Index

A

alignment() (co.translation.TranslationTable method)

alignment_str() (co.translation.TranslationTable method)

C

co (module), [1], [2], [3] co.mutation (module), [1] co.organism (module) co.translation (module)

Component (class in co) component (co.ComponentFeatureSet attribute) ComponentFeatureSet (class in co)

D

DEL (class in co.mutation) delete() (co.translation.MutableTranslationTable method)

diff() (co.organism.HaploidOrganism method)

E

end (co.mutation.Mutation attribute)

F

fdiff() (co.organism.HaploidOrganism method) Feature (class in co) features (co.Component attribute) (co.organism.HaploidOrganism attribute) FeatureSet (class in co) FeatureView (class in co.organism)

find() (co.organism.FeatureView method) freeze() (co.translation.MutableTranslationTable method) from_mutations() (co.translation.MutableTranslationTable class method) from_sequences() (co.translation.MutableTranslationTable class method)

G

ge() (co.translation.TranslationTable method)

get_lineage() (co.organism.HaploidOrganism method)

H

HaploidOrganism (class in co.organism)

I

id (co.Component attribute) (co.organism.HaploidOrganism attribute) INS (class in co.mutation) insert() (co.translation.MutableTranslationTable method) invert() (co.translation.TranslationTable method)

is_deletion() (co.mutation.Mutation method) is_insertion() (co.mutation.Mutation method) is_substitution() (co.mutation.Mutation method)

L

le() (co.translation.TranslationTable method)

M

MutableTranslationTable (class in co.translation)

Mutation (class in co.mutation)

N

new_sequence (co.mutation.Mutation attribute)

new_size (co.mutation.Mutation attribute)

O

OverlapError

P

parent (co.organism.HaploidOrganism attribute)

position (co.mutation.Mutation attribute)

R

remove() (co.organism.HaploidOrganism method)

removed_features (co.ComponentFeatureSet attribute)

S

set() (co.organism.HaploidOrganism method) size (co.mutation.Mutation attribute) SNP (class in co.mutation) source_end (co.translation.TranslationTable attribute)

source_start (co.translation.TranslationTable attribute) start (co.mutation.Mutation attribute) SUB (class in co.mutation) substitute() (co.translation.MutableTranslationTable method)

T

total_ungapped_size (co.translation.TranslationTable attribute)

TranslationTable (class in co.translation)