#include <sequence_handle.hh>

Inherits ConstGenericPropContainer< ConstSequenceHandle >.

Public Types
typedef String::const_iterator	iterator

Public Member Functions
	ConstSequenceHandle ()

int	GetResidueIndex (int pos) const

int	GetPos (int residue_index) const

int	GetFirstNonGap () const

int	GetLastNonGap () const

const String &	GetName () const

const String &	GetString () const

String	GetGaplessString () const

int	GetOffset () const

int	GetLength () const

int	GetIndex (const String &substr) const

char	GetOneLetterCode (int position) const

mol::ResidueView	GetResidue (int position) const

mol::EntityView	GetAttachedView () const

SequenceHandle	Copy () const

bool	HasAttachedView () const

const String &	GetRole () const

bool	operator== (const ConstSequenceHandle &rhs) const

bool	operator!= (const ConstSequenceHandle &rhs) const

char	operator[] (int index) const

iterator	begin () const

iterator	end () const

bool	IsValid () const

	ConstSequenceHandle (const impl::SequenceImplPtr &impl)

impl::SequenceImplPtr &	Impl () const

Public Member Functions inherited from ConstGenericPropContainer< ConstSequenceHandle >
bool	HasProp (const String &key) const

String	GetPropAsString (const String &key) const

String	GetStringProp (const String &key) const

String	GetStringProp (const String &key, const String &def) const

Real	GetFloatProp (const String &key) const

Real	GetFloatProp (const String &key, Real def) const

int	GetIntProp (const String &key) const

int	GetIntProp (const String &key, int def) const

bool	GetBoolProp (const String &key) const

bool	GetBoolProp (const String &key, bool def) const

geom::Vec3	GetVec3Prop (const String &key) const

std::map< String, GenericPropValue >	GetPropMap () const

std::vector< String >	GetPropList () const

Protected Member Functions
GenericPropContainerImpl *	GpImpl ()

const GenericPropContainerImpl *	GpImpl () const

Protected Member Functions inherited from ConstGenericPropContainer< ConstSequenceHandle >
T	gp_get (const String &key) const

T	gp_get (const String &key, const T &def) const

GenericPropContainerImpl *	GetImpl ()

const GenericPropContainerImpl *	GetImpl () const

Friends
class	ConstGenericPropContainer< ConstSequenceHandle >

class	AlignmentHandle

class	ConstSequenceList

class	SequenceList

Detailed Description

immutable sequence

The ConstSequenceHandle provides all read-only methods of the sequence handle.

Definition at line 48 of file sequence_handle.hh.

Member Typedef Documentation

typedef String::const_iterator iterator

Definition at line 56 of file sequence_handle.hh.

Constructor & Destructor Documentation

ConstSequenceHandle ( )

create invalid sequence handle

See Also: IsValid()

ConstSequenceHandle ( const impl::SequenceImplPtr & impl )

Member Function Documentation

iterator begin ( ) const

inline

Definition at line 132 of file sequence_handle.hh.

SequenceHandle Copy ( ) const

create copy sequence The newly created sequence has the same attached view.

iterator end ( ) const

inline

Definition at line 133 of file sequence_handle.hh.

mol::EntityView GetAttachedView ( ) const

get attached view. may be an invalid entity view

See Also: SequenceHandle::AttachView(const mol::EntityView&, const String&)

int GetFirstNonGap ( ) const

Get position of first non-gap character in sequence.

String GetGaplessString ( ) const

Get sequence as string ignoring gaps.

int GetIndex ( const String & substr ) const

get index of substring

int GetLastNonGap ( ) const

Get position of last non-gap character in sequence.

int GetLength ( ) const

Get lenght of sequence, including gaps.

const String& GetName ( ) const

Get name of sequence.

See Also: SequenceHandle::GetName()

int GetOffset ( ) const

Get sequence offset from N-terminus.

See Also: SequenceHandle::SetOffset

char GetOneLetterCode ( int position ) const

get one letter code of residue at position

int GetPos ( int residue_index ) const

Get zero-based index for given residue number.

Exceptions

out_of_range,if number is not included in sequence.

mol::ResidueView GetResidue ( int position ) const

get residue at position

will return the residue view at the given sequence position or an invalid residue view when no view is attached, the index is out of bounds or the position contains a gap.

int GetResidueIndex ( int pos ) const

Get residue index corresponding to given sequence position.

Parameters

pos	zero-based index

Exceptions

out_of_range if pos is not in [0, length-1].

const String& GetRole ( ) const

const String& GetString ( ) const

get sequence as a string, including all the gaps

See Also: GetGaplessString()

GenericPropContainerImpl* GpImpl ( )

protected

const GenericPropContainerImpl* GpImpl ( ) const

protected

bool HasAttachedView ( ) const

whether the sequence has an attached view

See Also: SequenceHandle::AttachView(const mol::EntityView&, const String&)

impl::SequenceImplPtr& Impl ( ) const

bool IsValid ( ) const

whether the sequence is valid

bool operator!= ( const ConstSequenceHandle & rhs ) const

bool operator== ( const ConstSequenceHandle & rhs ) const

char operator[] ( int index ) const

Friends And Related Function Documentation

friend class AlignmentHandle

friend

Definition at line 52 of file sequence_handle.hh.

friend class ConstGenericPropContainer< ConstSequenceHandle >

friend

Definition at line 51 of file sequence_handle.hh.

friend class ConstSequenceList

friend

Definition at line 53 of file sequence_handle.hh.

friend class SequenceList

friend

Definition at line 54 of file sequence_handle.hh.

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

build-2.7-doc/stage/include/ost/seq/sequence_handle.hh

Public Types

Public Member Functions

Protected Member Functions

Friends

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation