bpp-seq
2.2.0
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#include <Bpp/Seq/SequenceWithAnnotationTools.h>
Public Member Functions | |
void | init (const Sequence &seq) |
const std::string & | getType () const |
bool | isValidWith (const SequenceWithAnnotation &sequence, bool throwException=true) const |
Test is the annotation is valid for a given sequence. More... | |
bool | isRemovable () const |
bool | isShared () const |
void | beforeSequenceChanged (const SymbolListEditionEvent &event) |
void | afterSequenceChanged (const SymbolListEditionEvent &event) |
void | beforeSequenceInserted (const SymbolListInsertionEvent &event) |
void | afterSequenceInserted (const SymbolListInsertionEvent &event) |
void | beforeSequenceDeleted (const SymbolListDeletionEvent &event) |
void | afterSequenceDeleted (const SymbolListDeletionEvent &event) |
void | beforeSequenceSubstituted (const SymbolListSubstitutionEvent &event) |
void | afterSequenceSubstituted (const SymbolListSubstitutionEvent &event) |
size_t | getSize () const |
const bool | operator[] (size_t i) const |
void | setMask (const std::vector< bool > &mask) |
const std::vector< bool > & | getMask () const |
void | setMask (size_t pos, bool mask) |
void | setMask (size_t pos, const std::vector< bool > &mask) |
bool | merge (const SequenceAnnotation &anno) |
Merge the input annotation with the current one. More... | |
SequenceAnnotation * | getPartAnnotation (size_t pos, size_t len) const throw (Exception) |
Constructors | |
SequenceMask (size_t size=0, bool removable=true) | |
Build a new SequenceMask object. More... | |
SequenceMask (const std::vector< bool > &mask, bool removable=true) | |
Build a new SequenceMask object. More... | |
Destructor | |
virtual | ~SequenceMask () |
The Clonable interface | |
SequenceMask * | clone () const |
Static Public Attributes | |
static const std::string | MASK = "Boolean mask" |
Private Attributes | |
bool | removable_ |
std::vector< bool > | mask_ |
Definition at line 51 of file SequenceWithAnnotationTools.h.
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inline |
Build a new SequenceMask object.
Build a new SequenceMask object and set the mask to false.
size | The size of the sequence. |
removable | Tell if this listener can be removed by the user. |
Definition at line 76 of file SequenceWithAnnotationTools.h.
Referenced by clone(), and getPartAnnotation().
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inline |
Build a new SequenceMask object.
Build a new SequenceMask object and set the mask as a vector of bool.
mask | The boolean mask |
removable | Tell if this listener can be removed by the user. |
Definition at line 90 of file SequenceWithAnnotationTools.h.
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inlinevirtual |
Definition at line 101 of file SequenceWithAnnotationTools.h.
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virtual |
Implements bpp::SymbolListListener.
Definition at line 50 of file SequenceWithAnnotationTools.cpp.
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virtual |
Implements bpp::SymbolListListener.
Definition at line 66 of file SequenceWithAnnotationTools.cpp.
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virtual |
Implements bpp::SymbolListListener.
Definition at line 58 of file SequenceWithAnnotationTools.cpp.
References bpp::SymbolListInsertionEvent::getLength().
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inlinevirtual |
Implements bpp::SymbolListListener.
Definition at line 140 of file SequenceWithAnnotationTools.h.
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inlinevirtual |
Implements bpp::SymbolListListener.
Definition at line 133 of file SequenceWithAnnotationTools.h.
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inlinevirtual |
Implements bpp::SymbolListListener.
Definition at line 137 of file SequenceWithAnnotationTools.h.
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inlinevirtual |
Implements bpp::SymbolListListener.
Definition at line 135 of file SequenceWithAnnotationTools.h.
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inlinevirtual |
Implements bpp::SymbolListListener.
Definition at line 139 of file SequenceWithAnnotationTools.h.
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inlinevirtual |
Implements bpp::SequenceAnnotation.
Definition at line 113 of file SequenceWithAnnotationTools.h.
References SequenceMask().
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inline |
Definition at line 155 of file SequenceWithAnnotationTools.h.
References mask_.
Referenced by merge().
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inlinevirtual |
pos | Starting point of the region. |
len | The length of the region, in number of positions. |
Implements bpp::SequenceAnnotation.
Definition at line 179 of file SequenceWithAnnotationTools.h.
References mask_, removable_, and SequenceMask().
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inline |
Definition at line 142 of file SequenceWithAnnotationTools.h.
References mask_.
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inlinevirtual |
Implements bpp::SequenceAnnotation.
Definition at line 123 of file SequenceWithAnnotationTools.h.
References MASK.
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inlinevirtual |
Creates a default annotation according to a given sequence.
seq | The template sequence (typically the one with which the annotation will be attached). |
Implements bpp::SequenceAnnotation.
Definition at line 117 of file SequenceWithAnnotationTools.h.
References mask_, and bpp::SymbolList::size().
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inlinevirtual |
Implements bpp::SymbolListListener.
Definition at line 131 of file SequenceWithAnnotationTools.h.
References removable_.
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inlinevirtual |
Implements bpp::SymbolListListener.
Definition at line 132 of file SequenceWithAnnotationTools.h.
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inlinevirtual |
Test is the annotation is valid for a given sequence.
sequence | The sequence to be validated against. |
throwException | If set to yes, throw an exception if the sequence is not valid. |
Implements bpp::SequenceAnnotation.
Definition at line 125 of file SequenceWithAnnotationTools.h.
References mask_, and bpp::EdSymbolList::size().
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inlinevirtual |
Merge the input annotation with the current one.
anno | The annotation to fuse. |
Implements bpp::SequenceAnnotation.
Definition at line 169 of file SequenceWithAnnotationTools.h.
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inline |
Definition at line 144 of file SequenceWithAnnotationTools.h.
References mask_.
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inline |
Definition at line 146 of file SequenceWithAnnotationTools.h.
References mask_.
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inline |
Definition at line 157 of file SequenceWithAnnotationTools.h.
References mask_.
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inline |
Definition at line 163 of file SequenceWithAnnotationTools.h.
References mask_.
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static |
Definition at line 59 of file SequenceWithAnnotationTools.h.
Referenced by getType().
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private |
Definition at line 56 of file SequenceWithAnnotationTools.h.
Referenced by getMask(), getPartAnnotation(), getSize(), init(), isValidWith(), merge(), operator[](), and setMask().
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private |
Definition at line 55 of file SequenceWithAnnotationTools.h.
Referenced by getPartAnnotation(), and isRemovable().