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1 --$Revision: 1.57 $
2 --**********************************************************************
3 --
4 -- NCBI ASN.1 macro editing language specifications
5 --
6 -- by Colleen Bollin, 2007
7 --
8 --**********************************************************************
9
10 NCBI-Macro DEFINITIONS ::=
11 BEGIN
12
13 EXPORTS AECR-action, Parse-action, Macro-action-list;
14
15 -- simple constraints --
16
17 String-location ::= ENUMERATED {
18 contains (1) ,
19 equals (2) ,
20 starts (3) ,
21 ends (4) ,
22 inlist (5) }
23
24 String-constraint ::= SEQUENCE {
25 match-text VisibleString ,
26 match-location String-location DEFAULT contains ,
27 case-sensitive BOOLEAN DEFAULT FALSE ,
28 whole-word BOOLEAN DEFAULT FALSE ,
29 not-present BOOLEAN DEFAULT FALSE }
30
31 Strand-constraint ::= ENUMERATED {
32 any (0) ,
33 plus (1) ,
34 minus (2) }
35
36 Seqtype-constraint ::= ENUMERATED {
37 any (0) ,
38 nuc (1) ,
39 prot (2) }
40
41 Partial-constraint ::= ENUMERATED {
42 either (0) ,
43 partial (1) ,
44 complete (2) }
45
46 Location-constraint ::= SEQUENCE {
47 strand Strand-constraint DEFAULT any ,
48 seq-type Seqtype-constraint DEFAULT any ,
49 partial5 Partial-constraint DEFAULT either ,
50 partial3 Partial-constraint DEFAULT either }
51
52 Object-type-constraint ::= ENUMERATED {
53 any (0) ,
54 feature (1) ,
55 descriptor (2) }
56
57
58 -- feature values --
59
60 Feature-type ::= ENUMERATED {
61 any (0) ,
62 gene (1) ,
63 org (2) ,
64 cds (3) ,
65 prot (4) ,
66 preRNA (5) ,
67 mRNA (6) ,
68 tRNA (7) ,
69 rRNA (8) ,
70 snRNA (9) ,
71 scRNA (10) ,
72 otherRNA (11) ,
73 pub (12) ,
74 seq (13) ,
75 imp (14) ,
76 allele (15) ,
77 attenuator (16) ,
78 c-region (17) ,
79 caat-signal (18) ,
80 imp-CDS (19) ,
81 conflict (20) ,
82 d-loop (21) ,
83 d-segment (22) ,
84 enhancer (23) ,
85 exon (24) ,
86 gC-signal (25) ,
87 iDNA (26) ,
88 intron (27) ,
89 j-segment (28) ,
90 ltr (29) ,
91 mat-peptide (30) ,
92 misc-binding (31) ,
93 misc-difference (32) ,
94 misc-feature (33) ,
95 misc-recomb (34) ,
96 misc-RNA (35) ,
97 misc-signal (36) ,
98 misc-structure (37) ,
99 modified-base (38) ,
100 mutation (39) ,
101 n-region (40) ,
102 old-sequence (41) ,
103 polyA-signal (42) ,
104 polyA-site (43) ,
105 precursor-RNA (44) ,
106 prim-transcript (45) ,
107 primer-bind (46) ,
108 promoter (47) ,
109 protein-bind (48) ,
110 rbs (49) ,
111 repeat-region (50) ,
112 rep-origin (51) ,
113 s-region (52) ,
114 sig-peptide (53) ,
115 source (54) ,
116 stem-loop (55) ,
117 sts (56) ,
118 tata-signal (57) ,
119 terminator (58) ,
120 transit-peptide (59) ,
121 unsure (60) ,
122 v-region (61) ,
123 v-segment (62) ,
124 variation (63) ,
125 virion (64) ,
126 n3clip (65) ,
127 n3UTR (66) ,
128 n5clip (67) ,
129 n5UTR (68) ,
130 n10-signal (69) ,
131 n35-signal (70) ,
132 site-ref (71) ,
133 region (72) ,
134 comment (73) ,
135 bond (74) ,
136 site (75) ,
137 rsite (76) ,
138 user (77) ,
139 txinit (78) ,
140 num (79) ,
141 psec-str (80) ,
142 non-std-residue (81) ,
143 het (82) ,
144 biosrc (83) ,
145 preprotein (84) ,
146 mat-peptide-aa (85) ,
147 sig-peptide-aa (86) ,
148 transit-peptide-aa (87) ,
149 snoRNA (88) ,
150 gap (89) ,
151 operon (90) ,
152 oriT (91) ,
153 ncRNA (92) ,
154 tmRNA (93) }
155
156 Feat-qual-legal ::= ENUMERATED {
157 allele (1) ,
158 activity (2) ,
159 anticodon (3) ,
160 bound-moiety (4) ,
161 chromosome (5),
162 citation (6),
163 codon (7) ,
164 codon-start (8) ,
165 codons-recognized (9) ,
166 compare (10) ,
167 cons-splice (11) ,
168 db-xref (12) ,
169 description (13) ,
170 direction (14) ,
171 ec-number (15) ,
172 environmental-sample (16) ,
173 evidence (17) ,
174 exception (18) ,
175 experiment (19) ,
176 focus (20) ,
177 frequency (21) ,
178 function (22) ,
179 gene (23) ,
180 gene-description (24) ,
181 inference (25) ,
182 label (26) ,
183 locus-tag (27) ,
184 map (28) ,
185 mobile-element (29) ,
186 mod-base (30) ,
187 mol-type (31) ,
188 ncRNA-class (32) ,
189 note (33) ,
190 number (34) ,
191 old-locus-tag (35) ,
192 operon (36) ,
193 organism (37) ,
194 organelle (38) ,
195 partial (39) ,
196 phenotype (40) ,
197 plasmid (41) ,
198 product (42) ,
199 protein-id (43) ,
200 pseudo (44) ,
201 rearranged (45) ,
202 replace (46) ,
203 rpt-family (47) ,
204 rpt-type (48) ,
205 rpt-unit (49) ,
206 rpt-unit-seq (50) ,
207 rpt-unit-range (51) ,
208 segment (52) ,
209 sequenced-mol (53) ,
210 standard-name (54) ,
211 synonym (55) ,
212 transcript-id (56) ,
213 transgenic (57) ,
214 translation (58) ,
215 transl-except (59) ,
216 transl-table (60) ,
217 usedin (61),
218 mobile-element-type (62),
219 mobile-element-name (63),
220 gene-comment (64) ,
221 satellite (65) ,
222 satellite-type (66) ,
223 satellite-name (67) ,
224 location (68) ,
225 tag-peptide (69) }
226
227 Feat-qual-legal-val ::= SEQUENCE {
228 qual Feat-qual-legal ,
229 val VisibleString }
230
231 Feat-qual-legal-val-choice ::= CHOICE {
232 qual Feat-qual-legal-val }
233
234 Feat-qual-legal-set ::= SET OF Feat-qual-legal-val-choice
235
236 Feat-qual-choice ::= CHOICE {
237 legal-qual Feat-qual-legal ,
238 illegal-qual String-constraint }
239
240 Feature-field ::= SEQUENCE {
241 type Feature-type ,
242 field Feat-qual-choice }
243
244 Feature-field-legal ::= SEQUENCE {
245 type Feature-type ,
246 field Feat-qual-legal }
247
248 Feature-field-pair ::= SEQUENCE {
249 type Feature-type ,
250 field-from Feat-qual-choice ,
251 field-to Feat-qual-choice }
252
253 Rna-feat-type ::= CHOICE {
254 preRNA NULL ,
255 mRNA NULL ,
256 tRNA NULL ,
257 rRNA NULL ,
258 ncRNA VisibleString ,
259 tmRNA NULL,
260 miscRNA NULL }
261
262 Rna-field ::= ENUMERATED {
263 product (1) ,
264 comment (2) ,
265 codons-recognized (3) ,
266 ncrna-class (4) ,
267 anticodon (5) ,
268 transcript-id (6) ,
269 gene-locus (7) ,
270 gene-description (8) ,
271 gene-maploc (9) ,
272 gene-locus-tag (10) ,
273 gene-synonym (11) ,
274 gene-comment (12) ,
275 tag-peptide (13) }
276
277
278 Rna-qual ::= SEQUENCE {
279 type Rna-feat-type ,
280 field Rna-field }
281
282 Rna-qual-pair ::= SEQUENCE {
283 type Rna-feat-type ,
284 field-from Rna-field ,
285 field-to Rna-field }
286
287 Source-qual ::= ENUMERATED {
288 acronym (1) ,
289 anamorph (2) ,
290 authority (3) ,
291 bio-material (4) ,
292 biotype (5) ,
293 biovar (6) ,
294 breed (7) ,
295 cell-line (8) ,
296 cell-type (9) ,
297 chemovar (10) ,
298 chromosome (11) ,
299 clone (12) ,
