ASN.1 Type Definitions for Module NCBI-Macro

Top-level module index.

Colors and Styles Used


Type String-location

Is Used By

String-constraint Table-match String-location ::=
ENUMERATED {
contains 1
equals 2
starts 3
ends 4
inlist 5
}  


Type Word-substitution

Is Used By

Word-substitution-set Word-substitution ::=
SEQUENCE {
word VisibleString OPTIONAL
synonyms SET OF VisibleString OPTIONAL
case-sensitive BOOLEAN DEFAULT false
whole-word BOOLEAN DEFAULT false
}  


Type Word-substitution-set

Uses

Word-substitution

Is Used By

String-constraint Word-substitution-set ::= SET OF Word-substitution

Type String-constraint

Uses

String-location Word-substitution-set

Is Used By

CDSGeneProt-qual-constraint Constraint-choice Feat-qual-choice Field-constraint Pub-field-constraint Search-func Sequence-constraint Source-constraint String-constraint-set String-constraint ::=
SEQUENCE {
match-text VisibleString OPTIONAL
match-location String-location DEFAULT contains
case-sensitive BOOLEAN DEFAULT false
ignore-space BOOLEAN DEFAULT false
ignore-punct BOOLEAN DEFAULT false
ignore-words Word-substitution-set OPTIONAL
whole-word BOOLEAN DEFAULT false
not-present BOOLEAN DEFAULT false
is-all-caps BOOLEAN DEFAULT false
is-all-lower BOOLEAN DEFAULT false
is-all-punct BOOLEAN DEFAULT false
ignore-weasel BOOLEAN DEFAULT false
}  


Type String-constraint-set

Uses

String-constraint

Is Used By

Translation-constraint String-constraint-set ::= SET OF String-constraint

Type Strand-constraint

Is Used By

Location-constraint Strand-constraint ::=
ENUMERATED {
any 0
plus 1
minus 2
}  


Type Seqtype-constraint

Is Used By

Location-constraint Seqtype-constraint ::=
ENUMERATED {
any 0
nuc 1
prot 2
}  


Type Partial-constraint

Is Used By

Location-constraint Partial-constraint ::=
ENUMERATED {
either 0
partial 1
complete 2
}  


Type Location-type-constraint

Is Used By

Location-constraint Location-type-constraint ::=
ENUMERATED {
any 0
single-interval 1
joined 2
ordered 3
}  


Type Location-pos-constraint

Is Used By

Location-constraint Location-pos-constraint ::=
CHOICE {
dist-from-end INTEGER
max-dist-from-end INTEGER
min-dist-from-end INTEGER
}  


Type Location-constraint

Uses

Location-pos-constraint Location-type-constraint Partial-constraint Seqtype-constraint Strand-constraint

Is Used By

Constraint-choice Location-constraint ::=
SEQUENCE {
strand Strand-constraint DEFAULT any
seq-type Seqtype-constraint DEFAULT any
partial5 Partial-constraint DEFAULT either
partial3 Partial-constraint DEFAULT either
location-type Location-type-constraint DEFAULT any
end5 Location-pos-constraint OPTIONAL
end3 Location-pos-constraint OPTIONAL
}  


Type Object-type-constraint

Is Used By

Parse-dst-org Parse-src-org Source-constraint Object-type-constraint ::=
ENUMERATED {
any 0
feature 1
descriptor 2
}  


Type Macro-feature-type

Is Used By

Apply-feature-action Convert-feature-action Edit-feature-location-action Extend-to-feature Feature-field Feature-field-legal Feature-field-pair Gene-xref-type Make-gene-xref-action Remove-duplicate-feature-action Remove-feature-action Sequence-constraint Macro-feature-type ::=
ENUMERATED {
any 0
gene 1
org 2
cds 3
prot 4
preRNA 5
mRNA 6
tRNA 7
rRNA 8
snRNA 9
scRNA 10
otherRNA 11
pub 12
seq 13
imp 14
allele 15
attenuator 16
c-region 17
caat-signal 18
imp-CDS 19
conflict 20
d-loop 21
d-segment 22
enhancer 23
exon 24
gC-signal 25
iDNA 26
intron 27
j-segment 28
ltr 29
mat-peptide 30
misc-binding 31
misc-difference 32
misc-feature 33
misc-recomb 34
misc-RNA 35
misc-signal 36
misc-structure 37
modified-base 38
mutation 39
n-region 40
old-sequence 41
polyA-signal 42
polyA-site 43
precursor-RNA 44
prim-transcript 45
primer-bind 46
promoter 47
protein-bind 48
rbs 49
repeat-region 50
rep-origin 51
s-region 52
sig-peptide 53
source 54
stem-loop 55
sts 56
tata-signal 57
terminator 58
transit-peptide 59
unsure 60
v-region 61
v-segment 62
variation 63
virion 64
n3clip 65
n3UTR 66
n5clip 67
n5UTR 68
n10-signal 69
n35-signal 70
site-ref 71
region 72
comment 73
bond 74
site 75
rsite 76
user 77
txinit 78
num 79
psec-str 80
non-std-residue 81
het 82
biosrc 83
preprotein 84
mat-peptide-aa 85
sig-peptide-aa 86
transit-peptide-aa 87
snoRNA 88
gap 89
operon 90
oriT 91
ncRNA 92
tmRNA 93
mobile-element 94
}  


Type Feat-qual-legal

Is Used By

Feat-qual-choice Feat-qual-legal-val Feature-field-legal Feat-qual-legal ::=
ENUMERATED {
allele 1
activity 2
anticodon 3
bound-moiety 4
chromosome 5
citation 6
codon 7
codon-start 8
codons-recognized 9
compare 10
cons-splice 11
db-xref 12
description 13
direction 14
ec-number 15
environmental-sample 16
evidence 17
exception 18
experiment 19
focus 20
frequency 21
function 22
gene 23
gene-description 24
inference 25
label 26
locus-tag 27
map 28
mobile-element 29
mod-base 30
mol-type 31
ncRNA-class 32
note 33
number 34
old-locus-tag 35
operon 36
organism 37
organelle 38
partial 39
phenotype 40
plasmid 41
product 42
protein-id 43
pseudo 44
rearranged 45
replace 46
rpt-family 47
rpt-type 48
rpt-unit 49
rpt-unit-seq 50
rpt-unit-range 51
segment 52
sequenced-mol 53
standard-name 54
synonym 55
transcript-id 56
transgenic 57
translation 58
transl-except 59
transl-table 60
usedin 61
mobile-element-type 62
mobile-element-name 63
gene-comment 64
satellite 65
satellite-type 66
satellite-name 67
location 68
tag-peptide 69
mobile-element-type-type 70
name 71
pcr-conditions 72
}  


Type Feat-qual-legal-val

Uses

Feat-qual-legal

Is Used By

Feat-qual-legal-val-choice Feat-qual-legal-val ::=
SEQUENCE {
qual Feat-qual-legal
val VisibleString
}  


