CRef<CBioseq> MakeMaskingBioseq(const CSeq_id& new_id,
TSeqPos seq_length,
const CSeq_id& original_id,
const CSeq_loc& masking_loc)
{
return MakeMaskingBioseq(new_id, seq_length,
ConstRef(&original_id), masking_loc);
}
CSeqMap_CI::CSeqMap_CI(const CBioseq_Handle& bioseq,
const SSeqMapSelector& sel,
TSeqPos pos)
: m_Scope(&bioseq.GetScope()),
m_SearchPos(0),
m_SearchEnd(kInvalidSeqPos)
{
SSeqMapSelector tse_sel(sel);
tse_sel.SetLinkUsedTSE(bioseq.GetTSE_Handle());
x_Select(ConstRef(&bioseq.GetSeqMap()), tse_sel, pos);
}
CSeqMap_CI::CSeqMap_CI(const CBioseq_Handle& bioseq,
const SSeqMapSelector& sel,
const CRange<TSeqPos>& range)
: m_Scope(&bioseq.GetScope()),
m_SearchPos(range.GetFrom()),
m_SearchEnd(range.GetToOpen())
{
SSeqMapSelector tse_sel(sel);
tse_sel.SetLinkUsedTSE(bioseq.GetTSE_Handle());
x_Select(ConstRef(&bioseq.GetSeqMap()), tse_sel, range.GetFrom());
}
CConstRef<CSeq_interval> CSeqTable_column::GetSeq_int(size_t row) const
{
size_t index = row;
if ( IsSetSparse() ) {
index = GetSparse().GetIndexAt(row);
if ( index == CSeqTable_sparse_index::kSkipped ) {
if ( IsSetSparse_other() ) {
return ConstRef(&GetSparse_other().GetInterval());
}
return null;
}
}
if ( IsSetData() ) {
const CSeqTable_multi_data::TInterval& arr = GetData().GetInterval();
if ( index < arr.size() ) {
return arr[index];
}
}
if ( IsSetDefault() ) {
return ConstRef(&GetDefault().GetInterval());
}
return null;
}
int Foo (Packed &p, int i, int ui)
{
int r;
if ((r = Val (p.i, i)))
return r;
if ((r = Val (p.u.i, ui)))
return r + 2;
if ((r = Val (p.u, ui)))
return r + 4;
if ((r = ConstRef (p.i, &p.i, i)))
return r + 6;
return 0;
}
void CSeqTableLocColumns::AddExtraColumn(const CSeqTable_column& column,
const CSeqTableSetLocField* setter)
{
m_ExtraColumns.push_back(TColumnInfo(column, ConstRef(setter)));
m_Is_set = true;
}
{
dword tlen = s_strlen(lptstr, INT_MAX);
tmp.SetSize(__FILE__LINE__ tlen + 1);
s_strcpy(CastMutable(CPointer, tmp.GetString()), tlen + 1, lptstr);
GlobalUnlock(hglb);
}
}
CloseClipboard();
#endif
#ifdef OK_SYS_UNIX
tmp = _clipboardtext;
#endif
return tmp;
}
bool CConsoleClipboard::SetClipboardText(ConstRef(CStringBuffer) text)
{
#ifdef OK_SYS_WINDOWS
HWND hwnd = GetConsoleWindow();
HGLOBAL hglbCopy;
LPTSTR lptstrCopy;
if ( !hwnd )
return false;
if ( !OpenClipboard(hwnd) )
return false;
EmptyClipboard();
hglbCopy = GlobalAlloc(GMEM_MOVEABLE, text.GetSize() * sizeof(TCHAR));
if ( !hglbCopy )
{
CloseClipboard();
std::string SymbolicVal::toString() const
{
return (ConstPtr() != 0)? ConstRef().toString() : std::string("");
}
}
CListView::CListView(LPCTSTR name):
CControl(name),
m_SelectMode(TSelectModeDisabled),
m_editable(false),
m_hasSelection(false),
m_nodes(__FILE__LINE__ 64, 128),
m_selNodes(__FILE__LINE__ 64, 128),
m_images(),
m_currentNode(NULL),
m_editor(NULL)
{
}
CListView::CListView(ConstRef(CStringBuffer) name):
CControl(name),
m_SelectMode(TSelectModeDisabled),
