BALL::NucleicAcid Class Reference
[Molecular Datastructures]
#include <BALL/KERNEL/nucleicAcid.h>
Public Types | |
Enums | |
| enum | Property { NUMBER_OF_PROPERTIES = Molecule::NUMBER_OF_PROPERTIES } |
Public Member Functions | |
| bool | operator== (const NucleicAcid &nucleic_acid) const |
| bool | operator!= (const NucleicAcid &nucleic_acid) const |
Constructors and Destructors | |
| NucleicAcid () | |
| NucleicAcid (const NucleicAcid &nucleic_acid, bool deep=true) | |
| NucleicAcid (const String &name, const String &id=BALL_NUCLEICACID_DEFAULT_ID) | |
| virtual | ~NucleicAcid () |
| virtual void | clear () |
| virtual void | destroy () |
Persistence | |
| void | persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException) |
| void | persistentRead (PersistenceManager &pm) throw (Exception::GeneralException) |
Assignment Methods | |
| void | set (const NucleicAcid &nucleic_acid, bool deep=true) |
| NucleicAcid & | operator= (const NucleicAcid &nucleic_acid) |
| void | get (NucleicAcid &nucleic_acid, bool deep=true) const |
| void | swap (NucleicAcid &nucleic_acid) |
Accessors | |
| Nucleotide * | getNucleotide (Position position) |
| const Nucleotide * | getNucleotide (Position position) const |
| Nucleotide * | get3Prime () |
| const Nucleotide * | get3Prime () const |
| Nucleotide * | get5Prime () |
| const Nucleotide * | get5Prime () const |
| void | setID (const String &id) |
| const String & | getID () const |
| Size | countNucleotides () const |
Debugging and Diagnostics | |
| virtual bool | isValid () const |
| virtual void | dump (std::ostream &s=std::cout, Size depth=0) const |
Private Attributes | |
| String | id_ |
Detailed Description
Nucleic acid class.
Definition at line 29 of file nucleicAcid.h.
Member Enumeration Documentation
Constructor & Destructor Documentation
| BALL::NucleicAcid::NucleicAcid | ( | ) |
Default constructor.
| BALL::NucleicAcid::NucleicAcid | ( | const NucleicAcid & | nucleic_acid, | |
| bool | deep = true | |||
| ) |
Copy constructor.
| BALL::NucleicAcid::NucleicAcid | ( | const String & | name, | |
| const String & | id = BALL_NUCLEICACID_DEFAULT_ID | |||
| ) |
Detailed constructor.
| virtual BALL::NucleicAcid::~NucleicAcid | ( | ) | [virtual] |
Destructor.
Member Function Documentation
| virtual void BALL::NucleicAcid::clear | ( | ) | [virtual] |
Clear the contents of the nucleic acid.
Reimplemented from BALL::AtomContainer.
| Size BALL::NucleicAcid::countNucleotides | ( | ) | const |
Return the number of Nucleotides contained in this instance NucleicAcid.
- Returns:
- Size - number of Nucleotides
| virtual void BALL::NucleicAcid::destroy | ( | ) | [virtual] |
Clear the contents of the nucleic acid and remove it from parent kernel objects.
Reimplemented from BALL::AtomContainer.
| virtual void BALL::NucleicAcid::dump | ( | std::ostream & | s = std::cout, |
|
| Size | depth = 0 | |||
| ) | const [virtual] |
Internal state dump. Dump the current internal state of this instance to the output ostream s with dumping depth depth .
- Parameters:
-
s - output stream where to output the internal state of this instance depth - the dumping depth
Reimplemented from BALL::Molecule.
| void BALL::NucleicAcid::get | ( | NucleicAcid & | nucleic_acid, | |
| bool | deep = true | |||
| ) | const |
Assign a NucleicAcid object from another.
| const Nucleotide* BALL::NucleicAcid::get3Prime | ( | ) | const |
Retrieve a const pointer to the nucleotide at the 3'-end of this instance. The pointer is 0 if this instance does not have a Nucleotide.
