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/dports/science/py-DendroPy/DendroPy-4.4.0/src/dendropy/legacy/
H A Dpopgenstat.py27 def num_segregating_sites(char_matrix, ignore_uncertain=True): argument
41 …return popgenstat.average_number_of_pairwise_differences(char_matrix=char_matrix, ignore_uncertain…
43 def nucleotide_diversity(char_matrix, ignore_uncertain=True): argument
49 … return popgenstat.nucleotide_diversity(char_matrix=char_matrix, ignore_uncertain=ignore_uncertain)
51 def tajimas_d(char_matrix, ignore_uncertain=True): argument
57 return popgenstat.tajimas_d(char_matrix=char_matrix, ignore_uncertain=ignore_uncertain)
59 def wattersons_theta(char_matrix, ignore_uncertain=True): argument
65 return popgenstat.wattersons_theta(char_matrix=char_matrix, ignore_uncertain=ignore_uncertain)
67 def derived_state_matrix(char_matrix, ancestral_seq=None): argument
74 char_matrix=char_matrix,
[all …]
H A Dseqsim.py42 …char_matrix = dataset.new_char_matrix(char_matrix_type="dna", taxon_namespace=tree_model.taxon_nam…
50 char_matrix=char_matrix,
60 char_matrix=None, argument
73 char_matrix=char_matrix,
H A Dcontinuous.py39 char_matrix, argument
48 char_matrix=char_matrix,
/dports/science/py-DendroPy/DendroPy-4.4.0/src/dendropy/calculate/
H A Dpopgenstat.py170 char_matrix.sequences(),
184 …return _nucleotide_diversity(char_matrix.sequences(), char_matrix.default_state_alphabet, ignore_u…
190 sequences = char_matrix.sequences()
203 sequences = char_matrix.sequences()
338 char_matrix, argument
380 ancestral_sequence = char_matrix[0]
387 for taxon in char_matrix:
388 s1 = char_matrix[taxon]
401 char_matrix, argument
412 char_matrix=char_matrix,
[all …]
/dports/science/py-DendroPy/DendroPy-4.4.0/src/dendropy/dataio/
H A Dphylipwriter.py70 for char_matrix in char_matrices:
72 and char_matrix.taxon_namespace is not self.attached_taxon_namespace):
74 self._write_char_matrix(stream, char_matrix)
76 def _write_char_matrix(self, stream, char_matrix): argument
80 taxon_label_map = self.get_taxon_label_map(char_matrix.taxon_namespace)
87 for taxon in char_matrix.taxon_namespace:
94 n_seqs = len(char_matrix)
95 n_sites = char_matrix.max_sequence_size
97 for taxon in char_matrix.taxon_namespace:
99 if taxon in char_matrix:
[all …]
H A Dnexuswriter.py279 for char_matrix in char_matrices:
282 self._write_char_block(stream=stream, char_matrix=char_matrix)
366 for taxon in char_matrix:
384 if char_matrix.data_type == "continuous":
389 for taxon in char_matrix:
392 for state in char_matrix[taxon]:
399 def _compose_format_terms(self, char_matrix): argument
401 if char_matrix.data_type == "dna":
404 elif char_matrix.data_type == "rna":
410 elif char_matrix.data_type == "protein":
[all …]
H A Dphylipreader.py125 self.char_matrix = None
143 self.char_matrix = None
160 self.char_matrix = char_matrix_factory(
167 self.char_matrix = char_matrix_factory(
199 char_matrices=[self.char_matrix])
222 if current_taxon not in self.char_matrix:
223 self.char_matrix[current_taxon] = self.char_matrix.new_sequence(taxon=current_taxon)
225 if len(self.char_matrix[current_taxon]) >= self.nchar:
242 self.char_matrix[current_taxon].append(state)
254 self.char_matrix[current_taxon].append(state)
[all …]
H A Dnexmlwriter.py179 for char_matrix in char_matrices:
180 self._write_char_matrix(char_matrix=char_matrix, dest=body)
265 if char_matrix.label:
268 if char_matrix.data_type == "dna":
270 elif char_matrix.data_type == "rna":
272 elif char_matrix.data_type == "protein":
