Index

A

ALGEBRA (class in cgt.enums) all_adjacent_transpositions_representatives() (in module cgt.rearrangements)

all_inversions (cgt.enums.MODEL attribute) all_inversions_representatives() (in module cgt.rearrangements) arrows (cgt.enums.DISPLAY attribute)

C

C_2 (cgt.enums.SYMMETRY attribute) canonical_instance() (cgt.position_paradigm.PositionParadigmFramework method) cgt.distances module cgt.enums module cgt.examples module cgt.genome module cgt.models module cgt.position_paradigm module cgt.rearrangements module cgt.structures module

cgt.tests module cgt.tests.test_conversions module cgt.visualisation module circular (cgt.enums.SYMMETRY attribute) CLASSES (class in cgt.enums) coefficient_in() (cgt.position_paradigm.PositionParadigmFramework method) collect_genome_terms() (cgt.position_paradigm.PositionParadigmFramework method) conjugacy_class() (in module cgt.rearrangements) conjugacy_classes (cgt.enums.CLASSES attribute) cosets (cgt.enums.CLASSES attribute) css() (in module cgt.rearrangements) cuts() (in module cgt.rearrangements) cycles (cgt.enums.DISPLAY attribute) cycles() (cgt.position_paradigm.PositionParadigmFramework method)

D

D_n (cgt.enums.SYMMETRY attribute) dictionary (cgt.enums.FORMAT attribute) dihedral (cgt.enums.SYMMETRY attribute) DISPLAY (class in cgt.enums)

double_coset() (in module cgt.rearrangements) double_cosets (cgt.enums.CLASSES attribute) draw_genome_instance() (in module cgt.visualisation) draw_instance() (cgt.position_paradigm.PositionParadigmFramework method)

E

equiv_classes (cgt.enums.FORMAT attribute)

example() (in module cgt.examples) example_framework() (in module cgt.tests.test_conversions)

F

flip (cgt.enums.SYMMETRY attribute)

formal_sum (cgt.enums.FORMAT attribute) FORMAT (class in cgt.enums)

G

genome (cgt.enums.ALGEBRA attribute) Genome (class in cgt.genome) genome() (cgt.position_paradigm.PositionParadigmFramework method) genome_class (cgt.enums.ALGEBRA attribute)

genome_equivalence_classes() (cgt.position_paradigm.PositionParadigmFramework method) genome_group() (cgt.position_paradigm.PositionParadigmFramework method) genomes() (cgt.position_paradigm.PositionParadigmFramework method) group (cgt.enums.ALGEBRA attribute) group_algebra() (cgt.position_paradigm.PositionParadigmFramework method)

H

HyperoctahedralGroup() (in module cgt.structures)

I

irreps() (cgt.position_paradigm.PositionParadigmFramework method)

L

likelihood_function() (in module cgt.distances)

linear (cgt.enums.SYMMETRY attribute)

M

matrix() (cgt.position_paradigm.PositionParadigmFramework method) maximise() (in module cgt.distances) MFPT() (in module cgt.distances) min_distance() (in module cgt.distances) mle() (in module cgt.distances) mles() (in module cgt.distances) MODEL (class in cgt.enums) Model (class in cgt.models) module cgt.distances cgt.enums cgt.examples cgt.genome cgt.models cgt.position_paradigm cgt.rearrangements cgt.structures cgt.tests cgt.tests.test_conversions cgt.visualisation

N

named_model_with_relative_probs() (cgt.models.Model class method)

num_genomes() (cgt.position_paradigm.PositionParadigmFramework method)

O

one_region_inversions (cgt.enums.MODEL attribute) one_region_swaps (cgt.enums.MODEL attribute) one_row (cgt.enums.DISPLAY attribute) (cgt.enums.SET attribute)

one_row() (cgt.position_paradigm.PositionParadigmFramework method) only_reps (cgt.enums.FORMAT attribute)

P

pos_to_signed_reg (cgt.enums.TYPE attribute)

PositionParadigmFramework (class in cgt.position_paradigm)

R

random_genome() (cgt.position_paradigm.PositionParadigmFramework method) random_instance() (cgt.position_paradigm.PositionParadigmFramework method) reflection (cgt.enums.SYMMETRY attribute)

reg_rep_of_zs() (cgt.models.Model method) (cgt.position_paradigm.PositionParadigmFramework method) reg_to_signed_pos (cgt.enums.TYPE attribute) regular_representation() (cgt.position_paradigm.PositionParadigmFramework method)

S

S_2 (cgt.enums.SYMMETRY attribute) s_element() (cgt.models.Model method) SET (class in cgt.enums) set_plus_minus() (in module cgt.structures) signed_cycles (cgt.enums.SET attribute) signed_pos_to_reg (cgt.enums.TYPE attribute)

signed_reg_to_pos (cgt.enums.TYPE attribute) single_coset() (in module cgt.rearrangements) standard_reflection() (cgt.position_paradigm.PositionParadigmFramework method) standard_rotation() (cgt.position_paradigm.PositionParadigmFramework method) SYMMETRY (class in cgt.enums) symmetry_element() (cgt.position_paradigm.PositionParadigmFramework method) symmetry_group() (cgt.position_paradigm.PositionParadigmFramework method)

T

test_matrix_and_cycles_random() (in module cgt.tests.test_conversions) test_one_row_and_cycles_random() (in module cgt.tests.test_conversions)

two_region_adjacent_transpositions (cgt.enums.MODEL attribute) two_region_inversions (cgt.enums.MODEL attribute) TYPE (class in cgt.enums)

U

unsigned_cycles (cgt.enums.SET attribute)

W

wreath (cgt.enums.SET attribute)

wreath_s2 (cgt.enums.SET attribute)