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Diffstat (limited to 'exon_position.py')
| -rw-r--r-- | exon_position.py | 118 |
1 files changed, 118 insertions, 0 deletions
diff --git a/exon_position.py b/exon_position.py new file mode 100644 index 0000000..efe560a --- /dev/null +++ b/exon_position.py @@ -0,0 +1,118 @@ +# coding: UTF8 +# Copyright 2009 Thomas Jourdan +# +# 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 3 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, write to the Free Software +# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + +import random +import cairo +import ka_extensionpoint +import ka_random +import model_constraintpool +import model_allele + +EPSILON = 0.00001 +POSITION_CONSTRAINT = 'positionconstraint' + +class Position(model_allele.Allele): + """Position + """ + + cdef = [{'bind' : POSITION_CONSTRAINT, + 'name' : 'Position', + 'domain': model_constraintpool.STRING_1_OF_N, + 'enum' : ka_extensionpoint.list_extensions(POSITION_CONSTRAINT) + }, + ] + + def __init__(self, trunk, x_pos, y_pos): + """Position constructor + """ + super(Position, self).__init__(trunk) + cpool = model_constraintpool.ConstraintPool.get_pool() + constraint_name = cpool.get(self, POSITION_CONSTRAINT)[0] + self.constraint = ka_extensionpoint.create(constraint_name, self.path) + self.x_pos, self.y_pos = self.constraint.filter(x_pos, y_pos) + + def __eq__(self, other): + """Equality based on color components.""" + return isinstance(other, Position) \ + and abs(self.x_pos - other.x_pos) < EPSILON \ + and abs(self.y_pos - other.y_pos) < EPSILON + + def randomize(self): + """Set x_pos, y_pos to random values.""" + cpool = model_constraintpool.ConstraintPool.get_pool() + constraints = cpool.get(self, POSITION_CONSTRAINT) + self.constraint = ka_extensionpoint.create(random.choice(constraints), self.path) + self.x_pos, self.y_pos = self.constraint.randomize() + + def mutate(self): + """Make small random changes in position.""" + if ka_random.is_mutating(): + if ka_random.is_mutating(): + cpool = model_constraintpool.ConstraintPool.get_pool() + constraints = cpool.get(self, POSITION_CONSTRAINT) + self.constraint = ka_extensionpoint.create(random.choice(constraints), self.path) + self.x_pos, self.y_pos = self.constraint.mutate(self.x_pos, self.y_pos) + + def shuffle(self): + """Exchange x- and y-coordinate.""" + temp0, temp1 = self.x_pos, self.y_pos + self.x_pos, self.y_pos = temp1, temp0 + + def crossingover(self, other): + """Returns either a copy of self or a copy of other. + pre: isinstance(other, Position) + # check for distinct references, needs to copy content, not references + post: __return__ is not self + post: __return__ is not other + """ + randseq = ka_random.crossing_sequence(1) + return self.copy() if randseq[0] else other.copy() + + def copy(self): + """A position copy constructor + post: isinstance(__return__, Position) + # check for distinct references, needs to copy content, not references + post: __return__ is not self + """ + new_one = Position(self.get_trunk(), 0.0, 0.0) + new_one.x_pos, new_one.y_pos = self.x_pos, self.y_pos + new_one.constraint = self.constraint + return new_one + + def explain(self): + return u'%4.3f, %4.3f' % (self.x_pos, self.y_pos) + + @staticmethod + def make_icon(position_list, width, height): + surface = cairo.ImageSurface(cairo.FORMAT_ARGB32, width, height) + ctx = cairo.Context(surface) + ctx.scale(width, height) + # paint background + ctx.set_operator(cairo.OPERATOR_OVER) + ctx.set_source_rgb(1.0, 1.0, 1.0) + ctx.paint() + radius = 0.1 + ctx.set_line_width(0.02) + for position in position_list: + # paint a cross for each position + ctx.set_source_rgb(0.0, 0.0, 0.0) + ctx.move_to(position.x_pos-radius, position.y_pos-radius) + ctx.line_to(position.x_pos+radius, position.y_pos+radius) + ctx.move_to(position.x_pos+radius, position.y_pos-radius) + ctx.line_to(position.x_pos-radius, position.y_pos+radius) + ctx.stroke() + return surface |