Index

_ | A | B | C | D | E | F | G | H | L | M | P | R | S | T | U | W | Y

_

__del__() (tffm_module.TFFM method)
__eq__() (hit_module.HIT method)
__ge__() (hit_module.HIT method)
__gt__() (hit_module.HIT method)
__init__() (hit_module.HIT method)
(tffm_module.TFFM method)
__le__() (hit_module.HIT method)
__len__() (hit_module.HIT method)
(tffm_module.TFFM method)
__lt__() (hit_module.HIT method)
__module__ (hit_module.HIT attribute)
(tffm_module.TFFM attribute)
__ne__() (hit_module.HIT method)
__str__() (hit_module.HIT method)
_construct_hits() (tffm_module.TFFM method)
_get_hits() (tffm_module.TFFM method)
_get_posterior_proba() (tffm_module.TFFM method)
_get_trimmed_hmm() (tffm_module.TFFM method)

A

ALPHABET (in module constants)

B

background_emission_proba() (tffm_module.TFFM method)
background_emission_proba_1storder() (in module tffm_module)
background_emission_proba_detailed() (in module tffm_module)
best_hit() (in module tffm_module)
BLACK (in module constants)
BLUE (in module constants)

C

compute_entropy() (in module tffm_module)
constants (module)
create_0order_hmm() (in module tffm_module)
create_1storder_hmm() (in module tffm_module)
create_detailed_hmm() (in module tffm_module)

D

draw_axis() (in module drawing)
draw_dense_letters() (in module drawing)
draw_ellipse() (in module drawing)
draw_frame() (in module drawing)
draw_left_letters() (in module drawing)
draw_letter_a() (in module drawing)
draw_letter_c() (in module drawing)
draw_letter_g() (in module drawing)
draw_letter_t() (in module drawing)
draw_logo() (in module drawing)
draw_logo_letters() (in module drawing)
draw_polygon() (in module drawing)
draw_rectangle() (in module drawing)
draw_summary_letters() (in module drawing)
draw_y_axis() (in module drawing)
drawing (module)

E

enum() (in module constants)
exceptions_errors (module)
EXTENDED_ALPHABET (in module constants)

F

final_states() (tffm_module.TFFM method)

G

get_emission_update_pos_proba() (tffm_module.TFFM method)
get_information_content() (tffm_module.TFFM method)
get_position_start() (tffm_module.TFFM method)
get_positions_ic() (tffm_module.TFFM method)
get_sequences_info() (in module utils)
get_significant_positions() (tffm_module.TFFM method)
get_start_end_strand() (in module hit_module)
get_trimmed() (tffm_module.TFFM method)
GREEN (in module constants)

H

HIT (class in hit_module)
hit_module (module)

L

LOGO_TYPE (in module constants)

M

merge_hits() (in module tffm_module)

P

parse_fasta() (in module utils)
pocc_sequences() (tffm_module.TFFM method)
print_dense_logo() (tffm_module.TFFM method)
print_footer() (in module drawing)
print_header() (in module drawing)
print_ic() (in module drawing)
print_summary_logo() (tffm_module.TFFM method)

R

RED (in module constants)
roundrobin() (in module utils)

S

scan_sequence() (tffm_module.TFFM method)
scan_sequences() (tffm_module.TFFM method)
sequence() (hit_module.HIT method)
set_sequences_weight() (in module utils)

T

TFFM (class in tffm_module)
tffm_from_meme() (in module tffm_module)
tffm_from_motif() (in module tffm_module)
tffm_from_xml() (in module tffm_module)
TFFM_KIND (in module constants)
tffm_module (module)
TFFMKindError
train() (tffm_module.TFFM method)
trim_in_place() (tffm_module.TFFM method)

U

utils (module)

W

WHITE (in module constants)

Y

YELLOW (in module constants)