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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/split__cache_8cpp_source.html below:

NCBI C++ ToolKit: src/app/split_cache/split_cache.cpp Source File

: m_App(app), m_Stream(0)

m_Stream = &m_App->Info();

<

T>

<

T>

: m_DumpAsnText(

), m_DumpAsnBinary(

),

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddDefaultKey

(

,

,

,

arg_desc->AddDefaultKey

(

,

,

,

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

prog_description =

;

arg_desc->SetUsageContext(

().GetProgramBasename(),

prog_description,

);

(

<<

);

( args[

] ) {

cache_dir = args[

].AsString();

cache_dir = reg.

(

,

, cache_dir);

( !cache_dir.empty() ) {

(

<< cache_dir <<

);

( 0 && !cache_dir.empty() ) {

( blob_age <= 0 ) {

cache->

(cache_dir.c_str(),

);

time_t age = time_stamp.

();

age -= 60 * 60 * 24 * blob_age;

( 0 && !cache_dir.empty() ) {

cache->

(cache_dir.c_str(),

);

( cache_dir.empty() ) {

().

(

,

, cache_dir);

().

(

,

, cache_dir);

readers =

;

( !cache_dir.empty() ) {

);

& suffix,

( !suffix.empty() && !ext.empty() ) {

( args[

] ) {

args[

].AsInteger();

( args[

] ) {

( args[

] ) {

( args[

] ) {

id(args[

].AsString());

( args[

] ) {

( args[

] ) {

(args[

].AsString(),

, vv);

( vv.size() != 2 && vv.size() != 3 ) {

( vv.size() == 3 )

( args[

] ) {

( args[

] ) {

= args[

].AsString();

= args[

].AsString();

p =

.rfind(

);

&

,

& suffix =

)

: ext =

;

;

&

,

& suffix =

)

(

);

ids.

(it.GetRefSeqid());

( (*entry)->IsSet() ) {

seq_desc_set, set_desc_set);

( (*entry)->GetSeq().IsSetDescr() ) {

seq_desc_set, set_desc_set;

( tse.

() ) {

<<

<< seq_desc_set.

() <<

pair<size_t, size_t>(seq_desc_set.

(), set_desc_set.

());

(

);

(

<< blob_id);

<<

;

(

);

( !splitter.

(*seq_entry) ) {

(

);

<<

;

pair<size_t, size_t> desc_counts =

<< *it->second;

<<

<<it->first;

(

<<

);

<<

;

(

);

( !splitter.

(*seq_entry) ) {

(

);

<<

;

pair<size_t, size_t> desc_counts =

<< *it->second;

<<

<<it->first;

~(kMask_low + kMask_high);

( content.

() ) {

( (

.GetType_mask() & kMask_low) != 0 ) {

( (

.GetType_mask() & kMask_high) != 0 ) {

( (

.GetType_mask() & kMask_other) != 0 ) {

(

.IsSetBioseqs() ) {

(

.IsSetBioseq_sets() ) {

*

,

).GetLoader());

<<

<<

.AsString() <<

;

check_set_desc =

;

check_high_desc =

;

check_assembly =

;

check_high_desc =

;

check_set_desc =

;

check_assembly =

;

( check_set_desc || check_high_desc ) {

( check_set_desc ) {

( check_high_desc ) {

(

desc_ci(*seq, choices); desc_ci; ++desc_ci) {

( !check_set_desc ) {

( check_assembly ) {

( !seq->IsSetInst_Hist() ) {

seq->GetInst_Length();

seq->GetInst_Hist();

<<

<< seq->GetSeqId()->AsFastaString() <<

;

(tse_core == complete_tse);

( seh.

() ) {

(hcount >

) {

(

argc,

* argv[])

ncbi::objects::CSplitCacheApp().AppMain(argc, argv);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

ICache interface implementation on top of Berkeley DB.

