#include <OrderedFragSet.hh>

Inheritance diagram for core::fragment::OrderedFragSet:

Collaboration diagram for core::fragment::OrderedFragSet:

Public Types
typedef FragSet	Parent

typedef std::map< Size, FrameList >	FrameMap

Public Member Functions
	OrderedFragSet ()

	~OrderedFragSet ()

virtual FragSetOP	clone () const
	clone and copy the pointer of all Frames (Frames will not be copied) More...

virtual FragSetOP	empty_clone () const
	create an empty clone More...

virtual Size	region (kinematics::MoveMap const &mm, core::Size start, core::Size end, core::Size, core::Size, FrameList &frames) const
	get fragments that start somewhere between start and end More...

virtual Size	frames (Size pos, FrameList &frames) const
	Accessor for the Frame at the specified insertion position. Returns false if there is no frame at the specified position. More...

virtual FrameIterator	begin () const
	iterate over contents More...

virtual FrameIterator	end () const

virtual bool	empty () const

Public Member Functions inherited from core::fragment::FragSet
	FragSet ()

virtual	~FragSet ()

virtual Size	region_simple (core::Size start, core::Size end, FrameList &frames) const
	returns fragments that exactly span seq_pos start...end More...

virtual Size	region_all (core::Size start, core::Size end, core::Size min_overlap, core::Size min_length, FrameList &frames) const
	return a list of frames that all sample the specified region, assume all motions are allowed More...

virtual void	generate_insert_map (kinematics::MoveMap const &mm, InsertMap &insert_map, InsertSize &insert_size) const
	InsertMap and InsertSize gives quick overview which residues can be affected by fragments. insert_map — list of start-positions, insert_size corresponding list of longest fragment at position x. More...

Size	max_pos () const
	returns the maximal sequence position that can be affected by fragments in this set More...

Size	min_pos () const
	returns the first sequence position that can be affected by fragments in this set More...

Size	max_frag_length () const
	returns the longest fragment stored in this FragSet. More...

void	add (FrameOP aFrame)
	add a single frame. if compatible frame is already in set the frames will be merged More...

void	add (FrameList const &frames)
	add all Frames in list More...

void	add (FragSet const &frames)
	add all Frames in FragSet More...

void	add (FragID const &)
	add single fragment More...

void	add (FragID_List &list)

void	insert_fragID_list (FragID_List &list)
	add all fragments in FragID_List More...

Size	size () const
	returns total size–> counts together all frags in each frame More...

Size	nr_frames () const
	counts number of frames ( slow! - it really counts ) More...

Protected Member Functions
virtual void	add_ (FrameOP aframe)
	storage classes have to overload this one to add frames to their container More...

Protected Member Functions inherited from core::fragment::FragSet
void	set_max_frag_length (Size setting)
	setter for max_frag_length_ More...

void	set_max_pos (Size pos)

void	set_min_pos (Size pos)

Private Attributes
FrameMap	frames_

Detailed Description

Definition at line 45 of file OrderedFragSet.hh.

Member Typedef Documentation

typedef std::map< Size, FrameList > core::fragment::OrderedFragSet::FrameMap

Definition at line 48 of file OrderedFragSet.hh.

typedef FragSet core::fragment::OrderedFragSet::Parent

Definition at line 47 of file OrderedFragSet.hh.

Constructor & Destructor Documentation

core::fragment::OrderedFragSet::OrderedFragSet ( )

Definition at line 57 of file OrderedFragSet.cc.

core::fragment::OrderedFragSet::~OrderedFragSet ( )

Definition at line 58 of file OrderedFragSet.cc.

Member Function Documentation

void core::fragment::OrderedFragSet::add_ ( FrameOP aFrame)

protectedvirtual

storage classes have to overload this one to add frames to their container

Implements core::fragment::FragSet.

Definition at line 112 of file OrderedFragSet.cc.

FrameIterator core::fragment::OrderedFragSet::begin ( ) const

virtual

iterate over contents

Implements core::fragment::FragSet.

Definition at line 98 of file OrderedFragSet.cc.

FragSetOP core::fragment::OrderedFragSet::clone ( ) const

virtual

clone and copy the pointer of all Frames (Frames will not be copied)

Implements core::fragment::FragSet.

Definition at line 60 of file OrderedFragSet.cc.

bool core::fragment::OrderedFragSet::empty ( ) const

virtual

Implements core::fragment::FragSet.

Definition at line 106 of file OrderedFragSet.cc.

FragSetOP core::fragment::OrderedFragSet::empty_clone ( ) const

virtual

create an empty clone

Implements core::fragment::FragSet.

Definition at line 63 of file OrderedFragSet.cc.

FrameIterator core::fragment::OrderedFragSet::end ( ) const

virtual

Implements core::fragment::FragSet.

Definition at line 102 of file OrderedFragSet.cc.

Size core::fragment::OrderedFragSet::frames	(	Size	pos,
		FrameList &	frames
	)		const

virtual

Accessor for the Frame at the specified insertion position. Returns false if there is no frame at the specified position.

Reimplemented from core::fragment::FragSet.

Definition at line 86 of file OrderedFragSet.cc.

Size core::fragment::OrderedFragSet::region	(	kinematics::MoveMap const &	mm,
		core::Size	start,
		core::Size	end,
		core::Size	,
		core::Size	,
		FrameList &	frames
	)		const

virtual

get fragments that start somewhere between start and end

Implements core::fragment::FragSet.

Definition at line 68 of file OrderedFragSet.cc.

References core::sequence::end.

Member Data Documentation

FrameMap core::fragment::OrderedFragSet::frames_

private

Definition at line 83 of file OrderedFragSet.hh.

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

src/core/fragment/OrderedFragSet.hh
src/core/fragment/OrderedFragSet.cc

Public Types

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation