bpp-seq
2.2.0
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An implementation of the Sequence interface that supports annotation. More...
#include <Bpp/Seq/SequenceWithAnnotation.h>
Public Member Functions | |
SequenceWithAnnotation (const Alphabet *alpha) | |
Empty constructor: build a void Sequence with just an Alphabet. More... | |
SequenceWithAnnotation (const std::string &name, const std::string &sequence, const Alphabet *alpha) throw (BadCharException) | |
Direct constructor: build a Sequence object from a std::string You can use it safely for RNA, DNA and protein sequences. More... | |
SequenceWithAnnotation (const std::string &name, const std::string &sequence, const Comments &comments, const Alphabet *alpha) throw (BadCharException) | |
Direct constructor: build a Sequence object from a std::string. More... | |
SequenceWithAnnotation (const std::string &name, const std::vector< std::string > &sequence, const Alphabet *alpha) throw (BadCharException) | |
General purpose constructor, can be used with any alphabet. More... | |
SequenceWithAnnotation (const std::string &name, const std::vector< std::string > &sequence, const Comments &comments, const Alphabet *alpha) throw (BadCharException) | |
General purpose constructor, can be used with any alphabet. More... | |
SequenceWithAnnotation (const std::string &name, const std::vector< int > &sequence, const Alphabet *alpha) throw (BadIntException) | |
General purpose constructor, can be used with any alphabet. More... | |
SequenceWithAnnotation (const std::string &name, const std::vector< int > &sequence, const Comments &comments, const Alphabet *alpha) throw (BadIntException) | |
General purpose constructor, can be used with any alphabet. More... | |
SequenceWithAnnotation (const Sequence &s) | |
The Sequence generic copy constructor. This does not perform a hard copy of the alphabet object. More... | |
SequenceWithAnnotation (const SequenceWithAnnotation &s) | |
The Sequence copy constructor. This does not perform a hard copy of the alphabet object. More... | |
SequenceWithAnnotation & | operator= (const Sequence &s) |
The Sequence generic assignment operator. This does not perform a hard copy of the alphabet object. More... | |
SequenceWithAnnotation & | operator= (const SequenceWithAnnotation &s) |
The Sequence assignment operator. This does not perform a hard copy of the alphabet object. More... | |
virtual | ~SequenceWithAnnotation () |
virtual void | addAnnotation (SequenceAnnotation *anno) throw (Exception) |
Add a new annotation to the sequence. More... | |
virtual bool | hasAnnotation (const std::string &type) const |
virtual const SequenceAnnotation & | getAnnotation (const std::string &type) const |
virtual SequenceAnnotation & | getAnnotation (const std::string &type) |
virtual std::vector< std::string > | getAnnotationTypes () const |
virtual void | merge (const SequenceWithAnnotation &swa) throw (AlphabetMismatchException, Exception) |
Merge a sequence with the current one. More... | |
virtual const Alphabet * | getAlphabet () const =0 |
Get the alphabet associated to the list. More... | |
virtual size_t | size () const =0 |
Get the number of elements in the list. More... | |
virtual std::string | toString () const =0 |
Convert the list as a string. More... | |
virtual const Alphabet * | getAlphabet () const |
Get the alphabet associated to the list. More... | |
virtual size_t | size () const |
Get the number of elements in the list. More... | |
virtual const std::vector< int > & | getContent () const |
Get the whole content of the list as a vector of int. More... | |
virtual std::string | toString () const |
Convert the list as a string. More... | |
virtual void | addElement (const std::string &c) throw (BadCharException) |
Add a character to the end of the list. More... | |
virtual void | addElement (size_t pos, const std::string &c) throw (BadCharException, IndexOutOfBoundsException) |
Add a character at a certain position in the list. More... | |
virtual void | addElement (int v) throw (BadIntException) |
Add a character to the end of the list. More... | |
virtual void | addElement (size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) |
Add a character at a certain position in the list. More... | |
virtual void | setElement (size_t pos, const std::string &c) throw (BadCharException, IndexOutOfBoundsException) |
Set the element at position 'pos' to character 'c'. More... | |
virtual void | setElement (size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException) |
Set the element at position 'pos' to character 'v'. More... | |
virtual void | deleteElement (size_t pos) throw (IndexOutOfBoundsException) |
Delete the element at position 'pos'. More... | |
virtual void | deleteElements (size_t pos, size_t len) throw (IndexOutOfBoundsException) |
Delete the elements at position 'pos'. More... | |
virtual std::string | getChar (size_t pos) const throw (IndexOutOfBoundsException) |
Get the element at position 'pos' as a character. More... | |
virtual int | getValue (size_t pos) const throw (IndexOutOfBoundsException) |
Get the element at position 'pos' as an int. More... | |
virtual const int & | operator[] (size_t i) const |
Operator [] overloaded for quick access to a character in list. More... | |
virtual int & | operator[] (size_t i) |
Operator [] overloaded for quick access to a character in list. More... | |
virtual void | shuffle () |
Randomly shuffle the content of the list, with linear complexity. More... | |
The Clonable interface | |
SequenceWithAnnotation * | clone () const |
Setting/getting the name of the sequence. | |
const std::string & | getName () const |
Get the name of this sequence. More... | |
void | setName (const std::string &name) |
Set the name of this sequence. More... | |
Setting/getting the comments associated to the sequence. | |
const Comments & | getComments () const |
Get the comments associated to this sequence. More... | |
void | setComments (const Comments &comments) |
Set the comments associated to this sequence. More... | |
Adjusting the size of the sequence. | |
virtual void | setContent (const std::string &sequence) throw (BadCharException) |
Set the whole content of the sequence. More... | |
void | setContent (const std::vector< int > &list) throw (BadIntException) |
Set the whole content of the list. More... | |
void | setContent (const std::vector< std::string > &list) throw (BadCharException) |
Set the whole content of the list. More... | |
virtual void | setToSizeR (size_t newSize) |
Set up the size of a sequence from the right side. More... | |
virtual void | setToSizeL (size_t newSize) |
Set up the size of a sequence from the left side. More... | |
void | append (const std::vector< int > &content) throw (BadIntException) |
Append the specified content to the sequence. More... | |
void | append (const std::vector< std::string > &content) throw (BadCharException) |
Append the specified content to the sequence. More... | |
void | append (const std::string &content) throw (BadCharException) |
Append the specified content to the sequence. More... | |
Acting on the content of the list. | |
virtual const std::vector< int > & | getContent () const =0 |
Get the whole content of the list as a vector of int. More... | |
Edition methods. | |
virtual void | addElement (const std::string &c)=0 throw (BadCharException) |
Add a character to the end of the list. More... | |
virtual void | addElement (size_t pos, const std::string &c)=0 throw (BadCharException, IndexOutOfBoundsException) |
Add a character at a certain position in the list. More... | |
virtual void | addElement (int v)=0 throw (BadIntException) |
Add a character to the end of the list. More... | |
virtual void | addElement (size_t pos, int v)=0 throw (BadIntException, IndexOutOfBoundsException) |
Add a character at a certain position in the list. More... | |
virtual void | setElement (size_t pos, const std::string &c)=0 throw (BadCharException, IndexOutOfBoundsException) |
Set the element at position 'pos' to character 'c'. More... | |
virtual void | setElement (size_t pos, int v)=0 throw (BadIntException, IndexOutOfBoundsException) |
Set the element at position 'pos' to character 'v'. More... | |
virtual void | deleteElement (size_t pos)=0 throw (IndexOutOfBoundsException) |
Delete the element at position 'pos'. More... | |
virtual void | deleteElements (size_t pos, size_t len)=0 throw (IndexOutOfBoundsException) |
Delete the elements at position 'pos'. More... | |
virtual std::string | getChar (size_t pos) const =0 throw (IndexOutOfBoundsException) |
Get the element at position 'pos' as a character. More... | |
virtual int | getValue (size_t pos) const =0 throw (IndexOutOfBoundsException) |
Get the element at position 'pos' as an int. More... | |
Provide direct access to the list content. | |
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virtual const int & | operator[] (size_t i) const =0 |
Operator [] overloaded for quick access to a character in list. More... | |
virtual int & | operator[] (size_t i)=0 |
Operator [] overloaded for quick access to a character in list. More... | |
virtual void | shuffle ()=0 |
Randomly shuffle the content of the list, with linear complexity. More... | |
Protected Member Functions | |
void | propagateEvents (bool yn) |
bool | propagateEvents () const |
Protected Attributes | |
std::vector< int > | content_ |
The list content. More... | |
std::vector< SymbolListListener * > | listeners_ |
Contains the listeners. More... | |
Private Attributes | |
std::string | name_ |
The sequence name. More... | |
Comments | comments_ |
The sequence comments. More... | |
An implementation of the Sequence interface that supports annotation.
This is a general purpose container, containing an ordered list of states. The states that allowed to be present in the sequence are defined by an alphabet object, which is passed to the sequence constructor by a pointer.
