def _get_block_title(self, block):
# if self.is_write_block_titles is False then no block titles;
# if only one taxon set, or attached taxon set mode, unless self.is_write_block_titles
# is explicitly True, then again, we do not write block titles
if not self._link_blocks():
return None
if block in self._block_title_map:
return self._block_title_map[block]
if not block.label:
title = str(id(block))
else:
title = block.label
idx = 1
original_title = title
title = nexusprocessing.escape_nexus_token(
original_title,
preserve_spaces=self.preserve_spaces,
quote_underscores=not self.unquoted_underscores)
while title in self._title_block_map:
raw_title = "{}.{}".format(original_title, idx)
title = nexusprocessing.escape_nexus_token(
raw_title,
preserve_spaces=self.preserve_spaces,
quote_underscores=not self.unquoted_underscores)
idx += 1
self._title_block_map[title] = block
self._block_title_map[block] = title
return title
def _get_block_title(self, block):
# if self.is_write_block_titles is False then no block titles;
# if only one taxon set, or attached taxon set mode, unless self.is_write_block_titles
# is explicitly True, then again, we do not write block titles
if not self._link_blocks():
return None
if block in self._block_title_map:
return self._block_title_map[block]
if not block.label:
title = str(id(block))
else:
title = block.label
idx = 1
original_title = title
title = nexusprocessing.escape_nexus_token(
original_title,
preserve_spaces=self.preserve_spaces,
quote_underscores=not self.unquoted_underscores)
while title in self._title_block_map:
raw_title = "{}.{}".format(original_title, idx)
title = nexusprocessing.escape_nexus_token(
raw_title,
preserve_spaces=self.preserve_spaces,
quote_underscores=not self.unquoted_underscores)
idx += 1
self._title_block_map[title] = block
self._block_title_map[block] = title
return title
def _write_char_block(self, stream, char_matrix):
taxon_label_map = collections.OrderedDict()
for taxon in char_matrix:
taxon_label_map[taxon] = nexusprocessing.escape_nexus_token(taxon.label, preserve_spaces=self.preserve_spaces, quote_underscores=not self.unquoted_underscores)
nchar = max([len(seq) for seq in char_matrix.values()])
if self.simple:
stream.write("BEGIN DATA;\n")
# note that this will only list the number of taxa for
# which sequences are available
ntaxstr = "NTAX={}".format(len(taxon_label_map))
else:
stream.write("BEGIN CHARACTERS;\n")
ntaxstr = ""
self._write_block_title(stream, char_matrix)
self._write_item_annotations(stream, char_matrix)
self._write_item_comments(stream, char_matrix)
self._write_link_to_taxa_block(stream, char_matrix.taxon_namespace)
stream.write(" DIMENSIONS{} NCHAR={};\n".format(ntaxstr, nchar))
stream.write(" FORMAT {};\n".format(self._compose_format_terms(char_matrix)))
stream.write(" MATRIX\n")
if char_matrix.data_type == "continuous":
state_value_writer = lambda x : stream.write("{} ".format(self.continuous_character_state_value_format_fn(x)))
else:
state_value_writer = lambda x : stream.write("{}".format(self.discrete_character_state_value_format_fn(x)))
max_label_len = max(len(v) for v in taxon_label_map.values())
for taxon in char_matrix:
stream.write(" {taxon_label:{field_len}} ".format(taxon_label=taxon_label_map[taxon],
field_len=max_label_len))
for state in char_matrix[taxon]:
state_value_writer(state)
stream.write("\n")
stream.write(" ;\n")
stream.write("END;\n\n\n")
self._write_character_subsets(stream, char_matrix)
def _write_char_block(self, stream, char_matrix):
taxon_label_map = collections.OrderedDict()
for taxon in char_matrix:
taxon_label_map[taxon] = nexusprocessing.escape_nexus_token(taxon.label, preserve_spaces=self.preserve_spaces, quote_underscores=not self.unquoted_underscores)
nchar = max([len(seq) for seq in char_matrix.values()])
if self.simple:
stream.write("BEGIN DATA;\n")
# note that this will only list the number of taxa for
# which sequences are available
ntaxstr = " NTAX={}".format(len(taxon_label_map))
else:
stream.write("BEGIN CHARACTERS;\n")
ntaxstr = ""
self._write_block_title(stream, char_matrix)
self._write_item_annotations(stream, char_matrix)
self._write_item_comments(stream, char_matrix)
self._write_link_to_taxa_block(stream, char_matrix.taxon_namespace)
