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Rosetta 3.5
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Rosetta 3.5
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#include <DerivedSequenceMapping.hh>
Public Member Functions | |
| DerivedSequenceMapping () | |
| ctor More... | |
| DerivedSequenceMapping (Size s1, Size s2) | |
| ctor More... | |
| ~DerivedSequenceMapping () | |
| dtor More... | |
| DerivedSequenceMapping (DerivedSequenceMapping const &src) | |
| copy constructor More... | |
| DerivedSequenceMapping & | operator= (DerivedSequenceMapping const &src) |
| std::string & | seq1 () |
| std::string & | seq2 () |
| std::string const & | seq1 () const |
| std::string const & | seq2 () const |
| Size const & | start_seq2 () const |
| void | seq1 (std::string const &s) |
| void | seq2 (std::string const &s) |
| void | start_seq2 (Size s) |
 Public Member Functions inherited from core::id::SequenceMapping | |
| SequenceMapping () | |
| ctor More... | |
| SequenceMapping (Size const s1, Size const s2) | |
| ctor More... | |
| SequenceMapping (utility::vector1< Size > const &mapping) | |
| ctor More... | |
| SequenceMapping (conformation::signals::LengthEvent const &event) | |
| convenience constructor from LengthEvent More... | |
| virtual | ~SequenceMapping () |
| dtor More... | |
| SequenceMapping (SequenceMapping const &src) | |
| copy constructor More... | |
| SequenceMapping & | operator= (SequenceMapping const &src) |
| void | resize (Size const s1, Size const s2) |
| resize More... | |
| void | reverse () |
| go from an A->B mapping to a B->A mapping More... | |
| void | downstream_combine (core::id::SequenceMapping const &smap_to_add) |
| Apply a B->C mapping to the current A->B mapping to get an A->C mapping i.e. smap[j] becomes smap_to_add[ smap[j] ]. More... | |
| void | upstream_combine (core::id::SequenceMapping const &smap_to_add) |
| Apply a C->A mapping to the current A->B mapping to get a C->B mapping i.e. smap[j] becomes smap[ smap_to_add[ j ] ]. More... | |
| Size | size1 () const |
| size of target sequence More... | |
| Size | size2 () const |
| size of aligned sequence ??? More... | |
| void | set_offset (int setting) |
| bool | all_aligned () const |
| bool | is_identity () const |
| bool | is_identity_ignore_gaps () const |
| void | size2 (Size const s2) |
| void | push_back (Size const al) |
| void | delete_source_residue (Size const pos1) |
| void | show () const |
| void | show (std::ostream &output) const |
| void | insert_source_residue (Size const pos1) |
| void | insert_aligned_residue (Size const pos1, Size const pos2) |
| void | insert_aligned_residue_safe (Size const pos1, Size const pos2) |
| same as insert_aligned_residue, but a couple of extra checks on size1 and size2. More... | |
| void | insert_target_residue (Size const pos) |
| void | delete_target_residue (Size const pos) |
| void | clear () |
| Size | operator[] (Size const pos1) const |
| Size & | operator[] (Size const pos1) |
| bool | operator== (SequenceMapping const &other) const |
| Equality operator. More... | |
| utility::vector1< core::Size > const & | mapping () const |
| void | mapping (utility::vector1< core::Size > const &mapping) |
| std::string | to_string () const |
Private Attributes | |
| std::string | seq1_ |
| std::string | seq2_ |
| Size | start_seq2_ |
Additional Inherited Members | |
| Static Public Member Functions inherited from core::id::SequenceMapping | |
| static SequenceMapping | identity (Size const size) |
| Construct an identity mapping, which means that for all positions, i in seq1 maps to i in seq2. More... | |
Definition at line 37 of file DerivedSequenceMapping.hh.
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inline |
ctor
Definition at line 42 of file DerivedSequenceMapping.hh.
ctor
Definition at line 50 of file DerivedSequenceMapping.hh.
| core::sequence::DerivedSequenceMapping::~DerivedSequenceMapping | ( | ) |
dtor
Definition at line 45 of file DerivedSequenceMapping.cc.
| core::sequence::DerivedSequenceMapping::DerivedSequenceMapping | ( | DerivedSequenceMapping const & | src) |
copy constructor
Definition at line 47 of file DerivedSequenceMapping.cc.
| DerivedSequenceMapping & core::sequence::DerivedSequenceMapping::operator= | ( | DerivedSequenceMapping const & | src) |
Definition at line 54 of file DerivedSequenceMapping.cc.
References core::id::SequenceMapping::mapping(), seq1(), seq1_, seq2(), seq2_, core::id::SequenceMapping::size2(), start_seq2(), and start_seq2_.
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inline |
Definition at line 65 of file DerivedSequenceMapping.hh.
References seq1_.
Referenced by operator=(), protocols::abinitio::Template::query_sequence(), and core::sequence::simple_mapping_from_file().
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inline |
Definition at line 73 of file DerivedSequenceMapping.hh.
References seq1_.
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inline |
Definition at line 85 of file DerivedSequenceMapping.hh.
References seq1_.
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inline |
Definition at line 69 of file DerivedSequenceMapping.hh.
References seq2_.
Referenced by operator=(), core::sequence::simple_mapping_from_file(), and protocols::abinitio::Template::Template().
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inline |
Definition at line 77 of file DerivedSequenceMapping.hh.
References seq2_.
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inline |
Definition at line 89 of file DerivedSequenceMapping.hh.
References seq2_.
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inline |
Definition at line 81 of file DerivedSequenceMapping.hh.
References start_seq2_.
Referenced by operator=(), core::sequence::simple_mapping_from_file(), and protocols::abinitio::Template::Template().
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inline |
Definition at line 93 of file DerivedSequenceMapping.hh.
References start_seq2_.
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private |
Definition at line 99 of file DerivedSequenceMapping.hh.
Referenced by operator=(), and seq1().
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private |
Definition at line 100 of file DerivedSequenceMapping.hh.
Referenced by operator=(), and seq2().
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private |
Definition at line 101 of file DerivedSequenceMapping.hh.
Referenced by operator=(), and start_seq2().
1.8.4