For programming convenience, the states are stored as integers, but the translation toward and from a char description is easily performed with the Alphabet classes.
Sequence objets also contain a name attribute and potentially several comment lines.
The gestion of sequence content is identical to the BasicSequence object, but edition events are properly fired. Listener are therefore properly handled.
Definition at line 118 of file SequenceWithAnnotation.h.
SequenceWithAnnotation::SequenceWithAnnotation | ( | const Alphabet * | alpha | ) |
SequenceWithAnnotation::SequenceWithAnnotation | ( | const std::string & | name, |
const std::string & | sequence, | ||
const Alphabet * | alpha | ||
) | |||
throw | ( | BadCharException | |
) |
Direct constructor: build a Sequence object from a std::string You can use it safely for RNA, DNA and protein sequences.
It can be used with codon sequences too, the std::string will be cut into parts of size 3. But for more complicated alphabets, you should use one complete constructors.
name | The sequence name. |
sequence | The whole sequence to be parsed as a std::string. |
alpha | A pointer toward the alphabet to be used with this sequence. |
Definition at line 61 of file SequenceWithAnnotation.cpp.
SequenceWithAnnotation::SequenceWithAnnotation | ( | const std::string & | name, |
const std::string & | sequence, | ||
const Comments & | comments, | ||
const Alphabet * | alpha | ||
) | |||
throw | ( | BadCharException | |
) |
Direct constructor: build a Sequence object from a std::string.
You can use it safely for RNA, DNA and protein sequences.
It can be used with codon sequences too, the std::string will be cut into tokens of size 3. But for more complicated alphabets, you should use one complete constructors.
name | The sequence name. |
sequence | The whole sequence to be parsed as a std::string. |
comments | Comments to add to the sequence. |
alpha | A pointer toward the alphabet to be used with this sequence. |
Definition at line 71 of file SequenceWithAnnotation.cpp.
SequenceWithAnnotation::SequenceWithAnnotation | ( | const std::string & | name, |
const std::vector< std::string > & | sequence, | ||
const Alphabet * | alpha | ||
) | |||
throw | ( | BadCharException | |
) |
General purpose constructor, can be used with any alphabet.
You should note that the sequence is stored as a std::vector of int. Hence each std::string in the std::vector will be translated using the alphabet object.
name | The sequence name. |
sequence | The sequence content. |
alpha | A pointer toward the alphabet to be used with this sequence. |
Definition at line 81 of file SequenceWithAnnotation.cpp.
SequenceWithAnnotation::SequenceWithAnnotation | ( | const std::string & | name, |
const std::vector< std::string > & | sequence, | ||
const Comments & | comments, | ||
const Alphabet * | alpha | ||
) | |||
throw | ( | BadCharException | |
) |
General purpose constructor, can be used with any alphabet.
You should note that the sequence is stored as a std::vector of int. Hence each std::string in the std::vector will be translated using the alphabet object.
name | The sequence name. |
sequence | The sequence content. |
comments | Comments to add to the sequence. |
alpha | A pointer toward the alphabet to be used with this sequence. |
Definition at line 88 of file SequenceWithAnnotation.cpp.
SequenceWithAnnotation::SequenceWithAnnotation | ( | const std::string & | name, |
const std::vector< int > & | sequence, | ||
const Alphabet * | alpha | ||
) | |||
throw | ( | BadIntException | |
) |
General purpose constructor, can be used with any alphabet.
name | The sequence name. |
sequence | The sequence content. |
alpha | A pointer toward the alphabet to be used with this sequence. |
Definition at line 95 of file SequenceWithAnnotation.cpp.
SequenceWithAnnotation::SequenceWithAnnotation | ( | const std::string & | name, |
const std::vector< int > & | sequence, | ||
const Comments & | comments, | ||
const Alphabet * | alpha | ||
) | |||
throw | ( | BadIntException | |
) |
General purpose constructor, can be used with any alphabet.
name | The sequence name. |
sequence | The sequence content. |
comments | Comments to add to the sequence. |
alpha | A pointer toward the alphabet to be used with this sequence. |
Definition at line 102 of file SequenceWithAnnotation.cpp.
SequenceWithAnnotation::SequenceWithAnnotation | ( | const Sequence & | s | ) |
The Sequence generic copy constructor. This does not perform a hard copy of the alphabet object.
Definition at line 111 of file SequenceWithAnnotation.cpp.
SequenceWithAnnotation::SequenceWithAnnotation | ( | const SequenceWithAnnotation & | s | ) |
The Sequence copy constructor. This does not perform a hard copy of the alphabet object.
