Sequence Class Reference

Search Toolkit Book for Sequence

#include <algo/structure/struct_util/su_sequence_set.hpp>

Inheritance diagram for Sequence:

Collaboration diagram for Sequence:

Public Types
typedef list< CRef< objects::CSeq_id > >	SeqIdList
typedef std::map< const MoleculeIdentifier *, std::vector< bool > >	MoleculeHighlightMap

Public Member Functions
	Sequence (ncbi::objects::CBioseq &bioseq)
	~Sequence (void)
unsigned int	Length (void) const
const ncbi::objects::CSeq_id &	GetPreferredIdentifier (void) const
const ncbi::objects::CBioseq::TId &	GetAllIdentifiers (void) const
bool	MatchesSeqId (const ncbi::objects::CSeq_id &seqID) const
std::string	IdentifierString (void) const
	Sequence (const objects::CBioseq &bioseq)
unsigned int	Length (void) const
bool	Matches (const objects::CSeq_id &seqID) const
bool	Matches (const SeqIdList &others) const
string	GetTitle (void) const
string	GetLabel (void) const
int	Status (void) const
	Sequence (SequenceSet *parent, ncbi::objects::CBioseq &bioseq)
std::string	GetDescription (void) const
unsigned int	Length (void) const
int	GetOrSetMMDBLink (void) const
void	AddMMDBAnnotTag (int mmdbID) const
ncbi::objects::CSeq_id *	CreateSeqId (void) const
void	FillOutSeqId (ncbi::objects::CSeq_id *sid) const
void	LaunchWebBrowserWithInfo (void) const
bool	HighlightPattern (const std::string &pattern, const MoleculeHighlightMap &restrictTo) const
Public Member Functions inherited from StructureBase
	StructureBase (StructureBase *parent)
virtual	~StructureBase (void)
virtual bool	DrawAll (const AtomSet *atomSet=NULL) const
virtual bool	Draw (const AtomSet *atomSet=NULL) const
template<class T >
bool	GetParentOfType (const T **ptr, bool warnIfNotFound=true) const

Public Attributes
ncbi::CRef< ncbi::objects::CBioseq >	m_bioseqASN
std::string	m_sequenceString
std::string	m_description
bool	m_isProtein
CConstRef< objects::CBioseq >	bioseqASN
const SeqIdList	seqIDs
string	sequenceString
string	description
int	mmdbLink
ncbi::CRef< ncbi::objects::CBioseq >	bioseqASN
const MoleculeIdentifier *	identifier
const Molecule *	molecule
bool	isProtein
std::string	sequenceString
std::string	title
std::string	taxonomy
Public Attributes inherited from StructureBase
StructureSet *	parentSet

Static Public Attributes
static const int	NOT_SET = -1

Private Attributes
int	status

Detailed Description

Definition at line 51 of file su_sequence_set.hpp.

Member Typedef Documentation

MoleculeHighlightMap

typedef std::map< const MoleculeIdentifier *, std::vector < bool > > Sequence::MoleculeHighlightMap

Definition at line 103 of file sequence_set.hpp.

SeqIdList

typedef list< CRef < objects::CSeq_id > > Sequence::SeqIdList

Definition at line 91 of file cav_seqset.hpp.

Constructor & Destructor Documentation

Sequence() [1/3]

Sequence::Sequence

(

ncbi::objects::CBioseq &

bioseq

)

Definition at line 183 of file su_sequence_set.cpp.

References CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_rna, CSeq_inst_Base::eRepr_raw, i, m_description, m_isProtein, m_sequenceString, string, StringFrom2na(), StringFrom4na(), StringFromStdaa(), THROW_MESSAGE, and toupper().

~Sequence()

Sequence::~Sequence

(

void

)

Definition at line 269 of file su_sequence_set.cpp.

Sequence() [2/3]

Sequence::Sequence

(

const objects::CBioseq &

bioseq

)

Sequence() [3/3]

Sequence::Sequence	(	SequenceSet *	parent,
		ncbi::objects::CBioseq &	bioseq
	)

Definition at line 202 of file sequence_set.cpp.

References a, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_rna, NStr::EndsWith(), NStr::eNocase, CSeq_inst_Base::eRepr_raw, ERRORMSG, MoleculeIdentifier::GetIdentifier(), i, identifier, isProtein, sequenceString, string, StringFrom2na(), StringFrom4na(), StringFromStdaa(), taxonomy, title, toupper(), and MoleculeIdentifier::VALUE_NOT_SET.

Member Function Documentation

AddMMDBAnnotTag()

void Sequence::AddMMDBAnnotTag

(

int

mmdbID

)

const

Definition at line 342 of file sequence_set.cpp.

