CTempString CShortReadFastaInputSource::x_ParseDefline(CTempString& line)
{
// set local sequence id for the new sequence as the string between '>'
// and the first space
size_t begin = 1;
size_t end = line.find(' ', 1);
CTempString id = line.substr(begin, end - begin);
return id;
}
static void s_ProcessECNumberLine(const CTempString& line,
CProt_ref::EECNumberStatus status)
{
if (status == CProt_ref::eEC_replaced) {
SIZE_TYPE tab_pos = line.find('\t');
if (tab_pos == NPOS) {
ERR_POST_X(1, Warning << "No tab in ecnum_replaced entry " << line
<< "; disregarding");
} else {
string lhs(line.substr(0, tab_pos)), rhs(line.substr(tab_pos + 1));
s_ECNumberStatusMap[lhs] = status;
s_ECNumberReplacementMap[lhs] = rhs;
}
} else {
SIZE_TYPE tab_pos = line.find('\t');
if (tab_pos == NPOS) {
s_ECNumberStatusMap[line] = status;
} else {
string lhs(line.substr(0, tab_pos));
s_ECNumberStatusMap[lhs] = status;
}
}
}
BEGIN_NCBI_SCOPE
//////////////////////////////////////////////////////////////////////////////
static
TSvrRef
make_server(const CTempString& specification, double& preference)
{
CTempString server;
// string host;
Uint4 host = 0;
Uint2 port = 0;
string::size_type pos = 0;
pos = specification.find_first_of("@(", pos);
if (pos != string::npos) {
server = specification.substr(0, pos);
if (specification[pos] == '@') {
// string::size_type old_pos = pos + 1;
pos = specification.find_first_of(":(", pos + 1);
if (pos != string::npos) {
// string host_str = specification.substr(old_pos, pos - old_pos);
// Ignore host in order to avoid dependebcy on libconnect.
// SOCK_StringToHostPort(specification.c_str() + old_pos, &host, &port);
if (specification[pos] == ':') {
port = NStr::StringToUInt(specification.substr(pos + 1),
NStr::fAllowLeadingSpaces |
NStr::fAllowTrailingSymbols |
NStr::fConvErr_NoThrow);
pos = specification.find("(", pos + 1);
if (pos != string::npos) {
// preference = NStr::StringToDouble(
preference = NStr::StringToUInt(
specification.substr(pos + 1),
NStr::fAllowLeadingSpaces |
NStr::fAllowTrailingSymbols |
NStr::fConvErr_NoThrow);
}
} else {
// preference = NStr::StringToDouble(
preference = NStr::StringToUInt(
specification.substr(pos + 1),
NStr::fAllowLeadingSpaces |
NStr::fAllowTrailingSymbols |
NStr::fConvErr_NoThrow);
}
} else {
// host = specification.substr(old_pos);
// Ignore host in order to avoid dependebcy on libconnect.
// SOCK_StringToHostPort(specification.c_str() + old_pos, &host, &port);
}
} else {
// preference = NStr::StringToDouble(
preference = NStr::StringToUInt(
specification.substr(pos + 1),
NStr::fAllowLeadingSpaces |
NStr::fAllowTrailingSymbols |
NStr::fConvErr_NoThrow);
}
} else {
server = specification;
}
if (server.empty() && host == 0) {
DATABASE_DRIVER_ERROR("Either server name or host name expected.",
110100 );
}
return TSvrRef(new CDBServer(server, host, port));
}
CTextseq_id& CTextseq_id::Set
(const CTempString& acc_in,
const CTempString& name_in,
int version,
const CTempString& release_in,
bool allow_dot_version)
{
// Perform general sanity checks up front.
if (version < 0) {
NCBI_THROW(CSeqIdException, eFormat,
"Unexpected negative version " + NStr::IntToString(version)
+ " for accession " + string(acc_in));
}
CTempString acc =
NStr::TruncateSpaces_Unsafe(acc_in, NStr::eTrunc_Both);
CTempString name =
NStr::TruncateSpaces_Unsafe(name_in, NStr::eTrunc_Both);
CTempString release =
NStr::TruncateSpaces_Unsafe(release_in, NStr::eTrunc_Both);
if (acc.empty() && name.empty()) {
}
if (acc.empty()) {
ResetAccession();
} else {
SIZE_TYPE idx = NPOS;
if (allow_dot_version) {
idx = acc.rfind('.');
}
if (idx == NPOS) {
// no version within acc
SetAccession(acc);
// any standalone version is ok
if (version > 0) {
SetVersion(version);
} else {
ResetVersion();
}
} else {
// accession.version
CTempString accession = acc.substr(0, idx);
CTempString acc_ver = acc.substr(idx + 1);
int ver = NStr::StringToNonNegativeInt(acc_ver);
if (ver <= 0) {
NCBI_THROW(CSeqIdException, eFormat,
"Version embedded in accession " + string(acc)
+ " is not a positive integer");
} else if (version > 0 && ver != version) {
NCBI_THROW(CSeqIdException, eFormat,
"Incompatible version " + NStr::IntToString(version)
+ " supplied for accession " + string(acc));
}
SetAccession(accession);
SetVersion(ver);
}
}
if (name.empty()) {
ResetName();
} else {
SetName(name);
}
if (acc.empty() && name.empty()) {
NCBI_THROW(CSeqIdException, eFormat,
"Accession and name missing for Textseq-id (but got"
" version " + NStr::IntToString(version) + ", release "
+ string(release) + ')');
} else if (release.empty()) {
ResetRelease();
} else {
SetRelease(release);
}
return *this;
}