BDB cache implementation.

const CSplitBlob & GetBlob(void) const

bool Split(const CSeq_entry &entry)

void SetSubSat(TSubSat v)

void SetSatKey(TSatKey v)

ICache * GetIdCache(void) const

ICache * GetBlobCache(void) const

CReadDispatcher & GetDispatcher(void)

TRealBlobId GetRealBlobId(const TBlobId &blob_id) const

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

CID2S_Seq_descr_Info –.

static void Compress(const SSplitterParams &params, list< vector< char > * > &dst, const char *data, size_t size)

CTSE_Split_Info & GetSplitInfo(void)

CFlusher & operator<<(const T &t)

CFlusher(CNcbiOstream &out)

CFlusher operator<<(const T &t)

CNcbiOstream & Start(void)

CLog(const CSplitCacheApp *app)

const CSplitCacheApp * m_App

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

void SaveDataAndSkel(CReaderRequestResult &result, const TBlobId &blob_id, TBlobState blob_state, TChunkId chunk_id, CWriter *writer, TSplitVersion split_version, const CID2_Reply_Data &split_data, const CID2_Reply_Data &skel_data) const

const CProcessor & GetProcessor(CProcessor::EType type) const

CWriter * GetWriter(const CReaderRequestResult &result, CWriter::EType type) const

@Seq_descr.hpp User-defined methods of the data storage class.

const TChunks & GetChunks(void) const

const CID2S_Split_Info & GetSplitInfo(void) const

const CSeq_entry & GetMainBlob(void) const

static string GetFileName(const string &key, const string &suffix, const string &ext)

void ProcessBlob(CBioseq_Handle &bh, const CSeq_id_Handle &idh)

virtual void Init(void)

Initialize the application.

TProcessedBlobs m_ProcessedBlobs

SSplitterParams m_SplitterParams

CRef< CObjectManager > m_ObjMgr

void ProcessSeqId(const CSeq_id &seq_id)

void TestSplitBioseq(CSeq_entry_Handle seh)

virtual int Run(void)

Run the application.

CNcbiOstream & Info(void) const

void PrintVersion(int version)

AutoPtr< ICache > m_IdCache

const CBlob_id & GetBlob_id(CSeq_entry_Handle tse)

void ProcessEntry(const CSeq_entry &entry)

AutoPtr< ICache > m_Cache

void TestSplitBlob(CSeq_id_Handle id, const CSplitContentIndex &content)

bool GetBioseqHandle(CBioseq_Handle &bh, const CSeq_id_Handle &idh)

const SSplitterParams GetParams(void) const

CRef< CGBDataLoader > m_Loader

void ProcessGi(TIntId gi)

TProcessedIds m_ProcessedIds

size_t GetDescCount(void) const

void SetSetDescCount(size_t count)

void SetSeqDescCount(size_t count)

size_t GetSetDescCount(void) const

bool HaveSplitAssembly(void) const

TContentFlags GetSplitContent(void) const

size_t GetSeqDescCount(void) const

TContentIndex m_ContentIndex

void IndexChunkContent(int chunk_id, const CID2S_Chunk_Content &content)

bool HaveSplitBioseq(void) const

const TContentIndex & GetContentIndex(void) const

TContentFlags m_SplitContent

CSplitDataMaker(const SSplitterParams &params, CID2_Reply_Data::EData_type data_type)

AutoPtr< CNcbiOstrstream > m_MStream

CObjectOStream & OpenDataStream(void)

void operator<<(const C &obj)

void CloseDataStream(void)

AutoPtr< CObjectOStream > m_OStream

const CID2_Reply_Data & GetData(void) const

CConstRef< CSeq_entry > GetCompleteTSE(void) const

void SetSplitVersion(TSplitVersion version)

@ eKeepAll

Do not delete other versions of cache entries.

virtual size_t GetSize(const string &key, TBlobVersion version, const string &subkey)=0

Check if BLOB exists, return BLOB size.

virtual void Remove(const string &key, TBlobVersion version, const string &subkey)=0

Remove specific cache entry.

@ fTimeStampOnCreate

Cache element is created with a certain timestamp (default)

@ fTimeStampOnRead

Timestamp is updated every on every access (read or write)

@ fExpireLeastFrequentlyUsed

Expire objects older than a certain time frame Example: If object is not accessed within a week it is...

@ fTrackSubKey

Timestamp full key-subkey pair.

@ fPurgeOnStartup

Expired objects should be deleted on cache mount (Open)

@ fCheckExpirationAlways

Expiration timeout is checked on any access to cache element.

int TTimeStampFlags

Holds a bitwise OR of "ETimeStampFlags".

iterator_bool insert(const value_type &val)

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

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

main entry point for tests

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

#define GI_FROM(T, value)

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

element_type * get(void) const

Get pointer.

