NCBI C++ ToolKit
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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_ReplyGetReply () const
 Get the reply that contains this item. More...
 
const stringGetProcessorId ()
 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

See also
EState

Definition at line 881 of file psg_client.hpp.

Member Enumeration Documentation

◆ 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

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

The documentation for this class was generated from the following files:
Modified on Sun Apr 14 05:28:55 2024 by modify_doxy.py rev. 669887