Type Feat-qual-legal-val-choice

Uses

Feat-qual-legal-val

Is Used By

Feat-qual-legal-set Feat-qual-legal-val-choice ::=
CHOICE {
qual Feat-qual-legal-val
}  


Type Feat-qual-legal-set

Uses

Feat-qual-legal-val-choice

Is Used By

Apply-feature-action Feat-qual-legal-set ::= SET OF Feat-qual-legal-val-choice

Type Feat-qual-choice

Uses

Feat-qual-legal String-constraint

Is Used By

Feature-field Feature-field-pair Feat-qual-choice ::=
CHOICE {
legal-qual Feat-qual-legal
illegal-qual String-constraint
}  


Type Feature-field

Uses

Feat-qual-choice Macro-feature-type

Is Used By

Field-type Feature-field ::=
SEQUENCE {
type Macro-feature-type
field Feat-qual-choice
}  


Type Feature-field-legal

Uses

Feat-qual-legal Macro-feature-type

Is Used By

Parse-dest Feature-field-legal ::=
SEQUENCE {
type Macro-feature-type
field Feat-qual-legal
}  


Type Feature-field-pair

Uses

Feat-qual-choice Macro-feature-type

Is Used By

Field-pair-type Feature-field-pair ::=
SEQUENCE {
type Macro-feature-type
field-from Feat-qual-choice
field-to Feat-qual-choice
}  


Type Rna-feat-type

Is Used By

Rna-qual Rna-qual-pair Rna-feat-type ::=
CHOICE {
any NULL
preRNA NULL
mRNA NULL
tRNA NULL
rRNA NULL
ncRNA VisibleString
tmRNA NULL
miscRNA NULL
}  


Type Rna-field

Is Used By

Rna-qual Rna-qual-pair Rna-field ::=
ENUMERATED {
product 1
comment 2
codons-recognized 3
ncrna-class 4
anticodon 5
transcript-id 6
gene-locus 7
gene-description 8
gene-maploc 9
gene-locus-tag 10
gene-synonym 11
gene-comment 12
tag-peptide 13
}  


Type Rna-qual

Uses

Rna-feat-type Rna-field

Is Used By

Field-type Rna-qual ::=
SEQUENCE {
type Rna-feat-type
field Rna-field
}  


Type Rna-qual-pair

Uses

Rna-feat-type Rna-field

Is Used By

Field-pair-type Rna-qual-pair ::=
SEQUENCE {
type Rna-feat-type
field-from Rna-field
field-to Rna-field
}  


Type Source-qual

Is Used By

Autodef-action Fix-caps-action Parse-src-org-choice Source-qual-choice Source-qual-pair Source-qual-text-val Source-qual ::=
ENUMERATED {
acronym 1
anamorph 2
authority 3
bio-material 4
biotype 5
biovar 6
breed 7
cell-line 8
cell-type 9
chemovar 10
chromosome 11
clone 12
clone-lib 13
collected-by 14
collection-date 15
common 16
common-name 17
country 18
cultivar 19
culture-collection 20
dev-stage 21
division 22
dosage 23
ecotype 24
endogenous-virus-name 25
environmental-sample 26
forma 27
forma-specialis 28
frequency 29
fwd-primer-name 30
fwd-primer-seq 31
gb-acronym 32
gb-anamorph 33
gb-synonym 34
genotype 35
germline 36
group 37
haplotype 38
identified-by 39
insertion-seq-name 40
isolate 41
isolation-source 42
lab-host 43
lat-lon 44
lineage 45
map 46
metagenome-source 47
metagenomic 48
old-lineage 49
old-name 50
orgmod-note 51
nat-host 52
pathovar 53
plasmid-name 54
plastid-name 55
pop-variant 56
rearranged 57
rev-primer-name 58
rev-primer-seq 59
segment 60
serogroup 61
serotype 62
serovar 63
sex 64
specimen-voucher 65
strain 66
subclone 67
subgroup 68
subsource-note 69
sub-species 70
substrain 71
subtype 72
synonym 73
taxname 74
teleomorph 75
tissue-lib 76
tissue-type 77
transgenic 78
transposon-name 79
type 80
variety 81
specimen-voucher-INST 82
specimen-voucher-COLL 83
specimen-voucher-SpecID 84
culture-collection-INST 85
culture-collection-COLL 86
culture-collection-SpecID 87
bio-material-INST 88
bio-material-COLL 89
bio-material-SpecID 90
all-notes 91
mating-type 92
linkage-group 93
haplogroup 94
all-quals 95
dbxref 96
taxid 97
all-primers 98
altitude 99
}  


Type Source-qual-pair

Uses

Source-qual

Is Used By

Field-pair-type Source-qual-pair ::=
SEQUENCE {
field-from Source-qual
field-to Source-qual
}  


Type Source-location

Is Used By

Source-qual-choice Source-qual-val-choice Source-location ::=
ENUMERATED {
unknown 0
genomic 1
chloroplast 2
chromoplast 3
kinetoplast 4
mitochondrion 5
plastid 6
macronuclear 7
extrachrom 8
plasmid 9
transposon 10
insertion-seq 11
cyanelle 12
proviral 13
virion 14
nucleomorph 15
apicoplast 16
leucoplast 17
proplastid 18
endogenous-virus 19
hydrogenosome 20
chromosome 21
chromatophore 22
}  


Type Source-origin

Is Used By

Source-qual-choice Source-qual-val-choice Source-origin ::=
ENUMERATED {
unknown 0
natural 1
natmut 2
mut 3
artificial 4
synthetic 5
other 255
}  


Type Source-qual-choice

Uses

Source-location Source-origin Source-qual

Is Used By

Field-type Parse-dst-org Source-constraint Table-match-type Source-qual-choice ::=
CHOICE {
textqual Source-qual
location Source-location
origin Source-origin
gcode INTEGER
mgcode INTEGER
}  


Type Source-qual-text-val

Uses

Source-qual

Is Used By

Source-qual-val-choice Source-qual-text-val ::=
SEQUENCE {
srcqual Source-qual
val VisibleString
}  


Type Source-qual-val-choice

Uses

Source-location Source-origin Source-qual-text-val

Is Used By

Source-qual-val-set Source-qual-val-choice ::=
CHOICE {
textqual Source-qual-text-val
location Source-location
origin Source-origin
gcode INTEGER
mgcode INTEGER
}  


Type Source-qual-val-set

Uses

Source-qual-val-choice

Is Used By

Apply-feature-action Source-qual-val-set ::= SET OF Source-qual-val-choice

Type CDSGeneProt-field

Is Used By

CDSGeneProt-constraint-field CDSGeneProt-field-pair Field-type CDSGeneProt-field ::=
ENUMERATED {
cds-comment 1
gene-locus 2
gene-description 3
gene-comment 4
gene-allele 5
gene-maploc 6
gene-locus-tag 7
gene-synonym 8
gene-old-locus-tag 9
mrna-product 10
mrna-comment 11
prot-name 12
prot-description 13
prot-ec-number 14
prot-activity 15
prot-comment 16
mat-peptide-name 17
mat-peptide-description 18
mat-peptide-ec-number 19
mat-peptide-activity 20
mat-peptide-comment 21
cds-inference 22
gene-inference 23
codon-start 24
}  


