SequenceImpl Class Reference

#include <sequence_impl.hh>

Inherits GenericPropContainerImpl.

Public Member Functions
int	GetResidueIndex (int pos) const
int	GetPos (int residue_index) const
int	GetFirstNonGap () const
int	GetLastNonGap () const
const String &	GetName () const
void	SetName (const String &name)
void	Cut (int start, int n)
void	ShiftRegion (int start, int end, int amount)
const String &	GetString () const
void	SetString (const String &seq)
void	Normalise ()
void	Replace (const String &str, int start, int end)
String	GetGaplessString () const
int	GetOffset () const
int	GetIndex (const String &substr) const
void	SetOffset (int offset)
int	GetLength () const
	SequenceImpl (const String &seq_name, const String &sequence_string, const String &role)
char	GetOneLetterCode (int position) const
void	SetOneLetterCode (int position, char new_char)
mol::ResidueView	GetResidue (int position) const
mol::EntityView	GetAttachedView () const
void	AttachView (const mol::EntityView &view)
SequenceImplPtr	Copy () const
void	AttachView (const mol::EntityView &view, const String &chain_name)
bool	HasAttachedView () const
void	Append (char olc)
char &	operator[] (size_t index)
char	operator[] (size_t index) const
const String &	GetRole () const
void	SetRole (const String &role)
Public Member Functions inherited from GenericPropContainerImpl
	GenericPropContainerImpl ()
	~GenericPropContainerImpl ()
	GenericPropContainerImpl (const GenericPropContainerImpl &rhs)
GenericPropContainerImpl &	operator= (const GenericPropContainerImpl &r)
GenericPropValue &	GenericProp (const String &key)
const GenericPropValue &	GenericProp (const String &key) const
bool	HasProp (const String &key) const
void	ClearProps ()
void	RemoveProp (const String &key)
void	Assign (const GenericPropContainerImpl &impl)
PropertyMap	GetPropMap () const
std::vector< String >	GetPropList () const

Static Public Member Functions
static SequenceImplPtr	FromString (const String &seq_name, const String &sequence_string, const String &role="UNKNOWN")

Detailed Description

Definition at line 49 of file sequence_impl.hh.

Constructor & Destructor Documentation

SequenceImpl	(	const String &	seq_name,
		const String &	sequence_string,
		const String &	role
	)

Construct new sequence object from sequence_string.

If you want to check whether the sequence String does only contain valid characters use CreateSequence instead.

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

SequenceImplPtr Copy

(

)

const

create copy sequence

The newly created sequence has the same attached view.

void Cut	(	int	start,
		int	n
	)

static SequenceImplPtr FromString ( const String &  seq_name, const String &  sequence_string, const String &  role = "UNKNOWN"  )

static

Construct new sequence object from sequence_string.

mol::EntityView GetAttachedView

(

)

const

get attached view. may be an invalid entity view

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

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

int GetOffset

(

)

const

Get sequence offset from N-terminus.

See Also

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

inline

Definition at line 156 of file sequence_impl.hh.

const String& GetString ( ) const

inline

Definition at line 78 of file sequence_impl.hh.

bool HasAttachedView

(

)

const

whether the sequence has an attached view

void Normalise

(

)

Remove everything 'unusual' from sequence.

char& operator[] ( size_t  index )

inline

Definition at line 148 of file sequence_impl.hh.

char operator[] ( size_t  index ) const

inline

Definition at line 152 of file sequence_impl.hh.

void Replace	(	const String &	str,
		int	start,
		int	end
	)

replace substring starting from start to end

void SetName

(

const String &

name

)

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 )

inline

Definition at line 161 of file sequence_impl.hh.

void SetString

(

const String &

seq

)

Set sequence String.

void ShiftRegion	(	int	start,
		int	end,
		int	amount
	)

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

• stage/include/ost/seq/impl/sequence_impl.hh