#include <Bpp/Seq/Container/SequencedValuesContainer.h>
Definition at line 30 of file SequencedValuesContainer.h.
◆ clear()
| virtual void bpp::SequencedValuesContainer::clear |
( |
| ) |
|
|
pure virtual |
Delete all data in the container.
◆ createEmptyContainer()
Return a copy of this container, but with no data inside.
This method creates a new SequencedValuesContainer object. The class of this container depends on the derivative class.
- Returns
- A new empty container, with the same alphabet as this one.
◆ deleteGeneralComments()
| virtual void bpp::SequencedValuesContainer::deleteGeneralComments |
( |
| ) |
|
|
pure virtual |
Delete the comments associated to this container.
◆ getAlphabet()
| virtual const Alphabet* bpp::SequencedValuesContainer::getAlphabet |
( |
| ) |
const |
|
pure virtual |
Get container's alphabet.
- Returns
- The alphabet associated to this container.
◆ getComments()
| virtual const Comments& bpp::SequencedValuesContainer::getComments |
( |
const std::string & |
name | ) |
const |
|
pure virtual |
Get comments of a particular sequence.
- Parameters
-
| name | The name of the sequence. |
- Returns
- The comments associated to sequence with name 'name'.
- Exceptions
-
◆ getGeneralComments()
| virtual const Comments& bpp::SequencedValuesContainer::getGeneralComments |
( |
| ) |
const |
|
pure virtual |
Get the comments of this container.
- Returns
- The comments associated to this container.
◆ getNumberOfSequences()
| virtual size_t bpp::SequencedValuesContainer::getNumberOfSequences |
( |
| ) |
const |
|
pure virtual |
Get the number of sequences in the container.
- Returns
- The number of sequences in the container.
◆ getSequenceNames()
| virtual std::vector<std::string> bpp::SequencedValuesContainer::getSequenceNames |
( |
| ) |
const |
|
pure virtual |
Get all the names of the sequences in the container.
- Returns
- A vector of strings with all sequence names.
◆ getStateValueAt()
| virtual double bpp::SequencedValuesContainer::getStateValueAt |
( |
size_t |
siteIndex, |
|
|
const std::string & |
sequenceName, |
|
|
int |
state |
|
) |
| const |
|
pure virtual |
get value of a state in a position
- Parameters
-
| siteIndex | index of the site |
| sequenceName | name of the sequence in the container |
| state | state in the alphabet |
◆ hasSequence()
| virtual bool bpp::SequencedValuesContainer::hasSequence |
( |
const std::string & |
name | ) |
const |
|
pure virtual |
Check if a sequence with a given name is present in the container.
- Parameters
-
| name | The name of the sequence. |
- Returns
- True if a sequence with the given name is present in the container.
◆ operator()()
| virtual double bpp::SequencedValuesContainer::operator() |
( |
size_t |
siteIndex, |
|
|
const std::string & |
sequenceName, |
|
|
int |
state |
|
) |
| const |
|
pure virtual |
◆ setComments()
| virtual void bpp::SequencedValuesContainer::setComments |
( |
const std::string & |
name, |
|
|
const Comments & |
comments |
|
) |
| |
|
pure virtual |
Set the comments of a particular sequence.
- Parameters
-
| name | The name of the sequence. |
| comments | The comments to set to sequence with name 'name'. |
- Exceptions
-
◆ setGeneralComments()
| virtual void bpp::SequencedValuesContainer::setGeneralComments |
( |
const Comments & |
comments | ) |
|
|
pure virtual |
Set the comments of this container.
- Parameters
-
| comments | The comments to be associated to this container. |
◆ setSequenceNames()
| virtual void bpp::SequencedValuesContainer::setSequenceNames |
( |
const std::vector< std::string > & |
names, |
|
|
bool |
checkNames |
|
) |
| |
|
pure virtual |
Set all sequence names.
- Parameters
-
| names | A vector of strings with all sequence names. Its size must be strictly equal to the the size of the container (the number of sequences). |
| checkNames | Tell if the container must check if the name of the sequence is already used in the container before adding it. |
- Exceptions
-
| Exception | If there are redundant names in the input vector. |
◆ toString()
| virtual std::string bpp::SequencedValuesContainer::toString |
( |
const std::string & |
name | ) |
const |
|
pure virtual |
Convert a particular sequence to a string.
- Parameters
-
| name | The name of the sequence. |
- Returns
- A string describing the content of the sequence.
- Exceptions
-
The documentation for this class was generated from the following file:
Inheritance diagram for bpp::SequencedValuesContainer:
