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= *it;

112 const char

& ch = *c_it;

113 unsigned char

chu = ch;

114 if

(ch > 127 || (ch < 32 && ch !=

'\t'

&& ch !=

'\r'

&& ch !=

'\n'

)) {

125 switch

( desc.

Which

() ) {

128 "Modif descriptor is obsolete"

, *

, desc);

129

CSeqdesc::TModif::const_iterator it2 = desc.

GetModif

().begin();

130 while

(it2 != desc.

GetModif

().end()) {

140 "MolType descriptor is obsolete"

, *

, desc);

145 "Method descriptor is obsolete"

, *

, desc);

173 "Name descriptor needs text"

, desc);

181 "OrgRef descriptor is obsolete"

, *

, desc);

194 "Region descriptor needs text"

, desc);

234 const string

& comment,

239 "Comment may refer to reference by serial number - " 240 "attach reference specific comments to the reference " 241 "REMARK instead."

, *

, desc);

245 "Comment descriptor needs text"

, *

, desc);

247 if

(

(comment,

"::"

) != string::npos) {

249 "Comment may be formatted to look like a structured comment."

, *

, desc);

259 "Title descriptor needs text"

, desc);

263 "Title descriptor has internal PMID"

, desc);

267 char

end = cpy.c_str()[cpy.length() - 1];

269 if

(end ==

'.'

&& cpy.length() > 4) {

270

end = cpy.c_str()[cpy.length() - 2];

277 "Title descriptor ends in bad punctuation"

, desc);

325 if

(

(

"is not a valid value"

) != string::npos) {

327

}

else if

(

(

"field is out of order"

) != string::npos) {

331

}

else if

(

(

"is not a valid field name"

) != string::npos

332

(

"field without label"

) != string::npos) {

353 if

(errors.size() > 0) {

382 if

(errors.size() > 0) {

398 "Evidence-For-Name-Assignment"

400 "Genome-Annotation-Data"

401 "Genome-Assembly-Data"

402 "GISAID_EpiFlu(TM)Data"

406 "International Barcode of Life (iBOL)Data"

422 "RefSeq-Attributes"

424 "SymbiotaSpecimenReference"

425 "Taxonomic-Update-Statistics"

430 return

sc_OfficialPrefixList.find(

val

) != sc_OfficialPrefixList.end();

440 if

((*it)->IsSetLabel() && (*it)->GetLabel().IsStr() &&

442

(*it)->IsSetData() && (*it)->GetData().IsStr()) {

443 const string

val

= (*it)->GetData().GetStr();

460 if

((*it)->IsSetLabel() && (*it)->GetLabel().IsStr() &&

462

(*it)->IsSetData() && (*it)->GetData().IsStr()) {

463 const string

val

= (*it)->GetData().GetStr();

478 const bool

report =

false

;

491 const string

& prefix,

499

report_prefix +

" is not a valid value for StructuredCommentPrefix"

, *

, desc);

508 const string

& prefix,

518 string

sfx = report_sfx;

527 "StructuredCommentSuffix '"

+ report_sfx +

"' does not match prefix"

, *

, desc);

545 auto

& fields =

tmp

.SetData();

565 "Structured Comment user object descriptor is empty"

, *

, desc);

576 "Structured Comment lacks prefix and/or suffix"

, *

, desc);

591 const bool

isV2Prefix =

592

(prefix ==

"HumanSTR"

&& usr.

HasField

(

"Bracketed record seq."

""

));

593 const string

queryPrefix = isV2Prefix ?

"HumanSTRv2"

: prefix;

606 if

(

auto

pSuffix = usr.

GetFieldRef

(

"StructuredCommentSuffix"

); pSuffix) {

618 "Structured Comment lacks prefix and/or suffix"

, *

, desc);

624 if

(

NStr::Equal

(prefix,

"Genome-Assembly-Data"

)) {

629 "Assembly Name should not start with 'NCBI' or 'GenBank' in structured comment"

, *

, desc);

638 "Genome Representation should not start with 'Partial' in structured comment"

, *

, desc);

646 "Structured Comment invalid; the field value and/or name are incorrect"

, *

, desc);

655 unsigned int

skip = 4;

657 if

(

.length() < 5)

return true

;

659 if

(

[0] !=

'S'

)

return true

;

660 if

(

[1] !=

'A'

)

return true

;

661 if

(

[2] !=

'M'

)

return true

;

662 if

(

[3] !=

'E'

[3] !=

'N'

[3] !=

'D'

)

return true

;

664 if

(

[3] ==

'E'

) {

671 for

(

= skip;

.length();

++) {

673 if

(ch))

return true

;

684 if

(

.length() < 9)

return true

;

686 if

(

[0] !=

'S'

)

return true

;

687 if

(

[1] !=

'R'

)

return true

;

688 if

(

[2] !=

'S'

)

return true

;

690 for

(

= 3;

.length();

++) {

692 if

(ch))

return true

;

703 if

(

.length() < 9)

return true

;

706 if

(ch !=

'S'

&& ch !=

'D'

&& ch !=

'E'

)

return true

;

708 if

isupper

(ch))

return true

;

710 if

isupper

(ch))

return true

;

712 for

(

= 3;

.length();

++) {

714 if

(ch))

return true

;

726 if

(

.length() < 6)

return true

;

728 if

(

[0] !=

'P'

)

return true

;

729 if

(

[1] !=

'R'

)

return true

;

730 if

(

[2] !=

'J'

)

return true

;

731 if

(

[3] !=

'E'

[3] !=

'N'

[3] !=

'D'

)

return true

;

732 if

(

[4] !=

'A'

[4] !=

'B'

)

return true

;

734 for

(

= 5;

.length();

++) {

736 if

(ch))

return true

;

744 "Trace Assembly Archive"

748 "Sequence Read Archive"

765 "DBLink user object descriptor is empty"

, *

, desc);

776 const auto

& fdata = fld.

GetData

();

777 if

(fdata.IsStrs()) {

780 const string

= *st_itr;

784 "Bad BioSample format - "

, *

, desc);

787 "Old BioSample format - "

, *

, desc);

791

}

else if

(fdata.IsStr()) {

792 const string

= fdata.GetStr();

796 "Bad BioSample format - "

+ fdata.GetStr(), *

, desc);

799 "Old BioSample format - "

+ fdata.GetStr(), *

, desc);

808 const string

= *st_itr;

811 "Bad Sequence Read Archive format - "

, *

, desc);

819 const string

= *st_itr;

822 "Bad BioProject format - "

, *

, desc);

830 const string

= *st_itr;

833 "Trace Asssembly Archive accession "

" does not begin with TI prefix"

, *

, desc);

839 for

(

auto

: s_legalDblinkNames) {

843 "Bad DBLink capitalization - "

+ label_str, *

, desc);

859 "User object with no type"

, *

, desc);

865 "User object with no type"

, *

, desc);

871 "User object with no data"

, *

, desc);

875 bool

has_ref_track_status =

false

;

877 if

( (*field)->CanGetLabel() ) {

878 const CObject_id

& obj_id = (*field)->GetLabel();

879 if

( !obj_id.

IsStr

() ) {

883

has_ref_track_status =

true

;

884 if

((*field)->IsSetData() && (*field)->GetData().IsStr()) {

887 "RefGeneTracking object has illegal Status '" 888

+ (*field)->GetData().GetStr() +

"'"

895 if

( !has_ref_track_status ) {

897 "RefGeneTracking object needs to have Status set"

, *

, desc);

914 "Molinfo-biomol unknown used"

, *