Type CDSGeneProt-field-pair

Uses

CDSGeneProt-field

Is Used By

Field-pair-type CDSGeneProt-field-pair ::=
SEQUENCE {
field-from CDSGeneProt-field
field-to CDSGeneProt-field
}  


Type Molecule-type

Is Used By

Molinfo-field Molinfo-molecule-pair Molecule-type ::=
ENUMERATED {
unknown 0
genomic 1
precursor-RNA 2
mRNA 3
rRNA 4
tRNA 5
genomic-mRNA 6
cRNA 7
transcribed-RNA 8
ncRNA 9
transfer-messenger-RNA 10
macro-other 11
}  


Type Technique-type

Is Used By

Molinfo-field Molinfo-technique-pair Technique-type ::=
ENUMERATED {
unknown 0
standard 1
est 2
sts 3
survey 4
genetic-map 5
physical-map 6
derived 7
concept-trans 8
seq-pept 9
both 10
seq-pept-overlap 11
seq-pept-homol 12
concept-trans-a 13
htgs-1 14
htgs-2 15
htgs-3 16
fli-cDNA 17
htgs-0 18
htc 19
wgs 20
barcode 21
composite-wgs-htgs 22
tsa 23
other 24
}  


Type Completedness-type

Is Used By

Molinfo-completedness-pair Molinfo-field Completedness-type ::=
ENUMERATED {
unknown 0
complete 1
partial 2
no-left 3
no-right 4
no-ends 5
has-left 6
has-right 7
other 6
}  


Type Molecule-class-type

Is Used By

Molinfo-field Molinfo-mol-class-pair Molecule-class-type ::=
ENUMERATED {
unknown 0
dna 1
rna 2
protein 3
nucleotide 4
other 5
}  


Type Topology-type

Is Used By

Molinfo-field Molinfo-topology-pair Topology-type ::=
ENUMERATED {
unknown 0
linear 1
circular 2
tandem 3
other 4
}  


Type Strand-type

Is Used By

Molinfo-field Molinfo-strand-pair Strand-type ::=
ENUMERATED {
unknown 0
single 1
double 2
mixed 3
mixed-rev 4
other 5
}  


Type Molinfo-field

Uses

Completedness-type Molecule-class-type Molecule-type Strand-type Technique-type Topology-type

Is Used By

Field-type Molinfo-field-constraint Molinfo-field-list Molinfo-field ::=
CHOICE {
molecule Molecule-type
technique Technique-type
completedness Completedness-type
mol-class Molecule-class-type
topology Topology-type
strand Strand-type
}  


Type Molinfo-molecule-pair

Uses

Molecule-type

Is Used By

Molinfo-field-pair Molinfo-molecule-pair ::=
SEQUENCE {
from Molecule-type
to Molecule-type
}  


Type Molinfo-technique-pair

Uses

Technique-type

Is Used By

Molinfo-field-pair Molinfo-technique-pair ::=
SEQUENCE {
from Technique-type
to Technique-type
}  


Type Molinfo-completedness-pair

Uses

Completedness-type

Is Used By

Molinfo-field-pair Molinfo-completedness-pair ::=
SEQUENCE {
from Completedness-type
to Completedness-type
}  


Type Molinfo-mol-class-pair

Uses

Molecule-class-type

Is Used By

Molinfo-field-pair Molinfo-mol-class-pair ::=
SEQUENCE {
from Molecule-class-type
to Molecule-class-type
}  


Type Molinfo-topology-pair

Uses

Topology-type

Is Used By

Molinfo-field-pair Molinfo-topology-pair ::=
SEQUENCE {
from Topology-type
to Topology-type
}  


Type Molinfo-strand-pair

Uses

Strand-type

Is Used By

Molinfo-field-pair Molinfo-strand-pair ::=
SEQUENCE {
from Strand-type
to Strand-type
}  


Type Molinfo-field-pair

Uses

Molinfo-completedness-pair Molinfo-mol-class-pair Molinfo-molecule-pair Molinfo-strand-pair Molinfo-technique-pair Molinfo-topology-pair

Is Used By

Field-pair-type Molinfo-field-pair ::=
CHOICE {
molecule Molinfo-molecule-pair
technique Molinfo-technique-pair
completedness Molinfo-completedness-pair
mol-class Molinfo-mol-class-pair
topology Molinfo-topology-pair
strand Molinfo-strand-pair
}  


Type Molinfo-field-list

Uses

Molinfo-field

Is Used By

Molinfo-block Molinfo-field-list ::= SET OF Molinfo-field

Type Molinfo-field-constraint

Uses

Molinfo-field

Is Used By

Constraint-choice Molinfo-field-constraint ::=
SEQUENCE {
field Molinfo-field
is-not BOOLEAN DEFAULT false
}  


Type Publication-field

Is Used By

Field-type Pub-field-constraint Pub-field-special-constraint Publication-field ::=
ENUMERATED {
cit 1
authors 2
journal 3
volume 4
issue 5
pages 6
date 7
serial-number 8
title 9
affiliation 10
affil-div 11
affil-city 12
affil-sub 13
affil-country 14
affil-street 15
affil-email 16
affil-fax 17
affil-phone 18
affil-zipcode 19
authors-initials 20
pmid 21
pub-class 22
}  


Type Structured-comment-field

Is Used By

Field-type Structured-comment-field-pair Structured-comment-field ::=
CHOICE {
database NULL
named VisibleString
field-name NULL
}  


Type Structured-comment-field-pair

Uses

Structured-comment-field

Is Used By

Field-pair-type Structured-comment-field-pair ::=
SEQUENCE {
from Structured-comment-field
to Structured-comment-field
}  


Type Misc-field

Is Used By

Field-type Misc-field ::=
ENUMERATED {
genome-project-id 1
comment-descriptor 2
defline 3
keyword 4
}  


Type DBLink-field-type

Is Used By

DBLink-field-pair Field-type DBLink-field-type ::=
ENUMERATED {
trace-assembly 1
bio-sample 2
probe-db 3
sequence-read-archve 4
bio-project 5
assembly 6
}  


Type DBLink-field-pair

Uses

DBLink-field-type

Is Used By

Field-pair-type DBLink-field-pair ::=
SEQUENCE {
from DBLink-field-type
to DBLink-field-type
}  


Type Pub-type

Is Used By

Publication-constraint Pub-type ::=
ENUMERATED {
any 0
published 1
unpublished 2
in-press 3
submitter-block 4
}  


Type Pub-field-constraint

Uses

Publication-field String-constraint

Is Used By

Publication-constraint Pub-field-constraint ::=
SEQUENCE {
field Publication-field
constraint String-constraint
}  


Type Pub-field-special-constraint-type

Is Used By

Pub-field-special-constraint Pub-field-special-constraint-type ::=
CHOICE {
is-present NULL
is-not-present NULL
is-all-caps NULL
is-all-lower NULL
is-all-punct NULL
}  