References a, bioseqASN, ERRORMSG, i, identifier, MoleculeIdentifier::mmdbID, CSeq_annot_Base::SetData(), CDbtag_Base::SetDb(), CSeq_id_Base::SetGeneral(), CDbtag_Base::SetTag(), MoleculeIdentifier::ToString(), TRACEMSG, and MoleculeIdentifier::VALUE_NOT_SET.

CreateSeqId()

CSeq_id * Sequence::CreateSeqId

(

void

)

const

Definition at line 375 of file sequence_set.cpp.

References FillOutSeqId().

Referenced by CreatePairwiseSeqAlignFromMultipleRow().

FillOutSeqId()

void Sequence::FillOutSeqId

(

ncbi::objects::CSeq_id *

sid

)

const

Definition at line 382 of file sequence_set.cpp.

References bioseqASN, ERRORMSG, CConstRef< C, Locker >::GetObject(), i, identifier, and MoleculeIdentifier::ToString().

Referenced by CreateSeqId(), CDDAnnotateDialog::GetCurrentHighlightedIntervals(), IBISAnnotateDialog::GetIntervalsForSet(), and IBISInteraction::Initialize().

GetAllIdentifiers()

const ncbi::objects::CBioseq::TId& Sequence::GetAllIdentifiers ( void  ) const

inline

Definition at line 65 of file su_sequence_set.hpp.

GetDescription()

string Sequence::GetDescription

(

void

)

const

Definition at line 320 of file sequence_set.cpp.

References StructureBase::GetParentOfType(), StructureObject::graph, molecule, ChemicalGraph::name, taxonomy, and title.

Referenced by SequenceDisplay::MouseOver().

GetLabel()

string Sequence::GetLabel

(

void

)

const

Definition at line 313 of file cav_seqset.cpp.

References eContent, kEmptyStr, label, and seqIDs.

GetOrSetMMDBLink()

int Sequence::GetOrSetMMDBLink

(

void

)

const

Definition at line 421 of file sequence_set.cpp.

References ERRORMSG, StructureBase::GetParentOfType(), identifier, MoleculeIdentifier::mmdbID, StructureObject::mmdbID, molecule, and MoleculeIdentifier::VALUE_NOT_SET.

Referenced by AlignmentManager::RealignAllDependentStructures().

GetPreferredIdentifier()

const CSeq_id & Sequence::GetPreferredIdentifier

(

void

)

const

Definition at line 278 of file su_sequence_set.cpp.

References i, m_bioseqASN, and RETURN_FIRST_SEQID_THAT_.

Referenced by CreatePairwiseSeqAlignFromMultipleRow(), AlignmentUtility::IsRowPDB(), and SequenceIdToString().

GetTitle()

string Sequence::GetTitle

(

void

)

const

Definition at line 290 of file cav_seqset.cpp.

References kEmptyStr, NStr::NumericToString(), seqIDs, string, and title.

Referenced by AlignmentSet::AlignmentSet().

HighlightPattern()

bool Sequence::HighlightPattern	(	const std::string &	pattern,
		const MoleculeHighlightMap &	restrictTo
	)		const

Definition at line 456 of file sequence_set.cpp.

References Messenger::AddHighlights(), ERRORMSG, CRegexp::fCompile_ungreedy, CRegexp::fMatch_default, GlobalMessenger(), i, identifier, Length(), Prosite2Regex(), r(), sequenceString, and TRACEMSG.

Referenced by ViewerWindowBase::OnFindPattern().

IdentifierString()

string Sequence::IdentifierString

(

void

)

const

Definition at line 300 of file su_sequence_set.cpp.

References CSeq_id::eFormat_FastA, CSeq_id::GetStringDescr(), and m_bioseqASN.

Referenced by AlignmentSet::AlignmentSet(), AlignmentUtility::DoLeaveNOut(), and AlignmentUtility::DoLeaveOneOut().

LaunchWebBrowserWithInfo()

void Sequence::LaunchWebBrowserWithInfo

(

void

)

const

Definition at line 436 of file sequence_set.cpp.

References MoleculeIdentifier::GetLabel(), MoleculeIdentifier::gi, MoleculeIdentifier::GI_NOT_SET, identifier, isProtein, label, LaunchWebPage(), MoleculeIdentifier::pdbChain, and MoleculeIdentifier::pdbID.

Referenced by SequenceDisplay::MouseDown().

Length() [1/3]

unsigned int Sequence::Length ( void  ) const

inline

Definition at line 61 of file su_sequence_set.hpp.

