def trackselector(block_ptr, string_ptr, data_ptr): b = Block(block_ptr) string = Str(string_ptr) ret = func(b) if not ret: gterror("Track selector callback function must return a string!") string.append_cstr(ret)
def create_new(cls, seqid, start, end): if start > end: raise "start > end" seq_str = Str(str(seqid)) fn = gtlib.gt_region_node_new(seq_str, start, end) n = cls.create_from_ptr(fn, True) return n
def load_str(self, string): err = Error() strg = Str(str(string.encode("utf-8"))) rval = gtlib.gt_style_load_str(self.style, strg._as_parameter_, err._as_parameter_) if rval != 0: gterror(err)
def create_new(cls, seqid, start, end): if start > end: raise Error("start > end") seq_str = Str(str(seqid)) fn = gtlib.gt_region_node_new(seq_str._as_parameter_, start, end) n = cls.create_from_ptr(fn, True) return n
def to_str(self): err = Error() string = Str() if gtlib.gt_style_to_str(self.style, string, err) == 0: return str(string) else: gterror(err)
def to_str(self): err = Error() string = Str() if gtlib.gt_style_to_str(self.style, string._as_parameter_, err._as_parameter_) == 0: return str(string) else: gterror(err)
def create_new(cls, seqid, type, start, end, strand): from gt.extended.strand import strandchars if not strand in strandchars: gterror("Invalid strand '%s' -- must be one of %s" % (strand, strandchars)) s = Str(str(seqid.encode("utf-8"))) fn = gtlib.gt_feature_node_new(s, type, start, end, \ strandchars.index(strand)) n = cls.create_from_ptr(fn, True) n.depth_first = True return n
def get_cstr(self, section, key, gn=None): string = Str() err = Error() rval = gtlib.gt_style_get_str(self.style, section, key, string, gn, err) if rval == STYLE_OK: return str(string) elif rval == STYLE_NOT_SET: return None elif rval == STYLE_ERROR: gterror(err)
def get_cstr(self, section, key, gn=None): string = Str() err = Error() gnp = None if gn: gnp = gn._as_parameter_ rval = gtlib.gt_style_get_str(self.style, section, key, string._as_parameter_, gnp, err._as_parameter_) if rval == STYLE_OK: return str(string) elif rval == STYLE_NOT_SET: return None elif rval == STYLE_ERROR: gterror(err)
def get_caption(self): s = Str(gtlib.gt_block_get_caption(self.block)) return str(s)
def get_seqid(self): strptr = gtlib.gt_genome_node_get_seqid(self.gn) if strptr: return str(Str(strptr)) else: return None
def to_stream(self): from ctypes import string_at s = Str(None) gtlib.gt_graphics_save_to_stream(self.g, s._as_parameter_) return string_at(s.get_mem(), s.length())
def decode_seq(self, encoded): encstr = (c_ubyte * len(encoded))(*encoded) str_p = gtlib.gt_alphabet_decode_seq_to_str(self.alpha, encstr, len(encstr)) s = Str(str_p) return str(s)
def to_stream(self): from ctypes import string_at s = Str(None) gtlib.gt_graphics_save_to_stream(self.g, s) return string_at(s.get_mem(), s.length())
def create_new(cls, description, sequence): seq_str = Str(sequence.encode('UTF-8')) description = description.encode('UTF-8') fn = gtlib.gt_sequence_node_new(description, seq_str._as_parameter_) n = cls.create_from_ptr(fn, True) return n
def set_symbolmap_file(self, fn): gtlib.gt_encseq_encoder_set_symbolmap_file(self.ee, Str(str(fn.encode("utf-8"))))
def set_representation_type(self, sat): gtlib.gt_encseq_encoder_set_access_type(self.ee, Str(str(sat.encode("utf-8"))))
def to_stream(self): from ctypes import string_at str = Str(None) gtlib.gt_canvas_cairo_file_to_stream(self.canvas, str) return string_at(str.get_mem(), str.length())
def create_new(cls, description, sequence): seq_str = Str(str(sequence.encode("utf-8"))) fn = gtlib.gt_sequence_node_new(description, seq_str) n = cls.create_from_ptr(fn, True) return n
def set_source(self, source): s = Str(str(source.encode("utf-8"))) gtlib.gt_feature_node_set_source(self.gn, s._as_parameter_)
def set_cstr(self, section, key, value): string = Str(str(value.encode("utf-8"))) gtlib.gt_style_set_str(self.style, section, key, string)
def to_stream(self): from ctypes import string_at str = Str(None) gtlib.gt_canvas_cairo_file_to_stream(self.canvas, str._as_parameter_) return string_at(str.get_mem(), str.length())
def get_title_w(ptr, str): s = Str(str) title = self.get_title() s.append_cstr(title) return 0
def load_str(self, string): err = Error() strg = Str(str(string).encode("utf-8")) rval = gtlib.gt_style_load_str(self.style, strg, err) if rval != 0: gterror(err)