucleicAcid* na2 = new NucleicAcid(*na1, true);
TEST_NOT_EQUAL(na2, 0)
if (na2 != 0)
{
TEST_EQUAL(na2->getName(), "testname")
TEST_EQUAL(na2->getNucleotide(0)->getName(), "a")
delete na2;
}
na2 = new NucleicAcid(*na1, false);
TEST_NOT_EQUAL(na2, 0)
if (na2 != 0)
{
TEST_EQUAL(na2->getName(), "testname")
delete na2;
}
delete na1;
RESULT
CHECK(NucleicAcid(const String& name, const String& id = BALL_NUCLEICACID_DEFAULT_ID) throw())
NucleicAcid* na1 = new NucleicAcid("na1", "id");
TEST_NOT_EQUAL(na1, 0)
if (na1 != 0)
{
TEST_EQUAL(na1->getName(), "na1")
TEST_EQUAL(na1->getID(), "id")
delete na1;
}
NucleicAcid* na2 = new NucleicAcid("na1");
TEST_NOT_EQUAL(na2, 0)
if (na2 != 0)
{
TEST_EQUAL(na2->getName(), "na1")
TEST_EQUAL(na2->getID(), "")
delete na2;
}
RESULT
CHECK(void clear() throw())
NucleicAcid na("na1", "id");
Nucleotide a("a");
na.insert(a);
na.clear();
TEST_EQUAL(na.countNucleotides(), 0)
TEST_EQUAL(na.getID(), "")
RESULT
CHECK(void destroy() throw())
NucleicAcid na("na1", "id");
Nucleotide a("a");
na.insert(a);
na.destroy();
TEST_EQUAL(na.countNucleotides(), 0)
TEST_EQUAL(na.getID(), "")
RESULT
CHECK(void set(const NucleicAcid& nucleic_acid, bool deep = true) throw())
NucleicAcid na1("na1");
Nucleotide a("a");
na1.insert(a);
NucleicAcid na2("na2");
na2.set(na1, false);
TEST_EQUAL(na2.getName(), "na1")
TEST_EQUAL(na2.countNucleotides(), 0)
na2.setName("a");
na2.set(na1);
TEST_EQUAL(na2.getName(), "na1")
TEST_EQUAL(na2.countNucleotides(), 1)
RESULT
CHECK(NucleicAcid& operator = (const NucleicAcid& nucleic_acid) throw())
NucleicAcid na1("na1");
Nucleotide a("a");
na1.insert(a);
NucleicAcid na2("na2");
na2 = na1;
TEST_EQUAL(na2.getName(), "na1")
TEST_EQUAL(na2.countNucleotides(), 1)
RESULT
CHECK(void get(NucleicAcid& nucleic_acid, bool deep = true) const throw())
NucleicAcid na1("na1");
Nucleotide a("a");
na1.insert(a);
NucleicAcid na2("na2");
na1.get(na2, false);
TEST_EQUAL(na2.getName(), "na1")
TEST_EQUAL(na2.countNucleotides(), 0)
na2.setName("a");
na1.get(na2);
TEST_EQUAL(na2.getName(), "na1")
TEST_EQUAL(na2.countNucleotides(), 1)
RESULT
CHECK(void swap(NucleicAcid& nucleic_acid) throw())
NucleicAcid na1("na1");
NucleicAcid na2("na2");
Nucleotide n1("n1");
Nucleotide n2("n2");
na1.insert(n1);
na2.insert(n2);
na1.swap(na2);
TEST_EQUAL(na1.getName(), "na2")
TEST_EQUAL(na1.getNucleotide(0), &n2)
TEST_EQUAL(na2.getName(), "na1")
TEST_EQUAL(na2.getNucleotide(0), &n1)
RESULT
CHECK(Nucleotide* get3Prime() throw())
NucleicAcid na1("na1");
Nucleotide n1("n1");
na1.insert(n1);
na1.get3Prime()->setName("X");
TEST_EQUAL(na1.get3Prime()->getName(), "X")
RESULT
CHECK(const Nucleotide* get3Prime() const throw())
NucleicAcid na1("na1");
TEST_EQUAL(na1.get3Prime(), 0)
Nucleotide n1("n1");
Nucleotide n2("n2");
Nucleotide n3("n3");
na1.insert(n1);
TEST_EQUAL(na1.get3Prime(), &n1)
na1.insert(n2);
TEST_EQUAL(na1.get3Prime(), &n1)
na1.prepend(n3);
TEST_EQUAL(na1.get3Prime(), &n3)
RESULT
CHECK(Nucleotide* get5Prime() throw())
NucleicAcid na1("na1");
Nucleotide n1("n1");
na1.insert(n1);
na1.get5Prime()->setName("X");
TEST_EQUAL(na1.get5Prime()->getName(), "X")
RESULT
CHECK(const Nucleotide* get5Prime() const throw())
NucleicAcid na1("na1");
TEST_EQUAL(na1.get5Prime(), 0)
Nucleotide n1("n1");
Nucleotide n2("n2");
Nucleotide n3("n3");
na1.insert(n1);
TEST_EQUAL(na1.get5Prime(), &n1)
na1.prepend(n2);
TEST_EQUAL(na1.get5Prime(), &n1)
na1.insert(n3);
TEST_EQUAL(na1.get5Prime(), &n3)
RESULT
CHECK(const String& getID() const throw())
NucleicAcid na1("na1");
TEST_EQUAL(na1.getID(), BALL_NUCLEICACID_DEFAULT_ID)
na1.setID("X");
TEST_EQUAL(na1.getID(), "X")
RESULT
CHECK(void setID(const String& id) throw())
NucleicAcid na1("na1");
na1.setID("");
TEST_EQUAL(na1.getID(), BALL_NUCLEICACID_DEFAULT_ID)
na1.setID("X");
TEST_EQUAL(na1.getID(), "X")
RESULT
CHECK(Size countNucleotides() const throw())
NucleicAcid na1("na1");
TEST_EQUAL(na1.countNucleotides(), 0)
Nucleotide n1("n1");
na1.insert(n1);
TEST_EQUAL(na1.countNucleotides(), 1)
RESULT
CHECK([EXTRA]NucleicAcid::isValid())
NucleicAcid na1("");
TEST_EQUAL(na1.isValid(), true)
na1.setID("");
TEST_EQUAL(na1.isValid(), true)
na1.setID("X");
TEST_EQUAL(na1.isValid(), true)
RESULT
CHECK([EXTRA]NucleicAcid::dump(ostream&, Size))
NucleicAcid na1("NA1");
Nucleotide n1("N1");
na1.insert(n1);
NEW_TMP_FILE(filename)
std::ofstream outfile(filename.c_str(), std::ios::out);
na1.dump(outfile);
outfile.close();
TEST_FILE_REGEXP(filename.c_str(), BALL_TEST_DATA_PATH(NucleicAcid_test.txt))
RESULT
TextPersistenceManager pm;
using namespace RTTI;
NEW_TMP_FILE(filename)
CHECK(void persistentWrite(PersistenceManager& pm, const char* name = 0) const)
std::ofstream ofile(filename.c_str(), std::ios::out);
NucleicAcid* f1 = new NucleicAcid("name1");
Nucleotide* f2= new Nucleotide("name2");
Nucleotide* f3= new Nucleotide("name3");
f1->insert(*f2);
f1->insert(*f3);
pm.setOstream(ofile);
*f1 >> pm;
ofile.close();
delete f1;
RESULT
CHECK(void persistentRead(PersistenceManager& pm))
std::ifstream ifile(filename.c_str());
pm.setIstream(ifile);
PersistentObject* ptr = pm.readObject();
TEST_NOT_EQUAL(ptr, 0)
if (ptr != 0)
{
TEST_EQUAL(isKindOf<NucleicAcid>(ptr), true)
NucleicAcid* f1 = castTo<NucleicAcid>(*ptr);
TEST_EQUAL(f1->getName(), "name1")
TEST_EQUAL(f1->countNucleotides(), 2)
TEST_EQUAL(f1->getNucleotide(0)->getName(), "name2")
TEST_EQUAL(f1->getNucleotide(1)->getName(), "name3")
delete f1;
}
else
{
throw Exception::NullPointer(__FILE__, __LINE__);
}
RESULT
CHECK(bool operator == (const NucleicAcid& nucleic_acid) const throw())
NucleicAcid b1;
NucleicAcid b2;
TEST_EQUAL(b1 == b2, false)
b1 = b2;
TEST_EQUAL(b1 == b1, true)
RESULT
CHECK(bool operator != (const NucleicAcid& nucleic_acid) const throw())
NucleicAcid b1;
NucleicAcid b2;
TEST_EQUAL(b1 != b2, true)
b1 = b2;
TEST_EQUAL(b1 != b1, false)
RESULT
NucleicAcid na1("na1");
Nucleotide n1("n1");
Nucleotide n2("n2");
na1.insert(n1);
na1.insert(n2);
CHECK(BALL_CREATE_DEEP(NucleicAcid))
NucleicAcid* na2 = (NucleicAcid*) na1.create(false, true);
TEST_EQUAL(na2->getName(), "")
TEST_EQUAL(na2->countNucleotides(), 0)
delete na2;
na2 = (NucleicAcid*) na1.create(true, false);
TEST_EQUAL(na2->getName(), "na1")
TEST_EQUAL(na2->countNucleotides(), 2)
delete na2;
RESULT
CHECK(Nucleotide* getNucleotide(Position position) throw())
na1.getNucleotide(0)->setName("na1");
na1.getNucleotide(1)->setName("na2");
TEST_EQUAL(n1.getName(), "na1")
TEST_EQUAL(n2.getName(), "na2")
RESULT
CHECK(const Nucleotide* getNucleotide(Position position) const throw())
const NucleicAcid& na = na1;
TEST_EQUAL(na.getNucleotide(0)->getName(), "na1")
TEST_EQUAL(na.getNucleotide(1)->getName(), "na2")
TEST_EQUAL(na.getNucleotide(2), 0)
RESULT
CHECK([EXTRA] iterators)
NucleicAcid na;
Nucleotide n1,n2;
na.insert(n1);
na.insert(n2);
TEST_EQUAL(&*na.beginNucleotide(), &n1)
TEST_EQUAL(&*--na.endNucleotide(), &n2)
TEST_EQUAL(&*na.rbeginNucleotide(), &n2)
RESULT
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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