CPSG_BioseqInfo Class Reference

Search Toolkit Book for CPSG_BioseqInfo

Bio-sequence metainfo – result of the bio-id resolution. More...

#include <objtools/pubseq_gateway/client/psg_client.hpp>

Inheritance diagram for CPSG_BioseqInfo:

Collaboration diagram for CPSG_BioseqInfo:

Public Types
enum	EState {   eDead = 0 , eSought = 1 , eReserved = 5 , eMerged = 7 ,   eLive = 10 }
	State of the bio-sequence's seq-id. More...
typedef int	TState
Public Types inherited from CPSG_ReplyItem
enum	EType {   eBlobData , eBlobInfo , eSkippedBlob , eBioseqInfo ,   eNamedAnnotInfo , ePublicComment , eProcessor , eIpgInfo ,   eNamedAnnotStatus , eEndOfReply }

Public Member Functions
CPSG_BioId	GetCanonicalId () const
	Get canonical bio-id for the bioseq (usually "accession.version") More...
CPSG_BioIds	GetOtherIds () const
	Get non-canonical bio-ids (aliases) for the bioseq. More...
objects::CSeq_inst::TMol	GetMoleculeType () const
	The bioseq's molecule type (DNA, RNA, protein, etc) More...
Uint8	GetLength () const
	Length of bio-sequence. More...
TState	GetChainState () const
	State of the bio-sequence's seq-id chain, i.e. More...
TState	GetState () const
	State of this exact bio-sequence's seq-id. More...
CPSG_BlobId	GetBlobId () const
	Get coordinates of the TSE blob that contains the bioseq itself. More...
TTaxId	GetTaxId () const
	Get the bioseq's taxonomy ID. More...
int	GetHash () const
	Get the bioseq's (pre-calculated) hash. More...
CTime	GetDateChanged () const
	Date when the bioseq was changed last time. More...
TGi	GetGi () const
	Get GI. More...
CPSG_Request_Resolve::TIncludeInfo	IncludedInfo () const
	What data is immediately available now. More...
Public Member Functions inherited from CPSG_ReplyItem
EType	GetType () const
EPSG_Status	GetStatus (CDeadline deadline) const
	Get the final result of this blob's retrieval. More...
SPSG_Message	GetNextMessage (EDiagSev min_severity=eDiag_Error) const
	Unstructured text containing auxiliary info about the result – such as messages and errors that came from the PSG server or occured while trying to send request or to read and to process the reply. More...
shared_ptr< CPSG_Reply >	GetReply () const
	Get the reply that contains this item. More...
const string &	GetProcessorId ()
	Get processor ID. More...
virtual	~CPSG_ReplyItem ()

Private Member Functions
	CPSG_BioseqInfo ()

Private Attributes
CJsonNode	m_Data

Friends
class	CPSG_Reply

Additional Inherited Members
Protected Member Functions inherited from CPSG_ReplyItem
	CPSG_ReplyItem (EType type)

Detailed Description

Bio-sequence metainfo – result of the bio-id resolution.

It can be used to identify which data blobs (related to the requested bio-id retrieval) server is sending right away. It also contains resolution information as well as the information about which other biodata-related blobs are also available on the server and how they can be explicitly requested for later retrieval, if needed.

Note

Most of the data comes from table "BIOSEQ_INFO" and from the named annotation tables.

Definition at line 858 of file psg_client.hpp.

Member Typedef Documentation

TState

typedef int CPSG_BioseqInfo::TState

See also

EState

Definition at line 881 of file psg_client.hpp.

Member Enumeration Documentation

EState

enum CPSG_BioseqInfo::EState

State of the bio-sequence's seq-id.

Enumerator
eDead
eSought
eReserved
eMerged
eLive

Definition at line 874 of file psg_client.hpp.

Constructor & Destructor Documentation

CPSG_BioseqInfo()

CPSG_BioseqInfo::CPSG_BioseqInfo ( )

private

Definition at line 1164 of file psg_client.cpp.

Member Function Documentation

GetBlobId()

CPSG_BlobId CPSG_BioseqInfo::GetBlobId

(

void

)

const

Get coordinates of the TSE blob that contains the bioseq itself.

Definition at line 1226 of file psg_client.cpp.

References m_Data, and s_GetBlobId().

Referenced by SPsgBioseqInfo::Update().

GetCanonicalId()

CPSG_BioId CPSG_BioseqInfo::GetCanonicalId

(

)

const

Get canonical bio-id for the bioseq (usually "accession.version")

Definition at line 1169 of file psg_client.cpp.

References m_Data, and s_GetBioId().

Referenced by SPsgBioseqInfo::Update().

