core::fragment::OrderedFragSet Class Reference

#include <OrderedFragSet.hh>

Inheritance diagram for core::fragment::OrderedFragSet:

Public Types
typedef FragSet	Parent
typedef std::map< Size, FrameList >	FrameMap

Public Member Functions
	OrderedFragSet ()
	~OrderedFragSet () override
FragSetOP	clone () const override
	clone and copy the pointer of all Frames (Frames will not be copied) More...
FragSetOP	empty_clone () const override
	create an empty clone More...
Size	region (kinematics::MoveMap const &mm, core::Size start, core::Size end, core::Size, core::Size, FrameList &frames) const override
	get fragments that start somewhere between start and end More...
Size	frames (Size pos, FrameList &frames) const override
	Accessor for the Frame at the specified insertion position. Returns false if there is no frame at the specified position. More...
ConstFrameIterator	begin () const override
	iterate over contents More...
ConstFrameIterator	end () const override
FrameIterator	nonconst_begin () override
	iterate over contents More...
FrameIterator	nonconst_end () override
bool	empty () const override
Public Member Functions inherited from core::fragment::FragSet
	FragSet ()
	~FragSet () override=default
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 Size	overlapping_with_region (kinematics::MoveMap const &mm, core::Size start, core::Size end, core::Size min_overlap, core::Size min_length, FrameList &frames) const
	returns the number and list of all fragment alignment frames that somehow overlap with the given region (also allows those frames that start before the region and reach into it) 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 (FrameCOP 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...
virtual void	shift_by (int offset)
	shift all frames in FragSet by offset More...
int	global_offset () const
void	global_offset (int)
	resets global_offset of FragSet and shifts FragSet if necessary by calling shift_to More...
FragSetOP	clone_shifted (int) const

Protected Member Functions
void	add_ (FrameOP aframe) override
	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_

Member Typedef Documentation

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

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

Constructor & Destructor Documentation

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

default

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

overridedefault

Member Function Documentation

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

overrideprotectedvirtual

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

Implements core::fragment::FragSet.

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

overridevirtual

iterate over contents

Implements core::fragment::FragSet.

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

overridevirtual

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

Implements core::fragment::FragSet.

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

overridevirtual

Implements core::fragment::FragSet.

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

overridevirtual

create an empty clone

Implements core::fragment::FragSet.

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

overridevirtual

Implements core::fragment::FragSet.

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

overridevirtual

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.

FrameIterator core::fragment::OrderedFragSet::nonconst_begin ( )

overridevirtual

iterate over contents

Implements core::fragment::FragSet.

FrameIterator core::fragment::OrderedFragSet::nonconst_end ( )

overridevirtual

Implements core::fragment::FragSet.

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

overridevirtual

get fragments that start somewhere between start and end

Implements core::fragment::FragSet.

References core::sequence::end.

Member Data Documentation

FrameMap core::fragment::OrderedFragSet::frames_

private

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

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