src/objects/macro/macro.asn
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--$Revision: 86883 $
--**********************************************************************
--
-- NCBI ASN.1 macro editing language specifications
--
-- by Colleen Bollin, 2007
--
--**********************************************************************
NCBI-Macro DEFINITIONS ::=
BEGIN
EXPORTS AECR-action, Parse-action, Macro-action-list, Suspect-rule-set;
-- simple constraints --
String-location ::= ENUMERATED {
contains (1) ,
equals (2) ,
starts (3) ,
ends (4) ,
inlist (5) }
Word-substitution ::= SEQUENCE {
word VisibleString OPTIONAL ,
synonyms SET OF VisibleString OPTIONAL ,
case-sensitive BOOLEAN DEFAULT FALSE ,
whole-word BOOLEAN DEFAULT FALSE }
Word-substitution-set ::= SET OF Word-substitution
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 ,
is-first-cap BOOLEAN DEFAULT FALSE ,
is-first-each-cap BOOLEAN DEFAULT FALSE }
String-constraint-set ::= SET OF String-constraint
Strand-constraint ::= ENUMERATED {
any (0) ,
plus (1) ,
minus (2) }
Seqtype-constraint ::= ENUMERATED {
any (0) ,
nuc (1) ,
prot (2) }
Partial-constraint ::= ENUMERATED {
either (0) ,
partial (1) ,
complete (2) }
Location-type-constraint ::= ENUMERATED {
any (0) ,
single-interval (1) ,
joined (2) ,
ordered (3) }
Location-pos-constraint ::= CHOICE {
dist-from-end INTEGER ,
max-dist-from-end INTEGER ,
min-dist-from-end INTEGER }
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 }
Object-type-constraint ::= ENUMERATED {
any (0) ,
feature (1) ,
descriptor (2) }
-- feature values --
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) ,
regulatory (95) }
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) ,
regulatory-class (73) }
Feat-qual-legal-val ::= SEQUENCE {
qual Feat-qual-legal ,
val VisibleString }
Feat-qual-legal-val-choice ::= CHOICE {
qual Feat-qual-legal-val }
Feat-qual-legal-set ::= SET OF Feat-qual-legal-val-choice
Feat-qual-choice ::= CHOICE {
legal-qual Feat-qual-legal ,
illegal-qual String-constraint }
Feature-field ::= SEQUENCE {
type Macro-feature-type ,
field Feat-qual-choice }
Feature-field-legal ::= SEQUENCE {
type Macro-feature-type ,
field Feat-qual-legal }
Feature-field-pair ::= SEQUENCE {
type Macro-feature-type ,
field-from Feat-qual-choice ,
field-to Feat-qual-choice }
Rna-feat-type ::= CHOICE {
any NULL ,
preRNA NULL ,
mRNA NULL ,
tRNA NULL ,
rRNA NULL ,
ncRNA VisibleString ,
tmRNA NULL,
miscRNA NULL }
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) }
Rna-qual ::= SEQUENCE {
type Rna-feat-type ,
field Rna-field }
Rna-qual-pair ::= SEQUENCE {
type Rna-feat-type ,
field-from Rna-field ,
field-to Rna-field }
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-material (100)
}
Source-qual-pair ::= SEQUENCE {
field-from Source-qual ,
field-to Source-qual }
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) }
Source-origin ::= ENUMERATED {
unknown (0) ,
natural (1) ,
natmut (2) ,
mut (3) ,
artificial (4) ,
synthetic (5) ,
other (255) }
Source-qual-choice ::= CHOICE {
textqual Source-qual ,
location Source-location,
origin Source-origin ,
gcode INTEGER ,
mgcode INTEGER }
Source-qual-text-val ::= SEQUENCE {
srcqual Source-qual ,
val VisibleString }
Source-qual-val-choice ::= CHOICE {
textqual Source-qual-text-val ,
location Source-location,
origin Source-origin ,
gcode INTEGER ,
mgcode INTEGER }
Source-qual-val-set ::= SET OF Source-qual-val-choice