300 clone-lib (13) ,
301 collected-by (14) ,
302 collection-date (15) ,
303 common (16) ,
304 common-name (17) ,
305 country (18) ,
306 cultivar (19) ,
307 culture-collection (20) ,
308 dev-stage (21) ,
309 division (22) ,
310 dosage (23) ,
311 ecotype (24) ,
312 endogenous-virus-name (25) ,
313 environmental-sample (26) ,
314 forma (27) ,
315 forma-specialis (28) ,
316 frequency (29) ,
317 fwd-primer-name (30) ,
318 fwd-primer-seq (31) ,
319 gb-acronym (32) ,
320 gb-anamorph (33) ,
321 gb-synonym (34) ,
322 genotype (35) ,
323 germline (36) ,
324 group (37) ,
325 haplotype (38) ,
326 identified-by (39) ,
327 insertion-seq-name (40) ,
328 isolate (41) ,
329 isolation-source (42) ,
330 lab-host (43) ,
331 lat-lon (44) ,
332 lineage (45) ,
333 map (46) ,
334 metagenome-source (47) ,
335 metagenomic (48) ,
336 old-lineage (49) ,
337 old-name (50) ,
338 orgmod-note (51) ,
339 nat-host (52) ,
340 pathovar (53) ,
341 plasmid-name (54) ,
342 plastid-name (55) ,
343 pop-variant (56) ,
344 rearranged (57) ,
345 rev-primer-name (58) ,
346 rev-primer-seq (59) ,
347 segment (60) ,
348 serogroup (61) ,
349 serotype (62) ,
350 serovar (63) ,
351 sex (64) ,
352 specimen-voucher (65) ,
353 strain (66) ,
354 subclone (67) ,
355 subgroup (68) ,
356 subsource-note (69),
357 sub-species (70) ,
358 substrain (71) ,
359 subtype (72) ,
360 synonym (73) ,
361 taxname (74) ,
362 teleomorph (75) ,
363 tissue-lib (76) ,
364 tissue-type (77) ,
365 transgenic (78) ,
366 transposon-name (79) ,
367 type (80) ,
368 variety (81) ,
369 specimen-voucher-INST (82) ,
370 specimen-voucher-COLL (83) ,
371 specimen-voucher-SpecID (84) ,
372 culture-collection-INST (85) ,
373 culture-collection-COLL (86) ,
374 culture-collection-SpecID (87) ,
375 bio-material-INST (88) ,
376 bio-material-COLL (89) ,
377 bio-material-SpecID (90),
378 all-notes (91),
379 mating-type (92),
380 linkage-group (93) ,
381 haplogroup (94),
382 all-quals (95),
383 dbxref (96)
384 }
385
386 Source-qual-pair ::= SEQUENCE {
387 field-from Source-qual ,
388 field-to Source-qual }
389
390 Source-location ::= ENUMERATED {
391 unknown (0) ,
392 genomic (1) ,
393 chloroplast (2) ,
394 chromoplast (3) ,
395 kinetoplast (4) ,
396 mitochondrion (5) ,
397 plastid (6) ,
398 macronuclear (7) ,
399 extrachrom (8) ,
400 plasmid (9) ,
401 transposon (10) ,
402 insertion-seq (11) ,
403 cyanelle (12) ,
404 proviral (13) ,
405 virion (14) ,
406 nucleomorph (15) ,
407 apicoplast (16) ,
408 leucoplast (17) ,
409 proplastid (18) ,
410 endogenous-virus (19) ,
411 hydrogenosome (20) ,
412 chromosome (21) ,
413 chromatophore (22) }
414
415 Source-origin ::= ENUMERATED {
416 unknown (0) ,
417 natural (1) ,
418 natmut (2) ,
419 mut (3) ,
420 artificial (4) ,
421 synthetic (5) ,
422 other (255) }
423
424 Source-qual-choice ::= CHOICE {
425 textqual Source-qual ,
426 location Source-location,
427 origin Source-origin ,
428 gcode INTEGER ,
429 mgcode INTEGER }
430
431 Source-qual-text-val ::= SEQUENCE {
432 srcqual Source-qual ,
433 val VisibleString }
434
435 Source-qual-val-choice ::= CHOICE {
436 textqual Source-qual-text-val ,
437 location Source-location,
438 origin Source-origin ,
439 gcode INTEGER ,
440 mgcode INTEGER }
441
