RetroSearch Browse

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/reader__snp_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/data_loaders/genbank/reader_snp.cpp Source File

123

: m_SetObjectInfo(&set_info),

124

m_Seq_annot_hook(new CSeq_annot_hook)

141

~CSNP_Seq_feat_hook(

void

);

157 _ASSERT

(m_Seq_annot_hook->m_Seq_annot);

165

CSNP_Seq_feat_hook hook(*snp_info,

data

.SetFtable());

168

snp_info->x_FinishParsing();

169 if

( !snp_info->empty() ) {

170

m_SetObjectInfo->m_Seq_annot_InfoMap[m_Seq_annot_hook->m_Seq_annot].m_SNP_annot_Info = snp_info;

177

: m_Seq_annot_SNP_Info(annot_snp_info),

187

CSNP_Seq_feat_hook::~CSNP_Seq_feat_hook(

void

)

192 NcbiCout

"CSeq_annot_SNP_Info statistic (gi = "

193

m_Seq_annot_SNP_Info.GetSeq_id().AsFastaString() <<

"):\n"

;

195 if

( !m_Count[

] ) {

200

setw(6) << m_Count[

] <<

" "

201

setw(3) <<

int

(m_Count[

]*100.0/total+.5) <<

"%\n"

;

202

s_TotalCount[

] += m_Count[

];

208 NcbiCout

"cumulative CSeq_annot_SNP_Info statistic:\n"

;

210 if

( !s_TotalCount[

] ) {

215

setw(6) << s_TotalCount[

] <<

" "

216

setw(3) <<

int

(s_TotalCount[

]*100.0/total+.5) <<

"%\n"

;

235 in

.ReadObject(&*m_Feat, m_Feat->GetTypeInfo());

241

m_Seq_annot_SNP_Info.x_AddSNP(snp_info);

248 "CSNP_Seq_feat_hook::ReadContainerElement: complex SNP: "

253

m_Ftable.push_back(m_Feat);

315 if

(

sizeof

(

) > 4 &&

Uint4

(

) !=

) {

317 "write_unsigned overflow for "

<<name<<

": "

);

325

stream.write(c,

sizeof

(c));

333

stream.read(c,

sizeof

(c));

336 string

(

"Cannot read "

)+name);

339

(

Uint1

(c[0])<<24) |

340

(

Uint1

(c[1])<<16) |

341

(

Uint1

(c[2])<< 8) |

352 for

(

int i

= 7;

>= 0; --

) {

356

stream.write(c,

sizeof

(c));

364

stream.read(c,

sizeof

(c));

367 string

(

"Cannot read "

)+name);

370

(

Uint1

(c[4])<<24) |

371

(

Uint1

(c[5])<<16) |

372

(

Uint1

(c[6])<< 8) |

375

(

Uint1

(c[0])<<24) |

376

(

Uint1

(c[1])<<16) |

377

(

Uint1

(c[2])<< 8) |

382 if

( n2 != (

>>31) ) {

384 string

(

"GI overflow "

)+name);

395 while

(

size

>= (1<<7) ) {

396

stream.put(

char

(

size

| (1<<7)));

399

stream.put(

char

(

size

));

407 static const int

total_bits =

sizeof

(

size

)*8;

414 string

(

"Cannot read "

)+name);

416 size_t

bits = c & ((1<<7)-1);

417 if

( shift+7 > total_bits && (c>>(total_bits-shift)) != 0 ) {

419 string

(

"read_size overflow for "

)+name);

421 size

|= bits << shift;

423

}

while

( c & (1<<7) );

433

stream.write(

str

.data(),

size

);

441 if

(

size

> max_length ) {

443 "SNP table string is too long"

);

449 "Cannot read SNP table string"

);

475 for

(

size_t

idx = 0; idx <

strings

.GetSize(); ++idx) {

488 if

(

count

unsigned

(max_index+1) ) {

490 "SNP table string count is too big"

);

493 for

(

size_t

idx = 0; idx <

strings

.GetSize(); ++idx) {

502 size_t

element_size =

strings

.GetElementSize();

504 if

( element_size ) {

518 size_t

element_size =

519 read_size

(stream,

"SNP table OCTET STRING element size"

);

520 if

( element_size ) {

522 read_size

(stream,

"SNP table OCTET STRING total size"

);

523 if

( element_size == 0 ||

total_size

%element_size != 0 ||

526 "SNP table OCTET STRING count is too big"

);

534 "Cannot read SNP table OCTET STRING"

);

536 strings

.SetTotalString(element_size, s);

569

m_Index.push_back(

Ref

(ptr));

579 static const unsigned MAGIC

= 0x12340008;

592

obj_stream.

