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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2014 Daniel Standage <daniel.standage@gmail.com>
# Copyright (c) 2008 Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
# Copyright (c) 2008 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 gterror
from gt.core.gtrange import Range
from gt.core.gtstr import Str
from gt.extended.strand import strandchars
from gt.extended.feature_node import FeatureNode
class Block(object):
def __init__(self, ptr):
if ptr == 0 or ptr == None:
gterror("Block pointer cannot be NULL (was: " + str(ptr) +
")")
self.block = gtlib.gt_block_ref(ptr)
self._as_parameter_ = self.block
def __del__(self):
try:
gtlib.gt_block_delete(self.block)
except AttributeError:
pass
def get_range(self):
r = gtlib.gt_block_get_range(self.block)
return (r.start, r.end)
def get_type(self):
return gtlib.gt_block_get_type(self.block).decode('UTF-8')
def has_only_one_fullsize_element(self):
return gtlib.gt_block_has_only_one_fullsize_element(self.block) == \
1
def merge(self, block2):
gtlib.gt_block_merge(self.block, block2._as_parameter_)
def clone(self):
return Block(gtlib.gt_block_clone(self.block))
def get_caption(self):
s = Str(gtlib.gt_block_get_caption(self.block))
return str(s)
def set_strand(self, strand):
if not strand in strandchars:
gterror("Invalid strand '%s' -- must be one of %s" % (strand,
strandchars))
gtlib.gt_block_set_strand(self.block, strandchars.index(strand))
def get_strand(self):
return strandchars[gtlib.gt_block_get_strand(self.block)]
def get_top_level_feature(self):
f = gtlib.gt_block_get_top_level_feature(self.block)
if f != 0:
return FeatureNode.create_from_ptr(f, True)
else:
return None
def get_size(self):
return int(gtlib.gt_block_get_size(self.block))
def from_param(cls, obj):
if not isinstance(obj, Block):
raise TypeError("argument must be a Block")
return obj._as_parameter_
from_param = classmethod(from_param)
def register(cls, gtlib):
from ctypes import c_char_p, c_void_p, c_int, c_ulong
gtlib.gt_block_caption_is_visible.restype = c_int
gtlib.gt_block_caption_is_visible.argtypes = [c_void_p]
gtlib.gt_block_clone.restype = c_void_p
gtlib.gt_block_clone.argtypes = [c_void_p]
gtlib.gt_block_delete.restype = None
gtlib.gt_block_delete.argtypes = [c_void_p]
gtlib.gt_block_get_caption.restype = c_void_p
gtlib.gt_block_get_caption.argtypes = [c_void_p]
gtlib.gt_block_get_range.restype = Range
gtlib.gt_block_get_range.argtypes = [c_void_p]
gtlib.gt_block_get_size.restype = c_ulong
gtlib.gt_block_get_size.argtypes = [c_void_p]
gtlib.gt_block_get_strand.restype = c_int
gtlib.gt_block_get_strand.argtypes = [c_void_p]
gtlib.gt_block_get_top_level_feature.restype = c_void_p
gtlib.gt_block_get_top_level_feature.argtypes = [c_void_p]
gtlib.gt_block_get_type.restype = c_char_p
gtlib.gt_block_get_type.argtypes = [c_void_p]
gtlib.gt_block_has_only_one_fullsize_element.restype = c_int
gtlib.gt_block_has_only_one_fullsize_element.argtypes = [c_void_p]
gtlib.gt_block_merge.restype = None
gtlib.gt_block_merge.argtypes = [c_void_p, c_void_p]
gtlib.gt_block_ref.restype = c_void_p
gtlib.gt_block_ref.argtypes = [c_void_p]
gtlib.gt_block_set_caption_visibility.restype = None
gtlib.gt_block_set_caption_visibility.argtypes = [c_void_p,
c_int]
gtlib.gt_block_set_strand.restype = None
gtlib.gt_block_set_strand.argtypes = [c_void_p, c_int]
register = classmethod(register)
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