slib.sglib.io.loader.bio.gaf2
Class GraphLoader_GAF_2
java.lang.Object
slib.sglib.io.loader.bio.gaf2.GraphLoader_GAF_2
- All Implemented Interfaces:
- GraphLoader
public class GraphLoader_GAF_2
- extends Object
- implements GraphLoader
GAF 2 parser used to construct a graph from a GAF 2.0 annotation file
The parser consider considering GAF 2.0 specification provided at
http://wiki.geneontology.org/index.php/GO_Consortium_web_GAF2.0_documentation
http://www.geneontology.org/GO.format.gaf-2_0.shtml
TODO - Manage multiple organism specification : taxon:1|taxon:1000
Method Summary |
slib.sglib.model.graph.G |
load(GraphConf conf)
Load a new Graph considering the given configuration |
void |
populate(GDataConf conf,
slib.sglib.model.graph.G graph)
Method used to load an annotation repository considering a specific
configuration and a potential mapping restriction i.e. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
DB
public static final int DB
- See Also:
- Constant Field Values
DB_OBJECT_ID
public static final int DB_OBJECT_ID
- See Also:
- Constant Field Values
DB_OBJECT_SYMBOL
public static final int DB_OBJECT_SYMBOL
- See Also:
- Constant Field Values
QUALIFIER
public static final int QUALIFIER
- See Also:
- Constant Field Values
GOID
public static final int GOID
- See Also:
- Constant Field Values
REFERENCE
public static final int REFERENCE
- See Also:
- Constant Field Values
EVIDENCE_CODE
public static final int EVIDENCE_CODE
- See Also:
- Constant Field Values
WITH
public static final int WITH
- See Also:
- Constant Field Values
ASPECT
public static final int ASPECT
- See Also:
- Constant Field Values
DB_OBJECT_NAME
public static final int DB_OBJECT_NAME
- See Also:
- Constant Field Values
DB_OBJECT_SYNONYM
public static final int DB_OBJECT_SYNONYM
- See Also:
- Constant Field Values
DB_OBJECT_TYPE
public static final int DB_OBJECT_TYPE
- See Also:
- Constant Field Values
TAXON
public static final int TAXON
- See Also:
- Constant Field Values
DATE
public static final int DATE
- See Also:
- Constant Field Values
ASSIGNED_BY
public static final int ASSIGNED_BY
- See Also:
- Constant Field Values
ANNOTATION_XP
public static final int ANNOTATION_XP
- See Also:
- Constant Field Values
GENE_PRODUCT_ISOFORM
public static final int GENE_PRODUCT_ISOFORM
- See Also:
- Constant Field Values
GraphLoader_GAF_2
public GraphLoader_GAF_2()
load
public slib.sglib.model.graph.G load(GraphConf conf)
throws slib.utils.ex.SLIB_Exception
- Description copied from interface:
GraphLoader
- Load a new Graph considering the given configuration
- Specified by:
load
in interface GraphLoader
- Parameters:
conf
- a GraphConf
object specifying the configuration the loader must takes into account
- Returns:
- a graph
G
- Throws:
slib.utils.ex.SLIB_Exception
populate
public void populate(GDataConf conf,
slib.sglib.model.graph.G graph)
throws slib.utils.ex.SLIB_Ex_Critic
- Method used to load an annotation repository considering a specific
configuration and a potential mapping restriction i.e. a
G
containing the concepts to consider. A FilterKB_GAF2
can be
associated to the KBConf
/ KBConf_GAF2
object in order to
define restrictions to consider during the parsing (e.g. taxons, Evidence
Code, origin knowledge base)
- Specified by:
populate
in interface GraphLoader
- Parameters:
conf
- a KBConf
object defining a configuration. If the
configuration file define a Filter
of class
FilterKB_GAF2
, it will be evaluated during the parsing.graph
- a graph defining the concepts to consider, can be set to
null if no mapping restriction have to be take into account If a graph is
specified only annotation corresponding a graph Node will be loaded.
- Throws:
slib.utils.ex.SLIB_Ex_Critic
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