Search Toolkit Book for CNAUtils
#include <gui/objutils/na_utils.hpp>
Collaboration diagram for CNAUtils:
Public Types | |
| enum | EEntrezDB { EEDB_Undef , EEDB_Nucleotide , EEDB_Protein , EEDB_All } |
| eutils databases that can be used More... | |
| enum | EMetaDataSource { EMetaDataSource_Undef , EMetaDataSource_Cache , EMetaDataSource_Mixed , EMetaDataSource_Eutils , EMetaDataSource_EmptyRequest , EMetaDataSource_EmptyAfterFilteringRequest } |
| source of obtained NA metadata were internal caches hit, partially hit or totally missed during some cached operations More... | |
| enum | EUidsSource { EUidsSource_Undef , EUidsSource_Cache , EUidsSource_Mixed , EUidsSource_Eutils , EUidsSource_EmptyRequest } |
| typedef string | TNAA |
| typedefs for NAA meta-data More... | |
| typedef list< TNAA > | TNAAs |
| typedef map< string, CRef< CAnnotMetaData > > | TNAMetaDataSet |
| typedef CTrackInfo::TTrackInfoList | TTrackInfoList |
| using | TEntrezIds = CSeqUtils::TEntrezIds |
| typedef set< TGi > | TGis |
| get all GIs for a given NA accession More... | |
Public Member Functions | |
| CNAUtils () | |
| Default ctor. More... | |
| CNAUtils (const objects::CSeq_id &id) | |
| Ctor with target sequence id. More... | |
| CNAUtils (const objects::CSeq_id &id, objects::CScope &scope) | |
| Ctor with target sequence id and a scope. More... | |
| void | GetAllNAAs (TNAAs &naas, const string &context="") const |
| Get a list of NAAs associated with the target sequence. More... | |
| void | GetNAMetaData (TNAMetaDataSet &md_set, const string &na, bool filtering=false, EMetaDataSource *pMDSource=NULL, EUidsSource *pUidsSource=NULL, bool isGetLinks=true) const |
| Get meta-data for a specific NA. More... | |
| void | GetNAMetaData (TNAMetaDataSet &md_set, const TNAAs &naas, bool filtering=false, EMetaDataSource *pMDSource=NULL, EUidsSource *pUidsSource=NULL, bool isGetLinks=true) const |
| Get meta-data for a list of NAAs. More... | |
| void | GetAllNAMetaData (TNAMetaDataSet &md_set, const string &context="", ICanceled *canceledCallback=0) const |
| Get meta-data for a given NAA associated with seq_id. More... | |
| void | GetNATrackInfo (TTrackInfoList &track_info, const string &naa) const |
| Do data track discovery for a given NA. More... | |
| void | GetNATrackInfo (TTrackInfoList &track_info, const string &naa, const TNAMetaDataSet &md_set) const |
| Do data track discovery for a given NA with meta-data. More... | |
| void | GetNATrackInfo (TTrackInfoList &track_info, const TNAAs &naas) const |
| Do data track discovery for a list of NAs. More... | |
| void | GetNATrackInfo (TTrackInfoList &track_info, const TNAAs &naas, const TNAMetaDataSet &md_set) const |
| Do data track discovery for a list of NAs with meta-data. More... | |
| void | SetMaxNAs (int size) |
Static Public Member Functions | |
| static void | GetAllGIs (const TNAA &naa, EEntrezDB eedb, TGis &gis, EUidsSource *pUidsSource=NULL) |
Private Types | |
| typedef map< TNAA, TEntrezId > | TNAAtoUidCache |
| caching of eutils-related data: x_GetNAId(): NAA string to its numeric uid More... | |
| typedef map< TEntrezId, CRef< CAnnotMetaData > > | TEntrezIdtoMetaDataCache |
| x_GetNAMetaData() NAA numeric uid to CAnnotMetaData More... | |
| typedef map< string, TGis > | TEntrezIdtoGiCache |
| x_GetAllGIs(): NA uid+dbfrom to GIs which are associated with this NA More... | |
Private Member Functions | |
| void | x_Init () |