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) }
CDSGeneProt-field-pair ::= SEQUENCE {
field-from CDSGeneProt-field ,
field-to CDSGeneProt-field }
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) }
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) ,
targeted (24) ,
other (25) }
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 (8) }
Molecule-class-type ::= ENUMERATED {
unknown (0) ,
dna (1) ,
rna (2) ,
protein (3) ,
nucleotide (4),
other (5) }
Topology-type ::= ENUMERATED {
unknown (0) ,
linear (1) ,
circular (2) ,
tandem (3) ,
other (4) }
Strand-type ::= ENUMERATED {
unknown (0) ,
single (1) ,
double (2) ,
mixed (3) ,
mixed-rev (4) ,
other (5) }
Molinfo-field ::= CHOICE {
molecule Molecule-type ,
technique Technique-type ,
completedness Completedness-type ,
mol-class Molecule-class-type ,
topology Topology-type ,
strand Strand-type }
Molinfo-molecule-pair ::= SEQUENCE {
from Molecule-type ,
to Molecule-type }
Molinfo-technique-pair ::= SEQUENCE {
from Technique-type ,
to Technique-type }
Molinfo-completedness-pair ::= SEQUENCE {
from Completedness-type ,
to Completedness-type }
Molinfo-mol-class-pair ::= SEQUENCE {
from Molecule-class-type ,
to Molecule-class-type }
Molinfo-topology-pair ::= SEQUENCE {
from Topology-type ,
to Topology-type }
Molinfo-strand-pair ::= SEQUENCE {
from Strand-type ,
to Strand-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 }
Molinfo-field-list ::= SET OF Molinfo-field
Molinfo-field-constraint ::= SEQUENCE {
field Molinfo-field ,
is-not BOOLEAN DEFAULT FALSE }
-- publication fields --
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)
}
-- structured comment fields --
Structured-comment-field ::= CHOICE {
database NULL ,
named VisibleString ,
field-name NULL
}
Structured-comment-field-pair ::= SEQUENCE {
from Structured-comment-field ,
to Structured-comment-field
}
-- misc fields --
-- these would not appear in pairs --
Misc-field ::= ENUMERATED {
genome-project-id (1) ,
comment-descriptor (2) ,
defline (3) ,
keyword (4)
}
-- dblink fields --
DBLink-field-type ::= ENUMERATED {
trace-assembly (1) ,
bio-sample (2) ,
probe-db (3) ,
sequence-read-archve (4) ,
bio-project (5) ,
assembly (6) }
DBLink-field-pair ::= SEQUENCE {
from DBLink-field-type ,
to DBLink-field-type
}
-- complex constraints --
Pub-type ::= ENUMERATED {
any (0) ,
published (1) ,
unpublished (2) ,
in-press (3) ,
submitter-block (4) }
Pub-field-constraint ::= SEQUENCE {
field Publication-field ,
constraint String-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 }
Pub-field-special-constraint ::= SEQUENCE {
field Publication-field ,
constraint Pub-field-special-constraint-type }
Publication-constraint ::= SEQUENCE {
type Pub-type ,
field Pub-field-constraint OPTIONAL ,
special-field Pub-field-special-constraint OPTIONAL }
Source-constraint ::= SEQUENCE {
field1 Source-qual-choice OPTIONAL ,
field2 Source-qual-choice OPTIONAL ,
constraint String-constraint OPTIONAL ,
type-constraint Object-type-constraint OPTIONAL }
CDSGeneProt-feature-type-constraint ::= ENUMERATED {
gene (1) ,
mRNA (2) ,
cds (3) ,
prot (4) ,
exon (5) ,
mat-peptide (6) }
CDSGeneProt-pseudo-constraint ::= SEQUENCE {
feature CDSGeneProt-feature-type-constraint ,
is-pseudo BOOLEAN DEFAULT TRUE }
CDSGeneProt-constraint-field ::= CHOICE {
field CDSGeneProt-field }
CDSGeneProt-qual-constraint ::= SEQUENCE {
field1 CDSGeneProt-constraint-field OPTIONAL ,
