ConstSequenceHandle Class Reference

#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.

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

• stage/include/ost/seq/sequence_handle.hh