ASN.1 Type Definitions for Module NCBI-Cdd

Top-level module index.

Colors and Styles Used


Type Cdd-org-ref

Uses

Org-ref

Is Used By

Cdd-org-ref-set Cdd-org-ref ::=
SEQUENCE {
reference Org-ref
active BOOLEAN DEFAULT true
parent-tax-id INTEGER OPTIONAL
rank VisibleString OPTIONAL
}  


Type Cdd-org-ref-set

Uses

Cdd-org-ref

Is Used By

Cdd-pref-nodes Cdd-org-ref-set ::= SET OF Cdd-org-ref

Type Cdd-pref-node-descr

Uses

Date

Is Used By

Cdd-pref-node-descr-set Cdd-pref-node-descr ::=
CHOICE {
create-date Date
description VisibleString
}  


Type Cdd-pref-node-descr-set

Uses

Cdd-pref-node-descr

Is Used By

Cdd-pref-nodes Cdd-pref-node-descr-set ::= SET OF Cdd-pref-node-descr

Type Cdd-pref-nodes

Uses

Cdd-org-ref-set Cdd-pref-node-descr-set Cdd-pref-nodes ::=
SEQUENCE {
preferred-nodes Cdd-org-ref-set
model-organisms Cdd-org-ref-set OPTIONAL
optional-nodes Cdd-org-ref-set OPTIONAL
description Cdd-pref-node-descr-set OPTIONAL
}  


Type Global-id

Is Used By

Cdd-id Global-id ::=
SEQUENCE {
accession VisibleString
release VisibleString OPTIONAL
version INTEGER OPTIONAL
database VisibleString OPTIONAL
}  


Type Cdd-id

Uses

Global-id

Is Used By

Cdd Cdd-id-set Cdd-tree Domain-parent Cdd-id ::=
CHOICE {
uid INTEGER
gid Global-id
}  


Type Cdd-id-set

Uses

Cdd-id

Is Used By

Cdd Cdd-descr Cdd-Project Cdd-tree Cdd-id-set ::= SEQUENCE OF Cdd-id

Type Cdd-repeat

Uses

Seq-loc

Is Used By

Cdd-descr Cdd-repeat ::=
SEQUENCE {
count INTEGER
location Seq-loc OPTIONAL
avglen INTEGER OPTIONAL
}  


Type Cdd-book-ref

Is Used By

Cdd-descr Feature-evidence Cdd-book-ref ::=
SEQUENCE {
bookname VisibleString
textelement
ENUMERATED {
unassigned 0
section 1
figgrp 2
table 3
chapter 4
biblist 5
box 6
glossary 7
appendix 8
other 255
}  
elementid INTEGER OPTIONAL
subelementid INTEGER OPTIONAL
celementid VisibleString OPTIONAL
csubelementid VisibleString OPTIONAL
}  


Type Cdd-descr

Uses

Cdd-book-ref Cdd-id-set Cdd-repeat Date Org-ref Pub

Is Used By

Cdd-descr-set Cdd-descr ::=
CHOICE {
othername VisibleString
category VisibleString
comment VisibleString
reference Pub
create-date Date
tax-source Org-ref
source VisibleString
status
INTEGER {
unassigned 0
finished-ok 1
pending-release 2
other-asis 3
matrix-only 4
update-running 5
auto-updated 6
claimed 7
curated-complete 8
other 255
}  
update-date Date
scrapbook SEQUENCE OF VisibleString
source-id Cdd-id-set
repeats Cdd-repeat
old-root Cdd-id-set
curation-status
INTEGER {
unassigned 0
prein 1
ofc 2
iac 3
ofv1 4
iav1 5
ofv2 6
iav2 7
postin 8
other 255
}  
readonly-status
INTEGER {
unassigned 0
readonly 1
readwrite 2
other 255
}  
book-ref Cdd-book-ref
attribution Pub
title VisibleString
}  


Type Cdd-descr-set

Uses

Cdd-descr

Is Used By

Cdd Cdd-tree Cdd-descr-set ::= SET OF Cdd-descr

Type Cdd-tree

Uses

Cdd-descr-set Cdd-id Cdd-id-set

Is Used By

Cdd-tree-set Cdd-tree ::=
SEQUENCE {
name VisibleString
id Cdd-id-set
description Cdd-descr-set OPTIONAL
parent Cdd-id OPTIONAL
children Cdd-id-set OPTIONAL
siblings Cdd-id-set OPTIONAL
neighbors Cdd-id-set OPTIONAL
}  


Type Cdd-tree-set

Uses

Cdd-tree Cdd-tree-set ::= SEQUENCE OF Cdd-tree

Type Matrix

Is Used By

Cdd Matrix ::=
SEQUENCE {
ncolumns INTEGER
nrows INTEGER
row-labels SEQUENCE OF VisibleString OPTIONAL
scale-factor INTEGER
columns SEQUENCE OF INTEGER
}  


Type Triangle

Uses

Score-set

Is Used By

Cdd Triangle ::=
SEQUENCE {
nelements INTEGER
scores Score-set OPTIONAL
div-ranks SEQUENCE OF INTEGER OPTIONAL
}  


Type Update-comment

Uses

Pub Seq-loc

Is Used By

Reject-id Update-align Update-comment ::=
CHOICE {
comment VisibleString
addthis Seq-loc
replaces Seq-loc
reject-loc Seq-loc
reference Pub
}  


Type Update-align

Uses

Seq-annot Update-comment

Is Used By

Cdd Update-align ::=
SEQUENCE {
description SEQUENCE OF Update-comment OPTIONAL
seqannot Seq-annot OPTIONAL
type
INTEGER {
unassigned 0
update 1
update-3d 2
demoted 51
demoted-3d 52
other 255
}  
}  


Type Reject-id

Uses

Seq-id Update-comment

Is Used By

Cdd Reject-id ::=
SEQUENCE {
description SEQUENCE OF Update-comment OPTIONAL
ids SET OF Seq-id
}  


Type Feature-evidence

Uses

Biostruc-annot-set Cdd-book-ref Pub Seq-feat

Is Used By

Align-annot Feature-evidence ::=
CHOICE {
comment VisibleString
reference Pub
bsannot Biostruc-annot-set
seqfeat Seq-feat
book-ref Cdd-book-ref
}  


Type Align-annot

Uses

Feature-evidence Seq-loc

Is Used By

Align-annot-set Align-annot ::=
SEQUENCE {
location Seq-loc
description VisibleString OPTIONAL
evidence SEQUENCE OF Feature-evidence OPTIONAL
type INTEGER OPTIONAL
aliases SEQUENCE OF VisibleString OPTIONAL
motif VisibleString OPTIONAL
motifuse INTEGER OPTIONAL
}  


Type Align-annot-set

Uses

Align-annot

Is Used By

Cdd Align-annot-set ::= SEQUENCE OF Align-annot

Type Domain-parent

Uses

Cdd-id Seq-annot

Is Used By

Cdd Domain-parent ::=
SEQUENCE {
parent-type
INTEGER {
classical 0
fusion 1
deletion 2
permutation 3
other 255
}  
parentid Cdd-id
seqannot Seq-annot OPTIONAL
}  


Type Sequence-tree

Uses

Algorithm-type SeqTree-node

Is Used By

Cdd Sequence-tree ::=
SEQUENCE {
cdAccession VisibleString OPTIONAL
algorithm Algorithm-type
isAnnotated BOOLEAN DEFAULT false
root SeqTree-node
}  


Type SeqTree-node

Uses

Node-annotation Seq-interval SeqTree-node

Is Used By

SeqTree-node Sequence-tree SeqTree-node ::=
SEQUENCE {
isAnnotated BOOLEAN DEFAULT false
name VisibleString OPTIONAL
distance REAL OPTIONAL
children
CHOICE {
children SEQUENCE OF SeqTree-node
footprint
SEQUENCE {
seqRange Seq-interval
rowId INTEGER OPTIONAL
}  
}  
annotation Node-annotation OPTIONAL
}  