field2 CDSGeneProt-constraint-field OPTIONAL ,
constraint String-constraint OPTIONAL }
Field-constraint ::= SEQUENCE {
field Field-type ,
string-constraint String-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) }
Sequence-constraint-mol-type-constraint ::= CHOICE {
any NULL ,
nucleotide NULL ,
dna NULL ,
rna Sequence-constraint-rnamol ,
protein NULL }
Quantity-constraint ::= CHOICE {
equals INTEGER ,
greater-than INTEGER ,
less-than INTEGER }
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) }
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 }
Match-type-constraint ::= ENUMERATED {
dont-care (0) ,
yes (1) ,
no (2) }
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 }
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 }
Constraint-choice-set ::= SET OF Constraint-choice
Text-marker ::= CHOICE {
free-text VisibleString ,
digits NULL ,
letters NULL }
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 }
Field-edit-location ::= ENUMERATED {
anywhere (0) ,
beginning (1) ,
end (2) }
Field-edit ::= SEQUENCE {
find-txt VisibleString ,
repl-txt VisibleString OPTIONAL ,
location Field-edit-location DEFAULT anywhere ,
case-insensitive BOOLEAN DEFAULT FALSE }
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 }
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}
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) }
Apply-action ::= SEQUENCE {
field Field-type ,
value VisibleString ,
existing-text ExistingTextOption }
Edit-action ::= SEQUENCE {
edit Field-edit ,
field Field-type }
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)
}
Text-transform ::= CHOICE {
edit Field-edit ,
caps Cap-change ,
remove Text-portion }
Text-transform-set ::= SET OF Text-transform
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 }
Copy-action ::= SEQUENCE {
fields Field-pair-type ,
existing-text ExistingTextOption }
Swap-action ::= SEQUENCE {
fields Field-pair-type }
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 }
Remove-action ::= SEQUENCE {
field Field-type }
Remove-outside-action ::= SEQUENCE {
portion Text-portion ,
field Field-type ,
remove-if-not-found BOOLEAN DEFAULT FALSE }
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 }
AECR-action ::= SEQUENCE {
action Action-choice ,
also-change-mrna BOOLEAN DEFAULT FALSE ,
constraint Constraint-choice-set OPTIONAL }
Parse-src-org-choice ::= CHOICE {
source-qual Source-qual ,
taxname-after-binomial NULL }
Parse-src-org ::= SEQUENCE {
field Parse-src-org-choice ,
type Object-type-constraint DEFAULT any }
-- For Parse-src-general-id tag, specify the db of the id from which you
-- want to retrieve the tag. If empty or null, any db will do.
Parse-src-general-id ::= CHOICE {
whole-text NULL ,
db NULL ,
tag VisibleString }
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 }
Parse-dst-org ::= SEQUENCE {
field Source-qual-choice ,
type Object-type-constraint DEFAULT any }
Parse-dest ::= CHOICE {
defline NULL ,
org Parse-dst-org ,
featqual Feature-field-legal ,
comment-descriptor NULL ,
dbxref VisibleString }
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 }
Location-interval ::= SEQUENCE {
from INTEGER ,
to INTEGER }
Location-choice ::= CHOICE {
interval Location-interval ,
whole-sequence NULL ,
point INTEGER }
Sequence-list ::= SET OF VisibleString
Sequence-list-choice ::= CHOICE {
list Sequence-list ,
all NULL }
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 }
