def decode(self: object) -> None:
"""The main decoding method of the controller.
Returns
-------
None
Fills all the properties of an object and writes out the original
sequence to a file.
"""
self.bwm = list(BurrosWheeler.reconstruct_bwm(self.seq.read()))
self.original = BurrosWheeler.decode_bwt(self.bwm[-1])
Sequence(self.debwt_output).write(self.original)
def encode(self: object) -> None:
"""The main encoding method of the controller.
Returns
-------
None
Fills all the properties of an object and writes out the
transformed sequence to a file.
"""
self.rotations = list(BurrosWheeler.string_rotations(self.seq.read()))
self.bwm = BurrosWheeler.construct_bwm(self.rotations[-1])
self.bwt = BurrosWheeler.encode_bwt(self.bwm)
Sequence(self.bwt_output).write(self.bwt)
def save_random(self: object) -> None:
"""This method is used to save a randomly generated DNA sequence
to a file.
"""
seq_to_save = self.entry.get()
if seq_to_save:
path = filedialog.asksaveasfilename(
initialdir= os.getcwd(),title="Select File", filetypes=(
("Text Files", "*.txt"), ("all files","*.*")))
if path:
Sequence(path).write(seq_to_save)
messagebox.showinfo("Sequence saved", "The sequence was saved to %s" %(
path))
else:
messagebox.showerror("No sequence entered", "The sequence box is empty")
def encode(self: object) -> None:
"""The main encoding method of the controller.
Returns
-------
None
Fills all the properties of an object and writes out the
compressed sequence to a file.
"""
tree = HuffmanTree(self.seq.read())
tree.get_codings(tree.root)
self.binary = tree.seq_to_binstr()
self.unicode = HuffmanTree.binstr_to_unicode(self.binary)
self.header = tree.codes_to_header()
self.compressed = self.header + self.unicode
Sequence(self.huff_output).write_bytes(self.compressed)
def __init__(self: object, path: str) -> None:
"""Class constructor.
Parameters
----------
path : str
The path of the file to be read.
Returns
-------
None
A class instance.
"""
self.path = os.path.splitext(path)[0]
self.seq = Sequence(path)
self.debwt_output = self.path + '_debwt.txt'
self.bwm = None
self.original = None
def decode(self: object) -> None:
"""The main decoding method of the controller.
Returns
-------
None
Fills all the properties of an object and writes out the
decompressed sequence to a file.
"""
seq = self.seq.read_bytes()
self.header = seq[:seq.index('\n')]
self.unicode = seq[seq.index('\n') + 1:]
re_codes = HuffmanTree.header_to_codes(self.header)
binary = HuffmanTree.unicode_to_binstr(self.unicode)
padding = int(re_codes['pad'])
self.binary = HuffmanTree.remove_padding(binary, padding)
self.decompressed = HuffmanTree.binstr_to_seq(self.binary, re_codes)
Sequence(self.dehuffman_output).write(self.decompressed)
def __init__(self: object, path: str) -> None:
"""Class constructor.
Parameters
----------
path : str
The path of the file to be read.
Returns
-------
None
A class instance.
"""
self.path = os.path.splitext(path)[0]
self.seq = Sequence(path)
self.huff_output = self.path + '_compressed.txt'
self.binary = None
self.header = None
self.unicode = None
self.compressed = None
def generate_random(self: object) -> None:
"""This method is used to generate random sequences of DNA of length
50 and show them inside the random text box tkinter entry.
"""
self.random.set(Sequence.generate(length=50))