1 #ifndef SRA__READER__SRA__SRAREAD__HPP
2 #define SRA__READER__SRA__SRAREAD__HPP
83 const string& vol_path));
86 static string GetDefaultRepPath(
void);
88 static string GetDefaultVolPath(
void);
91 void AddRepPath(
const string& rep_path);
94 void AddVolPath(
const string& vol_path);
96 string FindAccPath(
const string& acc)
const;
111 CSraMgr(
const string& rep_path,
const string& vol_path,
112 ETrim trim = eNoTrim);
120 string FindAccPath(
const string& acc)
const;
128 static void RegisterFunctions(
void);
139 :
public CSraRef<const SRAColumn>
150 rc_t TryInitRc(
const CSraRun& run,
const char* name,
const char*
type);
156 :
public CSraRef<const SRATable>
179 void x_DoInit(
CSraMgr& mgr,
const string& acc);
201 ECheckRc check_rc = eCheckRc);
234 return static_cast<const char*
>(
m_Data);
CSraColumn(const CSraRun &run, const char *name, const char *type)
const string & GetAccession(void) const
CSraRun(CSraMgr &mgr, const string &acc)
CSraStringValue(const CSraColumn &col, spotid_t id, ECheckRc check_rc=eCheckRc)
const char * data(void) const
const TValue & Value(void) const
const TValue & operator[](size_t i) const
const TValue * operator->(void) const
CSraValueFor(const CSraColumn &col, spotid_t id, CSraValue::ECheckRc check_rc=CSraValue::eCheckRc)
DECLARE_OPERATOR_BOOL(!m_Error)
size_t GetLength(void) const
Include a standard set of the NCBI C++ Toolkit most basic headers.
#define NCBI_DEPRECATED_CTOR(decl)
Macro used to mark a constructor as deprecated.
unsigned int TSeqPos
Type for sequence locations and lengths.
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define END_SCOPE(ns)
End the previously defined scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
#define BEGIN_SCOPE(ns)
Define a new scope.
#define NCBI_SRAREAD_EXPORT
EMol
molecule class in living organism
Uint4 GetSequenceType(const CBioseq_Handle &bsh)
Return a (corrected) set of flags identifying the sequence type.
DECLARE_SRA_REF_TRAITS(SRAMgr, const)
CSraValueFor< uint16_t > CSraUInt16Value
CSraValueFor< char > CSraBytesValue
static rc_t x_Release(const SRAPath *t)
static rc_t x_AddRef(const SRAPath *t)