bool CAuthor::x_GetLabelV2(string* label, TLabelFlags flags, CTempString name,
CTempString initials, CTempString suffix)
{
if (name.empty()) {
return false;
}
if (name.size() <= 6 && (SWNC(name, "et al") || SWNC(name, "et,al"))) {
name = "et al.";
if (NStr::EndsWith(*label, " and ")) {
label->replace(label->size() - 5, NPOS, ", ");
}
}
SIZE_TYPE pos = label->size();
*label += name;
if (HasText(initials)) {
*label += ',';
*label += initials;
}
if (HasText(suffix)) {
*label += ' ';
*label += suffix;
}
if ((flags & fLabel_FlatEMBL) != 0) {
NStr::ReplaceInPlace(*label, ",", " ", pos);
}
return true;
}
CBlastDbBlob::CBlastDbBlob(CTempString data, bool copy)
: m_Owner(copy), m_ReadOffset(0), m_WriteOffset(0)
{
if (m_Owner) {
m_DataHere.assign(data.data(), data.data() + data.size());
} else {
m_DataRef = data;
}
}
void CVDBCursor::SetParam(const char* name, const CTempString& value) const
{
if ( rc_t rc = VCursorParamsSet
((struct VCursorParams *)GetPointer(),
name, "%.*s", value.size(), value.data()) ) {
NCBI_THROW2_FMT(CSraException, eNotFound,
"Cannot set VDB cursor param: "<<*this<<": "<<name,
rc);
}
}
void CTL_BCPInCmd::SetHints(CTempString hints)
{
#ifdef FTDS_IN_USE
m_Hints.clear();
if (Check(blk_sethints(x_GetSybaseCmd(), (CS_CHAR*)hints.data(), CS_INT(hints.size()))) == CS_FAIL) {
DATABASE_DRIVER_ERROR("blk_sethints failed." + GetDbgInfo(), 123018);
}
#else
_ASSERT(false);
#endif
}
///
/// This is the normative copy of the function
///
double ComputeNormalizedEntropy(const CTempString& sequence,
size_t word_size)
{
typedef map<CTempString, double> TCounts;
TCounts counts;
double total = sequence.size() - word_size;
for (size_t i = word_size; i < sequence.size(); ++i) {
CTempString t(sequence, i - word_size, word_size);
TCounts::iterator it =
counts.insert(TCounts::value_type(t, 0)).first;
it->second += 1;
}
NON_CONST_ITERATE (TCounts, it, counts) {
it->second /= total;
}
double entropy = 0;
ITERATE (TCounts, it, counts) {
entropy += it->second * log(it->second);
}
inline
TSqlString x_MakeTSqlString(const CTempString& s, EEncoding enc)
{
#if defined(UNICODE) || defined(_UNICODE) || defined(UCS2)
return CUtf8::AsBasicString<TSqlChar>(CUtf8::AsUTF8(s, enc));
#else
if (enc == eEncoding_Unknown || enc == eEncoding_UTF8) {
return CUtf8::AsSingleByteString(CUtf8::AsUTF8(s, enc),
eEncoding_ISO8859_1);
} else {
return CSqlString(s.data(), s.size());
}
#endif
}
const char * CBlastDbBlob::x_ReadRaw(int size, int * offsetp) const
{
_ASSERT(offsetp);
_ASSERT(size >= 0);
CTempString s = Str();
int begin = *offsetp;
int end = begin + size;
if (begin > end || end > (int)s.size()) {
NCBI_THROW(CSeqDBException,
eFileErr,
"CBlastDbBlob::x_ReadRaw: hit end of data");
}
*offsetp = end;
return s.data() + begin;
}
CTempString CBlastDbBlob::x_ReadString(EStringFormat fmt, int * offsetp) const
{
int sz = 0;
if (fmt == eSize4) {
sz = x_ReadIntFixed<int,4>(offsetp);
} else if (fmt == eSizeVar) {
sz = x_ReadVarInt(offsetp);
}
const char * datap = "";
if (fmt == eNUL) {
CTempString ts = Str();
int zoffset = -1;
for(size_t i = *offsetp; i < ts.size(); i++) {
if (ts[i] == (char)0) {
zoffset = i;
break;
}
}
if (zoffset == -1) {
NCBI_THROW(CSeqDBException,
eFileErr,
"CBlastDbBlob::ReadString: Unterminated string.");
}
datap = ts.data() + *offsetp;
sz = zoffset - *offsetp;
*offsetp = zoffset+1;
} else {
datap = x_ReadRaw(sz, offsetp);
}
return CTempString(datap, sz);
}
Int8 CBlastDbBlob::x_ReadVarInt(int * offsetp) const
{
CTempString all = Str();
