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static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)
static void ReleaseOM(void)
Release the class's reference to the object manager; for use by certain shut-down procedures.
static CRef< CObjectManager > sm_OM
Reference to our object manager.
static CRef< CObjectManager > x_GetOM(void)
Get our object manager, initializing if necessary.
static CRef< CScope > NewScope(bool with_defaults=true)
Return a new scope, possibly (by default) with default loaders, which will include the Genbank loader...
static CSeqVector GetSeqVector(const CSeq_id &id, ENa_strand strand=eNa_strand_plus)
Return a sequence vector for some kind of id or location.
static CBioseq_Handle GetBioseqHandle(const CSeq_id &id)
Return a biosequence handle for some kind of id.
static string GetIupac(const CSeq_id &id, ENa_strand strand=eNa_strand_plus)
Return the IUPAC-format sequence for some kind of id or location.
static CRef< CObjectManager > GetInstance(void)
Return the existing object manager or create one.
CBioseq_Handle GetBioseqHandle(const CSeq_id &id)
Get bioseq handle by seq-id.
void AddDefaults(TPriority pri=kPriority_Default)
Add default data loaders from object manager.
CDataLoader * FindDataLoader(const string &loader_name) const
Try to find a registered data loader by name.
CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const
Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.
@ eCoding_Ncbi
Set coding to binary coding (Ncbi4na or Ncbistdaa)
void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const
Fill the buffer string with the sequence data for the interval [start, stop).
void SetIupacCoding(void)
Set coding to either Iupacaa or Iupacna depending on molecule type.
void Reset(void)
Reset reference object.
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
ENa_strand
strand of nucleic acid
TGi & SetGi(void)
Select the variant.
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