Index

_

_annotate_rows() (jdna.viewer.FASTAItem method) (jdna.viewer.SequenceViewer method) _asdict() (jdna.reaction.BindingEvent method) _break_connections() (jdna.linked_list.EmptyNode method) (jdna.linked_list.Node method) (jdna.sequence.Nucleotide method)

_colored() (in module jdna.utils) _complete_match() (jdna.linked_list.EmptyNode method) (jdna.linked_list.Node method) (jdna.sequence.Nucleotide method) _make() (jdna.reaction.BindingEvent class method) _replace() (jdna.reaction.BindingEvent method)

A

absolute_annotate() (jdna.viewer.SequenceRow method) add_feature() (jdna.sequence.Sequence method) add_multipart_feature() (jdna.sequence.Sequence method) add_next() (jdna.linked_list.EmptyNode method) (jdna.linked_list.Node method) (jdna.sequence.Nucleotide method) add_prev() (jdna.linked_list.EmptyNode method) (jdna.linked_list.Node method) (jdna.sequence.Nucleotide method)

Alphabet (class in jdna.alphabet) anneal() (jdna.sequence.Sequence method) anneal_forward() (jdna.sequence.Sequence method) anneal_reverse() (jdna.sequence.Sequence method) annotate() (jdna.sequence.Sequence method) (jdna.viewer.FASTAItem method) (jdna.viewer.SequenceRow method) (jdna.viewer.SequenceViewer method) Assembly (class in jdna.reaction)

B

batch_create() (jdna.linked_list.LinkedListMatch class method) (jdna.sequence.BindPos class method)

BindingEvent (class in jdna.reaction) BindPos (class in jdna.sequence)

C

c() (jdna.sequence.Sequence method) chunkify() (in module jdna.viewer) circular() (jdna.linked_list.DoubleLinkedList property) (jdna.sequence.Sequence property) collect_nodes() (jdna.linked_list.DoubleLinkedList static method) (jdna.sequence.Sequence static method) colored() (in module jdna.utils) colored_background() (in module jdna.utils) compare() (jdna.alphabet.Alphabet method) (jdna.linked_list.DoubleLinkedList method) (jdna.sequence.Sequence method)

complement() (jdna.sequence.Sequence method) condense() (jdna.viewer.StringColumn class method) copy_slice() (jdna.linked_list.DoubleLinkedList method) (jdna.sequence.Sequence method) count() (jdna.reaction.BindingEvent method) cut_next() (jdna.linked_list.EmptyNode method) (jdna.linked_list.Node method) (jdna.sequence.Nucleotide method) cut_prev() (jdna.linked_list.EmptyNode method) (jdna.linked_list.Node method) (jdna.sequence.Nucleotide method)

D

digest() (jdna.sequence.Sequence method) DoubleLinkedList (class in jdna.linked_list)

DoubleLinkedList.Direction (class in jdna.linked_list) dsanneal() (jdna.sequence.Sequence method)

E

EmptyNode (class in jdna.linked_list) equivalent() (jdna.linked_list.EmptyNode method) (jdna.linked_list.Node method) (jdna.sequence.Nucleotide method)

F

FASTAItem (class in jdna.viewer) Feature (class in jdna.sequence) features() (jdna.sequence.Sequence property) features_list() (jdna.sequence.Sequence property) find_ends() (jdna.linked_list.DoubleLinkedList static method) (jdna.sequence.Sequence static method) find_feature_by_name() (jdna.sequence.Sequence method) find_first() (jdna.linked_list.EmptyNode method) (jdna.linked_list.Node method) (jdna.sequence.Nucleotide method)

find_iter() (jdna.linked_list.DoubleLinkedList method) (jdna.sequence.Sequence method) find_last() (jdna.linked_list.EmptyNode method) (jdna.linked_list.Node method) (jdna.sequence.Nucleotide method) from_match() (jdna.sequence.BindPos class method) fwd() (jdna.linked_list.EmptyNode method) (jdna.linked_list.Node method) (jdna.sequence.Nucleotide method)

