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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2014 Daniel Standage <daniel.standage@gmail.com>
# Copyright (c) 2008-2015 Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
# Copyright (c) 2008-2009 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#
from gt.dlload import gtlib
from gt.core.error import Error, gterror
from gt.extended.node_visitor import NodeVisitor
from gt.core.gtstr import Str
from gt.props import cachedproperty
class GenomeNode(object):
def __init__(self):
pass
@classmethod
def create_from_ptr(cls, node_ptr, newref=False):
if node_ptr == 0 or node_ptr == None:
gterror("GenomeNode pointer cannot be NULL (was: " + str(node_ptr) +
")")
n = cls()
if newref:
n.own = True
n.gn = gtlib.gt_genome_node_ref(node_ptr)
else:
n.own = False
n.gn = node_ptr
n._as_parameter_ = n.gn
return n
def __repr__(self):
c = self.__class__.__name__
return "%s(start=%i, end=%i, seqid=\"%s\")" % (c, self.start,
self.end, self.seqid)
def __del__(self):
if self.own:
try:
gtlib.gt_genome_node_delete(self.gn)
except AttributeError:
pass
def __eq__(self, node):
try:
return self.gn == node.gn
except AttributeError:
return False
def from_param(cls, obj):
if not isinstance(obj, GenomeNode):
raise TypeError("argument must be a GenomeNode")
return obj._as_parameter_
from_param = classmethod(from_param)
def get_range(self):
return (gtlib.gt_genome_node_get_start(self.gn), gtlib.gt_genome_node_get_end(self.gn))
range = property(get_range)
def get_seqid(self):
strptr = gtlib.gt_genome_node_get_seqid(self.gn)
if strptr:
return Str(strptr).get()
else:
return None
seqid = cachedproperty(get_seqid)
def get_start(self):
if not self.__class__.__name__ == "EOFNode":
return gtlib.gt_genome_node_get_start(self.gn)
else:
return None
start = cachedproperty(get_start)
def get_end(self):
if not self.__class__.__name__ == "EOFNode":
return gtlib.gt_genome_node_get_end(self.gn)
else:
return None
end = cachedproperty(get_end)
def get_filename(self):
return gtlib.gt_genome_node_get_filename(self.gn)
filename = property(get_filename)
def get_line_number(self):
return gtlib.gt_genome_node_get_line_number(self.gn)
line_number = property(get_line_number)
def accept(self, visitor):
err = Error()
rval = gtlib.gt_genome_node_accept(self.gn, visitor._as_parameter_,
err._as_parameter_)
if rval != 0:
gterror(err)
def register(cls, gtlib):
from ctypes import c_char_p, c_ulong, c_int, c_void_p, c_uint
gtlib.gt_genome_node_get_filename.restype = c_char_p
gtlib.gt_genome_node_get_filename.argtypes = [c_void_p]
gtlib.gt_genome_node_get_start.restype = c_ulong
gtlib.gt_genome_node_get_start.argtypes = [c_void_p]
gtlib.gt_genome_node_get_end.restype = c_ulong
gtlib.gt_genome_node_get_end.argtypes = [c_void_p]
gtlib.gt_genome_node_get_seqid.argtypes = [c_void_p]
gtlib.gt_genome_node_get_seqid.restype = c_void_p
gtlib.gt_genome_node_get_filename.argtypes = [c_void_p]
gtlib.gt_genome_node_get_filename.restype = c_char_p
gtlib.gt_genome_node_get_line_number.argtypes = [c_void_p]
gtlib.gt_genome_node_get_line_number.restype = c_uint
gtlib.gt_genome_node_delete.restype = None
gtlib.gt_genome_node_delete.argtypes = [c_void_p]
gtlib.gt_genome_node_ref.restype = c_void_p
gtlib.gt_genome_node_ref.argtypes = [c_void_p]
gtlib.gt_genome_node_accept.restype = c_int
gtlib.gt_genome_node_accept.argtypes = [c_void_p, c_void_p,
c_void_p]
register = classmethod(register)
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