Definition at line 117 of file SequenceWithAnnotation.cpp.
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inlinevirtual |
Definition at line 244 of file SequenceWithAnnotation.h.
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inlinevirtual |
Add a new annotation to the sequence.
anno | The annotation object to be added. Unless the annotation is shared, the annotation object will be owned by the sequence object, and will be copied and deleted when needed. |
Exception | If the annotation is not valid for this sequence. |
Definition at line 380 of file SequenceWithAnnotation.h.
References bpp::EdSymbolList::addSymbolListListener().
Referenced by bpp::SequenceWithAnnotationTools::createMaskAnnotation(), and bpp::SequenceWithQuality::SequenceWithQuality().
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pure virtualinherited |
Add a character to the end of the list.
c | The character to add, given as a string. |
Implemented in bpp::SequenceWithQuality, bpp::EdSymbolList, and bpp::BasicSymbolList.
Referenced by bpp::SequenceTools::getPutativeHaplotypes(), bpp::AbstractReverseTransliterator::reverse(), and bpp::AbstractTransliterator::translate().
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pure virtualinherited |
Add a character at a certain position in the list.
pos | The postion where to insert the element. |
c | The character to add, given as a string. |
Implemented in bpp::SequenceWithQuality, bpp::EdSymbolList, and bpp::BasicSymbolList.
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pure virtualinherited |
Add a character to the end of the list.
v | The character to add, given as an int. |
Implemented in bpp::SequenceWithQuality, bpp::EdSymbolList, and bpp::BasicSymbolList.
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pure virtualinherited |
Add a character at a certain position in the list.
pos | The postion where to insert the element. |
v | The character to add, given as an int. |
Implemented in bpp::SequenceWithQuality, bpp::EdSymbolList, and bpp::BasicSymbolList.
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virtualinherited |
Add a character to the end of the list.
c | The character to add, given as a string. |
Implements bpp::SymbolList.
Reimplemented in bpp::SequenceWithQuality.
Definition at line 321 of file SymbolList.cpp.
Referenced by bpp::SequenceWithQuality::addElement().
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virtualinherited |
Add a character at a certain position in the list.
pos | The postion where to insert the element. |
c | The character to add, given as a string. |
Implements bpp::SymbolList.
Reimplemented in bpp::SequenceWithQuality.
Definition at line 331 of file SymbolList.cpp.
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virtualinherited |
Add a character to the end of the list.
v | The character to add, given as an int. |
Implements bpp::SymbolList.
Reimplemented in bpp::SequenceWithQuality.
Definition at line 394 of file SymbolList.cpp.
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virtualinherited |
Add a character at a certain position in the list.
pos | The postion where to insert the element. |
v | The character to add, given as an int. |
Implements bpp::SymbolList.
Reimplemented in bpp::SequenceWithQuality.
Definition at line 406 of file SymbolList.cpp.
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inlinevirtualinherited |
Definition at line 657 of file SymbolList.h.
References bpp::EdSymbolList::listeners_.
Referenced by addAnnotation().
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inlineprotectedvirtualinherited |
Definition at line 670 of file SymbolList.h.
Referenced by bpp::EdSymbolList::fireAfterSequenceChanged().
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inlineprotectedvirtualinherited |
Definition at line 674 of file SymbolList.h.
Referenced by bpp::EdSymbolList::fireAfterSequenceDeleted().
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inlineprotectedvirtualinherited |
Definition at line 672 of file SymbolList.h.
Referenced by bpp::EdSymbolList::fireAfterSequenceInserted().
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inlineprotectedvirtualinherited |
Definition at line 676 of file SymbolList.h.
Referenced by bpp::EdSymbolList::fireAfterSequenceSubstituted().
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virtual |
Append the specified content to the sequence.
content | The content to append to the sequence. |
BadIntException | If the content does not match the current alphabet. |
Implements bpp::Sequence.
Reimplemented in bpp::SequenceWithQuality.
Definition at line 206 of file SequenceWithAnnotation.cpp.
Referenced by bpp::SequenceWithQuality::append().
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virtual |
Append the specified content to the sequence.
content | The content to append to the sequence. |
BadCharException | If the content does not match the current alphabet. |
Implements bpp::Sequence.
Reimplemented in bpp::SequenceWithQuality.
Definition at line 221 of file SequenceWithAnnotation.cpp.
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virtual |
Append the specified content to the sequence.
content | The content to append to the sequence. |
BadCharException | If the content does not match the current alphabet. |
Implements bpp::Sequence.
