Package rosetta :: Package core :: Package fragment :: Module _core_fragment_ :: Class FragSet

Class FragSet

 object --+    
          |    
??.instance --+
              |
             FragSet

Known Subclasses:

Instance Methods

[hide private]

__init__(...)
Raises an exception This class cannot be instantiated from Python

__reduce__(...)
helper for pickle

__str__(...)
__str__( (FragSet)arg1) -> object :

add(...)
add( (FragSet)arg1, (__CPP_Frame__)aFrame) -> None : add a single frame.

begin(...)
begin( (FragSet)arg1) -> ConstFrameIterator : iterate over contents

clone(...)
clone( (FragSet)arg1) -> FragSet : clone and copy the pointer of all Frames (Frames will not be copied)

clone_shifted(...)
clone_shifted( (FragSet)arg1, (int)) -> FragSet : core/fragment/FragSet.hh:195

empty(...)
empty( (FragSet)arg1) -> bool : core/fragment/FragSet.hh:180

empty_clone(...)
empty_clone( (FragSet)arg1) -> FragSet : create an empty clone

end(...)
end( (FragSet)arg1) -> ConstFrameIterator : core/fragment/FragSet.hh:85

frames(...)
frames( (FragSet)arg1, (int)pos, (FrameList)frames) -> int : appends frames at sequence position pos to frames, returns nr of frames added

generate_insert_map(...)
generate_insert_map( (FragSet)arg1, (MoveMap)mm, (vector1_Size)insert_map, (vector1_Size)insert_size) -> None : InsertMap and InsertSize gives quick overview which residues can be affected by fragments.

global_offset(...)
global_offset( (FragSet)arg1) -> int : core/fragment/FragSet.hh:187

insert_fragID_list(...)
insert_fragID_list( (FragSet)arg1, (object)list) -> None : add all fragments in FragID_List

max_frag_length(...)
max_frag_length( (FragSet)arg1) -> int : returns the longest fragment stored in this FragSet.

max_pos(...)
max_pos( (FragSet)arg1) -> int : returns the maximal sequence position that can be affected by fragments in this set

min_pos(...)
min_pos( (FragSet)arg1) -> int : returns the first sequence position that can be affected by fragments in this set

nonconst_begin(...)
nonconst_begin( (FragSet)arg1) -> FrameIterator : iterate over contents

nonconst_end(...)
nonconst_end( (FragSet)arg1) -> FrameIterator : core/fragment/FragSet.hh:89

nr_frames(...)
nr_frames( (FragSet)arg1) -> int : counts number of frames ( slow! - it really counts )

overlapping_with_region(...)
overlapping_with_region( (FragSet)arg1, (MoveMap)mm, (int)start, (int)end, (int)min_overlap, (int)min_length, (FrameList)frames) -> int : 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)

region(...)
region( (FragSet)arg1, (MoveMap)move_map, (int)start, (int)end, (int)min_overlap, (int)min_length, (FrameList)frames) -> int : the region thing has to be thought-over.

region_all(...)
region_all( (FragSet)arg1, (int)start, (int)end, (int)min_overlap, (int)min_length, (FrameList)frames) -> int : return a list of frames that all sample the specified region, assume all motions are allowed

region_simple(...)
region_simple( (FragSet)arg1, (int)start, (int)end, (FrameList)frames) -> int : returns fragments that exactly span seq_pos start...end

shift_by(...)
shift_by( (FragSet)arg1, (int)offset) -> None : shift all frames in FragSet by offset

size(...)
size( (FragSet)arg1) -> int : returns total size--> counts together all frags in each frame

Inherited from unreachable.instance: __new__

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(...)
(Constructor)

Raises an exception This class cannot be instantiated from Python

Overrides: object.__init__

reduce(...)

helper for pickle

Overrides: object.__reduce__: (inherited documentation)

str(...)
(Informal representation operator)


__str__( (FragSet)arg1) -> object :

    C++ signature :
        _object* __str__(core::fragment::FragSet {lvalue})

Overrides: object.__str__

add(...)


add( (FragSet)arg1, (__CPP_Frame__)aFrame) -> None :
    add a single frame. if compatible frame is already in set the frames will be merged
    

