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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/vdbfile_8cpp_source.html below:

NCBI C++ ToolKit: src/sra/readers/bam/vdbfile.cpp Source File

38 #include <vfs/manager.h> 41 #ifndef NCBI_THROW2_FMT 42 # define NCBI_THROW2_FMT(exception_class, err_code, message, extra) \ 43 throw NCBI_EXCEPTION2(exception_class, err_code, FORMAT(message), extra) 62 return

s.length() >= 2 &&

isalpha

(s[0]&0xff) && s[1] ==

':'

;

71

acc_or_path.find_first_of(

"/\\"

) ==

NPOS

;

73 return

acc_or_path.find(

'/'

) ==

NPOS

;

110 if

(

rc_t

rc = VFSManagerMakeSysPath(mgr,

x_InitPtr

(), path.c_str())) {

112 "CBamVDBPath("

<< path <<

"): " 113 "cannot create VPath"

, rc);

117 if

(

rc_t

rc = VFSManagerMakePath(mgr,

x_InitPtr

(), path.c_str())) {

119 "CBamVDBPath("

<< path <<

"): " 120 "cannot create VPath"

, rc);

129 if

(

rc_t

rc = VPathGetPath(*

this

, &

str

) ) {

131 "CBamVDBPath::GetString(): " 132 "VPathGetPath() failed"

, rc);

147 if

(

rc_t

rc = VFSManagerOpenFileRead(mgr,

x_InitPtr

(), path) ) {

149 "CBamVDBFile("

<<path.

GetString

()<<

"): " 150 "cannot open KFile"

, rc);

159 if

(

rc_t

rc = KFileSize(*

this

, &

size

) ) {

161 "CBamVDBFile::GetSize(): " 166 "CBamVDBFile::GetSize(): " 169 return

size_t(

size

);

176 if

(

rc_t

rc = KFileRead(*

this

, pos,

buffer

, buffer_size, &nread) ) {

178 "CBamVDBFile::Read(): " 188 size_t

nread_total = 0;

189 while

( buffer_size ) {

191 if

(

rc_t

rc = KFileRead(*

this

, pos,

buffer

, buffer_size, &nread) ) {

193 "CBamVDBFile::ReadAll(): " 199

nread_total += nread;

202

buffer_size -= nread;

210 if

(

rc_t

rc = KFileReadExactly(*

this

, pos,

buffer

, buffer_size) ) {

212 "CBamVDBFile::ReadExactly(): "

TObject ** x_InitPtr(void)

void x_Init(const CBamVFSManager &mgr, const CBamVDBPath &path)

void ReadExactly(size_t file_pos, char *buffer, size_t buffer_size)

size_t ReadAll(size_t file_pos, char *buffer, size_t buffer_size)

size_t Read(size_t file_pos, char *buffer, size_t buffer_size)

static bool IsPlainAccession(const string &acc_or_path)

void x_Init(const CBamVFSManager &mgr, const string &path)

static bool IsSysPath(const string &path)

static bool HasSchemaPrefix(const string &path)

CTempString GetString() const

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

static const char * str(char *buf, int n)

#define NCBI_THROW_FMT(exception_class, err_code, message)

The same as NCBI_THROW but with message processed as output to ostream.

#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.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

const struct ncbi::grid::netcache::search::fields::SIZE size

static bool s_HasWindowsDriveLetter(const string &s)

DEFINE_BAM_REF_TRAITS(VPath,)

#define NCBI_THROW2_FMT(exception_class, err_code, message, extra)

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