Reimplemented in bpp::SequenceWithQuality.
Definition at line 237 of file SequenceWithAnnotation.cpp.
References bpp::StringSequenceTools::codeSequence().
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inlineprotectedvirtualinherited |
Definition at line 669 of file SymbolList.h.
Referenced by bpp::EdSymbolList::fireBeforeSequenceChanged().
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inlineprotectedvirtualinherited |
Definition at line 673 of file SymbolList.h.
Referenced by bpp::EdSymbolList::fireBeforeSequenceDeleted().
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inlineprotectedvirtualinherited |
Definition at line 671 of file SymbolList.h.
Referenced by bpp::EdSymbolList::fireBeforeSequenceInserted().
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inlineprotectedvirtualinherited |
Definition at line 675 of file SymbolList.h.
Referenced by bpp::EdSymbolList::fireBeforeSequenceSubstituted().
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inlinevirtual |
Implements bpp::Sequence.
Reimplemented in bpp::SequenceWithQuality.
Definition at line 253 of file SequenceWithAnnotation.h.
References SequenceWithAnnotation().
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pure virtualinherited |
Delete the element at position 'pos'.
pos | The position of the element to delete. |
Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.
Referenced by bpp::SequenceTools::getCDS(), bpp::SequenceTools::removeGaps(), and bpp::VectorSiteContainer::removeSequence().
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virtualinherited |
Delete the element at position 'pos'.
pos | The position of the element to delete. |
Implements bpp::SymbolList.
Definition at line 369 of file SymbolList.cpp.
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pure virtualinherited |
Delete the elements at position 'pos'.
pos | The position of the first element to delete. |
len | The length of the region to delete. |
Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.
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virtualinherited |
Delete the elements at position 'pos'.
pos | The position of the first element to delete. |
len | The length of the region to delete. |
Implements bpp::SymbolList.
Definition at line 381 of file SymbolList.cpp.
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inlineprotectedinherited |
Definition at line 685 of file SymbolList.h.
References bpp::EdSymbolList::afterSequenceChanged(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.
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inlineprotectedinherited |
Definition at line 713 of file SymbolList.h.
References bpp::EdSymbolList::afterSequenceDeleted(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.
Referenced by setToSizeL(), and setToSizeR().
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inlineprotectedinherited |
Definition at line 699 of file SymbolList.h.
References bpp::EdSymbolList::afterSequenceInserted(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.
Referenced by setToSizeL(), and setToSizeR().
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inlineprotectedinherited |
Definition at line 727 of file SymbolList.h.
References bpp::EdSymbolList::afterSequenceSubstituted(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.
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inlineprotectedinherited |
Definition at line 678 of file SymbolList.h.
References bpp::EdSymbolList::beforeSequenceChanged(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.
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inlineprotectedinherited |
Definition at line 706 of file SymbolList.h.
References bpp::EdSymbolList::beforeSequenceDeleted(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.
Referenced by setToSizeL(), and setToSizeR().
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inlineprotectedinherited |
Definition at line 692 of file SymbolList.h.
References bpp::EdSymbolList::beforeSequenceInserted(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.
Referenced by setToSizeL(), and setToSizeR().
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inlineprotectedinherited |
Definition at line 720 of file SymbolList.h.
References bpp::EdSymbolList::beforeSequenceSubstituted(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.
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pure virtualinherited |
Get the alphabet associated to the list.
Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.
Referenced by bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::SymbolListTools::changeUnresolvedCharactersToGaps(), bpp::SequenceTools::findFirstOf(), bpp::SequenceTools::getCDS(), bpp::SymbolListTools::getCounts(), bpp::SequenceTools::getNumberOfCompleteSites(), bpp::SequenceTools::getNumberOfSites(), bpp::SequenceTools::getNumberOfUnresolvedSites(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::SequenceTools::getSequenceWithCompleteSites(), bpp::SequenceTools::getSequenceWithoutGaps(), bpp::SequenceTools::invertComplement(), bpp::BasicSymbolList::operator=(), bpp::EdSymbolList::operator=(), and bpp::SequenceTools::removeGaps().
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inlinevirtualinherited |
Get the alphabet associated to the list.
Implements bpp::SymbolList.
Definition at line 599 of file SymbolList.h.
References bpp::EdSymbolList::alphabet_.
Referenced by bpp::SequenceWithQuality::append(), bpp::EdSymbolList::operator=(), bpp::SequenceWithQualityTools::removeGaps(), setToSizeL(), and setToSizeR().