Write

(

object

);

596 "number of SNP table annots"

);

600 if

( iter == hook->m_Index.end() ) {

602 "Orphan CSeq_annot_SNP_Info"

);

605 x_Write

(stream, *it->second.m_SNP_annot_Info);

609 "SNP table store failed"

);

618 unsigned

magic =

read_unsigned

(stream,

"SNP table magic number"

);

619 if

( magic !=

MAGIC

) {

621 "Incompatible version of SNP table"

);

628

obj_stream.

Read

(

object

);

632 for

(

unsigned i

= 0;

count

; ++

) {

633 unsigned

index =

read_unsigned

(stream,

"SNP table annot index"

);

634 if

( index >= hook->m_Index.size() ) {

636 "Orphan CSeq_annot_SNP_Info"

);

644 "Duplicate CSeq_annot_SNP_Info"

);

647 x_Read

(stream, *snp_info);

667 x_Read

(stream, snp_info);

674

obj_stream >> *annot;

678 "Bad format of SNP table"

);

691 write_gi

(stream, gi,

"SNP table GI"

);

706

stream.write(

reinterpret_cast<const char

>

(&snp_info.

m_SNP_Set

[0]),

717 unsigned

magic =

read_unsigned

(stream,

"SNP table magic number"

);

718 if

( magic !=

MAGIC

) {

720 "Incompatible version of SNP table"

);

758

stream.read(

reinterpret_cast<char

>

(&snp_info.

m_SNP_Set

[0]),

762 "Cannot read SNP table simple SNPs"

);

771 size_t

index = it->m_CommentIndex;

773

index >= comments_size ) {

776 "SNP table bad comment index"

);

778

index = it->m_ExtraIndex;

780

index >= extra_size ) {

783 "SNP table bad extra index"

);

789

index = it->m_QualityCodesIndex;

790 if

( index >= quality_str_size ) {

793 "SNP table bad quality code str index"

);

797

index = it->m_QualityCodesIndex;

798 if

( index >= quality_os_size ) {

801 "SNP table bad quality code os index"

);

807 "SNP table bad quality code type"

);

810

index = it->m_AllelesIndices[

];

812

index >= alleles_size ) {

815 "SNP table bad allele index"

);

size_t GetSize(void) const

vector< char > TOctetString

size_t GetSize(void) const

Data loader exceptions, used by GenBank loader.

Helper class: installs hooks in constructor, and uninstalls in destructor.

CObjectIStreamAsnBinary â.

CObjectOStreamAsnBinary â.

static bool TrySNPTable(void)

static void SetSNPReadHooks(CObjectIStream &in)

Read hook for a choice variant (CHOICE)

Read hook for a container element (SEQUENCE OF)

Read hook for a standalone object.

vector< TAnnotRef > TIndexToAnnot

static void Write(CNcbiOstream &stream, const CSeq_annot_SNP_Info &snp_info)

static CRef< CSeq_annot_SNP_Info > ParseAnnot(CObjectIStream &in)

static void Read(CNcbiIstream &stream, CSeq_annot_SNP_Info &snp_info)

static void Parse(CObjectIStream &in, CSeq_entry &tse, CTSE_SetObjectInfo &set_info)

static void x_Read(CNcbiIstream &stream, CSeq_annot_SNP_Info &snp_info)

static void x_Write(CNcbiOstream &stream, const CSeq_annot_SNP_Info &snp_info)

const CSeq_id & GetSeq_id(void) const

CIndexedStrings m_Alleles

void SetSeq_id(const CSeq_id &id)

CIndexedStrings m_Comments

CRef< CSeq_annot > m_Seq_annot

CIndexedStrings m_QualityCodesStr

vector< SSNP_Info > TSNP_Set

CIndexedOctetStrings m_QualityCodesOs

namespace ncbi::objects::

TSeq_annot_InfoMap m_Seq_annot_InfoMap

Write hook for a standalone object.

container_type::const_iterator const_iterator

const_iterator begin() const

container_type::value_type value_type

Abstract reader-writer interface classes.