stream.write(" DIMENSIONS{} NCHAR={};\n".format(ntaxstr, nchar))
stream.write(" FORMAT {};\n".format(self._compose_format_terms(char_matrix)))
stream.write(" MATRIX\n")
if char_matrix.data_type == "continuous":
state_value_writer = lambda x : stream.write("{} ".format(self.continuous_character_state_value_format_fn(x)))
else:
state_value_writer = lambda x : stream.write("{}".format(self.discrete_character_state_value_format_fn(x)))
max_label_len = max(len(v) for v in taxon_label_map.values())
for taxon in char_matrix:
stream.write(" {taxon_label:{field_len}} ".format(taxon_label=taxon_label_map[taxon],
field_len=max_label_len))
for state in char_matrix[taxon]:
state_value_writer(state)
stream.write("\n")
stream.write(" ;\n")
stream.write("END;\n\n\n")
self._write_character_subsets(stream, char_matrix)
def _write_character_subsets(self, stream, char_matrix):
if not hasattr(char_matrix, "character_subsets") or not char_matrix.character_subsets:
return
stream.write("BEGIN SETS;\n")
for label, char_set in char_matrix.character_subsets.items():
label = nexusprocessing.escape_nexus_token(char_set.label,
preserve_spaces=self.preserve_spaces,
quote_underscores=not self.unquoted_underscores)
ranges = nexusprocessing.group_ranges(char_set.character_indices)
pos = " ".join("-".join(str(c+1) for c in r) for r in ranges)
stream.write(" charset {} = {};\n".format(label, pos))
stream.write("END;\n\n\n")
def _write_character_subsets(self, stream, char_matrix):
if not hasattr(char_matrix, "character_subsets") or not char_matrix.character_subsets:
return
stream.write("BEGIN SETS;\n")
for label, char_set in char_matrix.character_subsets.items():
label = nexusprocessing.escape_nexus_token(char_set.label,
preserve_spaces=self.preserve_spaces,
quote_underscores=not self.unquoted_underscores)
ranges = nexusprocessing.group_ranges(char_set.character_indices)
pos = " ".join("-".join(str(c+1) for c in r) for r in ranges)
stream.write(" charset {} = {};\n".format(label, pos))
stream.write("END;\n\n\n")
def _render_node_tag(self, node):
"""
Based on current settings, the attributes of a node, and
whether or not the node is a leaf, returns an appropriate tag.
"""
tag = None
if self.node_label_compose_fn:
tag = self.node_label_compose_fn(node)
else:
tag_parts = []
is_leaf = len(node.child_nodes()) == 0
if is_leaf:
if hasattr(node, 'taxon') \
and node.taxon \
and node.taxon.label is not None \
and not self.suppress_leaf_taxon_labels:
tag_parts.append(self._get_taxon_tree_token(node.taxon))
if hasattr(node, 'label') \
and node.label \
and node.label is not None \
and not self.suppress_leaf_node_labels:
tag_parts.append(str(node.label))
if len(tag_parts) > 0:
tag = self.node_label_element_separator.join(tag_parts)
else:
return "" # anonymous leaf
else:
if hasattr(node, 'taxon') \
and node.taxon \
and node.taxon.label is not None \
and not self.suppress_internal_taxon_labels:
tag_parts.append(self._get_taxon_tree_token(node.taxon))
if hasattr(node, 'label') \
and node.label \
and node.label is not None \
and not self.suppress_internal_node_labels:
tag_parts.append(str(node.label))
if len(tag_parts) > 0:
tag = self.node_label_element_separator.join(tag_parts)
else:
return ""
if tag:
tag = nexusprocessing.escape_nexus_token(
tag,
preserve_spaces=self.preserve_spaces,
quote_underscores=not self.unquoted_underscores)
return tag
else:
return ""
def _write_taxa_block(self, stream, taxon_namespace):
stream.write("BEGIN TAXA;\n")
self._write_block_title(stream, taxon_namespace)
self._write_item_annotations(stream, taxon_namespace)
self._write_item_comments(stream, taxon_namespace)
stream.write(" DIMENSIONS NTAX={};\n".format(len(taxon_namespace)))
stream.write(" TAXLABELS\n")
for taxon in taxon_namespace:
stream.write(" {}\n".format(
nexusprocessing.escape_nexus_token(taxon.label, preserve_spaces=self.preserve_spaces, quote_underscores=not self.unquoted_underscores),
))
self._write_item_annotations(stream, taxon)
self._write_item_comments(stream, taxon)
stream.write(" ;\n")
stream.write("END;\n\n")
def _render_node_tag(self, node):
"""
Based on current settings, the attributes of a node, and
whether or not the node is a leaf, returns an appropriate tag.
