owltools.gaf.inference
Class ClassTaxonMatrix

java.lang.Object
  extended by 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
protected ClassTaxonMatrix(int classCount, int taxonCount)
           
 
Method Summary
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


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