ConstSequenceHandle Class Reference

immutable sequence More...

#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
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 StringGetRole () 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

Protected Member Functions

GenericPropContainerImplGpImpl ()
const GenericPropContainerImplGpImpl () const


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

create invalid sequence handle

See also:

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:
int GetOffset (  )  const

Get sequence offset from N-terminus.

See also:
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.

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.

pos zero-based index
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:
const GenericPropContainerImpl* GpImpl (  )  const [protected]
GenericPropContainerImpl* GpImpl (  )  [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.

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:
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