#include <FragSetCollection.hh>

Inheritance diagram for core::fragment::FragSetCollection:

Collaboration diagram for core::fragment::FragSetCollection:

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 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	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 (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)
	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_

Detailed Description

Definition at line 51 of file FragSetCollection.hh.

Member Typedef Documentation

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

private

Definition at line 85 of file FragSetCollection.hh.

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

Definition at line 53 of file FragSetCollection.hh.

Constructor & Destructor Documentation

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

Definition at line 50 of file FragSetCollection.cc.

Referenced by clone(), and empty_clone().

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

Definition at line 51 of file FragSetCollection.cc.

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

Definition at line 52 of file FragSetCollection.cc.

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.

Definition at line 110 of file FragSetCollection.cc.

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

Definition at line 82 of file FragSetCollection.cc.

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().

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

virtual

iterate over contents

Implements core::fragment::FragSet.

Definition at line 89 of file FragSetCollection.cc.

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

virtual

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

Implements core::fragment::FragSet.

Definition at line 57 of file FragSetCollection.cc.

References FragSetCollection().

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

virtual

Implements core::fragment::FragSet.

Definition at line 103 of file FragSetCollection.cc.

References fragset_list_.

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

virtual

create an empty clone

Implements core::fragment::FragSet.

Definition at line 60 of file FragSetCollection.cc.

References FragSetCollection().

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

virtual

Implements core::fragment::FragSet.

Definition at line 96 of file FragSetCollection.cc.

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.

Definition at line 66 of file FragSetCollection.cc.

References fragset_list_.