def test_acceptance_01(self):
nus = Nussinov('GGGAAAUCC')
ret = nus.compute()
self.assertEqual(len(ret), 3)
self.assertIn(ret, ([(1, 8), (2, 7),
(3, 6)], [(1, 8), (2, 7),
(4, 6)], [(1, 8), (2, 7), (5, 6)]))
def test_acceptance_02(self):
nus = Nussinov('GGAAACCGAAAC')
ret = nus.compute()
self.assertEqual(len(ret), 3)
self.assertIn(ret,([(0,6), (1,5), (7,11)],
[(0,11), (1,5), (6,7)])
)
class NussinovTest(unittest.TestCase):
def setUp(self):
self.basic_data = 'ACGU'
self.basic = Nussinov(self.basic_data)
def test_compute_return(self):
ret = self.basic.compute()
self.assertIsInstance(ret, list)
def test_init_matrix(self):
self.basic._init_matrix()
self.assertEqual(len(self.basic.matrix), len(self.basic_data))
for i in xrange(len(self.basic_data)):
for j in xrange(len(self.basic_data)):
if i-1 <= j:
self.assertEqual(self.basic.matrix[i][j], 0)
else:
self.assertEqual(self.basic.matrix[i][j], -1)
def test_fill_diagonal(self):
self.basic._fill_diagonal(1)
self.assertEqual(self.basic.matrix[1][2], 1)
self.basic._fill_diagonal(2)
self.basic._fill_diagonal(3)
self.assertEqual(self.basic.matrix[0][3], 2)
def test_build_matrix(self):
self.basic._build_matrix()
self.assertEqual(self.basic.matrix[0][3], 2)
self.assertEqual(self.basic.matrix[1][2], 1)
def test_generate_trace(self):
self.basic._build_matrix()
self.basic._generate_trace()
def test_acceptance_01(self):
nus = Nussinov('GGGAAAUCC')
ret = nus.compute()
self.assertEqual(len(ret), 3)
self.assertIn(ret, ([(1,8), (2,7), (3,6)],
[(1,8), (2,7), (4,6)],
[(1,8), (2,7), (5,6)])
)
def test_acceptance_02(self):
nus = Nussinov('GGAAACCGAAAC')
ret = nus.compute()
self.assertEqual(len(ret), 3)
self.assertIn(ret,([(0,6), (1,5), (7,11)],
[(0,11), (1,5), (6,7)])
)
def test_acceptance_03(self):
nus = Nussinov('GCGCGCGCGCGCGCGCGCGCGCGC')
ret = nus.compute()
self.assertEqual(len(ret), 12)
def test_acceptance_01(self):
nus = Nussinov('GGGAAAUCC')
ret = nus.compute()
self.assertEqual(len(ret), 3)
self.assertIn(ret, ([(1,8), (2,7), (3,6)],
[(1,8), (2,7), (4,6)],
[(1,8), (2,7), (5,6)])
)
class NussinovTest(unittest.TestCase):
def setUp(self):
self.basic_data = 'ACGU'
self.basic = Nussinov(self.basic_data)
def test_compute_return(self):
ret = self.basic.compute()
self.assertIsInstance(ret, list)
def test_init_matrix(self):
self.basic._init_matrix()
self.assertEqual(len(self.basic.matrix), len(self.basic_data))
for i in xrange(len(self.basic_data)):
for j in xrange(len(self.basic_data)):
if i - 1 <= j:
self.assertEqual(self.basic.matrix[i][j], 0)
else:
self.assertEqual(self.basic.matrix[i][j], -1)
def test_fill_diagonal(self):
self.basic._fill_diagonal(1)
self.assertEqual(self.basic.matrix[1][2], 1)
self.basic._fill_diagonal(2)
self.basic._fill_diagonal(3)
self.assertEqual(self.basic.matrix[0][3], 2)
def test_build_matrix(self):
self.basic._build_matrix()
self.assertEqual(self.basic.matrix[0][3], 2)
self.assertEqual(self.basic.matrix[1][2], 1)
