bool CCit_gen::GetLabelV1(string* label, TLabelFlags flags) const
{
bool unique = (flags & fLabel_Unique) != 0;
if (IsSetSerial_number()) {
*label += "[" + NStr::IntToString(GetSerial_number()) + "]";
}
if (IsSetMuid()) {
*label += "NLM" + NStr::IntToString(GetMuid());
}
string date;
string* date_ptr = 0;
if ( IsSetDate() ) {
date_ptr = &date;
GetDate().GetDate(date_ptr, true);
}
const string* title2 = 0;
const string* titleunique = 0;
bool unpublished = false;
const CTitle* title = IsSetJournal() ? &GetJournal() : 0;
const CAuth_list* authors = IsSetAuthors() ? &GetAuthors() : 0;
const string* volume = IsSetVolume() ? &GetVolume() : 0;
const string* issue = IsSetIssue() ? &GetIssue() : 0;
const string* pages = IsSetPages() ? &GetPages() : 0;
if (IsSetCit()) {
if ( NStr::EqualNocase( GetCit(), "Unpublished") ) {
unpublished = true;
} else if (!title) {
title2 = &GetCit();
}
}
if (IsSetTitle()) {
titleunique = &GetTitle();
} else if (title2) {
titleunique = title2;
} else if (!title && IsSetCit()) {
titleunique = &GetCit();
}
if (!title && !authors && !IsSetTitle() && !volume &&
!pages && !issue) {
titleunique = 0;
if (IsSetCit()) {
string cit(GetCit());
if (!unique) {
try {
cit.resize(cit.find_last_of('|'));
} catch(length_error&) {}
}
*label += cit;
}
return true;
}
return x_GetLabelV1(label, unique,
authors, 0, title, 0, 0, 0, title2, titleunique,
date_ptr, volume, issue, pages, unpublished);
}
int CPatent_seq_id::Compare(const CPatent_seq_id& psip2) const
{
int ret = GetSeqid() - psip2.GetSeqid();
if ( ret == 0 ) {
ret = GetCit().Match(psip2.GetCit())? 0: this < &psip2? -1: 1;
}
return ret;
}
// format a FASTA style string
ostream& CPatent_seq_id::AsFastaString(ostream& s) const
{
const CId_pat& idp = GetCit();
s << idp.GetCountry() << '|'; // no Upcase per Ostell - Karl 7/2001
if ( idp.GetId().IsNumber() ) {
s << idp.GetId().GetNumber();
} else {
s << idp.GetId().GetApp_number();
}
s << '|' << GetSeqid();
return s;
}
// comparison function
bool CPatent_seq_id::Match(const CPatent_seq_id& psip2) const
{
return GetSeqid() == psip2.GetSeqid() && GetCit().Match(psip2.GetCit());
}
// Based on FormatCitGen from the C Toolkit's api/asn2gnb5.c.
bool CCit_gen::GetLabelV2(string* label, TLabelFlags flags) const
{
if ( !CanGetCit() && !CanGetJournal() && !CanGetDate()
&& CanGetSerial_number() ) {
return false;
}
if ( !CanGetJournal() && CanGetCit() && SWNC(GetCit(), "unpublished")) {
if ((flags & fLabel_NoUnpubAffil) != 0) {
MaybeAddSpace(label);
*label += "Unpublished";
return true;
}
if (CanGetAuthors() && GetAuthors().CanGetAffil()) {
MaybeAddSpace(label);
*label += "Unpublished ";
GetAuthors().GetAffil().GetLabel(label, flags, eLabel_V2);
NStr::TruncateSpacesInPlace(*label, NStr::eTrunc_End);
return true;
}
if (CanGetCit() && HasText(GetCit())) {
MaybeAddSpace(label);
*label += NStr::TruncateSpaces(GetCit());
return true;
} else {
return false;
}
}
string year = CanGetDate() ? GetParenthesizedYear(GetDate()) : kEmptyStr;
string pages = CanGetPages() ? FixPages(GetPages()) : kEmptyStr;
string journal, inpress;
SIZE_TYPE pos;
if (CanGetJournal()) {
journal = GetJournal().GetTitle();
}
if (CanGetCit()) {
pos = GetCit().find("Journal=\"");
if (pos != NPOS) {
journal = GetCit().substr(pos + 9);
} else if (SWNC(GetCit(), "submitted")
|| SWNC(GetCit(), "unpublished")) {
if ((flags & fLabel_NoBadCitGen) == 0 || !journal.empty()) {
inpress = GetCit();
} else {
inpress = "Unpublished";
}
} else if (SWNC(GetCit(), "Online Publication")
|| SWNC(GetCit(), "Published Only in DataBase")
|| SWNC(GetCit(), "In press")) {
inpress = GetCit();
} else if (SWNC(GetCit(), "(er) ")) {
journal = GetCit();
} else if ((flags & fLabel_NoBadCitGen) == 0 && journal.empty()) {
journal = GetCit();
}
}
if ((!HasText(pages) || (flags & (fLabel_FlatNCBI | fLabel_FlatEMBL)) == 0)
&& journal.empty() && !HasText(inpress) && !HasText(year)
&& (!CanGetVolume() || !HasText(GetVolume()))) {
return false;
}
string prefix;
MaybeAddSpace(label);
if ( !journal.empty() ) {
pos = journal.find_first_of("=\"");
if (pos != NPOS) {
journal.resize(pos);
}
*label += journal;
prefix = " ";
}
if (HasText(inpress)) {
*label += prefix + inpress;
prefix = " ";
}
if (CanGetVolume() && HasText(GetVolume())) {
*label += prefix + GetVolume();
}
if (HasText(pages)) {
if ((flags & fLabel_FlatNCBI) != 0) {
*label += ", " + pages;
} else if ((flags & fLabel_FlatEMBL) != 0) {
*label += ':' + pages;
}
}
if (HasText(year)) {
*label += ' ' + year;
}
return true;
}
