#include <sequence_handle.hh>

Inherits GenericPropContainer< SequenceHandle >.

Public Types
typedef String::const_iterator	iterator

Public Member Functions
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

char	GetOneLetterCode (int position) const

int	GetIndex (const String &substr) const

mol::ResidueView	GetResidue (int position) const

mol::EntityView	GetAttachedView () const

void	Normalise ()

SequenceHandle	Copy () const

bool	HasAttachedView () const

bool	operator== (const SequenceHandle &rhs) const

bool	operator!= (const SequenceHandle &rhs) const

bool	IsValid () const

	SequenceHandle ()

void	SetName (const String &name)

void	SetString (const String &seq)

void	SetOffset (int offset)

void	AttachView (const mol::EntityView &view)

void	SetOneLetterCode (int position, char new_char)

char	operator[] (size_t index) const

iterator	begin () const

iterator	end () const

void	Append (char olc)

	operator ConstSequenceHandle () const

void	AttachView (const mol::EntityView &view, const String &chain_name)

	SequenceHandle (const impl::SequenceImplPtr &impl)

const String &	GetRole () const

void	SetRole (const String &role) const

impl::SequenceImplPtr &	Impl () const

GenericPropContainerImpl *	GpImpl ()

const GenericPropContainerImpl *	GpImpl () const

Public Member Functions inherited from GenericPropContainer< SequenceHandle >
void	ClearProps ()

void	SetStringProp (const String &key, const String &value)

void	SetFloatProp (const String &key, Real value)

void	SetIntProp (const String &key, int value)

void	SetBoolProp (const String &key, bool value)

void	SetVec3Prop (const String &key, geom::Vec3 value)

void	RemoveProp (const String &key)

Public Member Functions inherited from ConstGenericPropContainer< SequenceHandle >
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

Friends
class	GenericPropContainer< SequenceHandle >

class	SequenceList

class	AlignmentHandle

class	ConstSequenceList

Additional Inherited Members
Protected Member Functions inherited from ConstGenericPropContainer< SequenceHandle >
T	gp_get (const String &key) const

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

GenericPropContainerImpl *	GetImpl ()

const GenericPropContainerImpl *	GetImpl () const

Detailed Description

mutable sequence handle.

Sequences are mostly used as part of a multiple sequence alignment. The class allows for fast mapping between residue index and position in the sequence. The GetResidueIndex() method maps from position in the sequence to residue index, taking the sequence offset into account. The reverse mapping is done with GetPos().

Optionally, an entity view may be attached to the sequence with AttachView(). If HasAttachedView() is true, the GetResidue() method can be used directly to map from sequence position to residue. Note that it is required that the entity view has only one chain. Sequences are created from string as

*  String seq_str="ALGW--ALN"
*  SequenceHandle seq=CreateSequence("NAME", seq_str);
*  

Sequences IO is dealt with in the sequence module. For more information, consult this page.

Definition at line 172 of file sequence_handle.hh.

Member Typedef Documentation

typedef String::const_iterator iterator

Definition at line 175 of file sequence_handle.hh.

Constructor & Destructor Documentation

SequenceHandle ( )

create invalid sequence handle

See Also: IsValid()

SequenceHandle ( const impl::SequenceImplPtr & impl )

Member Function Documentation

void Append ( char olc )

void AttachView ( const mol::EntityView & view )

attach entity view to sequence

Exceptions

IntegrityError when the view contains more than one chain

void AttachView	(	const mol::EntityView &	view,
		const String &	chain_name
	)

attach entity view to sequence

The sequence is mapped onto the chain with given name

iterator begin ( ) const

inline

Definition at line 281 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 282 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::GetOffset

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 ( )

const GenericPropContainerImpl* GpImpl ( ) const

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

void Normalise ( )

remove '.', '-' as gaps and make sequence all-uppercase Changes happen in place.

operator ConstSequenceHandle ( ) const

bool operator!= ( const SequenceHandle & rhs ) const

bool operator== ( const SequenceHandle & rhs ) const

char operator[] ( size_t index ) const

void SetName ( const String & name )

set name of sequence

void SetOffset ( int offset )

Set sequence offset.

By default the sequence offset is zero, i.e. the beginning of the sequence lies exactly at the N-terminus. Setting the sequence offset to a positive number will shift the sequence towards the C-terminus.

void SetOneLetterCode	(	int	position,
		char	new_char
	)

void SetRole ( const String & role ) const

void SetString ( const String & seq )

Set sequence String.

Friends And Related Function Documentation

friend class AlignmentHandle

friend

Definition at line 179 of file sequence_handle.hh.

friend class ConstSequenceList

friend

Definition at line 180 of file sequence_handle.hh.

friend class GenericPropContainer< SequenceHandle >

friend

Definition at line 176 of file sequence_handle.hh.

friend class SequenceList

friend

Definition at line 177 of file sequence_handle.hh.

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

stage/include/ost/seq/sequence_handle.hh

Public Types

Public Member Functions

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation