Represents a gene with a single primary unique identifier, zero or more synonyms, and zero or more functional annotations. More...
#include <genome.h>
Public Member Functions | |
| CGene (const std::string &strID) | |
| Create a new gene with the given primary identifier. | |
| bool | AddSynonym (const std::string &strName) |
| Appends the given synonym to the gene's synonym list. | |
| bool | AddAnnotation (const IOntology *pOntology, size_t iTerm) |
| Adds an annotation in the gene object to a specific functional ontology term. | |
| bool | SetWeight (float weight) |
| bool | IsAnnotated (const IOntology *pOntology) const |
| Return true if the gene is annotated within the given ontology. | |
| bool | IsAnnotated (const IOntology *pOntology, size_t iTerm) const |
| Return true if the gene is directly annotated to the given ontology term. | |
| const std::string & | GetName () const |
| Return the gene's primary identifier. | |
| size_t | GetSynonyms () const |
| Return the number of synonyms of the current gene. | |
| const std::string & | GetSynonym (size_t iSynonym) const |
| Return the requested synonym of the current gene. | |
| void | SetGloss (const std::string &strGloss) |
| Sets the human-readable text description of the gene. | |
| const std::string & | GetGloss () const |
| Return the human-readable text description of the gene. | |
| void | SetDubious (bool fDubious) |
| Sets whether the gene encodes a dubious reading frame. | |
| bool | GetDubious () const |
| Return whether the gene encodes a dubious reading frame. | |
| void | SetRNA (bool fRNA) |
| Sets whether the gene encodes an RNA gene. | |
| bool | GetRNA () const |
| Return whether the gene encodes an RNA gene. | |
| const float | GetWeight () const |
| Return weight of the gene. | |
| size_t | GetOntologies () const |
| Return the number of different ontologies in which this gene is annotated. | |
| const IOntology * | GetOntology (size_t iOntology) const |
| Return the ontology at the requested index. | |
| size_t | GetAnnotations (size_t iOntology) const |
| Return the number of annotations of this gene within the requested ontology. | |
| size_t | GetAnnotation (size_t iOntology, size_t iAnnotation) const |
| Return the ontology term index of the requested annotation. | |
Detailed Description
Represents a gene with a single primary unique identifier, zero or more synonyms, and zero or more functional annotations.
Uniquely identifying genes is a daunting task in many organisms; in yeast, almost every gene has a single transcript, a single protein, a single systematic name, and at most a few common names. In higher organisms, multiple transcripts, multiple naming schemes, and a lack of standards make consistent gene identification nearly impossible.
Fortunately or unfortunately, Sleipnir ignores most of this complexity. A Sleipnir gene consists of at least one unique systematic name - but that's it. A gene's primary identifier should be unique within its genome, and it can have zero or more (optionally unique) synonyms; CGenome does its best to disambiguate overlapping synonyms, but the primary identifier must be unique within a gene set of interest.
Each gene can also have an optional textual description (gloss), zero or more functional annotations tying it to IOntology objects, and reflective of Sleipnir's roots in yeast biology, genes can also be decorated with a few features indicating whether they encode dubious ORFs or RNA genes.
- Remarks:
- For clarity, this documentation will refer to a gene's unique primary identifier as its ID and to its optional synonyms as either synonyms or simply names.
- See also:
- CGenes
Constructor & Destructor Documentation
| Sleipnir::CGene::CGene | ( | const std::string & | strID | ) |
Create a new gene with the given primary identifier.
- Parameters:
-
strID Unique primary identifier of the new gene.
- See also:
- GetName
Definition at line 39 of file genome.cpp.
Member Function Documentation
| bool Sleipnir::CGene::AddAnnotation | ( | const IOntology * | pOntology, |
| size_t | iTerm | ||
| ) |
Adds an annotation in the gene object to a specific functional ontology term.
- Parameters:
-
pOntology Ontology into which the gene should be annotated. iTerm Ontology term to which the gene should be annotated.
- Returns:
- True if the annotation was added successfully.
Adds an annotation directly to the current gene based on the given ontology and functional term. This is usually called from from the appropriate IOntology implementation during parsing and is used to provide a local cache of direct annotations to the gene object.
- Remarks:
- This does not inform pOntology of the annotation, so if it is not already reflected in that ontology, the annotation will only be visible from the CGene object, not from the IOntology.
- See also:
- IsAnnotated
Definition at line 100 of file genome.cpp.
Referenced by Sleipnir::COntologyKEGG::Open().
| bool Sleipnir::CGene::AddSynonym | ( | const std::string & | strName | ) |
Appends the given synonym to the gene's synonym list.
- Parameters:
-
strName Synonym to be added.
- Returns:
- True if the synonym was successfully added.
- Remarks:
- Addition will fail if the synonym is the same as the gene's name or an existing synonym.
- See also:
- GetSynonym
Definition at line 198 of file genome.cpp.
Referenced by Sleipnir::CGenome::AddSynonym().
| size_t Sleipnir::CGene::GetAnnotation | ( | size_t | iOntology, |
| size_t | iAnnotation | ||
| ) | const [inline] |
Return the ontology term index of the requested annotation.
- Parameters:
-
iOntology Ontology index of requested annotation. iAnnotation Requested annotation index.