CNcbiRegistry & GetRWConfig(void)

Get the application's cached configuration parameters, accessible for read-write for an application's...

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ eNoOwnership

No ownership is assumed.

@ fBinary

Open as binary file; for eInputFile, eOutputFile, eIOFile.

@ eInputFile

Name of file (must exist and be readable)

@ eDouble

Convertible into a floating point number (double)

@ eIntId

Convertible to TIntId (int or Int8 depending on NCBI_INT8_GI)

@ eString

An arbitrary string.

@ eInteger

Convertible into an integer number (int or Int8)

virtual void SetVersionRetention(EKeepVersions policy)

Set version retention policy.

void SetWriteSync(EWriteSyncMode wsync)

Set write syncronization.

virtual void Purge(time_t access_timeout)

Delete all BLOBs older than specified.

virtual void SetTimeStampPolicy(TTimeStampFlags policy, unsigned int timeout, unsigned int max_timeout=0)

Set timestamp update policy.

void Open(const string &cache_path, const string &cache_name, ELockMode lm=eNoLock, Uint8 cache_ram_size=0, ETRansact use_trans=eUseTrans, unsigned int log_mem_size=0)

Open local cache instance (read-write access) If cache does not exists it is created.

void SetReadUpdateLimit(unsigned)

Set update attribute limit (0 by default)

#define ERR_FATAL(message)

Posting fatal error and abort.

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

@ eDiag_Info

Informational message.

#define NCBI_THROW(exception_class, err_code, message)

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

void Fatal(CExceptionArgs_Base &args)

bool CreatePath(TCreateFlags flags=fCreate_Default) const

Create the directory path recursively possibly more than one at a time.

static string MakePath(const string &dir=kEmptyStr, const string &base=kEmptyStr, const string &ext=kEmptyStr)

Assemble a path from basic components.

virtual bool Exists(void) const

Check if directory "dirname" exists.

static char GetPathSeparator(void)

Get path separator symbol specific for the current platform.

bool Create(TCreateFlags flags=fCreate_Default) const

Create the directory using "dirname" passed in the constructor.

#define MSerial_AsnText

I/O stream manipulators –.

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

string AsString(void) const

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

void ResetHistory(EActionIfLocked action=eKeepIfLocked)

Clean all unused TSEs from the scope's cache and release the memory.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CSeq_entry_Handle GetSeq_entryHandle(CDataLoader *loader, const TBlobId &blob_id, EMissing action=eMissing_Default)

Get Seq-entry handle by its blob-id, with possible loading.

string GetName(void) const

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

virtual TTSE_Lock GetBlobById(const TBlobId &blob_id)

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

bool RevokeDataLoader(CDataLoader &loader)

Revoke previously registered data loader.

virtual TBlobId GetBlobId(const CSeq_id_Handle &idh)

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

bool IsEmptySeq_set(void) const

Check if the bioseq set is empty.

const CSeq_id_Handle & GetSeq_id_Handle(void) const

Get handle of id used to obtain this bioseq handle.

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

TBlobId GetBlobId(void) const

TBlobVersion GetBlobVersion(void) const

const CSeqMap & GetSeqMap(void) const

Get sequence map.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

CConstRef< CSeq_entry > GetSeq_entryCore(void) const

Get const reference to the seq-entry.

vector< CSeqdesc::E_Choice > TDescChoices

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

void Reset(void)

Reset reference object.

virtual int GetInt(const string &section, const string &name, int default_value, TFlags flags=0, EErrAction err_action=eThrow) const

Get integer value of specified parameter name.

virtual string GetString(const string &section, const string &name, const string &default_value, TFlags flags=0) const

Get the parameter string value.

bool Set(const string &section, const string &name, const string &value, TFlags flags=0, const string &comment=kEmptyStr)

Set the configuration parameter value.

@ eErrPost

Log the error message and return default value.

#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.

