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core::fragment::OrderedFragSet Class Reference

#include <OrderedFragSet.hh>

Inheritance diagram for core::fragment::OrderedFragSet:
Inheritance graph
[legend]

Public Types

typedef FragSet Parent
 
typedef std::map< Size, FrameListFrameMap
 

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

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

create an empty clone

Implements core::fragment::FragSet.

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

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