Type Pub-field-special-constraint

Uses

Pub-field-special-constraint-type Publication-field

Is Used By

Publication-constraint Pub-field-special-constraint ::=
SEQUENCE {
field Publication-field
constraint Pub-field-special-constraint-type
}  


Type Publication-constraint

Uses

Pub-field-constraint Pub-field-special-constraint Pub-type

Is Used By

Constraint-choice Publication-constraint ::=
SEQUENCE {
type Pub-type
field Pub-field-constraint OPTIONAL
special-field Pub-field-special-constraint OPTIONAL
}  


Type Source-constraint

Uses

Object-type-constraint Source-qual-choice String-constraint

Is Used By

Constraint-choice Source-constraint ::=
SEQUENCE {
field1 Source-qual-choice OPTIONAL
field2 Source-qual-choice OPTIONAL
constraint String-constraint OPTIONAL
type-constraint Object-type-constraint OPTIONAL
}  


Type CDSGeneProt-feature-type-constraint

Is Used By

CDSGeneProt-pseudo-constraint CDSGeneProt-feature-type-constraint ::=
ENUMERATED {
gene 1
mRNA 2
cds 3
prot 4
exon 5
mat-peptide 6
}  


Type CDSGeneProt-pseudo-constraint

Uses

CDSGeneProt-feature-type-constraint

Is Used By

Constraint-choice CDSGeneProt-pseudo-constraint ::=
SEQUENCE {
feature CDSGeneProt-feature-type-constraint
is-pseudo BOOLEAN DEFAULT true
}  


Type CDSGeneProt-constraint-field

Uses

CDSGeneProt-field

Is Used By

CDSGeneProt-qual-constraint CDSGeneProt-constraint-field ::=
CHOICE {
field CDSGeneProt-field
}  


Type CDSGeneProt-qual-constraint

Uses

CDSGeneProt-constraint-field String-constraint

Is Used By

Constraint-choice CDSGeneProt-qual-constraint ::=
SEQUENCE {
field1 CDSGeneProt-constraint-field OPTIONAL
field2 CDSGeneProt-constraint-field OPTIONAL
constraint String-constraint OPTIONAL
}  


Type Field-constraint

Uses

Field-type String-constraint

Is Used By

Constraint-choice Field-constraint ::=
SEQUENCE {
field Field-type
string-constraint String-constraint
}  


Type Sequence-constraint-rnamol

Is Used By

Sequence-constraint-mol-type-constraint Sequence-constraint-rnamol ::=
ENUMERATED {
any 0
genomic 1
precursor-RNA 2
mRNA 3
rRNA 4
tRNA 5
genomic-mRNA 6
cRNA 7
transcribed-RNA 8
ncRNA 9
transfer-messenger-RNA 10
}  


Type Sequence-constraint-mol-type-constraint

Uses

Sequence-constraint-rnamol

Is Used By

Sequence-constraint Sequence-constraint-mol-type-constraint ::=
CHOICE {
any NULL
nucleotide NULL
dna NULL
rna Sequence-constraint-rnamol
protein NULL
}  


Type Quantity-constraint

Is Used By

Extend-to-feature Sequence-constraint Translation-constraint Quantity-constraint ::=
CHOICE {
equals INTEGER
greater-than INTEGER
less-than INTEGER
}  


Type Feature-strandedness-constraint

Is Used By

Sequence-constraint Feature-strandedness-constraint ::=
ENUMERATED {
any 0
minus-only 1
plus-only 2
at-least-one-minus 3
at-least-one-plus 4
no-minus 5
no-plus 6
}  


Type Sequence-constraint

Uses

Feature-strandedness-constraint Macro-feature-type Quantity-constraint Sequence-constraint-mol-type-constraint String-constraint

Is Used By

Constraint-choice Sequence-constraint ::=
SEQUENCE {
seqtype Sequence-constraint-mol-type-constraint OPTIONAL
id String-constraint OPTIONAL
feature Macro-feature-type
num-type-features Quantity-constraint OPTIONAL
num-features Quantity-constraint OPTIONAL
length Quantity-constraint OPTIONAL
strandedness Feature-strandedness-constraint DEFAULT any
}  


Type Match-type-constraint

Is Used By

Translation-constraint Match-type-constraint ::=
ENUMERATED {
dont-care 0
yes 1
no 2
}  


Type Translation-constraint

Uses

Match-type-constraint Quantity-constraint String-constraint-set

Is Used By

Constraint-choice Translation-constraint ::=
SEQUENCE {
actual-strings String-constraint-set
transl-strings String-constraint-set
internal-stops Match-type-constraint DEFAULT dont-care
num-mismatches Quantity-constraint OPTIONAL
}  


Type Constraint-choice

Uses

CDSGeneProt-pseudo-constraint CDSGeneProt-qual-constraint Field-constraint Field-type Location-constraint Molinfo-field-constraint Publication-constraint Sequence-constraint Source-constraint String-constraint Translation-constraint

Is Used By

Constraint-choice-set Constraint-choice ::=
CHOICE {
string String-constraint
location Location-constraint
field Field-constraint
source Source-constraint
cdsgeneprot-qual CDSGeneProt-qual-constraint
cdsgeneprot-pseudo CDSGeneProt-pseudo-constraint
sequence Sequence-constraint
pub Publication-constraint
molinfo Molinfo-field-constraint
field-missing Field-type
translation Translation-constraint
}  


Type Constraint-choice-set

Uses

Constraint-choice

Is Used By

Add-descriptor-list-action AECR-action Author-fix-action Convert-feature-action Edit-feature-location-action Fix-pub-caps-action Make-gene-xref-action Molinfo-block Remove-descriptor-action Remove-duplicate-feature-action Remove-feature-action Remove-sequences-action Remove-xrefs-action Sort-fields-action Suspect-rule Constraint-choice-set ::= SET OF Constraint-choice

Type Text-marker

Is Used By

Text-portion Text-marker ::=
CHOICE {
free-text VisibleString
digits NULL
letters NULL
}  


Type Text-portion

Uses

Text-marker

Is Used By

AECRParse-action Create-TSA-ids-action Create-TSA-ids-src Parse-action Remove-outside-action Text-transform Text-portion ::=
SEQUENCE {
left-marker Text-marker OPTIONAL
include-left BOOLEAN
right-marker Text-marker OPTIONAL
include-right BOOLEAN
inside BOOLEAN
case-sensitive BOOLEAN DEFAULT false
whole-word BOOLEAN DEFAULT false
}  


Type Field-edit-location

Is Used By

Field-edit Field-edit-location ::=
ENUMERATED {
anywhere 0
beginning 1
end 2
}  


Type Field-edit

Uses

Field-edit-location

Is Used By

Edit-action Text-transform Field-edit ::=
SEQUENCE {
find-txt VisibleString
repl-txt VisibleString OPTIONAL
location Field-edit-location DEFAULT anywhere
case-insensitive BOOLEAN DEFAULT false
}  