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inlinevirtual |
Definition at line 397 of file SequenceWithAnnotation.h.
References bpp::EdSymbolList::getListener(), bpp::EdSymbolList::getNumberOfListeners(), and bpp::SequenceAnnotation::getType().
Referenced by bpp::SequenceWithQuality::operator=(), and bpp::SequenceWithQuality::SequenceWithQuality().
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inlinevirtual |
Definition at line 407 of file SequenceWithAnnotation.h.
References bpp::EdSymbolList::getListener(), bpp::EdSymbolList::getNumberOfListeners(), and bpp::SequenceAnnotation::getType().
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virtual |
Definition at line 244 of file SequenceWithAnnotation.cpp.
References bpp::EdSymbolList::getListener(), bpp::EdSymbolList::getNumberOfListeners(), and bpp::SequenceAnnotation::getType().
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pure virtualinherited |
Get the element at position 'pos' as a character.
pos | The position of the character to retrieve. |
Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.
Referenced by bpp::SiteContainerTools::resolveDottedAlignment().
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virtualinherited |
Get the element at position 'pos' as a character.
pos | The position of the character to retrieve. |
Implements bpp::SymbolList.
Definition at line 354 of file SymbolList.cpp.
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inlinevirtual |
Get the comments associated to this sequence.
Implements bpp::Sequence.
Definition at line 290 of file SequenceWithAnnotation.h.
References comments_.
Referenced by operator=().
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pure virtualinherited |
Get the whole content of the list as a vector of int.
Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.
Referenced by bpp::SequenceWithQualityTools::complement(), bpp::AbstractSequenceContainer::getContent(), bpp::SymbolListTools::getCounts(), bpp::BasicSymbolList::operator=(), bpp::EdSymbolList::operator=(), bpp::SequenceWithQualityTools::reverseTranscript(), and bpp::SequenceWithQualityTools::transcript().
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inlinevirtualinherited |
Get the whole content of the list as a vector of int.
Implements bpp::SymbolList.
Definition at line 603 of file SymbolList.h.
References bpp::EdSymbolList::content_.
Referenced by bpp::SequenceWithQualityTools::invert(), and bpp::EdSymbolList::operator=().
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inlinevirtualinherited |
Definition at line 647 of file SymbolList.h.
References bpp::EdSymbolList::listeners_.
Referenced by getAnnotation(), getAnnotationTypes(), and hasAnnotation().
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inlinevirtualinherited |
Definition at line 652 of file SymbolList.h.
References bpp::EdSymbolList::listeners_.
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inlinevirtual |
Get the name of this sequence.
Implements bpp::Sequence.
Definition at line 268 of file SequenceWithAnnotation.h.
References name_.
Referenced by operator=().
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inlinevirtualinherited |
Definition at line 645 of file SymbolList.h.
References bpp::EdSymbolList::listeners_.
Referenced by getAnnotation(), getAnnotationTypes(), and hasAnnotation().
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pure virtualinherited |
Get the element at position 'pos' as an int.
pos | The position of the character to retrieve. |
Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.
Referenced by bpp::SequenceTools::findFirstOf(), bpp::SequenceTools::invert(), and bpp::SequenceTools::invertComplement().
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virtualinherited |
Get the element at position 'pos' as an int.
pos | The position of the character to retrieve. |
Implements bpp::SymbolList.
Definition at line 434 of file SymbolList.cpp.
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inlinevirtual |
Definition at line 386 of file SequenceWithAnnotation.h.
References bpp::EdSymbolList::getListener(), bpp::EdSymbolList::getNumberOfListeners(), and bpp::SequenceAnnotation::getType().
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virtual |
Merge a sequence with the current one.
Sequences must have the same name and alphabets. Only first sequence's commentaries are kept. Annotations that could not be merged will not be added in the concatenated sequence. See the documentation of each annotation class for more details.
swa | The sequence to merge with. |
AlphabetMismatchException | If the two alphabets do not match. |
Exception | If the sequence names do not match. |
Definition at line 257 of file SequenceWithAnnotation.cpp.
References bpp::SequenceAnnotation::clone(), bpp::SequenceAnnotation::init(), and bpp::SequenceAnnotation::merge().
SequenceWithAnnotation & SequenceWithAnnotation::operator= | ( | const Sequence & | s | ) |
The Sequence generic assignment operator. This does not perform a hard copy of the alphabet object.
Definition at line 125 of file SequenceWithAnnotation.cpp.
References comments_, bpp::Sequence::getComments(), bpp::Sequence::getName(), name_, and bpp::EdSymbolList::operator=().