GetChainState()

CPSG_BioseqInfo::TState CPSG_BioseqInfo::GetChainState

(

)

const

State of the bio-sequence's seq-id chain, i.e.

the state of the very latest seq-id in this bio-sequence's seq-id chain

Definition at line 1216 of file psg_client.cpp.

References CJsonNode::GetInteger(), and m_Data.

Referenced by SPsgBioseqInfo::Update().

GetDateChanged()

CTime CPSG_BioseqInfo::GetDateChanged

(

)

const

Date when the bioseq was changed last time.

Definition at line 1241 of file psg_client.cpp.

References CJsonNode::GetInteger(), m_Data, and s_GetTime().

GetGi()

TGi CPSG_BioseqInfo::GetGi

(

void

)

const

Get GI.

Definition at line 1246 of file psg_client.cpp.

References CJsonNode::GetInteger(), and m_Data.

Referenced by SPsgBioseqInfo::Update().

GetHash()

int CPSG_BioseqInfo::GetHash

(

void

)

const

Get the bioseq's (pre-calculated) hash.

Definition at line 1236 of file psg_client.cpp.

References CJsonNode::GetInteger(), and m_Data.

Referenced by SPsgBioseqInfo::Update().

GetLength()

Uint8 CPSG_BioseqInfo::GetLength

(

void

)

const

Length of bio-sequence.

Definition at line 1211 of file psg_client.cpp.

References CJsonNode::GetInteger(), and m_Data.

Referenced by SPsgBioseqInfo::Update().

GetMoleculeType()

objects::CSeq_inst::TMol CPSG_BioseqInfo::GetMoleculeType

(

)

const

The bioseq's molecule type (DNA, RNA, protein, etc)

Definition at line 1206 of file psg_client.cpp.

References CJsonNode::GetInteger(), and m_Data.

Referenced by SPsgBioseqInfo::Update().

GetOtherIds()

vector< CPSG_BioId > CPSG_BioseqInfo::GetOtherIds

(

)

const

Get non-canonical bio-ids (aliases) for the bioseq.

Definition at line 1174 of file psg_client.cpp.

References _ASSERT, CJsonNode::GetByKey(), CPSG_ReplyItem::GetReply(), m_Data, NCBI_THROW_FMT, and s_GetRequestTypeName().

Referenced by SPsgBioseqInfo::Update().

GetState()

CPSG_BioseqInfo::TState CPSG_BioseqInfo::GetState

(

void

)

const

State of this exact bio-sequence's seq-id.

I.e., for the latest seq-id in a chain it is equal to GetState(), and for all other seq-ids in a chain it's zero (eDead).

Definition at line 1221 of file psg_client.cpp.

References CJsonNode::GetInteger(), and m_Data.

Referenced by SPsgBioseqInfo::Update().

GetTaxId()

TTaxId CPSG_BioseqInfo::GetTaxId

(

void

)

const

Get the bioseq's taxonomy ID.

Definition at line 1231 of file psg_client.cpp.

References CJsonNode::GetInteger(), m_Data, and TAX_ID_FROM.

Referenced by SPsgBioseqInfo::Update().

IncludedInfo()

CPSG_Request_Resolve::TIncludeInfo CPSG_BioseqInfo::IncludedInfo

(

)

const

What data is immediately available now.

Other data will require a separate hit to the server.

See also

CPSG_Request_Resolve::IncludeInfo()

Definition at line 1251 of file psg_client.cpp.

References CPSG_Request_Resolve::fBlobId, CPSG_Request_Resolve::fCanonicalId, CPSG_Request_Resolve::fChainState, CPSG_Request_Resolve::fDateChanged, CPSG_Request_Resolve::fGi, CPSG_Request_Resolve::fHash, CPSG_Request_Resolve::fLength, CPSG_Request_Resolve::fMoleculeType, CPSG_Request_Resolve::fName, CPSG_Request_Resolve::fOtherIds, CPSG_Request_Resolve::fState, CPSG_Request_Resolve::fTaxId, CJsonNode::GetByKey(), CJsonNode::GetSize(), CJsonNode::HasKey(), and m_Data.

Referenced by SPsgBioseqInfo::Update().

Friends And Related Function Documentation

CPSG_Reply

friend class CPSG_Reply

friend

Definition at line 917 of file psg_client.hpp.

Member Data Documentation

m_Data

CJsonNode CPSG_BioseqInfo::m_Data

private

Definition at line 915 of file psg_client.hpp.

Referenced by GetBlobId(), GetCanonicalId(), GetChainState(), GetDateChanged(), GetGi(), GetHash(), GetLength(), GetMoleculeType(), GetOtherIds(), GetState(), GetTaxId(), and IncludedInfo().

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The documentation for this class was generated from the following files:

• include/objtools/pubseq_gateway/client/psg_client.hpp
• src/objtools/pubseq_gateway/client/psg_client.cpp