Type Field-type

Uses

CDSGeneProt-field DBLink-field-type Feature-field Misc-field Molinfo-field Publication-field Rna-qual Source-qual-choice Structured-comment-field

Is Used By

Apply-action Constraint-choice Edit-action Field-constraint Remove-action Remove-outside-action Sort-fields-action Field-type ::=
CHOICE {
source-qual Source-qual-choice
feature-field Feature-field
rna-field Rna-qual
cds-gene-prot CDSGeneProt-field
molinfo-field Molinfo-field
pub Publication-field
struc-comment-field Structured-comment-field
misc Misc-field
dblink DBLink-field-type
}  


Type Field-pair-type

Uses

CDSGeneProt-field-pair DBLink-field-pair Feature-field-pair Molinfo-field-pair Rna-qual-pair Source-qual-pair Structured-comment-field-pair

Is Used By

AECRParse-action Convert-action Copy-action Swap-action Field-pair-type ::=
CHOICE {
source-qual Source-qual-pair
feature-field Feature-field-pair
rna-field Rna-qual-pair
cds-gene-prot CDSGeneProt-field-pair
molinfo-field Molinfo-field-pair
struc-comment-field Structured-comment-field-pair
dblink DBLink-field-pair
}  


Type ExistingTextOption

Is Used By

AECRParse-action Apply-action Convert-action Copy-action Parse-action ExistingTextOption ::=
ENUMERATED {
replace-old 1
append-semi 2
append-space 3
append-colon 4
append-comma 5
append-none 6
prefix-semi 7
prefix-space 8
prefix-colon 9
prefix-comma 10
prefix-none 11
leave-old 12
add-qual 13
}  


Type Apply-action

Uses

ExistingTextOption Field-type

Is Used By

Action-choice Apply-action ::=
SEQUENCE {
field Field-type
value VisibleString
existing-text ExistingTextOption
}  


Type Edit-action

Uses

Field-edit Field-type

Is Used By

Action-choice Edit-action ::=
SEQUENCE {
edit Field-edit
field Field-type
}  


Type Cap-change

Is Used By

Convert-action Parse-action Text-transform Cap-change ::=
ENUMERATED {
none 0
tolower 1
toupper 2
firstcap 3
firstcaprestnochange 4
firstlower-restnochange 5
cap-word-space 6
cap-word-space-punc 7
}  


Type Text-transform

Uses

Cap-change Field-edit Text-portion

Is Used By

Text-transform-set Text-transform ::=
CHOICE {
edit Field-edit
caps Cap-change
remove Text-portion
}  


Type Text-transform-set

Uses

Text-transform

Is Used By

AECRParse-action Parse-action Text-transform-set ::= SET OF Text-transform

Type Convert-action

Uses

Cap-change ExistingTextOption Field-pair-type

Is Used By

Action-choice Convert-action ::=
SEQUENCE {
fields Field-pair-type
strip-name BOOLEAN DEFAULT false
keep-original BOOLEAN DEFAULT false
capitalization Cap-change DEFAULT none
existing-text ExistingTextOption
}  


Type Copy-action

Uses

ExistingTextOption Field-pair-type

Is Used By

Action-choice Copy-action ::=
SEQUENCE {
fields Field-pair-type
existing-text ExistingTextOption
}  


Type Swap-action

Uses

Field-pair-type

Is Used By

Action-choice Swap-action ::=
SEQUENCE {
fields Field-pair-type
}  


Type AECRParse-action

Uses

ExistingTextOption Field-pair-type Text-portion Text-transform-set

Is Used By

Action-choice AECRParse-action ::=
SEQUENCE {
portion Text-portion
fields Field-pair-type
remove-from-parsed BOOLEAN DEFAULT false
remove-left BOOLEAN DEFAULT false
remove-right BOOLEAN DEFAULT false
transform Text-transform-set OPTIONAL
existing-text ExistingTextOption
}  


Type Remove-action

Uses

Field-type

Is Used By

Action-choice Remove-action ::=
SEQUENCE {
field Field-type
}  


Type Remove-outside-action

Uses

Field-type Text-portion

Is Used By

Action-choice Remove-outside-action ::=
SEQUENCE {
portion Text-portion
field Field-type
remove-if-not-found BOOLEAN DEFAULT false
}  


Type Action-choice

Uses

AECRParse-action Apply-action Convert-action Copy-action Edit-action Remove-action Remove-outside-action Swap-action

Is Used By

AECR-action Action-choice ::=
CHOICE {
apply Apply-action
edit Edit-action
convert Convert-action
copy Copy-action
swap Swap-action
remove Remove-action
parse AECRParse-action
remove-outside Remove-outside-action
}  


Type AECR-action

Uses

Action-choice Constraint-choice-set

Is Used By

Macro-action-choice AECR-action ::=
SEQUENCE {
action Action-choice
also-change-mrna BOOLEAN DEFAULT false
constraint Constraint-choice-set OPTIONAL
}  


Type Parse-src-org-choice

Uses

Source-qual

Is Used By

Parse-src-org Parse-src-org-choice ::=
CHOICE {
source-qual Source-qual
taxname-after-binomial NULL
}  


Type Parse-src-org

Uses

Object-type-constraint Parse-src-org-choice

Is Used By

Parse-src Parse-src-org ::=
SEQUENCE {
field Parse-src-org-choice
type Object-type-constraint DEFAULT any
}  


Type Parse-src-general-id

Is Used By

Parse-src Parse-src-general-id ::=
CHOICE {
whole-text NULL
db NULL
tag VisibleString
}  


Type Parse-src

Uses

Parse-src-general-id Parse-src-org

Is Used By

Parse-action Parse-src ::=
CHOICE {
defline NULL
flatfile NULL
local-id NULL
org Parse-src-org
comment NULL
bankit-comment NULL
structured-comment VisibleString
file-id NULL
general-id Parse-src-general-id
}  


Type Parse-dst-org

Uses

Object-type-constraint Source-qual-choice

Is Used By

Parse-dest Parse-dst-org ::=
SEQUENCE {
field Source-qual-choice
type Object-type-constraint DEFAULT any
}  


Type Parse-dest

Uses

Feature-field-legal Parse-dst-org

Is Used By

Parse-action Parse-dest ::=
CHOICE {
defline NULL
org Parse-dst-org
featqual Feature-field-legal
comment-descriptor NULL
dbxref VisibleString
}  


Type Parse-action

Uses

Cap-change ExistingTextOption Parse-dest Parse-src Text-portion Text-transform-set

Is Used By

Macro-action-choice Parse-action ::=
SEQUENCE {
portion Text-portion
src Parse-src
dest Parse-dest
capitalization Cap-change DEFAULT none
remove-from-parsed BOOLEAN DEFAULT false
transform Text-transform-set OPTIONAL
existing-text ExistingTextOption
}  