H

header() (jdna.viewer.FASTAItem property) (jdna.viewer.SequenceViewer property)

hex_to_color_name() (in module jdna.utils)

I

in_bounds() (jdna.viewer.SequenceRow method) inclusive_range() (jdna.linked_list.DoubleLinkedList method) (jdna.sequence.Sequence method)

indent() (in module jdna.viewer) index() (jdna.reaction.BindingEvent method)

J

jdna.alphabet (module) jdna.linked_list (module) jdna.reaction (module)

jdna.sequence (module) jdna.utils (module) jdna.viewer (module) json() (jdna.sequence.Sequence method)

L

LinkedListException LinkedListIndexError LinkedListMatch (class in jdna.linked_list)

load() (jdna.sequence.Sequence class method) longest_match() (jdna.linked_list.EmptyNode method) (jdna.linked_list.Node method) (jdna.sequence.Nucleotide method)

M

make_annotation() (jdna.viewer.SequenceRow static method)

N

new_slice() (jdna.linked_list.DoubleLinkedList class method) (jdna.sequence.Sequence class method) next() (jdna.linked_list.EmptyNode method) (jdna.linked_list.Node method) (jdna.sequence.Nucleotide method)

Node (class in jdna.linked_list) NODE_CLASS (jdna.linked_list.DoubleLinkedList attribute) (jdna.sequence.Sequence attribute) node_range() (jdna.linked_list.DoubleLinkedList method) (jdna.sequence.Sequence method) Nucleotide (class in jdna.sequence)

P

PCRException position() (jdna.reaction.BindingEvent property) prepend_lines() (in module jdna.viewer) prev() (jdna.linked_list.EmptyNode method) (jdna.linked_list.Node method) (jdna.sequence.Nucleotide method)

primer() (jdna.reaction.BindingEvent property) print() (jdna.reaction.Assembly method) (jdna.sequence.Sequence method)

R

random() (jdna.alphabet.Alphabet method) (jdna.sequence.Nucleotide class method) (jdna.sequence.Sequence class method) range() (jdna.linked_list.DoubleLinkedList method) (jdna.sequence.Sequence method) rc() (jdna.sequence.Sequence method) ReactionException

remove() (jdna.linked_list.EmptyNode method) (jdna.linked_list.Node method) (jdna.sequence.Nucleotide method) rev() (jdna.linked_list.EmptyNode method) (jdna.linked_list.Node method) (jdna.sequence.Nucleotide method) reverse_complement() (jdna.sequence.Sequence method)

S

Sequence (class in jdna.sequence) Sequence.DEFAULTS (class in jdna.sequence) Sequence.Direction (class in jdna.sequence) SequenceFlags (class in jdna.sequence) SequenceRow (class in jdna.viewer) SequenceViewer (class in jdna.viewer) set_next() (jdna.linked_list.EmptyNode method) (jdna.linked_list.Node method) (jdna.sequence.Nucleotide method)

set_prev() (jdna.linked_list.EmptyNode method) (jdna.linked_list.Node method) (jdna.sequence.Nucleotide method) set_window() (jdna.viewer.FASTAItem method) (jdna.viewer.SequenceViewer method) string_length() (jdna.viewer.StringColumn class method) StringColumn (class in jdna.viewer) swap() (jdna.linked_list.EmptyNode method) (jdna.linked_list.Node method) (jdna.sequence.Nucleotide method)

T

template() (jdna.reaction.BindingEvent property) tm() (jdna.sequence.Sequence method)

tms() (jdna.reaction.Assembly method) to_lines() (in module jdna.viewer)

V

view() (jdna.sequence.Sequence method)

ViewerAnnotationFlag (class in jdna.viewer)

W

with_traceback() (jdna.linked_list.LinkedListException method) (jdna.linked_list.LinkedListIndexError method) (jdna.reaction.PCRException method) (jdna.reaction.ReactionException method)