Referenced by Messenger::AddHighlights(), CalculateContactScore(), Threader::CalculateScores(), BLASTer::CalculateSelfHitScores(), Threader::CreateCorDef(), Threader::CreateFldMtf(), AlignmentManager::CreateMultipleFromPairwiseWithIBM(), BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), Threader::CreateQrySeq(), Threader::CreateSeqMtf(), DisplayRowFromSequence::DisplayRowFromSequence(), CommandProcessor::DoCommand_Highlight(), dpScoreFunction(), DumpText(), FillInAlignmentData(), GetAlignmentByBestNeighbor(), CDDAnnotateDialog::GetCurrentHighlightedIntervals(), MoleculeIdentifier::GetIdentifier(), PSSMWrapper::GetPSSMScore(), BlockMultipleAlignment::HighlightAlignedColumnsOfMasterRange(), Messenger::HighlightAndShowSequence(), HighlightPattern(), MapDependentToMaster(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), StructureSet::MatchSequenceToMoleculeInObject(), SequenceDisplay::MouseOver(), IBISAnnotateDialog::PopulateInteractionData(), SequenceDisplay::ProximitySort(), Messenger::RemoveHighlights(), ScoreByPSSM(), BlockMultipleAlignment::ShowGeometryViolations(), SU_PSSMInput::SU_PSSMInput(), and PSSMWrapper::UnpackMatrix().

Length() [2/3]

unsigned int Sequence::Length ( void  ) const

inline

Definition at line 98 of file cav_seqset.hpp.

References sequenceString.

Length() [3/3]

unsigned int Sequence::Length ( void  ) const

inline

Definition at line 88 of file sequence_set.hpp.

References sequenceString.

Matches() [1/2]

bool Sequence::Matches

(

const objects::CSeq_id &

seqID

)

const

Referenced by AlignmentSet::AlignmentSet(), and Matches().

Matches() [2/2]

bool Sequence::Matches

(

const SeqIdList &

others

)

const

Definition at line 350 of file cav_seqset.cpp.

References Matches().

MatchesSeqId()

bool Sequence::MatchesSeqId

(

const ncbi::objects::CSeq_id &

seqID

)

const

Definition at line 290 of file su_sequence_set.cpp.

References i, m_bioseqASN, and CSeq_id::Match().

Referenced by AlignmentSet::AlignmentSet(), and MasterSlaveAlignment::MasterSlaveAlignment().

Status()

int Sequence::Status ( void  ) const

inline

Definition at line 104 of file cav_seqset.hpp.

References status.

Referenced by SequenceSet::UnpackSeqEntry(), and SequenceSet::UnpackSeqSet().

Member Data Documentation

bioseqASN [1/2]

CConstRef< objects::CBioseq > Sequence::bioseqASN

Definition at line 90 of file cav_seqset.hpp.

Referenced by AddMMDBAnnotTag(), FillOutSeqId(), TaxonomyTree::GetTaxIDForSequence(), StructureSet::MatchSequenceToMoleculeInObject(), and PSSMWrapper::PSSMWrapper().

bioseqASN [2/2]

ncbi::CRef< ncbi::objects::CBioseq > Sequence::bioseqASN

Definition at line 77 of file sequence_set.hpp.

description

string Sequence::description

Definition at line 93 of file cav_seqset.hpp.

identifier

const MoleculeIdentifier* Sequence::identifier

Definition at line 79 of file sequence_set.hpp.

Referenced by Messenger::AddHighlights(), AddMMDBAnnotTag(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), DoesPatternMatchHighlightedResidues(), dpScoreFunction(), DumpFASTA(), DumpText(), FillOutSeqId(), StructureSet::FindOrCreateSequence(), GetAlignmentByBestNeighbor(), Threader::GetGeometryViolations(), GetOrSetMMDBLink(), SequenceDisplay::GetRowTitle(), TaxonomyTree::GetTaxIDForSequence(), UpdateViewer::GetVASTAlignments(), StructureSet::HasStructuredMaster(), Messenger::HighlightAndShowSequence(), CDDAnnotateDialog::HighlightInterval(), IBISAnnotateDialog::HighlightInterval(), HighlightPattern(), Messenger::IsHighlighted(), Messenger::KeepHighlightsOnlyOnSequence(), LaunchWebBrowserWithInfo(), StructureSet::LoadAlignmentsAndStructures(), ViewerWindowBase::MakeSequenceVisible(), MasterDependentAlignment::MasterDependentAlignment(), StructureSet::MatchSequenceToMoleculeInObject(), AlignmentManager::MergeUpdates(), SequenceViewerWindow::OnRealign(), SequenceViewerWindow::OnShowHideRows(), IBISAnnotateDialog::PopulateInteractionData(), AlignmentManager::PurgeSequence(), AlignmentManager::RealignAllDependentStructures(), StructureObject::RealignStructure(), Messenger::RemoveHighlights(), Sequence(), Messenger::ToggleHighlights(), UnpackSeqEntry(), and UnpackSeqSet().

isProtein

bool Sequence::isProtein

Definition at line 83 of file sequence_set.hpp.