Type Location-interval

Is Used By

Location-choice Location-interval ::=
SEQUENCE {
from INTEGER
to INTEGER
}  


Type Location-choice

Uses

Location-interval

Is Used By

Apply-feature-action Location-choice ::=
CHOICE {
interval Location-interval
whole-sequence NULL
point INTEGER
}  


Type Sequence-list

Is Used By

Sequence-list-choice Sequence-list ::= SET OF VisibleString

Type Sequence-list-choice

Uses

Sequence-list

Is Used By

Apply-feature-action Sequence-list-choice ::=
CHOICE {
list Sequence-list
all NULL
}  


Type Apply-feature-action

Uses

Feat-qual-legal-set Location-choice Macro-feature-type Sequence-list-choice Source-qual-val-set

Is Used By

Macro-action-choice Apply-feature-action ::=
SEQUENCE {
type Macro-feature-type
partial5 BOOLEAN DEFAULT false
partial3 BOOLEAN DEFAULT false
plus-strand BOOLEAN DEFAULT true
location Location-choice
seq-list Sequence-list-choice
add-redundant BOOLEAN DEFAULT true
add-mrna BOOLEAN DEFAULT false
apply-to-parts BOOLEAN DEFAULT false
only-seg-num INTEGER DEFAULT -1
fields Feat-qual-legal-set OPTIONAL
src-fields Source-qual-val-set OPTIONAL
}  


Type Remove-feature-action

Uses

Constraint-choice-set Macro-feature-type

Is Used By

Macro-action-choice Remove-feature-action ::=
SEQUENCE {
type Macro-feature-type
constraint Constraint-choice-set OPTIONAL
}  


Type Convert-from-CDS-options

Is Used By

Convert-feature-src-options Convert-from-CDS-options ::=
SEQUENCE {
remove-mRNA BOOLEAN
remove-gene BOOLEAN
remove-transcript-id BOOLEAN
}  


Type Convert-feature-src-options

Uses

Convert-from-CDS-options

Is Used By

Convert-feature-action Convert-feature-src-options ::=
CHOICE {
cds Convert-from-CDS-options
}  


Type Bond-type

Is Used By

Convert-feature-dst-options Bond-type ::=
ENUMERATED {
disulfide 1
thioester 2
crosslink 3
thioether 4
other 5
}  


Type Site-type

Is Used By

Convert-feature-dst-options Site-type ::=
ENUMERATED {
active 1
binding 2
cleavage 3
inhibit 4
modified 5
glycosylation 6
myristoylation 7
mutagenized 8
metal-binding 9
phosphorylation 10
acetylation 11
amidation 12
methylation 13
hydroxylation 14
sulfatation 15
oxidative-deamination 16
pyrrolidone-carboxylic-acid 17
gamma-carboxyglutamic-acid 18
blocked 19
lipid-binding 20
np-binding 21
dna-binding 22
signal-peptide 23
transit-peptide 24
transmembrane-region 25
nitrosylation 26
other 27
}  


Type Region-type

Is Used By

Convert-feature-dst-options Region-type ::=
SEQUENCE {
create-nucleotide BOOLEAN
}  


Type Convert-feature-dst-options

Uses

Bond-type Region-type Site-type

Is Used By

Convert-feature-action Convert-feature-dst-options ::=
CHOICE {
bond Bond-type
site Site-type
region Region-type
ncrna-class VisibleString
remove-original BOOLEAN
}  


Type Convert-feature-action

Uses

Constraint-choice-set Convert-feature-dst-options Convert-feature-src-options Macro-feature-type

Is Used By

Macro-action-choice Convert-feature-action ::=
SEQUENCE {
type-from Macro-feature-type
type-to Macro-feature-type
src-options Convert-feature-src-options OPTIONAL
dst-options Convert-feature-dst-options OPTIONAL
leave-original BOOLEAN
src-feat-constraint Constraint-choice-set OPTIONAL
}  


Type Feature-location-strand-from

Is Used By

Edit-location-strand Feature-location-strand-from ::=
ENUMERATED {
any 0
plus 1
minus 2
unknown 3
both 4
}  


Type Feature-location-strand-to

Is Used By

Edit-location-strand Feature-location-strand-to ::=
ENUMERATED {
plus 1
minus 2
unknown 3
both 4
reverse 5
}  


Type Edit-location-strand

Uses

Feature-location-strand-from Feature-location-strand-to

Is Used By

Location-edit-type Edit-location-strand ::=
SEQUENCE {
strand-from Feature-location-strand-from
strand-to Feature-location-strand-to
}  


Type Partial-5-set-constraint

Is Used By

Partial-5-set-action Partial-5-set-constraint ::=
ENUMERATED {
all 0
at-end 1
bad-start 2
frame-not-one 3
}  


Type Partial-5-set-action

Uses

Partial-5-set-constraint

Is Used By

Location-edit-type Partial-5-set-action ::=
SEQUENCE {
constraint Partial-5-set-constraint
extend BOOLEAN
}  


Type Partial-5-clear-constraint

Is Used By

Location-edit-type Partial-5-clear-constraint ::=
ENUMERATED {
all 0
not-at-end 1
good-start 2
}  


Type Partial-3-set-constraint

Is Used By

Partial-3-set-action Partial-3-set-constraint ::=
ENUMERATED {
all 0
at-end 1
bad-end 2
}  


Type Partial-3-set-action

Uses

Partial-3-set-constraint

Is Used By

Location-edit-type Partial-3-set-action ::=
SEQUENCE {
constraint Partial-3-set-constraint
extend BOOLEAN
}  


Type Partial-3-clear-constraint

Is Used By

Location-edit-type Partial-3-clear-constraint ::=
ENUMERATED {
all 0
not-at-end 1
good-end 2
}  


Type Partial-both-set-constraint

Is Used By

Partial-both-set-action Partial-both-set-constraint ::=
ENUMERATED {
all 0
at-end 1
}  


Type Partial-both-set-action

Uses

Partial-both-set-constraint

Is Used By

Location-edit-type Partial-both-set-action ::=
SEQUENCE {
constraint Partial-both-set-constraint
extend BOOLEAN
}  


Type Partial-both-clear-constraint

Is Used By

Location-edit-type Partial-both-clear-constraint ::=
ENUMERATED {
all 0
not-at-end 1
}  


Type Convert-location-type

Is Used By

Location-edit-type Convert-location-type ::=
ENUMERATED {
join 1
order 2
merge 3
}  


Type Extend-to-feature

Uses

Macro-feature-type Quantity-constraint

Is Used By

Location-edit-type Extend-to-feature ::=
SEQUENCE {
type Macro-feature-type
include-feat BOOLEAN
distance Quantity-constraint OPTIONAL
}  


Type Location-edit-type

Uses

Convert-location-type Edit-location-strand Extend-to-feature Partial-3-clear-constraint Partial-3-set-action Partial-5-clear-constraint Partial-5-set-action Partial-both-clear-constraint Partial-both-set-action