Type Algorithm-type

Is Used By

Sequence-tree Algorithm-type ::=
SEQUENCE {
scoring-Scheme
INTEGER {
unassigned 0
percent-id 1
kimura-corrected 2
aligned-score 3
aligned-score-ext 4
aligned-score-filled 5
blast-footprint 6
blast-full 7
hybrid-aligned-score 8
other 255
}  
clustering-Method
INTEGER {
unassigned 0
single-linkage 1
neighbor-joining 2
fast-minimum-evolution 3
other 255
}  
score-Matrix
INTEGER {
unassigned 0
blosum45 1
blosum62 2
blosum80 3
pam30 4
pam70 5
pam250 6
other 255
}  
OPTIONAL
gapOpen INTEGER OPTIONAL
gapExtend INTEGER OPTIONAL
gapScaleFactor INTEGER OPTIONAL
nTerminalExt INTEGER OPTIONAL
cTerminalExt INTEGER OPTIONAL
tree-scope
INTEGER {
allDescendants 0
immediateChildrenOnly 1
selfOnly 2
other 255
}  
OPTIONAL
coloring-scope
INTEGER {
allDescendants 0
immediateChildrenOnly 1
other 255
}  
OPTIONAL
}  


Type Node-annotation

Is Used By

SeqTree-node Node-annotation ::=
SEQUENCE {
presentInChildCD VisibleString OPTIONAL
note VisibleString OPTIONAL
}  


Type Cdd

Uses

Align-annot-set Bioseq Biostruc-annot-set Cdd-descr-set Cdd-id Cdd-id-set Cn3d-style-dictionary Cn3d-user-annotations Domain-parent Matrix PssmWithParameters Reject-id Seq-annot Seq-entry Seq-id Seq-interval Sequence-tree Triangle Update-align

Is Used By

Biostruc-seqs-aligns-cdd Cdd-Project Cdd-set Cdd ::=
SEQUENCE {
name VisibleString
id Cdd-id-set
description Cdd-descr-set OPTIONAL
seqannot SEQUENCE OF Seq-annot OPTIONAL
features Biostruc-annot-set OPTIONAL
sequences Seq-entry OPTIONAL
profile-range Seq-interval OPTIONAL
trunc-master Bioseq OPTIONAL
posfreq Matrix OPTIONAL
scoremat Matrix OPTIONAL
distance Triangle OPTIONAL
parent Cdd-id OPTIONAL
children Cdd-id-set OPTIONAL
siblings Cdd-id-set OPTIONAL
neighbors Cdd-id-set OPTIONAL
pending SEQUENCE OF Update-align OPTIONAL
rejects SEQUENCE OF Reject-id OPTIONAL
master3d SET OF Seq-id OPTIONAL
alignannot Align-annot-set OPTIONAL
style-dictionary Cn3d-style-dictionary OPTIONAL
user-annotations Cn3d-user-annotations OPTIONAL
ancestors SEQUENCE OF Domain-parent OPTIONAL
scoreparams PssmWithParameters OPTIONAL
seqtree Sequence-tree OPTIONAL
}  


Type Cdd-set

Uses

Cdd Cdd-set ::= SET OF Cdd

Type Cdd-Viewer-Rect

Is Used By

Cdd-Viewer Cdd-Viewer-Rect ::=
SEQUENCE {
top INTEGER
left INTEGER
width INTEGER
height INTEGER
}  


Type Cdd-Viewer

Uses

Cdd-Viewer-Rect

Is Used By

Cdd-Project Cdd-Viewer ::=
SEQUENCE {
ctrl
INTEGER {
unassigned 0
cd-info 1
align-annot 2
seq-list 3
seq-tree 4
merge-preview 5
cross-hits 6
notes 7
tax-tree 8
dart 9
dart-selected-rows 10
other 255
}  
rect Cdd-Viewer-Rect OPTIONAL
accessions SEQUENCE OF VisibleString
}  


Type Cdd-Script

Is Used By

Cdd-Project Cdd-Script ::=
SEQUENCE {
type
INTEGER {
unassigned 0
user-recorded 1
server-generated 2
other 255
}  
OPTIONAL
name VisibleString OPTIONAL
commands VisibleString
}  


Type Cdd-Project

Uses

Cdd Cdd-id-set Cdd-Script Cdd-Viewer Date Cdd-Project ::=
SEQUENCE {
cds SEQUENCE OF Cdd
cdcolor SEQUENCE OF INTEGER
viewers SEQUENCE OF Cdd-Viewer
log VisibleString
scripts SEQUENCE OF Cdd-Script OPTIONAL
id Cdd-id-set OPTIONAL
rids SEQUENCE OF VisibleString OPTIONAL
create-date Date OPTIONAL
update-date Date OPTIONAL
project-id INTEGER OPTIONAL
}  


Top-level module index.