def align(self, hard_region1, hard_region2):
len1 = align_util.get_character_lengths(hard_region1)
number_of_soft_regions1 = len(hard_region1)
len2 = align_util.get_character_lengths(hard_region2)
number_of_soft_regions2 = len(hard_region2)
if (self.alignment_type == 'original'):
alignment = self._seq_align(len1, len2, number_of_soft_regions1,
number_of_soft_regions2)
elif (self.alignment_type == 'extended'):
alignment = self._seq_align_extended(len1, len2,
number_of_soft_regions1,
number_of_soft_regions2)
if (self.output_format == 'text_tuples'):
(output_alignment, indices_mapping) = \
align_util.convert_bead_to_tuples(alignment, hard_region1, hard_region2)
if (self.print_flag):
align_util.print_alignment_text_mapping(output_alignment)
elif (self.output_format == 'index_tuples'):
(text_mapping, output_alignment) = \
align_util.convert_bead_to_tuples(alignment, hard_region1, hard_region2)
if (self.print_flag):
align_util.print_alignment_index_mapping(output_alignment)
else: # the Gale-Church alignment "bead" objects - a dictionary of objects
output_alignment = alignment
if (self.print_flag):
align_util.print_alignments(output_alignment, hard_region1,
hard_region2)
return output_alignment
def align(self, hard_region1, hard_region2):
len1 = align_util.get_character_lengths(hard_region1)
number_of_soft_regions1 = len(hard_region1)
len2 = align_util.get_character_lengths(hard_region2)
number_of_soft_regions2 = len(hard_region2)
if (self.alignment_type == 'original'):
alignment = self._seq_align(len1, len2, number_of_soft_regions1, number_of_soft_regions2)
elif (self.alignment_type == 'extended'):
alignment = self._seq_align_extended(len1, len2, number_of_soft_regions1, number_of_soft_regions2)
if (self.output_format == 'text_tuples'):
(output_alignment, indices_mapping) = \
align_util.convert_bead_to_tuples(alignment, hard_region1, hard_region2)
if (self.print_flag):
align_util.print_alignment_text_mapping(output_alignment)
elif (self.output_format == 'index_tuples'):
(text_mapping, output_alignment) = \
align_util.convert_bead_to_tuples(alignment, hard_region1, hard_region2)
if (self.print_flag):
align_util.print_alignment_index_mapping(output_alignment)
else: # the Gale-Church alignment "bead" objects - a dictionary of objects
output_alignment = alignment
if (self.print_flag):
align_util.print_alignments(output_alignment, hard_region1, hard_region2)
return output_alignment
def recursive_align(self, source, target, alignments):
"""
Apply L{self.align()} to the elements of the C{source} and C{target}
texts in a top-down manner
@rtype: C{list} of I{alignments}
"""
standard_alignment = self.align(source, target)
alignments.append(standard_alignment)
alignment_mapping = None
if (self.output_format == 'text_tuples'):
alignment_mapping = standard_alignment
import align_util
if (self.output_format == 'bead_objects'):
(alignment_mapping, alignment_mapping_indices) = align_util.convert_bead_to_tuples(standard_alignment, source, target)
for entry in alignment_mapping:
source_list = [item for item in entry[0]]
target_list = [item for item in entry[1]]
if len(source_list) == 0 or len(target_list) == 0:
break
if not(isinstance(source_list[0], list)) or not(isinstance(target_list[0], list)):
break
lower_align = self.recursive_align(source_list, target_list, alignments)
return alignments