    C++ signature :
        void add(core::fragment::FragSet {lvalue},boost::shared_ptr<core::fragment::Frame const>)

add( (FragSet)arg1, (FrameList)frames) -> None :
    add all Frames in list
    

    C++ signature :
        void add(core::fragment::FragSet {lvalue},core::fragment::FrameList)

add( (FragSet)arg1, (FragSet)frames) -> None :
    add all Frames in FragSet
    

    C++ signature :
        void add(core::fragment::FragSet {lvalue},core::fragment::FragSet)

add( (FragSet)arg1, (FragID)) -> None :
    add single fragment
    

    C++ signature :
        void add(core::fragment::FragSet {lvalue},core::fragment::FragID)

add( (FragSet)arg1, (object)list) -> None :
    core/fragment/FragSet.hh:167

    C++ signature :
        void add(core::fragment::FragSet {lvalue},utility::vector1<core::fragment::FragID, std::allocator<core::fragment::FragID> > {lvalue})

begin(...)


begin( (FragSet)arg1) -> ConstFrameIterator :
    iterate over contents
    

    C++ signature :
        core::fragment::ConstFrameIterator begin(core::fragment::FragSet {lvalue})

begin( (FragSet)arg1) -> None :

    C++ signature :
        void begin(boost::shared_ptr<core::fragment::FragSet> {lvalue})

clone(...)


clone( (FragSet)arg1) -> FragSet :
    clone and copy the pointer of all Frames (Frames will not be copied)
    

    C++ signature :
        boost::shared_ptr<core::fragment::FragSet> clone(core::fragment::FragSet {lvalue})

clone( (FragSet)arg1) -> None :

    C++ signature :
        void clone(boost::shared_ptr<core::fragment::FragSet> {lvalue})

clone_shifted(...)


clone_shifted( (FragSet)arg1, (int)) -> FragSet :
    core/fragment/FragSet.hh:195

    C++ signature :
        boost::shared_ptr<core::fragment::FragSet> clone_shifted(core::fragment::FragSet {lvalue},int)

empty(...)


empty( (FragSet)arg1) -> bool :
    core/fragment/FragSet.hh:180

    C++ signature :
        bool empty(core::fragment::FragSet {lvalue})

empty( (FragSet)arg1) -> None :

    C++ signature :
        void empty(boost::shared_ptr<core::fragment::FragSet> {lvalue})

empty_clone(...)


empty_clone( (FragSet)arg1) -> FragSet :
    create an empty clone
    

    C++ signature :
        boost::shared_ptr<core::fragment::FragSet> empty_clone(core::fragment::FragSet {lvalue})

empty_clone( (FragSet)arg1) -> None :

    C++ signature :
        void empty_clone(boost::shared_ptr<core::fragment::FragSet> {lvalue})

end(...)


end( (FragSet)arg1) -> ConstFrameIterator :
    core/fragment/FragSet.hh:85

    C++ signature :
        core::fragment::ConstFrameIterator end(core::fragment::FragSet {lvalue})

end( (FragSet)arg1) -> None :

    C++ signature :
        void end(boost::shared_ptr<core::fragment::FragSet> {lvalue})

frames(...)


frames( (FragSet)arg1, (int)pos, (FrameList)frames) -> int :
    appends frames at sequence position pos to frames, returns nr of frames added
    

    C++ signature :
        unsigned long frames(core::fragment::FragSet {lvalue},unsigned long,core::fragment::FrameList {lvalue})

generate_insert_map(...)


generate_insert_map( (FragSet)arg1, (MoveMap)mm, (vector1_Size)insert_map, (vector1_Size)insert_size) -> None :
    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
    

    C++ signature :
        void generate_insert_map(core::fragment::FragSet {lvalue},core::kinematics::MoveMap,utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue},utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue})

global_offset(...)


global_offset( (FragSet)arg1) -> int :
    core/fragment/FragSet.hh:187

    C++ signature :
        int global_offset(core::fragment::FragSet {lvalue})

global_offset( (FragSet)arg1, (int)) -> None :
    resets global_offset of FragSet and shifts FragSet if necessary by calling shift_to
    

    C++ signature :
        void global_offset(core::fragment::FragSet {lvalue},int)

insert_fragID_list(...)


insert_fragID_list( (FragSet)arg1, (object)list) -> None :
    add all fragments in FragID_List
    

    C++ signature :
        void insert_fragID_list(core::fragment::FragSet {lvalue},utility::vector1<core::fragment::FragID, std::allocator<core::fragment::FragID> > {lvalue})

max_frag_length(...)


max_frag_length( (FragSet)arg1) -> int :
    returns the longest fragment stored in this FragSet.
    