Referenced by bpp::SequenceWithQuality::operator=().
SequenceWithAnnotation & SequenceWithAnnotation::operator= | ( | const SequenceWithAnnotation & | s | ) |
The Sequence assignment operator. This does not perform a hard copy of the alphabet object.
Definition at line 133 of file SequenceWithAnnotation.cpp.
References comments_, getComments(), getName(), name_, and bpp::EdSymbolList::operator=().
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pure virtualinherited |
Operator [] overloaded for quick access to a character in list.
i | The position to retrieve. |
Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.
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pure virtualinherited |
Operator [] overloaded for quick access to a character in list.
i | The position to retrieve. |
Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.
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inlinevirtualinherited |
Operator [] overloaded for quick access to a character in list.
i | The position to retrieve. |
Implements bpp::SymbolList.
Definition at line 631 of file SymbolList.h.
References bpp::EdSymbolList::content_.
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inlinevirtualinherited |
Operator [] overloaded for quick access to a character in list.
i | The position to retrieve. |
Implements bpp::SymbolList.
Definition at line 633 of file SymbolList.h.
References bpp::EdSymbolList::content_.
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inlineprotectedinherited |
Definition at line 736 of file SymbolList.h.
References bpp::EdSymbolList::propagateEvents_.
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inlineprotectedinherited |
Definition at line 737 of file SymbolList.h.
References bpp::EdSymbolList::propagateEvents_.
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inlinevirtualinherited |
Definition at line 661 of file SymbolList.h.
References bpp::SymbolListListener::isRemovable(), and bpp::EdSymbolList::listeners_.
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inlinevirtual |
Set the comments associated to this sequence.
comments | The new comments of the sequence. |
Implements bpp::Sequence.
Definition at line 297 of file SequenceWithAnnotation.h.
References comments_.
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virtual |
Set the whole content of the sequence.
sequence | The new content of the sequence. |
Implements bpp::Sequence.
Definition at line 143 of file SequenceWithAnnotation.cpp.
References bpp::StringSequenceTools::codeSequence().
Referenced by bpp::SequenceWithQualityTools::removeGaps().
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inlinevirtual |
Set the whole content of the list.
list | The new content of the list. |
Implements bpp::Sequence.
Definition at line 315 of file SequenceWithAnnotation.h.
References bpp::EdSymbolList::setContent().
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inlinevirtual |
Set the whole content of the list.
list | The new content of the list. |
Implements bpp::Sequence.
Definition at line 319 of file SequenceWithAnnotation.h.
References bpp::EdSymbolList::setContent().
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pure virtualinherited |
Set the element at position 'pos' to character 'c'.
pos | The position of the character to set. |
c | The value of the element, given as a string. |
Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.
Referenced by bpp::SequenceTools::invert(), and bpp::SequenceTools::invertComplement().
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pure virtualinherited |
Set the element at position 'pos' to character 'v'.
pos | The position of the character to set. |
v | The value of the element, given as an int. |
Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.
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virtualinherited |
Set the element at position 'pos' to character 'c'.
pos | The position of the character to set. |
c | The value of the element, given as a string. |
Implements bpp::SymbolList.
Definition at line 342 of file SymbolList.cpp.
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virtualinherited |
Set the element at position 'pos' to character 'v'.
pos | The position of the character to set. |
v | The value of the element, given as an int. |
Implements bpp::SymbolList.
Definition at line 420 of file SymbolList.cpp.
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inlinevirtual |
Set the name of this sequence.
name | The new name of the sequence. |
Implements bpp::Sequence.
Definition at line 275 of file SequenceWithAnnotation.h.
References name_.
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virtual |
Set up the size of a sequence from the left side.
All new characters are filled with gaps. If the specified size is < to the sequence size, the sequence will be truncated.
newSize | The new size of the sequence. |
Implements bpp::Sequence.
Definition at line 180 of file SequenceWithAnnotation.cpp.
References bpp::EdSymbolList::content_, bpp::EdSymbolList::fireAfterSequenceDeleted(), bpp::EdSymbolList::fireAfterSequenceInserted(), bpp::EdSymbolList::fireBeforeSequenceDeleted(), bpp::EdSymbolList::fireBeforeSequenceInserted(), bpp::EdSymbolList::getAlphabet(), and bpp::Alphabet::getGapCharacterCode().
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virtual |
Set up the size of a sequence from the right side.
All new characters are filled with gaps. If the specified size is < to the sequence size, the sequence will be truncated.
newSize | The new size of the sequence. |
Implements bpp::Sequence.