290 … if char_matrix.has_annotations or (hasattr(char_matrix, "comments") and char_matrix.comments):
301 for taxon in char_matrix:
302 char_vector = char_matrix[taxon]
590 for taxon in char_matrix:
[all …]
H A Dnexmlreader.py315 char_matrix = self._char_matrix_factory(
320 self._char_matrices.append(char_matrix)
321 return char_matrix
640 char_matrix = self._char_matrix_factory(
649 self._parse_annotations(char_matrix, annotation)
656 self.create_standard_character_alphabet(char_matrix)
748 char_matrix[taxon] = character_vector
877 col = char_matrix.new_character_type()
887 char_matrix.character_types.append(col)
906 char_matrix.state_alphabets.append(state_alphabet)
[all …]
H A Dfastawriter.py50 for char_matrix in char_matrices:
52 and char_matrix.taxon_namespace is not self.attached_taxon_namespace):
54 self._write_char_matrix(stream, char_matrix)
56 def _write_char_matrix(self, stream, char_matrix): argument
57 for taxon in char_matrix:
59 seq = char_matrix[taxon]
H A Dfastareader.py64 char_matrix = char_matrix_factory(
71 char_matrix = char_matrix_factory(
75 symbol_state_map = char_matrix.default_state_alphabet.full_symbol_state_map
85 if curr_taxon in char_matrix:
89 curr_vec = char_matrix[curr_taxon]
107 char_matrices=[char_matrix])
/dports/audio/murmur/mumble-1.3.3/plugins/jc2/
H A Djc2.cpp99 Matrix4 char_matrix; in fetch() local
102 ok = peekProc(char_matrix_ptr, &char_matrix, sizeof(char_matrix)) && in fetch()
108 avatar_pos[0] = char_matrix.pos.x; in fetch()
109 avatar_pos[1] = char_matrix.pos.y; in fetch()
110 avatar_pos[2] = -char_matrix.pos.z; in fetch()
112 avatar_front[0] = char_matrix.front.x; in fetch()
113 avatar_front[1] = char_matrix.front.y; in fetch()
114 avatar_front[2] = char_matrix.front.z; in fetch()
116 avatar_top[0] = char_matrix.top.x; in fetch()
117 avatar_top[1] = char_matrix.top.y; in fetch()
[all …]
/dports/audio/mumble/mumble-1.3.3/plugins/jc2/
H A Djc2.cpp99 Matrix4 char_matrix; in fetch() local
102 ok = peekProc(char_matrix_ptr, &char_matrix, sizeof(char_matrix)) && in fetch()
108 avatar_pos[0] = char_matrix.pos.x; in fetch()
109 avatar_pos[1] = char_matrix.pos.y; in fetch()
110 avatar_pos[2] = -char_matrix.pos.z; in fetch()
112 avatar_front[0] = char_matrix.front.x; in fetch()
113 avatar_front[1] = char_matrix.front.y; in fetch()
114 avatar_front[2] = char_matrix.front.z; in fetch()
116 avatar_top[0] = char_matrix.top.x; in fetch()
117 avatar_top[1] = char_matrix.top.y; in fetch()
[all …]
/dports/science/py-DendroPy/DendroPy-4.4.0/src/dendropy/model/
H A Ddiscrete.py148 char_matrix,
170 return char_matrix
437 char_matrix=None,
439 dataset.add_char_matrix(char_matrix=char_matrix)
448 char_matrix=None, argument
498 if char_matrix is None:
504 char_matrix=char_matrix,
508 return char_matrix
517 char_matrix=None, argument
557 if char_matrix is None:
[all …]
H A Dcontinuous.py46 char_matrix, argument
77 self.char_matrix = char_matrix
95 for idx in range(len(self.char_matrix[0])):
123 def _set_char_matrix(self, char_matrix): argument
124 self._char_matrix = char_matrix
126 char_matrix = property(_get_char_matrix, _set_char_matrix) variable in PhylogeneticIndependentConstrasts
/dports/math/octave/octave-6.4.0/libinterp/operators/
H A Dop-chm.cc43 DEFUNOP (transpose, char_matrix) in DEFUNOP() argument
50 DEFNDCATOP_FN (chm_chm, char_matrix, char_matrix, char_array, char_array, in DEFNDCATOP_FN() argument
53 DEFCATOP (chm_s, char_matrix, scalar) in DEFNDCATOP_FN()
65 DEFCATOP (chm_m, char_matrix, matrix) in DEFCATOP() argument
77 DEFCATOP (s_chm, scalar, char_matrix) in DEFCATOP() argument
