phenote.datamodel
Class OboUtil

java.lang.Object
  phenote.datamodel.OboUtil

public class OboUtil
extends java.lang.Object

changing this from static to non-static so can build post comp object from multiple rel-diffs

Constructor Summary

OboUtil()

Method Summary

void	addRelDiff(org.obo.datamodel.OBOProperty rel, org.obo.datamodel.OBOClass diff)
static java.util.List<org.obo.datamodel.Link>	getAllDifferentia(org.obo.datamodel.OBOClass postComp)
static org.obo.datamodel.OBOClass	getAttributeForValue(org.obo.datamodel.OBOClass valueTerm) Finds and returns the closest attribute ancestor for a value term from PATO.
static org.obo.datamodel.OBOClass	getDifferentiaTerm(org.obo.datamodel.OBOClass postComp, org.obo.datamodel.OBOProperty diffRel) Assumes theres only one term with diffRel, returns the 1st one it finds null if none found - ex?
static org.obo.datamodel.OBOClass	getGenusTerm(org.obo.datamodel.OBOClass term) for non post comp returns term itself
static org.obo.datamodel.OBOClass	getIsaParentForTerm(org.obo.datamodel.OBOClass term) Returns the "is_a" parent for an OBO term, or null if one is not found.
static int	getNumOfDiffs(org.obo.datamodel.OBOClass term) Return number of rel-diffs a term has
static org.obo.datamodel.OBORestriction	getOboRestriction(org.obo.datamodel.Link l)
org.obo.datamodel.OBOClass	getPostCompTerm()
boolean	hasRelAndDiff()
static OboUtil	initPostCompTerm(org.obo.datamodel.OBOClass genus) even if genus is null returns an oboutil - should it return null if genus null? ex?
static boolean	isLinkToDiff(org.obo.datamodel.Link l)
static boolean	isLinkToDiff(org.obo.datamodel.OBORestriction r)
static boolean	isOboRestriction(org.obo.datamodel.Link l)
static boolean	isPostCompTerm(org.obo.datamodel.OBOObject term)
static org.obo.datamodel.OBOClass	makePostCompTerm(org.obo.datamodel.OBOClass genus, org.obo.datamodel.OBOProperty rel, org.obo.datamodel.OBOClass diff)

Methods inherited from class java.lang.Object

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

Constructor Detail

OboUtil

public OboUtil()

Method Detail

makePostCompTerm

public static org.obo.datamodel.OBOClass makePostCompTerm(org.obo.datamodel.OBOClass genus,
                                                          org.obo.datamodel.OBOProperty rel,
                                                          org.obo.datamodel.OBOClass diff)

initPostCompTerm

public static OboUtil initPostCompTerm(org.obo.datamodel.OBOClass genus)

even if genus is null returns an oboutil - should it return null if genus null? ex?

addRelDiff

public void addRelDiff(org.obo.datamodel.OBOProperty rel,
                       org.obo.datamodel.OBOClass diff)

hasRelAndDiff

public boolean hasRelAndDiff()

getPostCompTerm

public org.obo.datamodel.OBOClass getPostCompTerm()

getGenusTerm

public static org.obo.datamodel.OBOClass getGenusTerm(org.obo.datamodel.OBOClass term)

for non post comp returns term itself

isPostCompTerm

public static boolean isPostCompTerm(org.obo.datamodel.OBOObject term)

isLinkToDiff

public static boolean isLinkToDiff(org.obo.datamodel.Link l)

isLinkToDiff

public static boolean isLinkToDiff(org.obo.datamodel.OBORestriction r)

isOboRestriction

public static boolean isOboRestriction(org.obo.datamodel.Link l)

getOboRestriction

public static org.obo.datamodel.OBORestriction getOboRestriction(org.obo.datamodel.Link l)

getNumOfDiffs

public static int getNumOfDiffs(org.obo.datamodel.OBOClass term)

Return number of rel-diffs a term has

getDifferentiaTerm

public static org.obo.datamodel.OBOClass getDifferentiaTerm(org.obo.datamodel.OBOClass postComp,
                                                            org.obo.datamodel.OBOProperty diffRel)

Assumes theres only one term with diffRel, returns the 1st one it finds null if none found - ex?

getAllDifferentia

public static java.util.List<org.obo.datamodel.Link> getAllDifferentia(org.obo.datamodel.OBOClass postComp)

getAttributeForValue

public static org.obo.datamodel.OBOClass getAttributeForValue(org.obo.datamodel.OBOClass valueTerm)

Finds and returns the closest attribute ancestor for a value term from PATO. Returns the input term if it is itself an attribute, or null if no attribute is found.

getIsaParentForTerm

public static org.obo.datamodel.OBOClass getIsaParentForTerm(org.obo.datamodel.OBOClass term)

Returns the "is_a" parent for an OBO term, or null if one is not found.