442 Source-qual-val-set ::= SET OF Source-qual-val-choice
443
444 CDSGeneProt-field ::= ENUMERATED {
445 cds-comment (1) ,
446 gene-locus (2) ,
447 gene-description (3) ,
448 gene-comment (4) ,
449 gene-allele (5) ,
450 gene-maploc (6) ,
451 gene-locus-tag (7) ,
452 gene-synonym (8) ,
453 gene-old-locus-tag (9) ,
454 mrna-product (10) ,
455 mrna-comment (11) ,
456 prot-name (12) ,
457 prot-description (13) ,
458 prot-ec-number (14) ,
459 prot-activity (15) ,
460 prot-comment (16) ,
461 mat-peptide-name (17) ,
462 mat-peptide-description (18) ,
463 mat-peptide-ec-number (19) ,
464 mat-peptide-activity (20) ,
465 mat-peptide-comment (21) ,
466 cds-inference (22) ,
467 gene-inference (23) ,
468 codon-start (24) }
469
470 CDSGeneProt-field-pair ::= SEQUENCE {
471 field-from CDSGeneProt-field ,
472 field-to CDSGeneProt-field }
473
474 Molecule-type ::= ENUMERATED {
475 unknown (0) ,
476 genomic (1) ,
477 precursor-RNA (2) ,
478 mRNA (3) ,
479 rRNA (4) ,
480 tRNA (5) ,
481 genomic-mRNA (6) ,
482 cRNA (7) ,
483 transcribed-RNA (8) ,
484 ncRNA (9) ,
485 transfer-messenger-RNA (10) ,
486 other (11) }
487
488 Technique-type ::= ENUMERATED {
489 unknown (0) ,
490 standard (1) ,
491 est (2) ,
492 sts (3) ,
493 survey (4) ,
494 genetic-map (5) ,
495 physical-map (6) ,
496 derived (7) ,
497 concept-trans (8) ,
498 seq-pept (9) ,
499 both (10) ,
500 seq-pept-overlap (11) ,
501 seq-pept-homol (12) ,
502 concept-trans-a (13) ,
503 htgs-1 (14) ,
504 htgs-2 (15) ,
505 htgs-3 (16) ,
506 fli-cDNA (17) ,
507 htgs-0 (18) ,
508 htc (19) ,
509 wgs (20) ,
510 barcode (21) ,
511 composite-wgs-htgs (22) ,
512 tsa (23) ,
513 other (24) }
514
515 Completedness-type ::= ENUMERATED {
516 unknown (0) ,
517 complete (1) ,
518 partial (2) ,
519 no-left (3) ,
520 no-right (4) ,
521 no-ends (5) ,
522 has-left (6) ,
523 has-right (7) ,
524 other (6) }
525
526 Molecule-class-type ::= ENUMERATED {
527 unknown (0) ,
528 dna (1) ,
529 rna (2) ,
530 protein (3) ,
531 nucleotide (4),
532 other (5) }
533
534 Topology-type ::= ENUMERATED {
535 unknown (0) ,
536 linear (1) ,
537 circular (2) ,
538 tandem (3) ,
539 other (4) }
540
541 Strand-type ::= ENUMERATED {
542 unknown (0) ,
543 single (1) ,
544 double (2) ,
545 mixed (3) ,
546 mixed-rev (4) ,
547 other (5) }
548
549 Molinfo-field ::= CHOICE {
550 molecule Molecule-type ,
551 technique Technique-type ,
552 completedness Completedness-type ,
553 mol-class Molecule-class-type ,
554 topology Topology-type ,
555 strand Strand-type }
556
557 Molinfo-molecule-pair ::= SEQUENCE {
558 from Molecule-type ,
559 to Molecule-type }
560
561 Molinfo-technique-pair ::= SEQUENCE {
562 from Technique-type ,
563 to Technique-type }
564
565 Molinfo-completedness-pair ::= SEQUENCE {
566 from Completedness-type ,
567 to Completedness-type }
568
569 Molinfo-mol-class-pair ::= SEQUENCE {
570 from Molecule-class-type ,
571 to Molecule-class-type }
572
573 Molinfo-topology-pair ::= SEQUENCE {
574 from Topology-type ,
575 to Topology-type }
576
577 Molinfo-strand-pair ::= SEQUENCE {
578 from Strand-type ,
579 to Strand-type }
580
581 Molinfo-field-pair ::= CHOICE {
582 molecule Molinfo-molecule-pair ,
583 technique Molinfo-technique-pair ,
584 completedness Molinfo-completedness-pair ,
