void CDate_std::GetDate(string* label, const string& format) const
{
static const char* const kMonths[] = {
"0", "January", "February", "March", "April", "May", "June",
"July", "August", "September", "October", "November", "December"
};
static const int kNumMonths = sizeof (kMonths) / sizeof (char*);
if (!label) {
return;
}
unsigned int depth = 0;
vector<pair<SIZE_TYPE, SIZE_TYPE> > starts;
starts.push_back(make_pair(label->size(), (SIZE_TYPE)0));
ITERATE (string, it, format) {
if (*it != '%') {
*label += *it;
continue;
}
if (++it == format.end()) {
NCBI_THROW2(CGeneralParseException, eFormat,
"CDate_std::GetDate(): incomplete % expression",
it - format.begin());
}
// Check for things that can only immediately follow %
if (*it == '%') {
*label += '%';
continue;
}
else if (*it == '{') {
depth++;
starts.push_back(make_pair(label->size(),
SIZE_TYPE(it - format.begin())));
continue;
} else if (*it == '}') {
if (depth == 0) {
NCBI_THROW2(CGeneralParseException, eFormat,
"CDate_std::GetDate(): unbalanced %}",
it - format.begin());
}
depth--;
starts.pop_back();
continue;
} else if (*it == '|') {
// We survived, so just look for the appropriate %}.
if (depth == 0) {
return; // Can ignore rest of format
}
unsigned int depth2 = 0;
for (;;) {
while (++it != format.end() && *it != '%')
;
if (it == format.end() || ++it == format.end()) {
NCBI_THROW2(CGeneralParseException, eFormat,
"CDate_std::GetDate(): unbalanced %{",
starts.back().second);
}
if (*it == '}') {
if (depth2 == 0) {
depth--;
starts.pop_back();
break;
} else {
depth2--;
}
} else if (*it == '{') {
depth2++;
}
}
continue;
}
unsigned int length = 0;
int value = -1;
while (isdigit((unsigned char)(*it))) {
length = length * 10 + *it - '0';
if (++it == format.end()) {
NCBI_THROW2(CGeneralParseException, eFormat,
"CDate_std::GetDate(): incomplete % expression",
it - format.begin());
}
}
switch (*it) {
case 'Y': value = GetYear(); break;
case 'M':
case 'N': value = CanGetMonth() ? GetMonth() : -1; break;
case 'D': value = CanGetDay() ? GetDay() : -1; break;
case 'S': value = CanGetSeason() ? 1 : -1; break;
case 'h': value = CanGetHour() ? GetHour() : -1; break;
case 'm': value = CanGetMinute() ? GetMinute() : -1; break;
case 's': value = CanGetSecond() ? GetSecond() : -1; break;
default:
NCBI_THROW2(CGeneralParseException, eFormat,
"CDate_std::GetDate(): unrecognized format specifier",
it - format.begin());
}
if (value >= 0) {
if (*it == 'N') { // special cases
const char* name;
if (value >= kNumMonths) {
name = "inv";
} else {
name = kMonths[value];
}
if (length > 0) {
label->append(name, length);
} else {
*label += name;
}
} else if (*it == 'S') {
if (length > 0) {
label->append(GetSeason(), 0, length);
} else {
*label += GetSeason();
}
} else { // just a number
if (length > 0) {
// We want exactly <length> digits.
CNcbiOstrstream oss;
oss << setfill('0') << setw(length) << value;
string s = CNcbiOstrstreamToString(oss);
label->append(s, s.size() > length ? s.size() - length : 0,
length);
} else {
*label += NStr::IntToString(value);
}
}
} else {
// missing...roll back label and look for alternatives, or
// throw if at top level and none found
label->erase(starts.back().first);
char request = *it;
unsigned int depth2 = 0;
for (;;) {
while (++it != format.end() && *it != '%')
;
if (it == format.end() || ++it == format.end()) {
if (depth > 0 || depth2 > 0) {
NCBI_THROW2(CGeneralParseException, eFormat,
"CDate_std::GetDate(): unbalanced %{",
starts.back().second);
} else {
NCBI_THROW2(CGeneralParseException, eFormat,
string("CDate_std::GetDate():"
" missing required field %")
+ request, it - format.begin() - 1);
}
}
if (*it == '|' && depth2 == 0) {
break;
} else if (*it == '}') {
if (depth2 == 0) {
if (depth == 0) {
NCBI_THROW2(CGeneralParseException, eFormat,
"CDate_std::GetDate(): unbalanced %}",
it - format.begin());
}
depth--;
starts.pop_back();
break;
} else {
depth2--;
}
} else if (*it == '{') {
depth2++;
}
}
}
}
}
CRef<CBioseq_set> CMakeCdrProds::MakeCdrProds(CRef<CSeq_annot> annot,
CBioseq_Handle handle)
{
CRef<CBioseq_set> bioseq_set(new CBioseq_set);
if (!annot->GetData().IsFtable()) {
// Is this the right thing to do?
// Could throw, or could return null CRef instead.
return bioseq_set;
}
list<CRef<CSeq_feat> >& ftable = annot->SetData().SetFtable();
NON_CONST_ITERATE (list<CRef<CSeq_feat> >, feat, ftable) {
if (!(*feat)->GetData().IsCdregion()) {
// not interested if not a Cdregion
continue;
}
if ((*feat)->IsSetProduct()) {
// already has a product; don't make new one
continue;
}
string prot;
CSeqTranslator::Translate(**feat, handle.GetScope(), prot);
CRef<CSeq_data> seq_data(new CSeq_data(prot,
CSeq_data::e_Iupacaa));
CRef<CSeq_inst> seq_inst(new CSeq_inst);
seq_inst->SetSeq_data(*seq_data);
seq_inst->SetRepr(CSeq_inst_Base::eRepr_raw);
seq_inst->SetMol(CSeq_inst_Base::eMol_aa);
seq_inst->SetLength(prot.size());
CRef<CBioseq> bio_seq(new CBioseq);
string num = NStr::NumericToString(sm_Counter.Add(1));
// pad to five digits
if (num.size() < 5) {
num.insert(SIZE_TYPE(0), 5 - num.size(), '0');
}
string acc = "tp" + num;
string full_acc = "lcl|" + acc;
CRef<CSeq_id> id(new CSeq_id(full_acc));
bio_seq->SetId().push_back(id);
// a title
CRef<CSeqdesc> title(new CSeqdesc);
title->SetTitle(string("Translation product ") + acc);
bio_seq->SetDescr().Set().push_back(title);
// Mol_type
CRef<CSeqdesc> mol_type(new CSeqdesc);
mol_type->SetMol_type( eGIBB_mol_peptide);
bio_seq->SetDescr().Set().push_back(mol_type);
// set the instance
bio_seq->SetInst(*seq_inst);
// wrap this Bio_seq in an entry
CRef<CSeq_entry> seq_entry(new CSeq_entry);
seq_entry->SetSeq(*bio_seq);
// add this entry to our Bioseq_set
bioseq_set->SetSeq_set().push_back(seq_entry);
// record it as product in the annot we're handed
CRef<CSeq_loc> prod_loc(new CSeq_loc);
prod_loc->SetWhole(*id);
(*feat)->SetProduct(*prod_loc);
}
return bioseq_set;
}