Remove-feature-action ::= SEQUENCE {
type Macro-feature-type ,
constraint Constraint-choice-set OPTIONAL }
-- for convert features --
Convert-from-CDS-options ::= SEQUENCE {
remove-mRNA BOOLEAN ,
remove-gene BOOLEAN ,
remove-transcript-id BOOLEAN }
Convert-feature-src-options ::= CHOICE {
cds Convert-from-CDS-options }
Bond-type ::= ENUMERATED {
disulfide (1) ,
thioester (2) ,
crosslink (3) ,
thioether (4) ,
other (5) }
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) }
-- other choice is to create protein sequences, skipping bad --
Region-type ::= SEQUENCE {
create-nucleotide BOOLEAN }
Convert-feature-dst-options ::= CHOICE {
bond Bond-type ,
site Site-type ,
region Region-type ,
ncrna-class VisibleString ,
remove-original BOOLEAN }
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 }
Feature-location-strand-from ::= ENUMERATED {
any (0) ,
plus (1) ,
minus (2) ,
unknown (3) ,
both (4) }
Feature-location-strand-to ::= ENUMERATED {
plus (1) ,
minus (2) ,
unknown (3) ,
both (4) ,
reverse (5) }
Edit-location-strand ::= SEQUENCE {
strand-from Feature-location-strand-from ,
strand-to Feature-location-strand-to }
Partial-5-set-constraint ::= ENUMERATED {
all (0) ,
at-end (1) ,
bad-start (2) ,
frame-not-one (3) }
Partial-5-set-action ::= SEQUENCE {
constraint Partial-5-set-constraint ,
extend BOOLEAN }
Partial-5-clear-constraint ::= ENUMERATED {
all (0) ,
not-at-end (1) ,
good-start (2) }
Partial-3-set-constraint ::= ENUMERATED {
all (0) ,
at-end (1) ,
bad-end (2) }
Partial-3-set-action ::= SEQUENCE {
constraint Partial-3-set-constraint ,
extend BOOLEAN }
Partial-3-clear-constraint ::= ENUMERATED {
all (0) ,
not-at-end (1) ,
good-end (2) }
Partial-both-set-constraint ::= ENUMERATED {
all (0) ,
at-end (1) }
Partial-both-set-action ::= SEQUENCE {
constraint Partial-both-set-constraint ,
extend BOOLEAN }
Partial-both-clear-constraint ::= ENUMERATED {
all (0) ,
not-at-end (1) }
Convert-location-type ::= ENUMERATED {
join (1) ,
order (2) ,
merge (3) }
Extend-to-feature ::= SEQUENCE {
type Macro-feature-type ,
include-feat BOOLEAN ,
distance Quantity-constraint OPTIONAL }
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 }
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 }
Molinfo-block ::= SEQUENCE {
to-list Molinfo-field-list ,
from-list Molinfo-field-list OPTIONAL ,
constraint Constraint-choice-set OPTIONAL }
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) }
Remove-descriptor-action ::= SEQUENCE {
type Descriptor-type ,
constraint Constraint-choice-set OPTIONAL }
Autodef-list-type ::= ENUMERATED {
feature-list (1) ,
complete-sequence (2) ,
complete-genome (3) ,
sequence (4) }
Autodef-misc-feat-parse-rule ::= ENUMERATED {
use-comment-before-first-semicolon (1) ,
look-for-noncoding-products (2) }
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 }
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 }
Sort-order ::= ENUMERATED {
short-to-long (1) ,
long-to-short (2) ,
alphabetical (3) }
Sort-fields-action ::= SEQUENCE {
field Field-type ,
order Sort-order ,
constraint Constraint-choice-set OPTIONAL }
Fix-author-caps ::= SEQUENCE {
last-name-only BOOLEAN }
Fix-caps-action ::= CHOICE {
pub Fix-pub-caps-action ,
src-country NULL ,
mouse-strain NULL ,
src-qual Source-qual ,
author Fix-author-caps }
Fix-format-action ::= CHOICE {
collection-date NULL ,
lat-lon NULL ,
primers NULL ,
protein-name NULL }
Remove-duplicate-feature-action ::= SEQUENCE {