- Returns:
- Ontology term of the requested annotation.
- Remarks:
- For efficiency, no bounds checking is performed. The given indices must be smaller than GetOntologies and GetAnnotations.
| size_t Sleipnir::CGene::GetAnnotations | ( | size_t | iOntology | ) | const [inline] |
Return the number of annotations of this gene within the requested ontology.
- Parameters:
-
iOntology Ontology whose annotations should be counted.
- Returns:
- Number of annotations of this gene within the requested ontology.
- Remarks:
- For efficiency, no bounds checking is performed. The given index must be smaller than GetOntologies.
| bool Sleipnir::CGene::GetDubious | ( | ) | const [inline] |
Return whether the gene encodes a dubious reading frame.
- Returns:
- Dubious reading frame status.
- See also:
- SetDubious
| const std::string& Sleipnir::CGene::GetGloss | ( | ) | const [inline] |
Return the human-readable text description of the gene.
- Returns:
- Human-readable text description of the gene.
- See also:
- SetGloss
Definition at line 137 of file genome.h.
Referenced by Sleipnir::CDat::SaveMATISSE().
| const std::string& Sleipnir::CGene::GetName | ( | ) | const [inline] |
Return the gene's primary identifier.
- Returns:
- Gene's primary identifier.
Definition at line 78 of file genome.h.
Referenced by Sleipnir::CGenome::AddSynonym(), Sleipnir::CPCL::Distance(), Sleipnir::CDat::FilterGenes(), Sleipnir::CDat::Open(), Sleipnir::CGenes::Open(), Sleipnir::CDatasetCompact::Open(), Sleipnir::CGenes::OpenWeighted(), and Sleipnir::CDat::SaveDOT().
| size_t Sleipnir::CGene::GetOntologies | ( | ) | const [inline] |
Return the number of different ontologies in which this gene is annotated.
- Returns:
- Number of ontologies in which this gene is annotated.
- See also:
- GetOntology
| const IOntology* Sleipnir::CGene::GetOntology | ( | size_t | iOntology | ) | const [inline] |
| bool Sleipnir::CGene::GetRNA | ( | ) | const [inline] |
| const std::string& Sleipnir::CGene::GetSynonym | ( | size_t | iSynonym | ) | const [inline] |
Return the requested synonym of the current gene.
- Parameters:
-
iSynonym Synonym to retrieve.
- Returns:
- Requested synonym.
- Remarks:
- For efficiency, no bounds checking is performed. The given index must be smaller than GetSynonyms.
Definition at line 109 of file genome.h.
Referenced by Sleipnir::CGenome::FindGene(), Sleipnir::CDat::SaveDOT(), and Sleipnir::CDat::SaveMATISSE().
| size_t Sleipnir::CGene::GetSynonyms | ( | ) | const [inline] |
Return the number of synonyms of the current gene.
- Returns:
- Current gene's number of synonyms.
- See also:
- GetSynonym
Definition at line 92 of file genome.h.
Referenced by Sleipnir::CGenome::FindGene(), Sleipnir::CDat::SaveDOT(), and Sleipnir::CDat::SaveMATISSE().
| const float Sleipnir::CGene::GetWeight | ( | ) | const [inline] |
| bool Sleipnir::CGene::IsAnnotated | ( | const IOntology * | pOntology | ) | const |
Return true if the gene is annotated within the given ontology.
- Parameters:
-
pOntology Ontology to test for gene annotation.
- Returns:
- True if gene is annotated within the given ontology.
Definition at line 144 of file genome.cpp.
| bool Sleipnir::CGene::IsAnnotated | ( | const IOntology * | pOntology, |
| size_t | iTerm | ||
| ) | const |
Return true if the gene is directly annotated to the given ontology term.
- Parameters:
-
pOntology Ontology to test for gene annotation. iTerm Term to test for direct gene annotation.
- Returns:
- True if gene is directly annotated to the given ontology term.
- Remarks:
- Does not examine the ontology or term descendants directly, so will only return true if the gene has been directly annotated to the given term using AddAnnotation.
Definition at line 170 of file genome.cpp.
| void Sleipnir::CGene::SetDubious | ( | bool | fDubious | ) | [inline] |
Sets whether the gene encodes a dubious reading frame.
- Parameters:
-
fDubious Value to store for dubious reading frame status.
- See also:
- GetDubious
Definition at line 151 of file genome.h.
Referenced by Sleipnir::CGenome::Open().
| void Sleipnir::CGene::SetGloss | ( | const std::string & | strGloss | ) | [inline] |
Sets the human-readable text description of the gene.
- Parameters:
-
strGloss Text description of the gene.
- See also:
- GetGloss
Definition at line 123 of file genome.h.
Referenced by Sleipnir::CGenome::Open().
| void Sleipnir::CGene::SetRNA | ( | bool | fRNA | ) | [inline] |
Sets whether the gene encodes an RNA gene.
- Parameters:
-
fRNA Value to store for RNA gene status.
- See also:
- GetRNA
Definition at line 179 of file genome.h.
Referenced by Sleipnir::CGenome::Open().
The documentation for this class was generated from the following files:
- src/genome.h
- src/genome.cpp