Is Used By

Edit-feature-location-action Location-edit-type ::=
CHOICE {
strand Edit-location-strand
set-5-partial Partial-5-set-action
clear-5-partial Partial-5-clear-constraint
set-3-partial Partial-3-set-action
clear-3-partial Partial-3-clear-constraint
set-both-partial Partial-both-set-action
clear-both-partial Partial-both-clear-constraint
convert Convert-location-type
extend-5 NULL
extend-3 NULL
extend-5-to-feat Extend-to-feature
extend-3-to-feat Extend-to-feature
}  


Type Edit-feature-location-action

Uses

Constraint-choice-set Location-edit-type Macro-feature-type

Is Used By

Macro-action-choice Edit-feature-location-action ::=
SEQUENCE {
type Macro-feature-type
action Location-edit-type
retranslate-cds BOOLEAN OPTIONAL
also-edit-gene BOOLEAN OPTIONAL
constraint Constraint-choice-set OPTIONAL
}  


Type Molinfo-block

Uses

Constraint-choice-set Molinfo-field-list

Is Used By

Macro-action-choice Molinfo-block ::=
SEQUENCE {
to-list Molinfo-field-list
from-list Molinfo-field-list OPTIONAL
constraint Constraint-choice-set OPTIONAL
}  


Type Descriptor-type

Is Used By

Remove-descriptor-action Descriptor-type ::=
ENUMERATED {
all 0
title 1
source 2
publication 3
comment 4
genbank 5
user 6
create-date 7
update-date 8
mol-info 9
structured-comment 10
genome-project-id 11
}  


Type Remove-descriptor-action

Uses

Constraint-choice-set Descriptor-type

Is Used By

Macro-action-choice Remove-descriptor-action ::=
SEQUENCE {
type Descriptor-type
constraint Constraint-choice-set OPTIONAL
}  


Type Autodef-list-type

Is Used By

Autodef-action Autodef-list-type ::=
ENUMERATED {
feature-list 1
complete-sequence 2
complete-genome 3
sequence 4
}  


Type Autodef-misc-feat-parse-rule

Is Used By

Autodef-action Autodef-misc-feat-parse-rule ::=
ENUMERATED {
use-comment-before-first-semicolon 1
look-for-noncoding-products 2
}  


Type Autodef-action

Uses

Autodef-list-type Autodef-misc-feat-parse-rule Source-qual

Is Used By

Macro-action-choice Autodef-action ::=
SEQUENCE {
modifiers SET OF Source-qual OPTIONAL
clause-list-type Autodef-list-type
misc-feat-parse-rule Autodef-misc-feat-parse-rule DEFAULT look-for-noncoding-products
}  


Type Fix-pub-caps-action

Uses

Constraint-choice-set

Is Used By

Fix-caps-action Macro-action-choice Fix-pub-caps-action ::=
SEQUENCE {
title BOOLEAN OPTIONAL
authors BOOLEAN OPTIONAL
affiliation BOOLEAN OPTIONAL
affil-country BOOLEAN OPTIONAL
punct-only BOOLEAN DEFAULT false
constraint Constraint-choice-set OPTIONAL
}  


Type Sort-order

Is Used By

Sort-fields-action Sort-order ::=
ENUMERATED {
short-to-long 1
long-to-short 2
alphabetical 3
}  


Type Sort-fields-action

Uses

Constraint-choice-set Field-type Sort-order

Is Used By

Macro-action-choice Sort-fields-action ::=
SEQUENCE {
field Field-type
order Sort-order
constraint Constraint-choice-set OPTIONAL
}  


Type Fix-author-caps

Is Used By

Fix-caps-action Fix-author-caps ::=
SEQUENCE {
last-name-only BOOLEAN
}  


Type Fix-caps-action

Uses

Fix-author-caps Fix-pub-caps-action Source-qual

Is Used By

Macro-action-choice Fix-caps-action ::=
CHOICE {
pub Fix-pub-caps-action
src-country NULL
mouse-strain NULL
src-qual Source-qual
author Fix-author-caps
}  


Type Fix-format-action

Is Used By

Macro-action-choice Fix-format-action ::=
CHOICE {
collection-date NULL
lat-lon NULL
primers NULL
protein-name NULL
}  


Type Remove-duplicate-feature-action

Uses

Constraint-choice-set Macro-feature-type

Is Used By

Macro-action-choice Remove-duplicate-feature-action ::=
SEQUENCE {
type Macro-feature-type
ignore-partials BOOLEAN
case-sensitive BOOLEAN
remove-proteins BOOLEAN
rd-constraint Constraint-choice-set OPTIONAL
}  


Type Gene-xref-suppression-type

Is Used By

Gene-xref-type Gene-xref-suppression-type ::=
ENUMERATED {
any 0
suppressing 1
non-suppressing 2
}  


Type Gene-xref-necessary-type

Is Used By

Gene-xref-type Gene-xref-necessary-type ::=
ENUMERATED {
any 0
necessary 1
unnecessary 2
}  


Type Gene-xref-type

Uses

Gene-xref-necessary-type Gene-xref-suppression-type Macro-feature-type

Is Used By

Xref-type Gene-xref-type ::=
SEQUENCE {
feature Macro-feature-type
suppression Gene-xref-suppression-type
necessary Gene-xref-necessary-type
}  


Type Xref-type

Uses

Gene-xref-type

Is Used By

Remove-xrefs-action Xref-type ::=
CHOICE {
gene Gene-xref-type
}  


Type Remove-xrefs-action

Uses

Constraint-choice-set Xref-type

Is Used By

Macro-action-choice Remove-xrefs-action ::=
SEQUENCE {
xref-type Xref-type
constraint Constraint-choice-set OPTIONAL
}  


Type Make-gene-xref-action

Uses

Constraint-choice-set Macro-feature-type

Is Used By

Macro-action-choice Make-gene-xref-action ::=
SEQUENCE {
feature Macro-feature-type
constraint Constraint-choice-set OPTIONAL
}  


Type Author-fix-type

Is Used By

Author-fix-action Author-fix-type ::=
ENUMERATED {
truncate-middle-initials 1
strip-suffix 2
move-middle-to-first 3
}  


Type Author-fix-action

Uses

Author-fix-type Constraint-choice-set

Is Used By

Macro-action-choice Author-fix-action ::=
SEQUENCE {
fix-type Author-fix-type
constraint Constraint-choice-set OPTIONAL
}  


Type Update-sequences-action

Is Used By

Macro-action-choice Update-sequences-action ::=
SEQUENCE {
filename VisibleString
add-cit-subs BOOLEAN DEFAULT false
}  


Type Create-TSA-ids-src

Uses

Text-portion

Is Used By

Create-TSA-ids-action Create-TSA-ids-src ::=
CHOICE {
local-id NULL
defline Text-portion
}  


Type Create-TSA-ids-action

Uses

Create-TSA-ids-src Text-portion

Is Used By

Macro-action-choice Create-TSA-ids-action ::=
SEQUENCE {
src Create-TSA-ids-src
suffix VisibleString OPTIONAL
id-text-portion Text-portion OPTIONAL
}  


