def test_get_coord(self):
"""MagePoint _get_coord should return coordinate that is asked for"""
m = MagePoint([0, 1, 2])
self.assertEqual(m.X, m.Coordinates[0])
self.assertEqual(m.Y, m.Coordinates[1])
self.assertEqual(m.Z, m.Coordinates[2])
m = MagePoint()
self.assertEqual(m.X, m.Coordinates[0])
self.assertEqual(m.Y, m.Coordinates[1])
self.assertEqual(m.Z, m.Coordinates[2])
def setUp(self):
"""Define a few standard points and lists of points."""
self.null = MagePoint([0, 0, 0])
self.label = MagePoint([1, 1, 1], 'test')
self.properties = MagePoint(Width=1, Label='point', State='L',\
Color='blue', Coordinates=[2.0,4.0,6.0])
self.radius1 = MagePoint([2, 2, 2], Radius=.1)
self.radius2 = MagePoint([3, 3, 3], Radius=.5)
self.first_list = [self.null, self.properties]
self.empty_list = []
self.minimal_list = [self.null]
self.single_list = [self.label]
self.multi_list = [self.properties] * 10
self.radii = [self.radius1, self.radius2]
def test_set_coord(self):
"""MagePoint _get_coord should return coordinate that is asked for"""
m = MagePoint([0, 1, 2])
m.X, m.Y, m.Z = 2, 3, 4
self.assertEqual(m.Coordinates, [2, 3, 4])
m = MagePoint()
m.X, m.Y, m.Z = 5, 4, 3
self.assertEqual(m.Coordinates, [5, 4, 3])
m = MagePoint()
m.X = 5
self.assertEqual(m.Coordinates, [5, 0, 0])
def setUp(self):
self.point = MagePoint([0, 0, 0], 'x')
self.ml = MageList([self.point], Label='y', Color='green')
self.mg1 = MageGroup([self.ml], Label='z')
self.mg2 = MageGroup([self.ml, self.ml], Label='b')
self.kin = Kinemage(1)
self.kin.Groups = [self.mg1, self.mg2]
def test_fromCartesian(self):
"""MageList fromCartesian() should return new list with ACG coordinates
"""
point = MagePoint([.1, .2, .3])
m = MageList([point] * 5, Color='green')
res = m.toCartesian().fromCartesian()
self.assertEqual(str(m), str(res))
def test_init(self):
"""MagePoint should init correctly with normal cases"""
#label and coords
m = MagePoint([0.200, 0.000, 0.800], '0.800')
self.assertEqual(str(m), '{0.800} ' + \
' '.join(map(str, ([0.200,0.000,0.800]))))
#coords only
m = MagePoint([0.200, 0.000, 0.800])
self.assertEqual(str(m), ' '.join(map(str, ([0.200, 0.000, 0.800]))))
#label only
m = MagePoint(Label='abc')
self.assertEqual(str(m), '{abc} ' + ' '.join(map(str, [0, 0, 0])))
#all fields occupied
m = MagePoint(Label='abc', Coordinates=[3, 6, 1.5], Radius=0.5, \
Width=2, State='P', Color='green')
self.assertEqual(str(m), \
'{abc} P green width2 r=0.5 3 6 1.5')
def test_fromCartesian(self):
"""MageGroup fromCartesian should return a new MageGroup"""
point = MagePoint([.1, .2, .3])
l = MageList([point] * 5, Color='red')
m = MageGroup([l], Radius=0.02, Subgroup=True)
mg = MageGroup([m])
res = mg.toCartesian().fromCartesian()
self.assertEqual(str(mg), str(res))
def test_fromCartesian(self):
"""MagePoint fromCartesian should transform coordinates correctly"""
mp = MagePoint([2/3.0,1/3.0,2/3.0])
self.assertFloatEqual(mp.fromCartesian().Coordinates,[1/3.0,1/3.0,0])
points = [MagePoint([.1,.2,.3]),MagePoint([.25,.25,.25],Color='red',
Label='label',State='L'),MagePoint([1/3,1/3,0]),
MagePoint([0,0,0]),MagePoint([1/7,2/7,3/7])]
for m in points:
b = m.toCartesian().fromCartesian()
self.assertFloatEqual(m.Coordinates,b.Coordinates)
self.assertEqual(m.Color,b.Color)
self.assertEqual(m.Label,b.Label)
self.assertEqual(m.State,b.State)
#even after multiple iterations?
