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# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------
from skbio.metadata._repr import _MetadataReprBuilder
class _TabularMSAReprBuilder(_MetadataReprBuilder):
def __init__(self, msa, width, indent):
super(_TabularMSAReprBuilder, self).__init__(msa, width, indent)
self._ellipse_insert = ' ... '
def _process_header(self):
cls_name = self._obj.__class__.__name__
if self._obj.dtype is not None:
dtype_class = '[' + self._obj.dtype.__name__ + ']'
else:
dtype_class = ''
self._lines.add_line(cls_name + dtype_class)
self._lines.add_separator()
def _process_data(self):
num_sequences = self._obj.shape.sequence
num_positions = self._obj.shape.position
# catch case of all empty sequences
if num_positions > 0:
# display all sequences if we can, else display the first two and
# last two sequences separated by ellipsis
if num_sequences <= 5:
self._lines.add_lines(
self._format_sequences(range(num_sequences)))
else:
self._lines.add_lines(self._format_sequences(range(2)))
self._lines.add_line('...')
self._lines.add_lines(self._format_sequences(
range(num_sequences - 2, num_sequences)))
def _format_sequences(self, sequence_indices):
lines = []
for line_index in sequence_indices:
seq_str = str(self._obj._get_sequence_iloc_(line_index))
if len(seq_str) <= self._width:
formatted_seq = seq_str
else:
formatted_seq = (
seq_str[0:self._num_characters_before_ellipse()] +
self._ellipse_insert +
seq_str[-self._num_characters_after_ellipse():]
)
lines.append(formatted_seq)
return lines
def _num_characters_before_ellipse(self):
return int(self._num_characters_to_display() / 2)
def _num_characters_after_ellipse(self):
return (self._num_characters_to_display() -
self._num_characters_before_ellipse())
def _num_characters_to_display(self):
return self._width - len(self._ellipse_insert)
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