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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/psg__loader_8hpp_source.html below:

NCBI C++ ToolKit: include/objtools/data_loaders/genbank/psg_loader.hpp Source File

1 #ifndef OBJTOOLS_DATA_LOADERS_PSG___PSG_LOADER__HPP 2 #define OBJTOOLS_DATA_LOADERS_PSG___PSG_LOADER__HPP 41 #if defined(HAVE_PSG_LOADER) && !defined(HAVE_PSG_CLIENT) 42 # undef HAVE_PSG_LOADER 45 #if defined(HAVE_PSG_LOADER) 56  CPsgBlobId

(

const string

&

id

,

bool

is_dead);

57  CPsgBlobId

(

const string

&

id

,

const string

& id2_info);

65  virtual string ToString

(

void

)

const override

;

84  return

!m_TSEName.empty();

93  return

m_HasBioseqIsDead;

97  return

m_BioseqIsDead;

101

m_HasBioseqIsDead =

false

;

102

m_BioseqIsDead =

false

;

106

m_HasBioseqIsDead =

true

;

107

m_BioseqIsDead = is_dead;

110  bool

GetSatSatkey(

int

& sat,

int

& satkey)

const

;

118  bool

m_HasBioseqIsDead =

false

;

119  bool

m_BioseqIsDead =

false

;

136  TBlobId

GetBlobIdFromSatSatKey(

int

sat,

138  int

sub_sat)

const override

;

140  TBlobId

GetBlobIdFromString(

const string

&

str

)

const override

;

142  bool

CanGetBlobById(

void

)

const override

;

154  void

GetChunk(

TChunk

chunk)

override

;

155  void

GetChunks(

const TChunkSet

& chunks)

override

;

174  const string

& named_acc)

override

;

180

time_t

= 0)

override

{}

183  void

GetBulkIds(

const

TIds& ids, TLoaded& loaded, TBulkIds& ret)

override

;

184  void

GetAccVers(

const

TIds& ids, TLoaded& loaded, TIds& ret)

override

;

185  void

GetGis(

const

TIds& ids, TLoaded& loaded, TGis& ret)

override

;

186  void

GetLabels(

const

TIds& ids, TLoaded& loaded, TLabels& ret)

override

;

187  void

GetTaxIds(

const

TIds& ids, TLoaded& loaded, TTaxIds& ret)

override

;

188  void

GetSequenceStates(

const

TIds& ids, TLoaded& loaded, TSequenceStates& ret)

override

;

189  void

GetSequenceHashes(

const

TIds& ids, TLoaded& loaded, TSequenceHashes& ret, THashKnown& known)

override

;

190  void

GetSequenceLengths(

const

TIds& ids, TLoaded& loaded, TSequenceLengths& ret)

override

;

191  void

GetSequenceTypes(

const

TIds& ids, TLoaded& loaded, TSequenceTypes& ret)

override

;

CReaderCacheManager::TCacheType TCacheType

void PurgeCache(TCacheType, time_t=0) override

void CloseCache(void) override

CRef< CPSGDataLoader_Impl > m_Impl

bool HaveCache(TCacheType) override

void SetBioseqIsDead(bool is_dead=true)

void SetId2Info(const string &id2_info)

const string & GetId2Info() const

bool HasBioseqIsDead() const

const string & GetTSEName() const

const string & ToPsgId() const

bool BioseqIsDead() const

void SetTSEName(const string &name)

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

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

unsigned int TSeqPos

Type for sequence locations and lengths.

SStrictId_Tax::TId TTaxId

Taxon id type.

ESNPScaleLimit

SNP annotation scale limits.

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

vector< CTSE_Lock > TCDD_Locks

virtual bool operator<(const CBlobId &id) const =0

vector< CSeq_id_Handle > TIds

virtual string ToString(void) const =0

Get string representation of blob id.

EChoice

main blob is blob with sequence all other blobs are external and contain external annotations

vector< vector< CSeq_id_Handle > > TSeqIdSets

virtual bool operator==(const CBlobId &id) const

EIsDefault

Flag defining if the data loader is included in the "default" group.

vector< bool > TLoaded

Bulk loading interface for a small pieces of information per id.

vector< TChunk > TChunkSet

@ kPriority_NotSet

Deprecated: use kPriority_Default instead.

#define NCBI_XLOADER_GENBANK_EXPORT

const GenericPointer< typename T::ValueType > T2 value

static bool GetIds(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

CRef< objects::CObjectManager > om

Better replacement of GetAccVer(), this method should be defined in data loaders, GetAccVer() is left...

Better replacement of GetGi(), this method should be defined in data loaders, GetGi() is left for com...

Better replacement of GetSequenceHash(), this method should be defined in data loaders,...

Better replacement of GetSequenceType(), this method should be defined in data loaders,...

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