#include <FragSetCollection.hh>

Public Types
typedef FragSet	Parent

Public Member Functions
	FragSetCollection ()

	~FragSetCollection ()

	FragSetCollection (FragSetCollection const &)

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...

void	add_fragset (FragSetOP fragset)

virtual Size	region (kinematics::MoveMap const &move_map, Size start, Size end, Size min_overlap, Size min_length, FrameList &frames) const
	the region thing has to be thought-over. How do we really want to sample fragments? for now, we ignore everything in this call and just return frags that have "start" as there specified start() entry. More...

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

virtual ConstFrameIterator	end () const

virtual FrameIterator	nonconst_begin ()
	iterate over contents More...

virtual FrameIterator	nonconst_end ()

virtual bool	empty () const

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

virtual	~FragSet ()

virtual Size	frames (core::Size pos, FrameList &frames) const
	appends frames at sequence position pos to frames, returns nr of frames added More...

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 (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...

virtual void	shift_to (core::Size offset)
	shift all frames in FragSet to old position + offset More...

core::Size	global_offset () const

void	global_offset (core::Size offset)

void	set_global_offset (core::Size)
	resets global_offset of FragSet and shifts FragSet if necessary by calling shift_to More...

FragSetOP	clone_shifted (core::Size) const

Protected Member Functions
virtual void	add_ (FrameOP)
	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 Types
typedef utility::vector1 < FragSetOP >	FragSetList

Private Attributes
FragSetList	fragset_list_

Member Typedef Documentation

typedef utility::vector1< FragSetOP > core::fragment::FragSetCollection::FragSetList

private

typedef FragSet core::fragment::FragSetCollection::Parent

Constructor & Destructor Documentation

core::fragment::FragSetCollection::FragSetCollection ( )

Referenced by clone(), and empty_clone().

core::fragment::FragSetCollection::~FragSetCollection ( )

core::fragment::FragSetCollection::FragSetCollection ( FragSetCollection const & src )

Member Function Documentation

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

protectedvirtual

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

Implements core::fragment::FragSet.

References utility_exit_with_message.

void core::fragment::FragSetCollection::add_fragset ( FragSetOP fragset )

References fragset_list_, core::fragment::FragSet::max_frag_length(), core::fragment::FragSet::max_pos(), core::fragment::FragSet::min_pos(), core::fragment::FragSet::set_max_frag_length(), core::fragment::FragSet::set_max_pos(), and core::fragment::FragSet::set_min_pos().

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

virtual

iterate over contents

Implements core::fragment::FragSet.

References utility_exit_with_message.

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

virtual

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

Implements core::fragment::FragSet.

References FragSetCollection().

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

virtual

Implements core::fragment::FragSet.

References fragset_list_.

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

virtual

create an empty clone

Implements core::fragment::FragSet.

References FragSetCollection().

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

virtual

Implements core::fragment::FragSet.

References utility_exit_with_message.

FrameIterator core::fragment::FragSetCollection::nonconst_begin ( )

virtual

iterate over contents

Implements core::fragment::FragSet.

References utility_exit_with_message.

FrameIterator core::fragment::FragSetCollection::nonconst_end ( )

virtual

Implements core::fragment::FragSet.

References utility_exit_with_message.

Size core::fragment::FragSetCollection::region	(	kinematics::MoveMap const &	move_map,
		Size	start,
		Size	end,
		Size	min_overlap,
		Size	min_length,
		FrameList &	frames
	)		const

virtual

the region thing has to be thought-over. How do we really want to sample fragments? for now, we ignore everything in this call and just return frags that have "start" as there specified start() entry.

Implements core::fragment::FragSet.

References fragset_list_.

Member Data Documentation

FragSetList core::fragment::FragSetCollection::fragset_list_

private

Referenced by add_fragset(), empty(), and region().

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

symlinks/rosetta/src/core/fragment/FragSetCollection.hh
symlinks/rosetta/src/core/fragment/FragSetCollection.cc

Public Types

Public Member Functions

Protected Member Functions

Private Types

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation