Represents a set of ontology terms. More...
#include <annotation.h>
Public Member Functions | |
| bool | Open (std::istream &istmSlim, const IOntology *pOntology) |
| void | GetGeneNames (std::vector< std::string > &vecstrGenes) const |
| const CGene & | GetGene (size_t iSlim, size_t iGene) const |
| Returns the gene at the requested index below the requested slim term. | |
| size_t | GetSlims () const |
| Returns the number of ontology terms in this slim. | |
| size_t | GetGenes (size_t iSlim) const |
| Returns the number of genes annotated below the given slim term. | |
| const std::string & | GetSlim (size_t iSlim) const |
| Returns the string ID of the ontology term at the given slim index. | |
| size_t | GetNodes (size_t iSlim) const |
| Returns the number of ontology terms in the requested slim. | |
| size_t | GetNode (size_t iSlim, size_t iTerm) const |
| Returns the ontology term ID at the requested index in the requested slim. | |
Detailed Description
Represents a set of ontology terms.
Modeled after the "GO Slim" sets of GO terms, CSlim represents any set of IOntology terms. A slim is generally opened from a text file listing ontology IDs and can be used in a variety of settings, e.g. functional enrichment or gold standard generation.
- See also:
- CDat::Open | CDataPair::Open
Definition at line 651 of file annotation.h.
Member Function Documentation
| const CGene& Sleipnir::CSlim::GetGene | ( | size_t | iSlim, |
| size_t | iGene | ||
| ) | const [inline] |
Returns the gene at the requested index below the requested slim term.
- Parameters:
-
iSlim Index of the slim term for which a gene are retrieved. iGene Index of the gene to retrieve.
- Returns:
- Gene annotated at the requested index below the requested slim term.
- Remarks:
- iSlim must be less than CSlim::GetSlims; iGene must be less than CSlim::GetGenes. All genes annotated recursively to descendants of the slim terms are considered.
- See also:
- IOntology::GetGenes
Definition at line 676 of file annotation.h.
| size_t Sleipnir::CSlim::GetGenes | ( | size_t | iSlim | ) | const [inline] |
Returns the number of genes annotated below the given slim term.
- Parameters:
-
iSlim Index of the slim term for which genes are retrieved.
- Returns:
- Number of genes annotated below the given slim term.
- Remarks:
- iSlim must be less than CSlim::GetSlims.
Definition at line 704 of file annotation.h.
Referenced by Sleipnir::CDat::Open().
| size_t Sleipnir::CSlim::GetNode | ( | size_t | iSlim, |
| size_t | iTerm | ||
| ) | const [inline] |
Returns the ontology term ID at the requested index in the requested slim.
- Parameters:
-
iSlim ID of slim. iTerm Index of ontology term to be returned.
- Returns:
- Ontology term at the requested index within the given slim.
- Remarks:
- No bounds checking is performed; iSlim must be less than GetSlims, and iTerm must be less than GetNodes.
- See also:
- GetNodes
Definition at line 761 of file annotation.h.
| size_t Sleipnir::CSlim::GetNodes | ( | size_t | iSlim | ) | const [inline] |
Returns the number of ontology terms in the requested slim.
- Parameters:
-
iSlim ID of slim.
- Returns:
- Number of ontology terms in the requested slim.
- See also:
- GetNode
Definition at line 738 of file annotation.h.
| const std::string& Sleipnir::CSlim::GetSlim | ( | size_t | iSlim | ) | const [inline] |
Returns the string ID of the ontology term at the given slim index.
- Parameters:
-
iSlim Index of the slim term to identify.
- Returns:
- String ID of the requested slim index.
- Remarks:
- iSlim must be less than CSlim::GetSlims.
Definition at line 721 of file annotation.h.
Referenced by Sleipnir::CDat::Open().
| size_t Sleipnir::CSlim::GetSlims | ( | ) | const [inline] |
Returns the number of ontology terms in this slim.
- Returns:
- Number of ontology terms in this slim.
Definition at line 687 of file annotation.h.
Referenced by Sleipnir::CDat::Open().
The documentation for this class was generated from the following file:
- src/annotation.h
