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core::fragment::FragSet Class Referenceabstract

The FragSet: (Interface Definition – Virtual BaseClass ) More...

#include <FragSet.hh>

Inheritance diagram for core::fragment::FragSet:
Inheritance graph
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Public Member Functions

 FragSet ()
 
 ~FragSet () override=default
 
virtual FragSetOP clone () const =0
 clone and copy the pointer of all Frames (Frames will not be copied) More...
 
virtual FragSetOP empty_clone () const =0
 create an empty clone More...
 
virtual ConstFrameIterator begin () const =0
 iterate over contents More...
 
virtual ConstFrameIterator end () const =0
 
virtual FrameIterator nonconst_begin ()=0
 iterate over contents More...
 
virtual FrameIterator nonconst_end ()=0
 
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 Size region (kinematics::MoveMap const &move_map, core::Size start, core::Size end, core::Size min_overlap, core::Size min_length, FrameList &frames) const =0
 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 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 bool empty () const =0
 
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 set_max_frag_length (Size setting)
 setter for max_frag_length_ More...
 
void set_max_pos (Size pos)
 
void set_min_pos (Size pos)
 
virtual void add_ (FrameOP aFrame)=0
 storage classes have to overload this one to add frames to their container More...
 

Private Attributes

Size min_pos_
 
Size max_pos_
 
Size max_frag_length_
 
int global_offset_
 global offset of current Fragmentset. Default = 0 More...
 

Friends

std::ostream & operator<< (std::ostream &out, FragSet const &frags)
 

Detailed Description

The FragSet: (Interface Definition – Virtual BaseClass )

Constructor & Destructor Documentation

core::fragment::FragSet::FragSet ( )
inline
core::fragment::FragSet::~FragSet ( )
overridedefault

Member Function Documentation

void core::fragment::FragSet::add ( FrameCOP  aFrame)
void core::fragment::FragSet::add ( FrameList const &  frames)

add all Frames in list

References protocols::mean_field::add().

void core::fragment::FragSet::add ( FragSet const &  frames)

add all Frames in FragSet

References protocols::mean_field::add(), begin(), and end().

void core::fragment::FragSet::add ( FragID const &  frag_id)
void core::fragment::FragSet::add ( FragID_List list)
inline

References insert_fragID_list().

virtual void core::fragment::FragSet::add_ ( FrameOP  aFrame)
protectedpure virtual

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

Implemented in core::fragment::ConstantLengthFragSet, core::fragment::MinimalFragSet, core::fragment::FragSetCollection, and core::fragment::OrderedFragSet.

virtual ConstFrameIterator core::fragment::FragSet::begin ( ) const
pure virtual
virtual FragSetOP core::fragment::FragSet::clone ( ) const
pure virtual

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

Implemented in core::fragment::ConstantLengthFragSet, core::fragment::MinimalFragSet, core::fragment::FragSetCollection, and core::fragment::OrderedFragSet.

Referenced by core::fragment::merge_frags().

FragSetOP core::fragment::FragSet::clone_shifted ( int  offset) const

References core::sequence::end.

virtual bool core::fragment::FragSet::empty ( ) const
pure virtual
virtual FragSetOP core::fragment::FragSet::empty_clone ( ) const
pure virtual
virtual ConstFrameIterator core::fragment::FragSet::end ( ) const
pure virtual
virtual Size core::fragment::FragSet::frames ( core::Size  pos,
FrameList frames 
) const
inlinevirtual

appends frames at sequence position pos to frames, returns nr of frames added

Reimplemented in core::fragment::MinimalFragSet, and core::fragment::OrderedFragSet.

References region_simple().

Referenced by core::fragment::merge_frags(), and protocols::loops::select_loop_frags().

void core::fragment::FragSet::generate_insert_map ( kinematics::MoveMap const &  mm,
InsertMap insert_map,
InsertSize insert_size 
) const
virtual

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.

References core::sequence::end, core::kinematics::MoveMap::get_bb(), and core::fragment::tr().

Referenced by protocols::loops::select_loop_frags().

int core::fragment::FragSet::global_offset ( ) const
inline
void core::fragment::FragSet::global_offset ( int  offset)

resets global_offset of FragSet and shifts FragSet if necessary by calling shift_to

References core::fragment::tr().

void core::fragment::FragSet::insert_fragID_list ( FragID_List list)

add all fragments in FragID_List

References protocols::mean_field::add(), and core::fragment::tr().

Referenced by add().

Size core::fragment::FragSet::max_frag_length ( ) const
inline
Size core::fragment::FragSet::max_pos ( ) const
inline

returns the maximal sequence position that can be affected by fragments in this set

References max_pos_.

Referenced by core::fragment::chop_fragments(), core::fragment::SecondaryStructure::compute_fractions(), core::fragment::compute_per_residue_coverage(), and core::fragment::merge_frags().

Size core::fragment::FragSet::min_pos ( ) const
inline

returns the first sequence position that can be affected by fragments in this set

References min_pos_.

virtual FrameIterator core::fragment::FragSet::nonconst_begin ( )
pure virtual
virtual FrameIterator core::fragment::FragSet::nonconst_end ( )
pure virtual
Size core::fragment::FragSet::nr_frames ( ) const

counts number of frames ( slow! - it really counts )

References core::sequence::end.

Size core::fragment::FragSet::overlapping_with_region ( kinematics::MoveMap const &  mm,
core::Size  start,
core::Size  end,
core::Size  min_overlap,
core::Size  min_length,
FrameList frames 
) const
virtual

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)

Reimplemented in core::fragment::ConstantLengthFragSet.

virtual Size core::fragment::FragSet::region ( kinematics::MoveMap const &  move_map,
core::Size  start,
core::Size  end,
core::Size  min_overlap,
core::Size  min_length,
FrameList frames 
) const
pure 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.

Implemented in core::fragment::ConstantLengthFragSet, core::fragment::MinimalFragSet, core::fragment::FragSetCollection, and core::fragment::OrderedFragSet.

Size core::fragment::FragSet::region_all ( core::Size  start,
core::Size  end,
core::Size  min_overlap,
core::Size  min_length,
FrameList frames 
) const
virtual

return a list of frames that all sample the specified region, assume all motions are allowed

References core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), and core::kinematics::MoveMap::set_jump().

Referenced by region_simple().

virtual Size core::fragment::FragSet::region_simple ( core::Size  start,
core::Size  end,
FrameList frames 
) const
inlinevirtual

returns fragments that exactly span seq_pos start...end

References region_all().

Referenced by frames().

void core::fragment::FragSet::set_max_frag_length ( Size  setting)
inlineprotected

setter for max_frag_length_

References max_frag_length_.

Referenced by core::fragment::ConstantLengthFragSet::ConstantLengthFragSet().

void core::fragment::FragSet::set_max_pos ( Size  pos)
inlineprotected

References max_pos_.

void core::fragment::FragSet::set_min_pos ( Size  pos)
inlineprotected

References min_pos_.

void core::fragment::FragSet::shift_by ( int  offset)
virtual

shift all frames in FragSet by offset

References core::fragment::tr().

Size core::fragment::FragSet::size ( ) const

returns total size–> counts together all frags in each frame

References core::sequence::end.

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
FragSet const &  frags 
)
friend

Member Data Documentation

int core::fragment::FragSet::global_offset_
private

global offset of current Fragmentset. Default = 0

Referenced by global_offset().

Size core::fragment::FragSet::max_frag_length_
private
Size core::fragment::FragSet::max_pos_
private

Referenced by max_pos(), and set_max_pos().

Size core::fragment::FragSet::min_pos_
private

Referenced by min_pos(), and set_min_pos().


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