owltools.gaf.inference

Class ClassTaxonMatrix

java.lang.Object

owltools.gaf.inference.ClassTaxonMatrix

public class ClassTaxonMatrix
extends Object

Matrix representing the applicability of classes and taxa. Uses the TaxonConstraintsEngine to infer the taxon constraints. Use the static methods to create and write instances.

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	ClassTaxonMatrix(int classCount, int taxonCount)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	add(boolean applicable, org.semanticweb.owlapi.model.OWLClass owlClass, org.semanticweb.owlapi.model.OWLClass taxon)
static ClassTaxonMatrix	create(OWLGraphWrapper graph, Collection<org.semanticweb.owlapi.model.OWLClass> classes, Collection<org.semanticweb.owlapi.model.OWLClass> taxa) Create a new taxon-class-matrix for the given classes and taxa.
static ClassTaxonMatrix	create(OWLGraphWrapper graph, Collection<org.semanticweb.owlapi.model.OWLClass> classes, String... taxa) Create a new taxon-class-matrix for the given classes and taxa.
Boolean	get(org.semanticweb.owlapi.model.OWLClass cls, org.semanticweb.owlapi.model.OWLClass taxon)
static void	write(ClassTaxonMatrix matrix, OWLGraphWrapper graph, BufferedWriter writer) Write a ClassTaxonMatrix using the default delimiter.
static void	write(ClassTaxonMatrix matrix, OWLGraphWrapper graph, char delimiter, BufferedWriter writer) Write a ClassTaxonMatrix using the specified delimiter.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ClassTaxonMatrix

protected ClassTaxonMatrix(int classCount,
                int taxonCount)

Method Detail

add

protected void add(boolean applicable,
       org.semanticweb.owlapi.model.OWLClass owlClass,
       org.semanticweb.owlapi.model.OWLClass taxon)

get

public Boolean get(org.semanticweb.owlapi.model.OWLClass cls,
          org.semanticweb.owlapi.model.OWLClass taxon)

create

public static ClassTaxonMatrix create(OWLGraphWrapper graph,
                      Collection<org.semanticweb.owlapi.model.OWLClass> classes,
                      String... taxa)

Create a new taxon-class-matrix for the given classes and taxa.

Parameters:

graph -

classes -

taxa - taxa identifier

Returns:

matrix

create

public static ClassTaxonMatrix create(OWLGraphWrapper graph,
                      Collection<org.semanticweb.owlapi.model.OWLClass> classes,
                      Collection<org.semanticweb.owlapi.model.OWLClass> taxa)

Create a new taxon-class-matrix for the given classes and taxa.

Parameters:

graph -

classes -

taxa -

Returns:

matrix

write

public static void write(ClassTaxonMatrix matrix,
         OWLGraphWrapper graph,
         BufferedWriter writer)
                  throws IOException

Write a ClassTaxonMatrix using the default delimiter. Hint: Do not forget to close the writer after use.

Parameters:

matrix -

graph - required for rendering the OBO style identifiers

writer -

Throws:

IOException

write

public static void write(ClassTaxonMatrix matrix,
         OWLGraphWrapper graph,
         char delimiter,
         BufferedWriter writer)
                  throws IOException

Write a ClassTaxonMatrix using the specified delimiter. Hint: Do not forget to close the writer after use.

Parameters:

matrix -

graph - required for rendering the OBO style identifiers

delimiter -

writer -

Throws:

IOException