89 DEFCATOP (m_chm, matrix, char_matrix) in DEFCATOP() argument
/dports/science/py-DendroPy/DendroPy-4.4.0/src/dendropy/interop/
H A Dmuscle.py28 def muscle_align(char_matrix, muscle_args=None, muscle_path='muscle'): argument
36 stdout, stderr = processio.communicate(p, char_matrix.as_string("fasta"))
39 d = char_matrix.__class__.get_from_string(stdout,
41 taxon_namespace=char_matrix.taxon_namespace)
H A Dpaup.py573 char_matrix, argument
604 char_matrix.write_to_stream(cf, schema='nexus')
635 char_matrix, argument
645 ultrametric_tree = estimate_tree(char_matrix,
662 char_matrix.write_to_stream(cf, schema='nexus')
688 def estimate_tree(char_matrix, argument
712 char_matrix.write_to_stream(cf, schema='nexus', **char_matrix_writing_kwargs)
766 …t = dendropy.Tree.get_from_path(output_tree_filepath, "nexus", taxon_namespace=char_matrix.taxon_n…
771 def estimate_model(char_matrix, argument
794 assert tree_model.taxon_namespace is char_matrix.taxon_namespace
[all …]
/dports/science/py-DendroPy/DendroPy-4.4.0/src/dendropy/datamodel/
H A Ddatasetmodel.py481 for char_matrix in self.char_matrices:
482 char_matrix.migrate_taxon_namespace(
617 def add_char_matrix(self, char_matrix): argument
627 if char_matrix.taxon_namespace not in self.taxon_namespaces:
628 self.taxon_namespaces.add(char_matrix.taxon_namespace)
629 self.char_matrices.add(char_matrix)
630 return char_matrix
644 char_matrix = charmatrixmodel.new_char_matrix(
649 char_matrix = char_matrix_type(*args, **kwargs)
650 return self.add_char_matrix(char_matrix)
H A Dcharmatrixmodel.py530 char_matrix = char_matrices[matrix_offset]
531 if char_matrix.data_type != cls.data_type:
536 char_matrix.data_type,
538 return char_matrix
683 char_matrix=None, argument
748 if char_matrix is None:
749 char_matrix = cls(**kwargs)
756 if taxon not in char_matrix.taxon_namespace:
758 s = char_matrix.coerce_values(source_dict[key])
759 char_matrix[taxon] = s
[all …]
/dports/biology/py-biopython/biopython-1.79/Bio/Phylo/
H A D_utils.py150 char_matrix = [[" " for x in range(drawing_width)] for y in range(drawing_height)]
157 char_matrix[thisrow][col] = "_"
163 char_matrix[row][thiscol] = "|"
166 char_matrix[toprow][thiscol] = ","
173 for idx, row in enumerate(char_matrix):
/dports/emulators/dps8m/dps8m-572f79bb4f0f84a8b16c3892c894c2b9ed64b458/src/punutil/
H A Dpunutil.c614 static void log_char_matrix_pattern(uint8 *char_matrix) in log_char_matrix_pattern() argument
619 fprintf(stderr, " %03o\n", char_matrix[col_offset]); in log_char_matrix_pattern()
627 if ((char_matrix[col] >> (4 - row)) & 0x1) in log_char_matrix_pattern()
678 uint8 char_matrix[CHAR_MATRIX_BYTES]; in get_lace_char() local
682 char_matrix[col_offset] = (col_buffer[col_offset] >> (top ? 6 : 0)) & 0x1F; in get_lace_char()
685 char c = search_glyph_patterns(char_matrix); in get_lace_char()
/dports/www/chromium-legacy/chromium-88.0.4324.182/third_party/llvm/lldb/test/API/lang/c/array_types/
H A Dmain.c14 char char_matrix[3][3] = {{'a', 'b', 'c' }, {'d', 'e', 'f' }, {'g', 'h', 'i' }}; in main() local
/dports/devel/wasi-libcxx/llvm-project-13.0.1.src/lldb/test/API/lang/c/array_types/
H A Dmain.c14 char char_matrix[3][3] = {{'a', 'b', 'c' }, {'d', 'e', 'f' }, {'g', 'h', 'i' }}; in main() local
/dports/devel/llvm-cheri/llvm-project-37c49ff00e3eadce5d8703fdc4497f28458c64a8/lldb/test/API/lang/c/array_types/
H A Dmain.c14 char char_matrix[3][3] = {{'a', 'b', 'c' }, {'d', 'e', 'f' }, {'g', 'h', 'i' }}; in main() local

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