slib.sglib.io.loader.bio.gaf2
Class GraphLoader_GAF_2

java.lang.Object
  extended by 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


Field Summary
static int ANNOTATION_XP
           
static int ASPECT
           
static int ASSIGNED_BY
           
static int DATE
           
static int DB
           
static int DB_OBJECT_ID
           
static int DB_OBJECT_NAME
           
static int DB_OBJECT_SYMBOL
           
static int DB_OBJECT_SYNONYM
           
static int DB_OBJECT_TYPE
           
static int EVIDENCE_CODE
           
static int GENE_PRODUCT_ISOFORM
           
static int GOID
           
static int QUALIFIER
           
static int REFERENCE
           
static int TAXON
           
static int WITH
           
 
Constructor Summary
GraphLoader_GAF_2()
           
 
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
 

Field Detail

DB

public static final int DB
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Constant Field Values

DB_OBJECT_ID

public static final int DB_OBJECT_ID
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DB_OBJECT_SYMBOL

public static final int DB_OBJECT_SYMBOL
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QUALIFIER

public static final int QUALIFIER
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GOID

public static final int GOID
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REFERENCE

public static final int REFERENCE
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EVIDENCE_CODE

public static final int EVIDENCE_CODE
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WITH

public static final int WITH
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ASPECT

public static final int ASPECT
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DB_OBJECT_NAME

public static final int DB_OBJECT_NAME
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DB_OBJECT_SYNONYM

public static final int DB_OBJECT_SYNONYM
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DB_OBJECT_TYPE

public static final int DB_OBJECT_TYPE
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TAXON

public static final int TAXON
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DATE

public static final int DATE
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ASSIGNED_BY

public static final int ASSIGNED_BY
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ANNOTATION_XP

public static final int ANNOTATION_XP
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GENE_PRODUCT_ISOFORM

public static final int GENE_PRODUCT_ISOFORM
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Constant Field Values
Constructor Detail

GraphLoader_GAF_2

public GraphLoader_GAF_2()
Method Detail

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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