Type Autofix-action

Is Used By

Macro-action-choice Autofix-action ::=
SEQUENCE {
test-name VisibleString
}  


Type Fix-sets-action

Is Used By

Macro-action-choice Fix-sets-action ::=
CHOICE {
remove-single-item-set NULL
renormalize-nuc-prot-sets NULL
fix-pop-to-phy NULL
}  


Type Table-match-type

Uses

Source-qual-choice

Is Used By

Table-match Table-match-type ::=
CHOICE {
feature-id NULL
gene-locus-tag NULL
protein-id NULL
dbxref NULL
nuc-id NULL
src-qual Source-qual-choice
protein-name NULL
any NULL
}  


Type Table-match

Uses

String-location Table-match-type

Is Used By

Apply-table-action Table-match ::=
SEQUENCE {
match-type Table-match-type
match-location String-location DEFAULT equals
}  


Type Apply-table-extra-data

Is Used By

Add-file-action Apply-table-action Apply-table-extra-data ::=
CHOICE {
table NULL
}  


Type Apply-table-action

Uses

Apply-table-extra-data Table-match

Is Used By

Macro-action-choice Apply-table-action ::=
SEQUENCE {
filename VisibleString
match-type Table-match
in-memory-table Apply-table-extra-data OPTIONAL
also-change-mrna BOOLEAN DEFAULT false
skip-blanks BOOLEAN DEFAULT true
}  


Type Add-file-action

Uses

Apply-table-extra-data

Is Used By

Add-descriptor-list-action Add-file-action ::=
SEQUENCE {
filename VisibleString
in-memory-table Apply-table-extra-data OPTIONAL
}  


Type Add-descriptor-list-action

Uses

Add-file-action Constraint-choice-set

Is Used By

Macro-action-choice Add-descriptor-list-action ::=
SEQUENCE {
descriptor-list Add-file-action
constraint Constraint-choice-set OPTIONAL
}  


Type Remove-sequences-action

Uses

Constraint-choice-set

Is Used By

Macro-action-choice Remove-sequences-action ::=
SEQUENCE {
constraint Constraint-choice-set
}  


Type Update-replaced-ec-numbers-action

Is Used By

Macro-action-choice Update-replaced-ec-numbers-action ::=
SEQUENCE {
delete-improper-format BOOLEAN
delete-unrecognized BOOLEAN
delete-multiple-replacement BOOLEAN
}  


Type Retranslate-cds-action

Is Used By

Macro-action-choice Retranslate-cds-action ::=
SEQUENCE {
obey-stop-codon BOOLEAN
}  


Type Macro-action-choice

Uses

Add-descriptor-list-action AECR-action Apply-feature-action Apply-table-action Author-fix-action Autodef-action Autofix-action Convert-feature-action Create-TSA-ids-action Edit-feature-location-action Fix-caps-action Fix-format-action Fix-pub-caps-action Fix-sets-action Make-gene-xref-action Molinfo-block Parse-action Remove-descriptor-action Remove-duplicate-feature-action Remove-feature-action Remove-sequences-action Remove-xrefs-action Retranslate-cds-action Sort-fields-action Update-replaced-ec-numbers-action Update-sequences-action

Is Used By

Macro-action-list Macro-action-choice ::=
CHOICE {
aecr AECR-action
parse Parse-action
add-feature Apply-feature-action
remove-feature Remove-feature-action
convert-feature Convert-feature-action
edit-location Edit-feature-location-action
remove-descriptor Remove-descriptor-action
autodef Autodef-action
removesets NULL
trim-junk-from-primer-seq NULL
trim-stop-from-complete-cds NULL
fix-usa-and-states NULL
synchronize-cds-partials NULL
adjust-for-consensus-splice NULL
fix-pub-caps Fix-pub-caps-action
remove-seg-gaps NULL
sort-fields Sort-fields-action
apply-molinfo-block Molinfo-block
fix-caps Fix-caps-action
fix-format Fix-format-action
fix-spell NULL
remove-duplicate-features Remove-duplicate-feature-action
remove-lineage-notes NULL
remove-xrefs Remove-xrefs-action
make-gene-xrefs Make-gene-xref-action
make-bold-xrefs NULL
fix-author Author-fix-action
update-sequences Update-sequences-action
add-trans-splicing NULL
remove-invalid-ecnumbers NULL
create-tsa-ids Create-TSA-ids-action
perform-autofix Autofix-action
fix-sets Fix-sets-action
apply-table Apply-table-action
remove-sequences Remove-sequences-action
propagate-sequence-technology NULL
add-file-descriptors Add-descriptor-list-action
propagate-missing-old-name NULL
autoapply-structured-comments NULL
reorder-structured-comments NULL
remove-duplicate-structured-comments NULL
lookup-taxonomy NULL
lookup-pubs NULL
trim-terminal-ns NULL
update-replaced-ecnumbers Update-replaced-ec-numbers-action
instantiate-protein-titles NULL
retranslate-cds Retranslate-cds-action
}  


Type Macro-action-list

Uses

Macro-action-choice Macro-action-list ::= SET OF Macro-action-choice

Type Search-func

Uses

String-constraint

Is Used By

Suspect-rule Search-func ::=
CHOICE {
string-constraint String-constraint
contains-plural NULL
n-or-more-brackets-or-parentheses INTEGER
three-numbers NULL
underscore NULL
prefix-and-numbers VisibleString
all-caps NULL
unbalanced-paren NULL
too-long INTEGER
has-term VisibleString
}  


Type Simple-replace

Is Used By

Replace-func Simple-replace ::=
SEQUENCE {
replace VisibleString OPTIONAL
whole-string BOOLEAN DEFAULT false
weasel-to-putative BOOLEAN DEFAULT false
}  


Type Replace-func

Uses

Simple-replace

Is Used By

Replace-rule Replace-func ::=
CHOICE {
simple-replace Simple-replace
haem-replace VisibleString
}  


Type Replace-rule

Uses

Replace-func

Is Used By

Suspect-rule Replace-rule ::=
SEQUENCE {
replace-func Replace-func
move-to-note BOOLEAN DEFAULT false
}  


Type Fix-type

Is Used By

Suspect-rule Fix-type ::=
ENUMERATED {
none 0
typo 1
putative-typo 2
quickfix 3
no-organelle-for-prokaryote 4
might-be-nonfunctional 5
database 6
remove-organism-name 7
inappropriate-symbol 8
evolutionary-relationship 9
use-protein 10
hypothetical 11
british 12
description 13
gene 14
}  


Type Suspect-rule

Uses

Constraint-choice-set Fix-type Replace-rule Search-func

Is Used By

Suspect-rule-set Suspect-rule ::=
SEQUENCE {
find Search-func
except Search-func OPTIONAL
feat-constraint Constraint-choice-set OPTIONAL
rule-type Fix-type DEFAULT none
replace Replace-rule OPTIONAL
description VisibleString OPTIONAL
}  


Type Suspect-rule-set

Uses

Suspect-rule Suspect-rule-set ::= SET OF Suspect-rule

Top-level module index.