mutant = deepcopy(m)
for x in range(10):
mutant = mutant.toCartesian().fromCartesian()
self.assertFloatEqual(m.Coordinates,mutant.Coordinates)
def test_fromCartesian(self):
"""Kinemage fromCartesian should return Kinemage with A,C,G(,U) coords
"""
point = MagePoint([.1, .2, .3])
l = MageList([point] * 5, Color='red')
m1 = MageGroup([l], Radius=0.02, Subgroup=True)
m2 = MageGroup([l], Radius=0.02)
mg = MageGroup([m1])
k = Kinemage(Count=1, Groups=[mg, m2])
res = k.toCartesian().fromCartesian()
self.assertEqual(str(k), str(res))
def setUp(self):
"""Define some standard lists and groups."""
self.p1 = MagePoint([0, 1, 0], Color='green', Label='x')
self.p0 = MagePoint([0, 0, 0])
self.min_list = MageList([self.p0] * 2, 'y')
self.max_list = MageList([self.p1]*5,'z',Color='blue',Off=True, \
Style='ball')
self.min_group = MageGroup([self.min_list], Label="min_group")
self.max_group = MageGroup([self.min_list, self.max_list],
Color='red',
Label="max_group",
Style='dot')
self.nested = MageGroup([self.min_group, self.max_group],
Label='nest',
Color='orange',
Radius=0.3,
Style='vector')
self.empty = MageGroup(Label='empty',
Color='orange',
NoButton=True,
Style='vector',
RecessiveOn=False)
def test_set_coord(self):
"""MagePoint _get_coord should return coordinate that is asked for"""
m = MagePoint([0,1,2])
m.X, m.Y, m.Z = 2,3,4
self.assertEqual(m.Coordinates,[2,3,4])
m = MagePoint()
m.X, m.Y, m.Z = 5,4,3
self.assertEqual(m.Coordinates,[5,4,3])
m = MagePoint()
m.X = 5
self.assertEqual(m.Coordinates,[5,0,0])
def test_fromCartesian(self):
"""MagePoint fromCartesian should transform coordinates correctly"""
mp = MagePoint([2 / 3.0, 1 / 3.0, 2 / 3.0])
self.assertFloatEqual(mp.fromCartesian().Coordinates,
[1 / 3.0, 1 / 3.0, 0])
points = [
MagePoint([.1, .2, .3]),
MagePoint([.25, .25, .25], Color='red', Label='label', State='L'),
MagePoint([1 / 3, 1 / 3, 0]),
MagePoint([0, 0, 0]),
MagePoint([1 / 7, 2 / 7, 3 / 7])
]
for m in points:
b = m.toCartesian().fromCartesian()
self.assertFloatEqual(m.Coordinates, b.Coordinates)
self.assertEqual(m.Color, b.Color)
self.assertEqual(m.Label, b.Label)
self.assertEqual(m.State, b.State)
#even after multiple iterations?