585 mol-class Molinfo-mol-class-pair ,
586 topology Molinfo-topology-pair ,
587 strand Molinfo-strand-pair }
588
589 Molinfo-field-list ::= SET OF Molinfo-field
590
591 -- publication fields --
592
593 Publication-field ::= ENUMERATED {
594 cit (1) ,
595 authors (2) ,
596 journal (3) ,
597 volume (4) ,
598 issue (5) ,
599 pages (6) ,
600 date (7) ,
601 serial-number (8) ,
602 title (9) ,
603 affiliation (10) ,
604 affil-div (11) ,
605 affil-city (12) ,
606 affil-sub (13) ,
607 affil-country (14) ,
608 affil-street (15) ,
609 affil-email (16) ,
610 affil-fax (17) ,
611 affil-phone (18) ,
612 affil-zipcode (19),
613 authors-initials (20)
614 }
615
616 -- structured comment fields --
617
618 Structured-comment-field ::= CHOICE {
619 database NULL ,
620 named VisibleString ,
621 field-name NULL
622 }
623
624 Structured-comment-field-pair ::= SEQUENCE {
625 from Structured-comment-field ,
626 to Structured-comment-field
627 }
628
629 -- misc fields --
630 -- these would not appear in pairs --
631 Misc-field ::= ENUMERATED {
632 genome-project-id (1) ,
633 comment-descriptor (2) ,
634 defline (3) ,
635 keyword (4)
636 }
637
638 -- complex constraints --
639
640 Pub-type ::= ENUMERATED {
641 any (0) ,
642 published (1) ,
643 unpublished (2) ,
644 in-press (3) ,
645 submitter-block (4) }
646
647 Pub-field-constraint ::= SEQUENCE {
648 field Publication-field ,
649 constraint String-constraint }
650
651 Publication-constraint ::= SEQUENCE {
652 type Pub-type ,
653 field Pub-field-constraint OPTIONAL }
654
655 Source-constraint ::= SEQUENCE {
656 field1 Source-qual-choice OPTIONAL ,
657 field2 Source-qual-choice OPTIONAL ,
658 constraint String-constraint OPTIONAL ,
659 type-constraint Object-type-constraint OPTIONAL }
660
661 CDSGeneProt-feature-type-constraint ::= ENUMERATED {
662 gene (1) ,
663 mRNA (2) ,
664 cds (3) ,
665 prot (4) ,
666 exon (5) ,
667 mat-peptide (6) }
668
669 CDSGeneProt-pseudo-constraint ::= SEQUENCE {
670 feature CDSGeneProt-feature-type-constraint ,
671 is-pseudo BOOLEAN DEFAULT TRUE }
672
673 CDSGeneProt-constraint-field ::= CHOICE {
674 field CDSGeneProt-field }
675
676 CDSGeneProt-qual-constraint ::= SEQUENCE {
677 field1 CDSGeneProt-constraint-field OPTIONAL ,
678 field2 CDSGeneProt-constraint-field OPTIONAL ,
679 constraint String-constraint OPTIONAL }
680
681 Field-constraint ::= SEQUENCE {
682 field Field-type ,
683 string-constraint String-constraint }
684
685 Sequence-constraint-rnamol ::= ENUMERATED {
686 any (0) ,
687 genomic (1) ,
688 precursor-RNA (2) ,
689 mRNA (3) ,
690 rRNA (4) ,
691 tRNA (5) ,
692 genomic-mRNA (6) ,
693 cRNA (7) ,
694 transcribed-RNA (8) ,
695 ncRNA (9) ,
696 transfer-messenger-RNA (10) }
697
698 Sequence-constraint-mol-type-constraint ::= CHOICE {
699 any NULL ,
700 nucleotide NULL ,
701 dna NULL ,
702 rna Sequence-constraint-rnamol ,
703 protein NULL }
704
705 Sequence-constraint ::= SEQUENCE {
706 seqtype Sequence-constraint-mol-type-constraint OPTIONAL ,
707 id String-constraint OPTIONAL ,
708 feature Feature-type }
709
710 Constraint-choice ::= CHOICE {
711 string String-constraint ,
712 location Location-constraint ,
713 field Field-constraint ,
714 source Source-constraint ,