m_editable(false),
m_hasSelection(false),
m_nodes(__FILE__LINE__ 64, 128),
m_selNodes(__FILE__LINE__ 64, 128),
m_images(),
m_currentNode(NULL),
m_editor(NULL)
{
}
CListView::~CListView(void)
{
clear();
CConstRef<CSeq_align> CSeq_align_Handle::GetSeq_align(void) const
{
return ConstRef(&x_GetSeq_align());
}
bool CSeqMap_CI::x_Push(TSeqPos pos, bool resolveExternal)
{
const TSegmentInfo& info = x_GetSegmentInfo();
if ( !info.InRange() ) {
return false;
}
const CSeqMap::CSegment& seg = info.x_GetSegment();
CSeqMap::ESegmentType type = CSeqMap::ESegmentType(seg.m_SegType);
switch ( type ) {
case CSeqMap::eSeqSubMap:
{{
CConstRef<CSeqMap> push_map
(static_cast<const CSeqMap*>(info.m_SeqMap->x_GetObject(seg)));
// We have to copy the info.m_TSE into local variable push_tse because
// of TSegmentInfo referenced by info can be moved inside x_Push() call.
CTSE_Handle push_tse = info.m_TSE;
x_Push(push_map, info.m_TSE,
GetRefPosition(), GetLength(), GetRefMinusStrand(), pos);
break;
}}
case CSeqMap::eSeqRef:
{{
if ( !resolveExternal ) {
return false;
}
const CSeq_id& seq_id =
static_cast<const CSeq_id&>(*info.m_SeqMap->x_GetObject(seg));
CBioseq_Handle bh;
if ( m_Selector.x_HasLimitTSE() ) {
// Check TSE limit
bh = m_Selector.x_GetLimitTSE().GetBioseqHandle(seq_id);
if ( !bh ) {
return false;
}
}
else {
if ( !GetScope() ) {
NCBI_THROW(CSeqMapException, eNullPointer,
"Cannot resolve "+
seq_id.AsFastaString()+": null scope pointer");
}
bh = GetScope()->GetBioseqHandle(seq_id);
if ( !bh ) {
if ( GetFlags() & CSeqMap::fIgnoreUnresolved ) {
return false;
}
NCBI_THROW(CSeqMapException, eFail,
"Cannot resolve "+
seq_id.AsFastaString()+": unknown");
}
}
if ( (GetFlags() & CSeqMap::fByFeaturePolicy) &&
bh.GetFeatureFetchPolicy() == bh.eFeatureFetchPolicy_only_near ) {
return false;
}
if ( info.m_TSE ) {
if ( !info.m_TSE.AddUsedTSE(bh.GetTSE_Handle()) ) {
m_Selector.AddUsedTSE(bh.GetTSE_Handle());
}
}
size_t depth = m_Stack.size();
x_Push(ConstRef(&bh.GetSeqMap()), bh.GetTSE_Handle(),
GetRefPosition(), GetLength(), GetRefMinusStrand(), pos);
if (m_Stack.size() == depth) {
return false;
}
m_Selector.PushResolve();
if ( (m_Stack.size() & 63) == 0 ) {
// check for self-recursion every 64'th stack frame
const CSeqMap* top_seq_map = &m_Stack.back().x_GetSeqMap();
for ( int i = m_Stack.size()-2; i >= 0; --i ) {
if ( &m_Stack[i].x_GetSeqMap() == top_seq_map ) {
NCBI_THROW(CSeqMapException, eSelfReference,
"Self-reference in CSeqMap");
}
}
}
break;
}}
default:
return false;
}
return true;
}
CConstPointer vName = va_arg(argList, CConstPointer);
Ptr(CSqLite3Column) pColumn = OK_NEW_OPERATOR CSqLite3Column(vName, vDataType);
_pFuncInfo->Append(pColumn);
}
va_end(argList);
_lpImpl->create_function(_pFuncInfo);
}
}
CSqLite3Connection::create_function_infoclass::create_function_infoclass(Ptr(CSqLite3Connection) pConn, CConstPointer name, create_function_type funcbody, sword nArgs) :