type Macro-feature-type ,
ignore-partials BOOLEAN ,
case-sensitive BOOLEAN ,
remove-proteins BOOLEAN ,
rd-constraint Constraint-choice-set OPTIONAL }
Gene-xref-suppression-type ::= ENUMERATED {
any (0) ,
suppressing (1) ,
non-suppressing (2) }
Gene-xref-necessary-type ::= ENUMERATED {
any (0) ,
necessary (1) ,
unnecessary (2) }
Gene-xref-type ::= SEQUENCE {
feature Macro-feature-type ,
suppression Gene-xref-suppression-type ,
necessary Gene-xref-necessary-type }
Xref-type ::= CHOICE {
gene Gene-xref-type }
Remove-xrefs-action ::= SEQUENCE {
xref-type Xref-type ,
constraint Constraint-choice-set OPTIONAL }
Make-gene-xref-action ::= SEQUENCE {
feature Macro-feature-type ,
constraint Constraint-choice-set OPTIONAL }
Author-fix-type ::= ENUMERATED {
truncate-middle-initials (1) ,
strip-suffix (2) ,
move-middle-to-first (3) }
Author-fix-action ::= SEQUENCE {
fix-type Author-fix-type ,
constraint Constraint-choice-set OPTIONAL }
Update-sequences-action ::= SEQUENCE {
filename VisibleString ,
add-cit-subs BOOLEAN DEFAULT FALSE }
Create-TSA-ids-src ::= CHOICE {
local-id NULL ,
defline Text-portion
}
Create-TSA-ids-action ::= SEQUENCE {
src Create-TSA-ids-src ,
suffix VisibleString OPTIONAL ,
id-text-portion Text-portion OPTIONAL }
Autofix-action ::= SEQUENCE {
test-name VisibleString }
Fix-sets-action ::= CHOICE {
remove-single-item-set NULL ,
renormalize-nuc-prot-sets NULL ,
fix-pop-to-phy NULL
}
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 ,
bioproject NULL ,
any NULL
}
Table-match ::= SEQUENCE {
match-type Table-match-type ,
match-location String-location DEFAULT equals
}
Apply-table-extra-data ::= CHOICE {
table NULL }
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
}
Add-file-action ::= SEQUENCE {
filename VisibleString ,
in-memory-table Apply-table-extra-data OPTIONAL
}
Add-descriptor-list-action ::= SEQUENCE {
descriptor-list Add-file-action ,
constraint Constraint-choice-set OPTIONAL
}
Remove-sequences-action ::= SEQUENCE {
constraint Constraint-choice-set
}
Update-replaced-ec-numbers-action ::= SEQUENCE {
delete-improper-format BOOLEAN ,
delete-unrecognized BOOLEAN ,
delete-multiple-replacement BOOLEAN
}
Retranslate-cds-action ::= SEQUENCE {
obey-stop-codon BOOLEAN
}
Truncated-ends-partial-type ::= ENUMERATED {
always (1) ,
unless-pseudo (2) ,
never (3) }
Adjust-features-for-gaps-action ::= SEQUENCE {
type Macro-feature-type ,
adjust-for-unknown-length-gaps BOOLEAN ,
adjust-for-known-length-gaps BOOLEAN ,
make-truncated-ends-partial Truncated-ends-partial-type ,
trim-ends-in-gaps BOOLEAN ,
split-for-internal-gaps BOOLEAN ,
even-when-gaps-are-in-introns BOOLEAN
}
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 ,
add-selenocysteine-except NULL ,
join-short-trnas NULL ,
adjust-features-for-gaps Adjust-features-for-gaps-action }
Macro-action-list ::= SET OF Macro-action-choice
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 }
Simple-replace ::= SEQUENCE {
replace VisibleString OPTIONAL,
whole-string BOOLEAN DEFAULT FALSE ,
weasel-to-putative BOOLEAN DEFAULT FALSE }
Replace-func ::= CHOICE {
simple-replace Simple-replace ,
haem-replace VisibleString }
Replace-rule ::= SEQUENCE {
replace-func Replace-func ,
move-to-note BOOLEAN DEFAULT FALSE }
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) }
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 ,
fatal BOOLEAN DEFAULT FALSE }
Suspect-rule-set ::= SET OF Suspect-rule
END