CNcbiIstream & NcbiGetline(CNcbiIstream &is, string &str, char delim, string::size_type *count=NULL)

Read from "is" to "str" up to the delimiter symbol "delim" (or EOF)

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

NCBI_NS_STD::string::size_type SIZE_TYPE

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

string AsString(const CTimeFormat &format=kEmptyStr, TSeconds out_tz=eCurrentTimeZone) const

Transform time to string.

time_t GetTimeT(void) const

Get time in time_t format.

@ eCurrent

Use current time. See also CCurrentTime.

EData_type

index of negotiated types recommended types Seq-entry, ID2S-Split-Info, ID2S-Chunk

EData_compression

post serialization compression (plain, gzip, etc.) index of negotiated compressions

virtual void Reset(void)

Reset the whole object.

void SetData_compression(TData_compression value)

Assign a value to Data_compression data member.

TData & SetData(void)

Assign a value to Data data member.

void SetData_type(TData_type value)

Assign a value to Data_type data member.

void SetData_format(TData_format value)

Assign a value to Data_format data member.

@ eData_type_id2s_split_info

@ eData_compression_nlmzip

@ eData_format_asn_binary

list< CRef< CID2S_Chunk_Info > > TChunks

const TSeq_descr & GetSeq_descr(void) const

Get the variant data.

const TChunks & GetChunks(void) const

Get the Chunks member data.

E_Choice Which(void) const

Which variant is currently selected.

list< CRef< CID2S_Chunk_Content > > TContent

@ e_Seq_descr

place of Seq-descrs

@ e_Seq_data

place of sequence data

@ e_Seq_assembly

place of assembly history

@ e_Bioseq_place

place of Bioseqs

@ e_Seq_annot

locations and types of annotations

TGi & SetGi(void)

Select the variant.

const TSeq & GetSeq(void) const

Get the variant data.

const TDescr & GetDescr(void) const

Get the Descr member data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSetSeq_set(void) const

Check if a value has been assigned to Seq_set data member.

bool IsSetDescr(void) const

Check if a value has been assigned to Descr data member.

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

list< CRef< CSeq_entry > > TSeq_set

list< CRef< CSeqdesc > > Tdata

const TInst & GetInst(void) const

Get the Inst member data.

bool IsSetAssembly(void) const

how was this assembled? Check if a value has been assigned to Assembly data member.

const Tdata & Get(void) const

Get the member data.

const THist & GetHist(void) const

Get the Hist member data.

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

const TDescr & GetDescr(void) const

Get the Descr member data.

@ e_Pub

a reference to the publication

@ e_Comment

a more extensive comment

@ e_Molinfo

info on the molecule and techniques

@ e_Title

a title for this sequence

@ e_Source

source of materials, includes Org-ref

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

const string version

version string

const struct ncbi::grid::netcache::search::fields::KEY key

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

Defines: CTimeFormat - storage class for time format.

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

static CReadDispatcher & x_GetDispatcher(CDataLoader *loader_arg)

void CollectDescriptors(const CSeq_descr &descr, TDescSet &desc_set)

static const int kDefaultCacheBlobAge

set< CConstRef< CSeqdesc > > TDescSet

void Dump(CSplitCacheApp *app, const C &obj, ESerialDataFormat format, const string &key, const string &suffix=kEmptyStr)

static void x_InitBlob(CReaderRequestResult &result, const CBlob_id &blob_id, CDataLoader::TBlobVersion version)

static const int kDefaultCacheIdAge

int main(int argc, const char *argv[])

static string x_GetSubkey1(void)

void DumpData(CSplitCacheApp *app, const C &obj, CID2_Reply_Data::EData_type data_type, const string &key, const string &suffix=kEmptyStr)

static string x_GetSubkey0(void)

static string GetBlobSubkey(CLoadLockBlob &blob, int chunk_id=kMain_ChunkId)

BLOB cache subkeys:

static string GetBlobKey(const CBlob_id &blob_id)

Return BLOB cache key string based on Sat() and SatKey()

Selector used in CSeqMap methods returning iterators.

void SetChunkSize(size_t size)

bool m_DisableSplitDescriptions

bool m_DisableSplitAssembly

bool m_DisableSplitSequence

bool m_DisableSplitAnnotations

ECompression m_Compression

@ kDefaultSplitNonFeatureSeqTables

bool m_SplitNonFeatureSeqTables

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