715 cdsgeneprot-qual CDSGeneProt-qual-constraint ,
716 cdsgeneprot-pseudo CDSGeneProt-pseudo-constraint ,
717 sequence Sequence-constraint ,
718 pub Publication-constraint }
719
720 Constraint-choice-set ::= SET OF Constraint-choice
721
722 Text-portion ::= SEQUENCE {
723 left-text VisibleString OPTIONAL ,
724 include-left BOOLEAN ,
725 right-text VisibleString OPTIONAL ,
726 include-right BOOLEAN ,
727 inside BOOLEAN ,
728 case-sensitive BOOLEAN DEFAULT FALSE ,
729 whole-word BOOLEAN DEFAULT FALSE }
730
731 Field-edit-location ::= ENUMERATED {
732 anywhere (0) ,
733 beginning (1) ,
734 end (2) }
735
736 Field-edit ::= SEQUENCE {
737 find-txt VisibleString ,
738 repl-txt VisibleString OPTIONAL ,
739 location Field-edit-location DEFAULT anywhere }
740
741 Field-type ::= CHOICE {
742 source-qual Source-qual-choice ,
743 feature-field Feature-field ,
744 rna-field Rna-qual ,
745 cds-gene-prot CDSGeneProt-field ,
746 molinfo-field Molinfo-field ,
747 pub Publication-field ,
748 struc-comment-field Structured-comment-field ,
749 misc Misc-field }
750
751 Field-pair-type ::= CHOICE {
752 source-qual Source-qual-pair ,
753 feature-field Feature-field-pair ,
754 rna-field Rna-qual-pair ,
755 cds-gene-prot CDSGeneProt-field-pair ,
756 molinfo-field Molinfo-field-pair ,
757 struc-comment-field Structured-comment-field-pair }
758
759 ExistingTextOption ::= ENUMERATED {
760 replace-old (1) ,
761 append-semi (2) ,
762 append-space (3) ,
763 append-colon (4) ,
764 append-comma (5) ,
765 append-none (6) ,
766 prefix-semi (7) ,
767 prefix-space (8) ,
768 prefix-colon (9) ,
769 prefix-comma (10) ,
770 prefix-none (11) ,
771 leave-old (12) ,
772 add-qual (13) }
773
774
775 Apply-action ::= SEQUENCE {
776 field Field-type ,
777 value VisibleString ,
778 existing-text ExistingTextOption }
779
780 Edit-action ::= SEQUENCE {
781 edit Field-edit ,
782 field Field-type }
783
784 Convert-action ::= SEQUENCE {
785 fields Field-pair-type ,
786 strip-name BOOLEAN DEFAULT FALSE ,
787 keep-original BOOLEAN DEFAULT FALSE ,
788 existing-text ExistingTextOption }
789
790 Copy-action ::= SEQUENCE {
791 fields Field-pair-type ,
792 existing-text ExistingTextOption }
793
794 Swap-action ::= SEQUENCE {
795 fields Field-pair-type ,
796 field-to Field-type }
797
798 AECRParse-action ::= SEQUENCE {
799 portion Text-portion ,
800 fields Field-pair-type ,
801 remove-from-parsed BOOLEAN DEFAULT FALSE ,
802 remove-left BOOLEAN DEFAULT FALSE ,
803 remove-right BOOLEAN DEFAULT FALSE ,
804 existing-text ExistingTextOption }
805
806 Remove-action ::= SEQUENCE {
807 field Field-type }
808
809 Action-choice ::= CHOICE {
810 apply Apply-action ,
811 edit Edit-action ,
812 convert Convert-action ,
813 copy Copy-action ,
814 swap Swap-action ,
815 remove Remove-action ,
816 parse AECRParse-action }
817
818 AECR-action ::= SEQUENCE {
819 action Action-choice ,
820 also-change-mrna BOOLEAN DEFAULT FALSE ,
821 constraint Constraint-choice-set OPTIONAL }
822
823 Cap-change ::= ENUMERATED {
824 none (0) ,
825 tolower (1) ,
826 toupper (2) ,
827 firstcap (3) ,
828 firstcaprestnochange (4) }
829
830 Parse-src-org-choice ::= CHOICE {
831 source-qual Source-qual ,
832 taxname-after-binomial NULL }