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

static const char *const strings[]

#define GI_FROM(T, value)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

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

#define NCBI_THROW_FMT(exception_class, err_code, message)

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

#define MSerial_AsnText

I/O stream manipulators â.

static C * Get(const CTypesIterator &it)

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

void DefaultWrite(CObjectOStream &out, const CConstObjectInfo &object)

void Read(const CObjectInfo &object)

Read object of know type.

TFlags SetFlags(TFlags flags)

const CObjectInfo & GetChoiceObject(void) const

Get containing choice.

void DefaultRead(CObjectIStream &in, const CObjectInfo &object)

Default read.

virtual void ReadObject(CObjectIStream &in, const CObjectInfo &object)=0

This method will be called at approriate time when the object of requested type is to be read.

virtual void WriteObject(CObjectOStream &out, const CConstObjectInfo &object)=0

This method will be called at approriate time when the object of requested type is to be written.

void Write(const CConstObjectInfo &object)

void ReadContainer(CObjectIStream &in, CReadContainerElementHook &hook)

Read element data from stream.

virtual void ReadChoiceVariant(CObjectIStream &in, const CObjectInfoCV &variant)=0

This method will be called at approriate time when the object of requested type is to be read.

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

#define NCBI_PARAM_TYPE(section, name)

Generate typename for a parameter from its {section, name} attributes.

@ eParam_NoThread

Do not use per-thread values.

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

#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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

TGi & SetGi(void)

Select the variant.

list< CRef< CSeq_feat > > TFtable

unsigned int

A callback function used to compare two keys in a database.

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

string s_Value(TValue value)

std::istream & in(std::istream &in_, double &x_)

static const size_t kMax_ExtraLength

void StoreIndexedOctetStringsTo(CNcbiOstream &stream, const CIndexedOctetStrings &strings)

static TGi read_gi(CNcbiIstream &stream, const char *name)

void LoadIndexedStringsFrom(CNcbiIstream &stream, CIndexedStrings &strings, size_t max_index, size_t max_length)

static void write_string(CNcbiOstream &stream, const string &str)

void StoreIndexedStringsTo(CNcbiOstream &stream, const CIndexedStrings &strings)

static const unsigned MAGIC

static void write_gi(CNcbiOstream &stream, TGi gi, const char *name)

static size_t read_size(CNcbiIstream &stream, const char *name)

static const size_t kMax_StringLength

static const size_t kMax_AlleleLength

static void write_unsigned(CNcbiOstream &stream, size_t n, const char *name)

static void write_size(CNcbiOstream &stream, size_t size)

static void write_seq_id(CNcbiOstream &stream, const CSeq_id &id)

static unsigned read_unsigned(CNcbiIstream &stream, const char *name)

static CRef< CSeq_id > read_seq_id(CNcbiIstream &stream)

NCBI_PARAM_DECL(bool, GENBANK, SNP_TABLE_STAT)

void LoadIndexedOctetStringsFrom(CNcbiIstream &stream, CIndexedOctetStrings &strings, size_t max_index, size_t max_length)

static const size_t kMax_QualityLength

NCBI_PARAM_DEF_EX(bool, GENBANK, SNP_TABLE_STAT, false, eParam_NoThread, GENBANK_SNP_TABLE_STAT)

static const size_t kMax_CommentLength

static void read_string(CNcbiIstream &stream, string &str, size_t max_length)

static bool CollectSNPStat(void)

static sljit_uw total_size

static const char *const s_SNP_Type_Label[eSNP_Type_last]

ESNP_Type ParseSeq_feat(const CSeq_feat &feat, CSeq_annot_SNP_Info &annot_info)

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4