    C++ signature :
        unsigned long max_frag_length(core::fragment::FragSet {lvalue})

max_pos(...)


max_pos( (FragSet)arg1) -> int :
    returns the maximal sequence position that can be affected by fragments in this set
    

    C++ signature :
        unsigned long max_pos(core::fragment::FragSet {lvalue})

min_pos(...)


min_pos( (FragSet)arg1) -> int :
    returns the first sequence position that can be affected by fragments in this set
    

    C++ signature :
        unsigned long min_pos(core::fragment::FragSet {lvalue})

nonconst_begin(...)


nonconst_begin( (FragSet)arg1) -> FrameIterator :
    iterate over contents
    

    C++ signature :
        core::fragment::FrameIterator nonconst_begin(core::fragment::FragSet {lvalue})

nonconst_begin( (FragSet)arg1) -> None :

    C++ signature :
        void nonconst_begin(boost::shared_ptr<core::fragment::FragSet> {lvalue})

nonconst_end(...)


nonconst_end( (FragSet)arg1) -> FrameIterator :
    core/fragment/FragSet.hh:89

    C++ signature :
        core::fragment::FrameIterator nonconst_end(core::fragment::FragSet {lvalue})

nonconst_end( (FragSet)arg1) -> None :

    C++ signature :
        void nonconst_end(boost::shared_ptr<core::fragment::FragSet> {lvalue})

nr_frames(...)


nr_frames( (FragSet)arg1) -> int :
    counts number of frames ( slow! - it really counts )
    

    C++ signature :
        unsigned long nr_frames(core::fragment::FragSet {lvalue})

overlapping_with_region(...)


overlapping_with_region( (FragSet)arg1, (MoveMap)mm, (int)start, (int)end, (int)min_overlap, (int)min_length, (FrameList)frames) -> int :
    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)
    

    C++ signature :
        unsigned long overlapping_with_region(core::fragment::FragSet {lvalue},core::kinematics::MoveMap,unsigned long,unsigned long,unsigned long,unsigned long,core::fragment::FrameList {lvalue})

region(...)


region( (FragSet)arg1, (MoveMap)move_map, (int)start, (int)end, (int)min_overlap, (int)min_length, (FrameList)frames) -> int :
    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.
    

    C++ signature :
        unsigned long region(core::fragment::FragSet {lvalue},core::kinematics::MoveMap,unsigned long,unsigned long,unsigned long,unsigned long,core::fragment::FrameList {lvalue})

region( (FragSet)arg1, (MoveMap)arg2, (int)arg3, (int)arg4, (int)arg5, (int)arg6, (FrameList)arg7) -> None :

    C++ signature :
        void region(boost::shared_ptr<core::fragment::FragSet> {lvalue},core::kinematics::MoveMap,unsigned long,unsigned long,unsigned long,unsigned long,core::fragment::FrameList {lvalue})

region_all(...)


region_all( (FragSet)arg1, (int)start, (int)end, (int)min_overlap, (int)min_length, (FrameList)frames) -> int :
    return a list of frames that all sample the specified region, assume all motions are allowed
    

    C++ signature :
        unsigned long region_all(core::fragment::FragSet {lvalue},unsigned long,unsigned long,unsigned long,unsigned long,core::fragment::FrameList {lvalue})

region_simple(...)


region_simple( (FragSet)arg1, (int)start, (int)end, (FrameList)frames) -> int :
    returns fragments that exactly span seq_pos start...end
    

    C++ signature :
        unsigned long region_simple(core::fragment::FragSet {lvalue},unsigned long,unsigned long,core::fragment::FrameList {lvalue})

shift_by(...)


shift_by( (FragSet)arg1, (int)offset) -> None :
    shift all frames in FragSet by offset
    

    C++ signature :
        void shift_by(core::fragment::FragSet {lvalue},int)

size(...)


size( (FragSet)arg1) -> int :
    returns total size--> counts together all frags in each frame
    

    C++ signature :
        unsigned long size(core::fragment::FragSet {lvalue})

Class FragSet

__init__(...) (Constructor)

__reduce__(...)

__str__(...) (Informal representation operator)

add(...)

begin(...)

clone(...)

clone_shifted(...)

empty(...)

empty_clone(...)

end(...)

frames(...)

generate_insert_map(...)

global_offset(...)

insert_fragID_list(...)

max_frag_length(...)

max_pos(...)

min_pos(...)

nonconst_begin(...)

nonconst_end(...)

nr_frames(...)

overlapping_with_region(...)

region(...)

region_all(...)

region_simple(...)

shift_by(...)

size(...)

init(...)
(Constructor)

reduce(...)

str(...)
(Informal representation operator)