Definition at line 155 of file SequenceWithAnnotation.cpp.
References bpp::EdSymbolList::content_, bpp::EdSymbolList::fireAfterSequenceDeleted(), bpp::EdSymbolList::fireAfterSequenceInserted(), bpp::EdSymbolList::fireBeforeSequenceDeleted(), bpp::EdSymbolList::fireBeforeSequenceInserted(), bpp::EdSymbolList::getAlphabet(), and bpp::Alphabet::getGapCharacterCode().
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pure virtualinherited |
Randomly shuffle the content of the list, with linear complexity.
Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.
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inlinevirtualinherited |
Randomly shuffle the content of the list, with linear complexity.
Implements bpp::SymbolList.
Definition at line 635 of file SymbolList.h.
References bpp::EdSymbolList::content_.
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pure virtualinherited |
Get the number of elements in the list.
Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.
Referenced by bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::SymbolListTools::changeUnresolvedCharactersToGaps(), bpp::SequenceTools::findFirstOf(), bpp::SiteContainerTools::getAlignmentPositions(), bpp::SequenceTools::getCDS(), bpp::GeneticCode::getCodingSequence(), bpp::SymbolListTools::getFrequencies(), bpp::SequenceTools::getNumberOfCompleteSites(), bpp::SequenceTools::getNumberOfSites(), bpp::SequenceTools::getNumberOfUnresolvedSites(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::SiteContainerTools::getSequencePositions(), bpp::SequenceTools::getSequenceWithCompleteSites(), bpp::SequenceTools::getSequenceWithoutGaps(), bpp::SequenceMask::init(), bpp::SequenceQuality::init(), bpp::SequenceTools::invert(), bpp::SequenceTools::invertComplement(), bpp::SequenceTools::removeGaps(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::SequenceContainerTools::sequencesHaveTheSameLength(), and bpp::SequenceWalker::SequenceWalker().
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inlinevirtualinherited |
Get the number of elements in the list.
Implements bpp::SymbolList.
Definition at line 601 of file SymbolList.h.
References bpp::EdSymbolList::content_.
Referenced by bpp::SequenceWithQuality::addElement(), bpp::SequenceMask::isValidWith(), bpp::SequenceQuality::isValidWith(), and bpp::SequenceWithQualityTools::removeGaps().
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pure virtualinherited |
Convert the list as a string.
This method is useful for dumping a list to a file or to the screen for display.
Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.
Referenced by bpp::AbstractSequenceContainer::toString().
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virtualinherited |
Convert the list as a string.
This method is useful for dumping a list to a file or to the screen for display.
Implements bpp::SymbolList.
Definition at line 314 of file SymbolList.cpp.
References bpp::EdSymbolList::alphabet_, bpp::EdSymbolList::content_, and bpp::StringSequenceTools::decodeSequence().
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private |
The sequence comments.
Definition at line 132 of file SequenceWithAnnotation.h.
Referenced by getComments(), operator=(), and setComments().
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protectedinherited |
The list content.
Definition at line 518 of file SymbolList.h.
Referenced by bpp::EdSymbolList::getContent(), bpp::EdSymbolList::operator=(), bpp::EdSymbolList::operator[](), setToSizeL(), setToSizeR(), bpp::EdSymbolList::shuffle(), bpp::EdSymbolList::size(), and bpp::EdSymbolList::toString().
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protectedinherited |
Contains the listeners.
Definition at line 523 of file SymbolList.h.
Referenced by bpp::EdSymbolList::addSymbolListListener(), bpp::EdSymbolList::EdSymbolList(), bpp::EdSymbolList::fireAfterSequenceChanged(), bpp::EdSymbolList::fireAfterSequenceDeleted(), bpp::EdSymbolList::fireAfterSequenceInserted(), bpp::EdSymbolList::fireAfterSequenceSubstituted(), bpp::EdSymbolList::fireBeforeSequenceChanged(), bpp::EdSymbolList::fireBeforeSequenceDeleted(), bpp::EdSymbolList::fireBeforeSequenceInserted(), bpp::EdSymbolList::fireBeforeSequenceSubstituted(), bpp::EdSymbolList::getListener(), bpp::EdSymbolList::getNumberOfListeners(), bpp::EdSymbolList::operator=(), bpp::EdSymbolList::removeSymbolListListener(), and bpp::EdSymbolList::~EdSymbolList().
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private |
The sequence name.
Definition at line 127 of file SequenceWithAnnotation.h.
Referenced by getName(), operator=(), and setName().