def test_generate_trace(self):
self.basic._build_matrix()
self.basic._generate_trace()
def test_acceptance_01(self):
nus = Nussinov('GGGAAAUCC')
ret = nus.compute()
self.assertEqual(len(ret), 3)
self.assertIn(ret, ([(1, 8), (2, 7),
(3, 6)], [(1, 8), (2, 7),
(4, 6)], [(1, 8), (2, 7), (5, 6)]))
def test_acceptance_02(self):
nus = Nussinov('GGAAACCGAAAC')
ret = nus.compute()
self.assertEqual(len(ret), 3)
self.assertIn(ret, ([(0, 6), (1, 5), (7, 11)], [(0, 11), (1, 5),
(6, 7)]))
def test_acceptance_03(self):
nus = Nussinov('GCGCGCGCGCGCGCGCGCGCGCGC')
ret = nus.compute()
self.assertEqual(len(ret), 12)
def RunAlgorithm(self):
i = 0
text = self.RnaCodeTextEdit.toPlainText()
TextList = text.split(QRegExp("\\s+"))
if TextList.count() - 1 == 0:
msgBox = QMessageBox()
msgBox.setText("Can't run algorithm without data!")
msgBox.exec_()
return
self.ResultTabView.setRowCount(TextList.count())
for line in TextList:
nuss = Nussinov(line)
ret = nuss.compute()
item1 = QTableWidgetItem(line)
item2 = QTableWidgetItem(QString(("%s\n" % (ret))))
self.ResultTabView.setItem(i, 0, item1)
self.ResultTabView.setItem(i, 1, item2)
i = i + 1
#self.ResultTabView. .write("%s %s\n" % (len(ret), ret))
self.ResultTabView.resizeColumnsToContents()
def RunAlgorithm(self):
i = 0
text = self.RnaCodeTextEdit.toPlainText()
TextList = text.split(QRegExp("\\s+"))
if TextList.count() -1 == 0 :
msgBox = QMessageBox()
msgBox.setText("Can't run algorithm without data!")
msgBox.exec_()
return
self.ResultTabView.setRowCount(TextList.count())
for line in TextList:
nuss = Nussinov(line)
ret = nuss.compute()
item1 = QTableWidgetItem(line)
item2 = QTableWidgetItem(QString(("%s\n" % (ret)) ))
self.ResultTabView.setItem(i,0,item1)
self.ResultTabView.setItem(i,1,item2)
i = i + 1
#self.ResultTabView. .write("%s %s\n" % (len(ret), ret))
self.ResultTabView.resizeColumnsToContents()
#!/usr/bin/python
from file_reader import *
from nussinov import Nussinov
if __name__ == "__main__":
input_path = 'test_data'
output_path = 'out'
out = open(output_path, 'w')
reader = FileReader(input_path)
for line in reader:
nuss = Nussinov(line)
ret = nuss.compute()
out.write("%s %s\n" % (len(ret), ret))
out.close()
def test_acceptance_03(self):
nus = Nussinov('GCGCGCGCGCGCGCGCGCGCGCGC')
ret = nus.compute()
self.assertEqual(len(ret), 12)
def test_acceptance_03(self):
nus = Nussinov('GCGCGCGCGCGCGCGCGCGCGCGC')
ret = nus.compute()
self.assertEqual(len(ret), 12)
def test_acceptance_02(self):
nus = Nussinov('GGAAACCGAAAC')
ret = nus.compute()
self.assertEqual(len(ret), 3)
self.assertIn(ret, ([(0, 6), (1, 5), (7, 11)], [(0, 11), (1, 5),
(6, 7)]))
#!/usr/bin/python
from file_reader import *
from nussinov import Nussinov
if __name__ == "__main__":
input_path = 'test_data'
output_path = 'out'
out = open(output_path, 'w')
reader = FileReader(input_path)
for line in reader:
nuss = Nussinov(line)
ret = nuss.compute()
out.write("%s %s\n" % (len(ret), ret))
out.close()