mutant = deepcopy(m)
for x in range(10):
mutant = mutant.toCartesian().fromCartesian()
self.assertFloatEqual(m.Coordinates, mutant.Coordinates)
def test_toCartesian(self):
"""MagePoint toCartesian() should transform coordinates correctly"""
m = MagePoint([.1, .2, .3])
self.assertEqual(m.toCartesian().Coordinates, [.6, .7, .5])
m = MagePoint()
self.assertEqual(m.toCartesian().Coordinates, [1, 1, 1])
m = MagePoint([.25, .25, .25], Color='red', Label='label', State='L')
self.assertEqual(m.toCartesian().Coordinates, [.5, .5, .5])
self.assertEqual(m.toCartesian().Color, m.Color)
self.assertEqual(m.toCartesian().Label, m.Label)
self.assertEqual(m.toCartesian().State, m.State)
m = MagePoint([1 / 3.0, 1 / 3.0, 0])
self.assertFloatEqual(m.toCartesian().Coordinates,
[2 / 3.0, 1 / 3.0, 2 / 3.0])
m = MagePoint([1 / 3.0, 1 / 3.0, 1 / 3.0])
self.assertFloatEqual(m.toCartesian().Coordinates,
[1 / 3.0, 1 / 3.0, 1 / 3.0])
m = MagePoint([3, 4, 5])
self.assertRaises(ValueError, m.toCartesian)
def test_cmp(self):
"""MagePoint cmp should compare all fields"""
self.assertEqual(MagePoint([0, 0, 0]), MagePoint([0, 0, 0]))
self.assertNotEqual(MagePoint([0, 0, 0]),
MagePoint([0, 0, 0], Color='red'))
def test_init_empty(self):
"""MagePoint should init correctly with no data"""
m = MagePoint()
self.assertEqual(str(m), ' '.join(map(str, [0, 0, 0])))
def test_toCartesian(self):
"""MagePoint toCartesian() should transform coordinates correctly"""
m = MagePoint([.1,.2,.3])
self.assertEqual(m.toCartesian().Coordinates,[.6,.7,.5])
m = MagePoint()
self.assertEqual(m.toCartesian().Coordinates,[1,1,1])
m = MagePoint([.25,.25,.25],Color='red',Label='label',State='L')
self.assertEqual(m.toCartesian().Coordinates,[.5,.5,.5])
self.assertEqual(m.toCartesian().Color,m.Color)
self.assertEqual(m.toCartesian().Label,m.Label)
self.assertEqual(m.toCartesian().State,m.State)
m = MagePoint([1/3.0,1/3.0,0])
self.assertFloatEqual(m.toCartesian().Coordinates,
[2/3.0,1/3.0,2/3.0])
m = MagePoint([1/3.0,1/3.0,1/3.0])
self.assertFloatEqual(m.toCartesian().Coordinates,
[1/3.0,1/3.0,1/3.0])
m = MagePoint([3,4,5])
self.assertRaises(ValueError,m.toCartesian)
def MagePointFromString(line):
"""Constructs a new MagePoint from a one-line string."""
#handle the label if there is one: note that it might contain spaces
line = line.strip()
result = MagePoint()
label = extract_delimited(line, '{', '}')
if label:
pieces = line.replace('{'+label+'}', '').split()
else:
pieces = line.split()
fields = []
#also have to take into account the possibility of comma-delimited parts
for p in pieces:
fields.extend(filter(None, p.split(',')))
pieces = fields
result.Label = label
#get the coordinates and remove them from the list of items
result.Coordinates = map(float, pieces[-3:])
pieces = pieces[:-3]
#parse the remaining attributes in more detail
result.State = None
result.Width = None
result.Radius = None
result.Color = None
for attr in pieces:
#handle radius
if attr.startswith('r='): #radius: note case sensitivity
result.Radius = float(attr[2:])
#handle single-character attributes
elif len(attr) == 1:
result.State = attr
#handle line width
elif attr.startswith('width'):
result.Width = int(attr[5:])
else:
#otherwise assume it's a color label
result.Color = attr
return result
def test_toCartesian(self):
"""MagePoint toCartesian() should transform coordinates correctly"""
m = MagePoint([0.1, 0.2, 0.3])
self.assertEqual(m.toCartesian().Coordinates, [0.6, 0.7, 0.5])
m = MagePoint()
self.assertEqual(m.toCartesian().Coordinates, [1, 1, 1])
m = MagePoint([0.25, 0.25, 0.25], Color="red", Label="label", State="L")
self.assertEqual(m.toCartesian().Coordinates, [0.5, 0.5, 0.5])
self.assertEqual(m.toCartesian().Color, m.Color)
self.assertEqual(m.toCartesian().Label, m.Label)
self.assertEqual(m.toCartesian().State, m.State)
m = MagePoint([1 / 3.0, 1 / 3.0, 0])
self.assertFloatEqual(m.toCartesian().Coordinates, [2 / 3.0, 1 / 3.0, 2 / 3.0])
m = MagePoint([1 / 3.0, 1 / 3.0, 1 / 3.0])
self.assertFloatEqual(m.toCartesian().Coordinates, [1 / 3.0, 1 / 3.0, 1 / 3.0])
m = MagePoint([3, 4, 5])
self.assertRaises(ValueError, m.toCartesian)