833
834 Parse-src-org ::= SEQUENCE {
835 field Parse-src-org-choice ,
836 type Object-type-constraint DEFAULT any }
837
838 Parse-src ::= CHOICE {
839 defline NULL ,
840 flatfile NULL ,
841 local-id NULL ,
842 org Parse-src-org ,
843 comment NULL ,
844 bankit-comment NULL ,
845 structured-comment VisibleString ,
846 file-id NULL }
847
848 Parse-dst-org ::= SEQUENCE {
849 field Source-qual-choice ,
850 type Object-type-constraint DEFAULT any }
851
852 Parse-dest ::= CHOICE {
853 defline NULL ,
854 org Parse-dst-org ,
855 featqual Feature-field-legal ,
856 comment-descriptor NULL ,
857 dbxref VisibleString }
858
859 Parse-action ::= SEQUENCE {
860 portion Text-portion ,
861 src Parse-src ,
862 dest Parse-dest ,
863 capitalization Cap-change DEFAULT none ,
864 remove-from-parsed BOOLEAN DEFAULT FALSE ,
865 existing-text ExistingTextOption }
866
867
868 Location-interval ::= SEQUENCE {
869 from INTEGER ,
870 to INTEGER }
871
872 Location-choice ::= CHOICE {
873 interval Location-interval ,
874 whole-sequence NULL }
875
876 Sequence-list ::= SET OF VisibleString
877 Sequence-list-choice ::= CHOICE {
878 list Sequence-list ,
879 all NULL }
880
881 Apply-feature-action ::= SEQUENCE {
882 type Feature-type ,
883 partial5 BOOLEAN DEFAULT FALSE ,
884 partial3 BOOLEAN DEFAULT FALSE ,
885 plus-strand BOOLEAN DEFAULT TRUE ,
886 location Location-choice ,
887 seq-list Sequence-list-choice ,
888 add-redundant BOOLEAN DEFAULT TRUE ,
889 add-mrna BOOLEAN DEFAULT FALSE ,
890 apply-to-parts BOOLEAN DEFAULT FALSE ,
891 only-seg-num INTEGER DEFAULT -1 ,
892 fields Feat-qual-legal-set OPTIONAL,
893 src-fields Source-qual-val-set OPTIONAL }
894
895 Remove-feature-action ::= SEQUENCE {
896 type Feature-type ,
897 constraint Constraint-choice-set OPTIONAL }
898
899 -- for convert features --
900 Convert-from-CDS-options ::= SEQUENCE {
901 remove-mRNA BOOLEAN ,
902 remove-gene BOOLEAN ,
903 remove-transcript-id BOOLEAN }
904
905 Convert-feature-src-options ::= CHOICE {
906 cds Convert-from-CDS-options }
907
908 Bond-type ::= ENUMERATED {
909 disulfide (1) ,
910 thioester (2) ,
911 crosslink (3) ,
912 thioether (4) ,
913 other (5) }
914
915
916 Site-type ::= ENUMERATED {
917 active (1) ,
918 binding (2) ,
919 cleavage (3) ,
920 inhibit (4) ,
921 modified (5) ,
922 glycosylation (6) ,
923 myristoylation (7) ,
924 mutagenized (8) ,
925 metal-binding (9) ,
926 phosphorylation (10) ,
927 acetylation (11) ,
928 amidation (12) ,
929 methylation (13) ,
930 hydroxylation (14) ,
931 sulfatation (15) ,
932 oxidative-deamination (16) ,
933 pyrrolidone-carboxylic-acid (17) ,
934 gamma-carboxyglutamic-acid (18) ,
935 blocked (19) ,
936 lipid-binding (20) ,
937 np-binding (21) ,
938 dna-binding (22) ,
939 signal-peptide (23) ,
940 transit-peptide (24) ,
941 transmembrane-region (25) ,
942 nitrosylation (26) ,
943 other (27) }
944
945 -- other choice is to create protein sequences, skipping bad --
946 Region-type ::= SEQUENCE {
947 create-nucleotide BOOLEAN }
948
949 Convert-feature-dst-options ::= CHOICE {
950 bond Bond-type ,
951 site Site-type ,
952 region Region-type ,
953 ncrna-class VisibleString ,
954 remove-original BOOLEAN }
955
956
957 Convert-feature-action ::= SEQUENCE {
