Sequence weight

Collaboration diagram for Sequence weight:

Typedefs
typedef int	TGetProteinWeight
typedef map< CConstRef< CSeq_loc >, double >	TWeights

Enumerations
enum	FGetProteinWeight { fGetProteinWeight_ForceInitialMetTrim = 1 << 0 }

Functions
double	GetProteinWeight (const CBioseq_Handle &handle, const CSeq_loc *location=0, TGetProteinWeight opts=0)
	Handles the standard 20 amino acids and Sec and Pyl; treats Asx as Asp, Glx as Glu, and Xle as Leu; ignores Xxx, dash (gap), and asterisk (stop); throws CObjmgrUtilException on anything else. More...
double	GetProteinWeight (const CSeq_feat &prot_feat, CScope &scope, const CSeq_loc *location=0, TGetProteinWeight opts=0)
double	GetProteinWeight (const string &ncbieaa_sequence)
void	GetProteinWeights (const CBioseq_Handle &handle, TWeights &weights)
	Automatically picks reasonable ranges: in decreasing priority order,. More...

Detailed Description

Typedef Documentation

TGetProteinWeight

typedef int TGetProteinWeight

Definition at line 58 of file weight.hpp.

TWeights

typedef map<CConstRef<CSeq_loc>, double> TWeights

Definition at line 81 of file weight.hpp.

Enumeration Type Documentation

FGetProteinWeight

enum FGetProteinWeight

Enumerator
fGetProteinWeight_ForceInitialMetTrim

Definition at line 53 of file weight.hpp.

Function Documentation

GetProteinWeight() [1/3]

double GetProteinWeight	(	const CBioseq_Handle &	handle,
		const CSeq_loc *	location = 0,
		TGetProteinWeight	opts = 0
	)

Handles the standard 20 amino acids and Sec and Pyl; treats Asx as Asp, Glx as Glu, and Xle as Leu; ignores Xxx, dash (gap), and asterisk (stop); throws CObjmgrUtilException on anything else.

NOTE: The molecular weight excludes a leading 'M' on proteins with a known valid start, provided that the location is omitted or the location begins at residue 0

Definition at line 212 of file weight.cpp.

References CSeq_data_Base::e_Ncbieaa, CMolInfo_Base::eCompleteness_complete, CMolInfo_Base::eCompleteness_no_ends, CMolInfo_Base::eCompleteness_no_left, CMolInfo_Base::eCompleteness_partial, CMolInfo_Base::eCompleteness_unknown, CSeqVector::end(), fGetProteinWeight_ForceInitialMetTrim, CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeqVector(), location, s_GetProteinWeight(), and CSeqVector::SetCoding().

Referenced by BOOST_AUTO_TEST_CASE(), CFeatureItem::x_AddQualsProt(), and CGff3Writer::xWriteProteinFeature().

GetProteinWeight() [2/3]

double GetProteinWeight	(	const CSeq_feat &	prot_feat,
		CScope &	scope,
		const CSeq_loc *	location = 0,
		TGetProteinWeight	opts = 0
	)

Definition at line 111 of file weight.cpp.

References CSeq_data_Base::e_Ncbieaa, CSeqFeatData_Base::e_Prot, CMolInfo_Base::eCompleteness_complete, CMolInfo_Base::eCompleteness_no_ends, CMolInfo_Base::eCompleteness_no_left, CMolInfo_Base::eCompleteness_partial, CMolInfo_Base::eCompleteness_unknown, CSeqVector::end(), CProt_ref_Base::eProcessed_mature, CProt_ref_Base::eProcessed_not_set, CProt_ref_Base::eProcessed_preprotein, CProt_ref_Base::eProcessed_signal_peptide, CProt_ref_Base::eProcessed_transit_peptide, eUnknown, fGetProteinWeight_ForceInitialMetTrim, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeqVector_CI::GetBufferSize(), CSeq_feat_Base::GetData(), CSeq_feat_Handle::GetData(), CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), CSeq_feat_Base::GetLocation(), CProt_ref_Base::GetProcessed(), CSeqFeatData_Base::GetProt(), CSeq_loc::GetTotalRange(), location, NCBI_THROW, prot, s_GetProteinWeight(), CSeqVector::SetCoding(), and CSeqFeatData_Base::Which().

Referenced by GetProteinWeights().

GetProteinWeight() [3/3]

double GetProteinWeight

(

const string &

ncbieaa_sequence

)

Definition at line 269 of file weight.cpp.

References s_GetProteinWeight().

GetProteinWeights()

void GetProteinWeights	(	const CBioseq_Handle &	handle,
		TWeights &	weights
	)

Automatically picks reasonable ranges: in decreasing priority order,.

• Annotated cleavage products (mature peptides)
• What's left after removing the first signal peptide found
• The entire sequence (skipping a leading methionine if present)

Definition at line 276 of file weight.cpp.

References map_checker< Container >::clear(), NStr::CompareNocase(), data, CSeq_data_Base::e_Ncbieaa, CSeqFeatData_Base::e_Prot, CSeqFeatData_Base::e_Region, CSeqFeatData_Base::e_Site, CBioseq_Handle::eCoding_Iupac, CSeq_inst_Base::eMol_aa, set< Key, Compare >::empty(), CConstRef< C, Locker >::Empty(), CProt_ref_Base::eProcessed_mature, CProt_ref_Base::eProcessed_signal_peptide, CSeqFeatData_Base::eSite_signal_peptide, CSeqFeatData::eSubtype_mat_peptide_aa, CSeqFeatData::eSubtype_sig_peptide_aa, CBioseq_Handle::GetBioseqMolType(), GetProteinWeight(), CBioseq_Handle::GetSeqId(), CBioseq_Handle::GetSeqVector(), CRange_Base::GetTo(), CSeq_loc::GetTotalRange(), SAnnotSelector::IncludeFeatSubtype(), SAnnotSelector::IncludeFeatType(), set< Key, Compare >::insert(), ITERATE, NCBI_THROW, CConstRef< C, Locker >::NotEmpty(), CSeqVector::SetCoding(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), SAnnotSelector::SetOverlapIntervals(), SAnnotSelector::SetResolveTSE(), CSeq_interval_Base::SetTo(), CSeqVector::size(), weight, and whole.