OpenStructure
Public Types | Public Member Functions | Protected Member Functions | Friends
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 StringGetName () const
const StringGetString () const
String GetGaplessString () const
int GetOffset () const
int GetLength () const
char GetOneLetterCode (int position) const
mol::ResidueView GetResidue (int position) const
mol::EntityView GetAttachedView () const
SequenceHandle Copy () const
bool HasAttachedView () 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::SequenceImplPtrImpl () 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
std::map< String,
GenericPropValue
GetPropMap () const
std::vector< StringGetPropList () const

Protected Member Functions

GenericPropContainerImplGpImpl ()
const GenericPropContainerImplGpImpl () const
- Protected Member Functions inherited from ConstGenericPropContainer< ConstSequenceHandle >
gp_get (const String &key) const
gp_get (const String &key, const T &def) const
GenericPropContainerImplGetImpl ()
const GenericPropContainerImplGetImpl () 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 45 of file sequence_handle.hh.


Member Typedef Documentation

typedef String::const_iterator iterator

Definition at line 53 of file sequence_handle.hh.


Constructor & Destructor Documentation

create invalid sequence handle

See also:
IsValid()

Member Function Documentation

iterator begin ( ) const
inline

Definition at line 124 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 125 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 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,ifnumber 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:
poszero-based index
Exceptions:
out_of_rangeif pos is not in [0, length-1].
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 49 of file sequence_handle.hh.

Definition at line 48 of file sequence_handle.hh.

friend class ConstSequenceList
friend

Definition at line 50 of file sequence_handle.hh.

friend class SequenceList
friend

Definition at line 51 of file sequence_handle.hh.


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