_pConn(pConn), _name(__FILE__LINE__ name), _func(funcbody), _nArgs(nArgs), _args(__FILE__LINE__ 16, 16, CSqLite3ColumnsDeleteFunc)
{}
CSqLite3Connection::create_function_infoclass::create_function_infoclass(Ptr(CSqLite3Connection) pConn, ConstRef(CStringBuffer) name, create_function_type funcbody, sword nArgs) :
_pConn(pConn), _name(name), _func(funcbody), _nArgs(nArgs), _args(__FILE__LINE__ 16, 16, CSqLite3ColumnsDeleteFunc)
{}
CSqLite3Connection::create_function_infoclass::~create_function_infoclass() {}
void CSqLite3Connection::create_function_infoclass::Append(Ptr(CSqLite3Column) pArg)
{
_args.Append(pArg);
}
CSqLite3Statement::CSqLite3Statement(CSqLite3Environment* lpEnv, CSqLite3StatementImpl* lpStmtImpl) :
_lpEnv(lpEnv), _lpImpl(lpStmtImpl), _columns(__FILE__LINE__ 16, 16, CSqLite3ColumnsDeleteFunc)
{
if (_lpEnv)
_lpEnv->addRef();
#endif
{
SetString(ARGS_FILE_LINE _str.GetCurrent(), _str.GetLength());
}
CStringBuffer::CStringBuffer(DECL_FILE_LINE CStringLiteral _str):
CStringLiteral()
#ifdef __DEBUG__
, _file(file), _line(line)
#endif
{
SetString(ARGS_FILE_LINE _str.GetString(), _str.GetLength());
}
#ifdef QT_VERSION
CStringBuffer::CStringBuffer( ConstRef(QString) _str):
CStringLiteral()
#ifdef __DEBUG__
, _file(NULL), _line(0)
#endif
{
SetString(_str);
}
#endif
CStringBuffer::CStringBuffer(const CStringBuffer& copy):
CStringLiteral()
#ifdef __DEBUG__
, _file(copy._file), _line(copy._line)
#endif
{
#ifdef OK_SYS_WINDOWS
#include <winsock2.h>
#ifdef OK_COMP_MSC
#pragma comment (lib, "Ws2_32.lib")
#endif
#endif
#ifdef OK_SYS_UNIX
#include <netdb.h>
#endif
CWinException::CWinException():
CBaseException()
{
}
CWinException::CWinException(DECL_FILE_LINE ConstRef(CStringLiteral) format) :
CBaseException(ARGS_FILE_LINE format)
{
}
CWinException::CWinException(DECL_FILE_LINE ConstRef(CStringLiteral) format, CConstPointer sArg) :
CBaseException(ARGS_FILE_LINE format, sArg)
{
}
CWinException::CWinException(DECL_FILE_LINE ConstRef(CStringLiteral) format, CConstPointer sArg1, CConstPointer sArg2) :
CBaseException(ARGS_FILE_LINE format, sArg1, sArg2)
{
}
CWinException::CWinException(DECL_FILE_LINE ConstRef(CStringLiteral) format, int sArg) :
******************************************************************************/
#include "WS_PCH.H"
#include "AsyncFile.h"
#include "SecurityFile.h"
#include "WinDirectoryIterator.h"
CAsyncFile::CAsyncFile(Ptr(CAsyncIOManager) pManager):
CAsyncIOBuffer(pManager)
{
}
CAsyncFile::~CAsyncFile(void)
{
}
void CAsyncFile::Create(ConstRef(CFilePath) _path)
{
CWinDirectoryIterator::UnlinkFile(_path);
SECURITY_ATTRIBUTES sa;
HANDLE fHandle;
sa.nLength = sizeof(SECURITY_ATTRIBUTES);
sa.lpSecurityDescriptor = NULL;
sa.bInheritHandle = TRUE;
fHandle = CreateFile(
_path.get_Path().GetString(), // LPCTSTR lpFileName,
GENERIC_READ | GENERIC_WRITE, // DWORD dwDesiredAccess,
FILE_SHARE_READ, // DWORD dwShareMode,
&sa, // LPSECURITY_ATTRIBUTES lpSecurityAttributes,