| Initialize some internal states. More... | |
| void | x_GetNAIds (TEntrezIds &uids, const string &context="") const |
| Get all available NA uids w/wo a context. More... | |
| void | x_GetAllNAIds (TEntrezIds &uids) const |
| get all available NA uids for a given gi. More... | |
| void | x_FilterNAIds (TEntrezIds &uids, EUidsSource *pUidsSource=NULL) const |
| filter a given list of NA uids and keep only the ones that are related to a given gi (m_GI) More... | |
| bool | x_NAIdMatchesGI (TEntrezId uid, EUidsSource *pUidsSource=NULL) const |
| returns true if an uid is related to a given gi (m_GI) or GI is ZERO_GI More... | |
| void | x_GetAllNAIdsWithContext (TEntrezIds &uids, const string &context) const |
| get all available NA ids applied to a viewer context for a given gi. More... | |
| void | x_GetNAAs (TNAAs &naas, const TEntrezIds &uids) const |
| Retrieve NAAs for a list of NA uids. More... | |
| void | x_GetAllGIs (TEntrezId uid, TGis &gis, EUidsSource *pUidsSource=NULL) const |
| this uses m_SeqDB More... | |
| void | x_GetNAMetaData (TNAMetaDataSet &md_set, const TEntrezIds &uids, bool isGetLinks, EMetaDataSource *pSource=NULL) const |
| Retrieve NA meta data for a list of NA uids. More... | |
| void | x_SearchNAIds (TEntrezIds &uids, const TNAAs &naas, bool filtering, EUidsSource *pUidsSource=NULL) const |
| Search all NAAs for a given term. More... | |
| void | x_ParseNAMetaData (CAnnotMetaData &data, const char *xml_str) const |
| Parse the meta-data xml DocSum. More... | |
| void | x_GetNAEntrezLinks (CAnnotMetaData &data) const |
| Retrieve Entrez links for a given NA. More... | |
| DECLARE_CLASS_STATIC_FAST_MUTEX (sm_NAAtoUidCacheMutex) | |
| DECLARE_CLASS_STATIC_FAST_MUTEX (sm_UidtoMetaDataCacheMutex) | |
| DECLARE_CLASS_STATIC_FAST_MUTEX (sm_UidtoGiCacheMutex) | |
Static Private Member Functions | |
| static bool | x_GetNAId (TEntrezId &uid, const string &naa, EUidsSource *pUidsSource=NULL) |
| get an id for a given NAA string returns false if no id is found More... | |
| static void | x_GetAllGIs (TEntrezId uid, EEntrezDB eedb, TGis &gis, EUidsSource *pUidsSource=NULL, bool isIncremental=false) |
| get all GIs for a given uid this needs a given database where to search for GIs More... | |
Private Attributes | |
| CConstRef< objects::CSeq_id > | m_TargetSeq |
| The target sequence associating with the NAAs. More... | |
| CRef< objects::CScope > | m_Scope |
| Scope helping resolve sequences and retrieve annotations. More... | |
| objects::CBioseq_Handle | m_BioseqHandle |
| Derived values which make sense only if m_TargetSeq is set. More... | |
| objects::CSeq_id_Handle | m_SeqIdHandle |
| sequence handles More... | |
| TGi | m_Gi |
| GI of m_TargetSeq; it may be ZERO_GI for one of two reasons: either a target seq is not given at all or it does not have a GI. More... | |
| EEntrezDB | m_SeqDB {EEDB_Undef} |
| Entrez db name for m_TargetSeq: nucleotide/protein or Undef if no TargetSeq is given. More... | |
| int | m_MaxNAMeta |
| maximal number of NAAs for retrieving meta-data. More... | |
Static Private Attributes | |
| static TNAAtoUidCache | sm_NAAtoUidCache |
| static TEntrezIdtoMetaDataCache | sm_UidtoMetaDataCache |
| static TEntrezIdtoGiCache | sm_UidtoGiCache |
Detailed Description
Definition at line 115 of file na_utils.hpp.
The documentation for this class was generated from the following files:
- include/gui/objutils/na_utils.hpp
- src/gui/objutils/na_utils.cpp