958 type-from Feature-type ,
959 type-to Feature-type ,
960 src-options Convert-feature-src-options OPTIONAL ,
961 dst-options Convert-feature-dst-options OPTIONAL ,
962 leave-original BOOLEAN ,
963 src-feat-constraint Constraint-choice-set OPTIONAL }
964
965
966 Feature-location-strand-from ::= ENUMERATED {
967 any (0) ,
968 plus (1) ,
969 minus (2) ,
970 unknown (3) ,
971 both (4) }
972
973 Feature-location-strand-to ::= ENUMERATED {
974 plus (1) ,
975 minus (2) ,
976 unknown (3) ,
977 both (4) ,
978 reverse (5) }
979
980 Edit-location-strand ::= SEQUENCE {
981 strand-from Feature-location-strand-from ,
982 strand-to Feature-location-strand-to }
983
984 Partial-5-set-constraint ::= ENUMERATED {
985 all (0) ,
986 at-end (1) ,
987 bad-start (2) ,
988 frame-not-one (3) }
989
990 Partial-5-set-action ::= SEQUENCE {
991 constraint Partial-5-set-constraint ,
992 extend BOOLEAN }
993
994 Partial-5-clear-constraint ::= ENUMERATED {
995 all (0) ,
996 not-at-end (1) ,
997 good-start (2) }
998
999 Partial-3-set-constraint ::= ENUMERATED {
1000 all (0) ,
1001 at-end (1) ,
1002 bad-end (2) }
1003
1004 Partial-3-set-action ::= SEQUENCE {
1005 constraint Partial-3-set-constraint ,
1006 extend BOOLEAN }
1007
1008 Partial-3-clear-constraint ::= ENUMERATED {
1009 all (0) ,
1010 not-at-end (1) ,
1011 good-end (2) }
1012
1013 Convert-location-type ::= ENUMERATED {
1014 join (1) ,
1015 order (2) ,
1016 merge (3) }
1017
1018 Location-edit-type ::= CHOICE {
1019 strand Edit-location-strand ,
1020 set-5-partial Partial-5-set-action ,
1021 clear-5-partial Partial-5-clear-constraint ,
1022 set-3-partial Partial-3-set-action ,
1023 clear-3-partial Partial-3-clear-constraint ,
1024 convert Convert-location-type }
1025
1026 Edit-feature-location-action ::= SEQUENCE {
1027 type Feature-type ,
1028 action Location-edit-type ,
1029 constraint Constraint-choice-set OPTIONAL }
1030
1031 Molinfo-block ::= SEQUENCE {
1032 to-list Molinfo-field-list ,
1033 from-list Molinfo-field-list OPTIONAL ,
1034 constraint Constraint-choice-set OPTIONAL }
1035
1036 Descriptor-type ::= ENUMERATED {
1037 all (0) ,
1038 title (1) ,
1039 source (2) ,
1040 publication (3) ,
1041 comment (4) ,
1042 genbank (5) ,
1043 user (6) ,
1044 create-date (7) ,
1045 update-date (8) ,
1046 mol-info (9) ,
1047 structured-comment (10) ,
1048 genome-project-id (11) }
1049
1050 Remove-descriptor-action ::= SEQUENCE {
1051 type Descriptor-type ,
1052 constraint Constraint-choice-set OPTIONAL }
1053
1054 Autodef-list-type ::= ENUMERATED {
1055 feature-list (1) ,
1056 complete-sequence (2) ,
1057 complete-genome (3) }
1058
1059 Autodef-action ::= SEQUENCE {
1060 modifiers SET OF Source-qual OPTIONAL ,
1061 clause-list-type Autodef-list-type }
1062
1063 Macro-action-choice ::= CHOICE {
1064 aecr AECR-action ,
1065 parse Parse-action ,
1066 add-feature Apply-feature-action ,
1067 remove-feature Remove-feature-action ,
1068 convert-feature Convert-feature-action ,
1069 edit-location Edit-feature-location-action ,
1070 remove-descriptor Remove-descriptor-action ,
1071 autodef Autodef-action }
1072
1073
1074 Macro-action-list ::= SET OF Macro-action-choice
1075
1076 END
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