slib.sglib.io.loader.bio.obo
Class GraphLoader_OBO_1_2

java.lang.Object
  extended by slib.sglib.io.loader.bio.obo.GraphLoader_OBO_1_2
All Implemented Interfaces:
GraphLoader

public class GraphLoader_OBO_1_2
extends Object
implements GraphLoader

TODO update doc Graph Loader used to map an OBO 1.2 specification as a Graph loaded in RAM
OBO specification
Compatibility with other format-version than 1.2 is not supported.
The mapping consider

Meta informations:
[Term]
Each Term are loaded as a specific vertex in the graph.
A Term is then mapped as a of equals to V_TYPE_CLASS.
Note that obsolete Terms/Typedefs are excluded during graph construction (see below is_obsolete).

Flag considered :
  • id: Loaded as the URI of the current [Term/Class/Vertex] specification
  • is a: Loaded as an of IS_A with currently defined Vertex as source and specified as target Vertex
  • relationships: Loaded as an of specified with source as current Vertex and target specified by the precise The EdgeType have to be defined by a [TypeDef] specification to be taken into account.
  • is_obsolete: Specifying the validity of the current Term specification
  • intersection_of/XREF...: These information are not loaded.
[Typedef] as
Every Typedef definition is loaded as an .
This definition is used to specify the type authorized for specification
  • id: the URI of the
  • is_transitive: Specifying if the relationship have to be considered as transitive
  • inverse_of Used to defined the URI of the to consider as the inverse of the current specified EdgeType e.g if an edge type X is defined as the inverse of Y, a relationship of type X defined between A and B will lead to the creation of:
    • an edge of type X betwween v(A) -> v(B)
    • an edge of type Y betwween v(B) -> v(A)
  • is_symmetric Used to defined an EdgeType as the inverse of itself e.g if an edge type X is transitive, a relationship defined as an edge of type X betwween v(A) -> v(B) is defined will imply the creation of an edge of type X as v(B) -> v(A)
  • is_obsolete: Specifying the validity of the current Typedef specification
  • transitive_over/XREF...: These information are not loaded.
TODO : load instances


Constructor Summary
GraphLoader_OBO_1_2()
           
 
Method Summary
 boolean isAllow_all_gafVersion()
           
 slib.sglib.model.graph.G load(GraphConf conf)
          Load a new Graph considering the given configuration
static void main(String[] args)
           
 void populate(GDataConf conf, slib.sglib.model.graph.G g)
          Populate an existing graph considering the given configuration
 void setAllow_all_gafVersion(boolean allow_all_gafVersion)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

GraphLoader_OBO_1_2

public GraphLoader_OBO_1_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 g)
              throws slib.utils.ex.SLIB_Exception
Description copied from interface: GraphLoader
Populate an existing graph considering the given configuration

Specified by:
populate in interface GraphLoader
Parameters:
conf - a GraphConf object specifying the configuration the loader must takes into account
Throws:
slib.utils.ex.SLIB_Exception

isAllow_all_gafVersion

public boolean isAllow_all_gafVersion()
Returns:

setAllow_all_gafVersion

public void setAllow_all_gafVersion(boolean allow_all_gafVersion)
Parameters:
allow_all_gafVersion -

main

public static void main(String[] args)
                 throws slib.utils.ex.SLIB_Ex_Warning
Parameters:
args -
Throws:
slib.utils.ex.SLIB_Ex_Warning


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