"""
tag = None
if self.node_label_compose_fn:
tag = self.node_label_compose_fn(node)
else:
tag_parts = []
is_leaf = len(node.child_nodes()) == 0
if is_leaf:
if hasattr(node, 'taxon') \
and node.taxon \
and node.taxon.label is not None \
and not self.suppress_leaf_taxon_labels:
tag_parts.append(self._get_taxon_tree_token(node.taxon))
if hasattr(node, 'label') \
and node.label \
and node.label is not None \
and not self.suppress_leaf_node_labels:
tag_parts.append(str(node.label))
if len(tag_parts) > 0:
tag = self.node_label_element_separator.join(tag_parts)
else:
return "" # anonymous leaf
else:
if hasattr(node, 'taxon') \
and node.taxon \
and node.taxon.label is not None \
and not self.suppress_internal_taxon_labels:
tag_parts.append(self._get_taxon_tree_token(node.taxon))
if hasattr(node, 'label') \
and node.label \
and node.label is not None \
and not self.suppress_internal_node_labels:
tag_parts.append(str(node.label))
if len(tag_parts) > 0:
tag = self.node_label_element_separator.join(tag_parts)
else:
return ""
if tag:
tag = nexusprocessing.escape_nexus_token(tag,
preserve_spaces=self.preserve_spaces,
quote_underscores=not self.unquoted_underscores)
return tag
else:
return ""
def _write_taxa_block(self, stream, taxon_namespace):
stream.write("BEGIN TAXA;\n")
self._write_block_title(stream, taxon_namespace)
self._write_item_annotations(stream, taxon_namespace)
self._write_item_comments(stream, taxon_namespace)
taxon_to_include = self._get_taxa_to_include(taxon_namespace)
stream.write(" DIMENSIONS NTAX={};\n".format(len(taxon_to_include)))
stream.write(" TAXLABELS\n")
for taxon in taxon_to_include:
stream.write(" {}\n".format(
nexusprocessing.escape_nexus_token(taxon.label, preserve_spaces=self.preserve_spaces, quote_underscores=not self.unquoted_underscores),
))
self._write_item_annotations(stream, taxon)
self._write_item_comments(stream, taxon)
stream.write(" ;\n")
stream.write("END;\n\n")
def _write_trees_block(self, stream, tree_list):
stream.write("BEGIN TREES;\n")
self._write_block_title(stream, tree_list)
self._write_item_annotations(stream, tree_list)
self._write_item_comments(stream, tree_list)
self._write_link_to_taxa_block(stream, tree_list.taxon_namespace)
self._set_and_write_translate_block(stream, tree_list.taxon_namespace)
for tree_idx, tree in enumerate(tree_list):
if tree.label:
tree_name = tree.label
else:
tree_name = str(tree_idx+1)
tree_name = nexusprocessing.escape_nexus_token(
tree_name,
preserve_spaces=self.preserve_spaces,
quote_underscores=not self.unquoted_underscores)
stream.write(" TREE {} = ".format(tree_name))
self._newick_writer._write_tree(stream, tree)
stream.write("\n")
stream.write("END;\n\n")
def _write_trees_block(self, stream, tree_list):
stream.write("BEGIN TREES;\n")
self._write_block_title(stream, tree_list)
self._write_item_annotations(stream, tree_list)
self._write_item_comments(stream, tree_list)
self._write_link_to_taxa_block(stream, tree_list.taxon_namespace)
self._set_and_write_translate_block(stream, tree_list.taxon_namespace)
for tree_idx, tree in enumerate(tree_list):
if tree.label:
tree_name = tree.label
else:
tree_name = str(tree_idx + 1)
tree_name = nexusprocessing.escape_nexus_token(
tree_name,
preserve_spaces=self.preserve_spaces,
quote_underscores=not self.unquoted_underscores)
stream.write(" TREE {} = ".format(tree_name))
self._newick_writer._write_tree(stream, tree)
stream.write("\n")
stream.write("END;\n\n")
def _set_and_write_translate_block(self, stream, taxon_namespace):
if not self.translate_tree_taxa:
self._newick_writer.taxon_token_map = None
return
if self.translate_tree_taxa is True:
m = {}
for taxon_idx, t in enumerate(taxon_namespace):
m[t] = str(taxon_namespace.accession_index(t)+1)
# m[t] = str(taxon_idx)
self._newick_writer.taxon_token_map = m
else:
self._newick_writer.taxon_token_map = dict(self.translate_tree_taxa)
stream.write(" Translate\n")
statement = []
for taxon in taxon_namespace:
label = nexusprocessing.escape_nexus_token(str(taxon.label),
preserve_spaces=self.preserve_spaces,
quote_underscores=not self.unquoted_underscores)
statement.append(" {} {}".format(self._newick_writer.taxon_token_map[taxon], label))
statement = ",\n".join(statement)
stream.write("{}\n ;\n".format(statement))
def _set_and_write_translate_block(self, stream, taxon_namespace):
if not self.translate_tree_taxa:
self._newick_writer.taxon_token_map = None
return
if self.translate_tree_taxa is True:
m = {}
for taxon_idx, t in enumerate(taxon_namespace):
m[t] = str(taxon_namespace.accession_index(t)+1)
# m[t] = str(taxon_idx)
self._newick_writer.taxon_token_map = m
else:
self._newick_writer.taxon_token_map = dict(self.translate_tree_taxa)
stream.write(" Translate\n")
statement = []
for taxon in taxon_namespace:
label = nexusprocessing.escape_nexus_token(str(taxon.label),
preserve_spaces=self.preserve_spaces,
quote_underscores=not self.unquoted_underscores)
statement.append(" {} {}".format(self._newick_writer.taxon_token_map[taxon], label))
statement = ",\n".join(statement)
stream.write("{}\n ;\n".format(statement))