Int8 rv(0);
for(size_t i = *offsetp; i < all.size(); i++) {
int ch = all[i];
if (ch & 0x80) {
// middle
rv = (rv << 7) | (ch & 0x7F);
} else {
// end
rv = (rv << 6) | (ch & 0x3F);
*offsetp = i+1;
return (ch & 0x40) ? -rv : rv;
}
}
NCBI_THROW(CSeqDBException,
eFileErr,
"CBlastDbBlob::ReadVarInt: eof while reading integer.");
}
void Reset(const CTempString& line)
{
const char* line_buf = line.data();
Reset(line_buf, line_buf + line.size());
}
bool CODBC_BCPInCmd::x_AssignParams(void* pb)
{
RETCODE r;
if (!m_WasBound) {
for (unsigned int i = 0; i < GetBindParamsImpl().NofParams(); ++i) {
if (GetBindParamsImpl().GetParamStatus(i) == 0) {
r = bcp_bind(GetHandle(), (BYTE*) pb, 0, SQL_VARLEN_DATA, 0, 0, 0, i + 1);
}
else {
CDB_Object& param = *GetBindParamsImpl().GetParam(i);
EDB_Type data_type = param.GetType();
r = bcp_bind(GetHandle(),
static_cast<LPCBYTE>(const_cast<void*>(x_GetDataPtr(data_type, pb))),
0,
static_cast<DBINT>(x_GetBCPDataSize(data_type)),
static_cast<LPCBYTE>(x_GetDataTerminator(data_type)),
static_cast<INT>(x_GetDataTermSize(data_type)),
x_GetBCPDataType(data_type),
i + 1);
m_HasTextImage = m_HasTextImage || (data_type == eDB_Image || data_type == eDB_Text);
}
if (r != SUCCEED) {
ReportErrors();
return false;
}
}
GetBindParamsImpl().LockBinding();
m_WasBound = true;
}
for (unsigned int i = 0; i < GetBindParamsImpl().NofParams(); i++) {
if (GetBindParamsImpl().GetParamStatus(i) == 0) {
r = bcp_collen(GetHandle(), SQL_NULL_DATA, i + 1);
}
else {
CDB_Object& param = *GetBindParamsImpl().GetParam(i);
switch ( param.GetType() ) {
case eDB_Bit:
DATABASE_DRIVER_ERROR("Bit data type is not supported", 10005);
break;
case eDB_Int: {
CDB_Int& val = dynamic_cast<CDB_Int&> (param);
r = bcp_colptr(GetHandle(), (BYTE*) val.BindVal(), i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), val.IsNULL() ? SQL_NULL_DATA : sizeof(Int4), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_SmallInt: {
CDB_SmallInt& val = dynamic_cast<CDB_SmallInt&> (param);
// DBSMALLINT v = (DBSMALLINT) val.Value();
r = bcp_colptr(GetHandle(), (BYTE*) val.BindVal(), i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), val.IsNULL() ? SQL_NULL_DATA : sizeof(Int2), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_TinyInt: {
CDB_TinyInt& val = dynamic_cast<CDB_TinyInt&> (param);
// DBTINYINT v = (DBTINYINT) val.Value();
r = bcp_colptr(GetHandle(), (BYTE*) val.BindVal(), i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), val.IsNULL() ? SQL_NULL_DATA : sizeof(Uint1), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_BigInt: {
CDB_BigInt& val = dynamic_cast<CDB_BigInt&> (param);
r = bcp_colptr(GetHandle(), (BYTE*) val.BindVal(), i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), val.IsNULL() ? SQL_NULL_DATA : sizeof(Int8), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_Char:
case eDB_VarChar:
case eDB_LongChar: {
CDB_String& val = dynamic_cast<CDB_String&> (param);
CTempString data;
if (val.IsNULL()) {
data.assign(static_cast<char*>(pb), 0);
} else {
if (IsMultibyteClientEncoding()) {
const wstring& ws = val.AsWString(GetClientEncoding());
// hack
data.assign((const char*)(ws.data()),
ws.size() * sizeof(wchar_t));
} else {
data = val.Value();
}
}
DBINT length;
INT dummy; // Can't just supply NULL
if (val.IsNULL()) {
length = SQL_NULL_DATA;
} else if (bcp_getcolfmt(GetHandle(), i + 1, BCP_FMT_DATA_LEN,
&length, sizeof(length), &dummy)
== FAIL || length < 0) {
length = SQL_VARLEN_DATA; // Be conservative.
} else if (static_cast<SIZE_TYPE>(length) > data.size()) {
// Retain automatic truncation, which blindly supplying
// data.size() could lose.
length = data.size();
}
r = bcp_colptr(GetHandle(),
(BYTE*) data.data(),
i + 1)
== SUCCEED &&
bcp_collen(GetHandle(),
length,
i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_Binary: {
CDB_Binary& val = dynamic_cast<CDB_Binary&> (param);
r = bcp_colptr(GetHandle(), (!val.IsNULL())? ((BYTE*) val.Value()) : (BYTE*)pb, i + 1)
== SUCCEED &&
bcp_collen(GetHandle(),
val.IsNULL() ? SQL_NULL_DATA : (Int4) val.Size(), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_VarBinary: {
CDB_VarBinary& val = dynamic_cast<CDB_VarBinary&> (param);
r = bcp_colptr(GetHandle(), (!val.IsNULL())? ((BYTE*) val.Value()) : (BYTE*)pb, i + 1)
== SUCCEED &&
bcp_collen(GetHandle(),
val.IsNULL() ? SQL_NULL_DATA : (Int4) val.Size(), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_LongBinary: {
CDB_LongBinary& val = dynamic_cast<CDB_LongBinary&> (param);
r = bcp_colptr(GetHandle(), (!val.IsNULL())? ((BYTE*) val.Value()) : (BYTE*)pb, i + 1)
== SUCCEED &&
bcp_collen(GetHandle(),
val.IsNULL() ? SQL_NULL_DATA : (Int4) val.DataSize(), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_Float: {
CDB_Float& val = dynamic_cast<CDB_Float&> (param);
//DBREAL v = (DBREAL) val.Value();
r = bcp_colptr(GetHandle(), (BYTE*) val.BindVal(), i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), val.IsNULL() ? SQL_NULL_DATA : sizeof(float), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_Double: {
CDB_Double& val = dynamic_cast<CDB_Double&> (param);
//DBFLT8 v = (DBFLT8) val.Value();
r = bcp_colptr(GetHandle(), (BYTE*) val.BindVal(), i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), val.IsNULL() ? SQL_NULL_DATA : sizeof(double), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
break;
case eDB_SmallDateTime: {
CDB_SmallDateTime& val =
dynamic_cast<CDB_SmallDateTime&> (param);
DBDATETIM4* dt = (DBDATETIM4*) pb;
DBDATETIME4_days(dt) = val.GetDays();
DBDATETIME4_mins(dt) = val.GetMinutes();
r = bcp_colptr(GetHandle(), (BYTE*) dt, i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), val.IsNULL() ? SQL_NULL_DATA : sizeof(DBDATETIM4), i + 1)
== SUCCEED ? SUCCEED : FAIL;
pb = (void*) (dt + 1);
}
break;
case eDB_DateTime: {
CDB_DateTime& val = dynamic_cast<CDB_DateTime&> (param);
DBDATETIME* dt = (DBDATETIME*) pb;
if (val.IsNULL()) {
r = bcp_colptr(GetHandle(), (BYTE*) dt, i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), SQL_NULL_DATA, i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
else {
dt->dtdays = val.GetDays();
dt->dttime = val.Get300Secs();
r = bcp_colptr(GetHandle(), (BYTE*) dt, i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), sizeof(DBDATETIME), i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
pb = (void*) (dt + 1);
}
break;
case eDB_Text: {
CDB_Text& val = dynamic_cast<CDB_Text&> (param);
if (val.IsNULL()) {
r = bcp_colptr(GetHandle(), (BYTE*) pb, i + 1)
== SUCCEED &&
bcp_collen(GetHandle(), SQL_NULL_DATA, i + 1)
== SUCCEED ? SUCCEED : FAIL;
}
else {
r = bcp_bind(GetHandle(), (BYTE*) NULL, 0, (DBINT) val.Size(),
static_cast<LPCBYTE>(x_GetDataTerminator(eDB_Text)),
static_cast<INT>(x_GetDataTermSize(eDB_Text)),
x_GetBCPDataType(eDB_Text),
i + 1);
}
}
break;
case eDB_Image: {
CDB_Image& val = dynamic_cast<CDB_Image&> (param);
// Null images doesn't work in odbc
// (at least in those tests that exists in dbapi_unit_test)
r = bcp_collen(GetHandle(), (DBINT) val.Size(), i + 1);
}
break;
default:
return false;
}
}
if (r != SUCCEED) {
ReportErrors();
return false;
}
}
return true;
}