- Returns:
- Nucleotide* - constant pointer to the first child Nucleotide
| Nucleotide* BALL::NucleicAcid::get3Prime | ( | ) |
Retrieve a pointer to the Nucleotide at the 3'-end of this instance. The pointer is 0 if this instance does not have a Nucleotide.
- Returns:
- Nucleotide* - mutable pointer to the first child Nucleotide
| const Nucleotide* BALL::NucleicAcid::get5Prime | ( | ) | const |
Retrieve a const pointer to the Nucleotide at the 5'-end of this instance. The pointer is 0 if this instance does not have a Nucleotide.
- Returns:
- Nucleotide* - constant pointer to the last child Nucleotide
| Nucleotide* BALL::NucleicAcid::get5Prime | ( | ) |
Retrieve a pointer to the Nucleotide at the 5'-end of this instance. The pointer is 0 if this instance does not have a Nucleotide.
- Returns:
- Nucleotide* - mutable pointer to the last child Nucleotide
| const String& BALL::NucleicAcid::getID | ( | ) | const |
Retrieve the ID of the NucleicAcid.
- Returns:
- String the ID
| const Nucleotide* BALL::NucleicAcid::getNucleotide | ( | Position | position | ) | const |
Get a pointer to a child Nucleotide at a given position. The pointer is 0 if this instance does not have a Nucleotide at the given position.
- Parameters:
-
position the position of the child Nucleotide
- Returns:
- Nucleotide* - constant pointer to the child Nucleotide at positon
| Nucleotide* BALL::NucleicAcid::getNucleotide | ( | Position | position | ) |
Get a pointer to a child Nucleotide at a given position. The pointer is 0 if this instance does not have a Nucleotide at the given position.
- Parameters:
-
position the position of the child Nucleotide
- Returns:
- Nucleotide* - mutable pointer to the child Nucleotide at positon
| virtual bool BALL::NucleicAcid::isValid | ( | ) | const [virtual] |
Internal state and consistency self-validation.
- Returns:
- bool -
trueif the internal state of this instance atom is correct (self-validated) and consistent,falseotherwise
Reimplemented from BALL::AtomContainer.
| bool BALL::NucleicAcid::operator!= | ( | const NucleicAcid & | nucleic_acid | ) | const |
Inequality operator
- See also:
- operator ==
| NucleicAcid& BALL::NucleicAcid::operator= | ( | const NucleicAcid & | nucleic_acid | ) |
Assignment operator.
| bool BALL::NucleicAcid::operator== | ( | const NucleicAcid & | nucleic_acid | ) | const |
Equality operator. Two nucleic acids are equal if they have the same handle.
- See also:
- Object::operator ==.
| void BALL::NucleicAcid::persistentRead | ( | PersistenceManager & | pm | ) | throw (Exception::GeneralException) [virtual] |
Reads a NucleicAcid object from a persistent stream.
- Parameters:
-
pm the persistence manager
Reimplemented from BALL::Molecule.
| void BALL::NucleicAcid::persistentWrite | ( | PersistenceManager & | pm, | |
| const char * | name = 0 | |||
| ) | const throw (Exception::GeneralException) [virtual] |
Writes a NucleicAcid object to a persistent stream.
- Parameters:
-
pm the persistence manager
Reimplemented from BALL::Molecule.
| void BALL::NucleicAcid::set | ( | const NucleicAcid & | nucleic_acid, | |
| bool | deep = true | |||
| ) |
Assignment with cloning facility. The assignment is either deep or shallow (default).
- Parameters:
-
nucleic_acid the NucleicAcid to be copied (cloned) deep make a deep (= true) or shallow (=false) copy
| void BALL::NucleicAcid::setID | ( | const String & | id | ) |
Set the ID of the NucleicAcid.
- Parameters:
-
id the new ID
| void BALL::NucleicAcid::swap | ( | NucleicAcid & | nucleic_acid | ) |
Swap the contents of two NucleicAcid objects.
Member Data Documentation
String BALL::NucleicAcid::id_ [private] |
Definition at line 235 of file nucleicAcid.h.
