All Data Structures Namespaces Files Functions Variables Typedefs Enumerations Enumerator Properties Friends Macros Groups Pages
Public Types | Public Member Functions | Friends
SequenceHandle Class Reference

#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 StringGetName () const
const StringGetString () 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
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 StringGetRole () const
void SetRole (const String &role) const
impl::SequenceImplPtrImpl () const
GenericPropContainerImplGpImpl ()
const GenericPropContainerImplGpImpl () 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 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
std::map< String,
GetPropMap () const
std::vector< StringGetPropList () const


class GenericPropContainer< SequenceHandle >
class SequenceList
class AlignmentHandle
class ConstSequenceList

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

create invalid sequence handle

See also:

Member Function Documentation

void Append ( char  olc)
void AttachView ( const mol::EntityView view)

attach entity view to sequence

IntegrityErrorwhen 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

Definition at line 277 of file sequence_handle.hh.

SequenceHandle Copy ( ) const

create copy sequence The newly created sequence has the same attached view.

iterator end ( ) const

Definition at line 278 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,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.

poszero-based index
out_of_rangeif 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
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

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

Definition at line 179 of file sequence_handle.hh.

friend class ConstSequenceList

Definition at line 180 of file sequence_handle.hh.

friend class GenericPropContainer< SequenceHandle >

Definition at line 176 of file sequence_handle.hh.

friend class SequenceList

Definition at line 177 of file sequence_handle.hh.

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