Referenced by UpdateViewer::FetchSequencesViaHTTP(), BlockMultipleAlignment::GetCharacterTraitsAt(), SequenceDisplay::GetProteinSequences(), LaunchWebBrowserWithInfo(), and Sequence().

m_bioseqASN

ncbi::CRef< ncbi::objects::CBioseq > Sequence::m_bioseqASN

Definition at line 57 of file su_sequence_set.hpp.

Referenced by GetPreferredIdentifier(), IdentifierString(), and MatchesSeqId().

m_description

std::string Sequence::m_description

Definition at line 59 of file su_sequence_set.hpp.

Referenced by Sequence().

m_isProtein

bool Sequence::m_isProtein

Definition at line 60 of file su_sequence_set.hpp.

Referenced by Sequence().

m_sequenceString

std::string Sequence::m_sequenceString

Definition at line 59 of file su_sequence_set.hpp.

Referenced by AlignmentUtility::DoLeaveNOut(), AlignmentUtility::DoLeaveOneOut(), FillInAlignmentData(), BlockMultipleAlignment::GetCharacterAt(), UngappedAlignedBlock::GetCharacterAt(), ScoreByPSSM(), AlignmentUtility::ScoreRowByPSSM(), Sequence(), and SU_PSSMInput::SU_PSSMInput().

mmdbLink

int Sequence::mmdbLink

Definition at line 96 of file cav_seqset.hpp.

molecule

const Molecule* Sequence::molecule

Definition at line 82 of file sequence_set.hpp.

Referenced by Threader::CalculateScores(), StructureSet::CenterViewOnAlignedResidues(), Threader::CreateFldMtf(), BlockMultipleAlignment::GetCharacterTraitsAt(), DisplayRowFromSequence::GetCharacterTraitsAt(), GetDescription(), SequenceDisplay::GetDisplayCoordinates(), Threader::GetGeometryViolations(), GetOrSetMMDBLink(), BlockMultipleAlignment::GetRowForSequence(), SequenceDisplay::GetRowTitle(), HighlightResidues(), UpdateViewer::ImportStructure(), StructureSet::MatchSequenceToMoleculeInObject(), SequenceDisplay::MouseDown(), SequenceDisplay::MouseOver(), Threader::Realign(), AlignmentManager::RealignAllDependentStructures(), StructureObject::RealignStructure(), and SequenceDisplay::RedrawAlignedMolecules().

NOT_SET

const int Sequence::NOT_SET = -1

static

Definition at line 95 of file cav_seqset.hpp.

seqIDs

const SeqIdList Sequence::seqIDs

Definition at line 92 of file cav_seqset.hpp.

Referenced by GetLabel(), and GetTitle().

sequenceString [1/2]

string Sequence::sequenceString

Definition at line 93 of file cav_seqset.hpp.

Referenced by AlignmentDisplay::AlignmentDisplay(), Threader::CalculateScores(), Threader::CreateQrySeq(), Threader::CreateSeqMtf(), DoesPatternMatchHighlightedResidues(), dpScoreFunction(), BlockMultipleAlignment::GetCharacterTraitsAt(), DisplayRowFromSequence::GetCharacterTraitsAt(), PSSMWrapper::GetPSSMScore(), HighlightPattern(), Length(), AlignmentManager::MergeUpdates(), CDDAnnotateDialog::NewOrEditMotif(), SequenceDisplay::ProximitySort(), Sequence(), UpdateViewer::SortByPSSM(), and VerifyAlignmentData().

sequenceString [2/2]

std::string Sequence::sequenceString

Definition at line 85 of file sequence_set.hpp.

status

int Sequence::status

private

Definition at line 85 of file cav_seqset.hpp.

Referenced by Status().

taxonomy

std::string Sequence::taxonomy

Definition at line 85 of file sequence_set.hpp.

Referenced by GetDescription(), and Sequence().

title

std::string Sequence::title

Definition at line 85 of file sequence_set.hpp.

Referenced by GetDescription(), GetTitle(), and Sequence().

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

• include/algo/structure/struct_util/su_sequence_set.hpp
• include/objtools/cddalignview/cav_seqset.hpp
• src/app/cn3d/sequence_set.hpp
• src/algo/structure/struct_util/su_sequence_set.cpp
• src/app/cn3d/sequence_set.cpp
• src/objtools/cddalignview/cav_seqset.cpp