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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bamread__base_8hpp_source.html below:

NCBI C++ ToolKit: include/sra/readers/bam/bamread_base.hpp Source File

1 #ifndef SRA__READER__BAM__BAMREAD_BASE__HPP 2 #define SRA__READER__BAM__BAMREAD_BASE__HPP 48 #ifndef NCBI_EXCEPTION3_VAR 50 # define NCBI_EXCEPTION3_VAR(name, exc_cls, err_code, msg, extra1, extra2) \ 51 exc_cls name(DIAG_COMPILE_INFO, 0, exc_cls::err_code, msg, \ 55 #ifndef NCBI_EXCEPTION3 56 # define NCBI_EXCEPTION3(exc_cls, err_code, msg, extra1, extra2) \ 57 NCBI_EXCEPTION3_VAR(NCBI_EXCEPTION_EMPTY_NAME, \ 58 exc_cls, err_code, msg, extra1, extra2) 62 # define NCBI_THROW3(exc_cls, err_code, msg, extra1, extra2) \ 63 throw NCBI_EXCEPTION3(exc_cls, err_code, msg, extra1, extra2) 67 # define NCBI_RETHROW3(prev_exc, exc_cls, err_code, msg, extra1, extra2) \ 68 throw exc_cls(DIAG_COMPILE_INFO, &(prev_exc), exc_cls::err_code, msg, \ 112 const string

& message,

117 const string

& message,

123 const string

& message,

125 const string

& param,

134 virtual const char

GetType

(

void

)

const

;

153 static void

ReportError(

const char

msg

rc_t

rc);

168 template

class

Object>

173 #define SPECIALIZE_BAM_REF_TRAITS(T, Const) \ 175 struct CBamRefTraits<Const T> \ 177 static rc_t x_Release(const T* t); \ 178 static rc_t x_AddRef (const T* t); \ 180 #define DEFINE_BAM_REF_TRAITS(T, Const) \ 181 rc_t CBamRefTraits<Const T>::x_Release(const T* t) \ 182 { return T##Release(t); } \ 183 rc_t CBamRefTraits<Const T>::x_AddRef (const T* t) \ 184 { return T##AddRef(t); } 186 template

class

Object>

205 if

(

this

!= &ref ) {

230 "Null BAM pointer"

);

266 if

(

rc_t

rc = TTraits::x_AddRef(obj) ) {

268 "Cannot add ref"

, rc);

ostream & operator<<(ostream &out, const CBamRcFormatter &f)

EErrCode

Error types that CBamXxx classes can generate.

@ eAddRefFailed

AddRef failed.

@ eInvalidArg

Invalid argument error.

@ eInitFailed

Initialization failed.

@ eInvalidBAIFormat

Invalid data in BAM index file.

@ eInvalidBAMFormat

Invalid data in BAM file.

@ eBadCIGAR

Bad CIGAR string.

@ eNoData

Data not found.

@ eNullPtr

Null pointer error.

int TErrCode

Translate from the error code value to its string representation.

const string & GetParam(void) const

static void ReportError(const char *msg, rc_t rc)

CBamRef(const TSelf &ref)

static TObject * s_AddRef(const TSelf &ref)

void SetReferencedPointer(TObject *ptr)

TSelf & operator=(const TSelf &ref)

TObject ** x_InitPtr(void)

CBamRefTraits< Object > TTraits

TObject * operator->(void) const

TObject & operator*(void) const

TObject * GetPointer(void) const

Incapsulate compile time information such as __FILE__, __LINE__, NCBI_MODULE, current function.

Include a standard set of the NCBI C++ Toolkit most basic headers.

std::ofstream out("events_result.xml")

main entry point for tests

EDiagSev

Severity level for the posted diagnostics.

@ eDiag_Error

Error message.

virtual void ReportExtra(ostream &out) const

Report "non-standard" attributes.

virtual const char * GetType(void) const

Get class name as a string.

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

virtual const CException * x_Clone(void) const

Helper method for cloning the exception.

#define NCBI_THROW2(exception_class, err_code, message, extra)

Throw exception with extra parameter.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

#define EXCEPTION_VIRTUAL_BASE

Do not use virtual base classes in exception declaration at all, because in this case derived class s...

#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_BAMREAD_EXPORT

Defines NCBI C++ exception handling.

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

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