Uses of Interface
org.forester.phylogeny.data.PhylogenyData

Packages that use PhylogenyData

Package	Description
org.forester.archaeopteryx.phylogeny.data
org.forester.go
org.forester.io.parsers.phyloxml.data
org.forester.phylogeny
org.forester.phylogeny.data

Uses of PhylogenyData in org.forester.archaeopteryx.phylogeny.data

Subinterfaces of PhylogenyData in org.forester.archaeopteryx.phylogeny.data

Modifier and Type	Interface and Description
interface	RenderablePhylogenyData

Classes in org.forester.archaeopteryx.phylogeny.data that implement PhylogenyData

Modifier and Type	Class and Description
class	RenderableDomainArchitecture
class	RenderableMsaSequence
class	RenderableVector

Methods in org.forester.archaeopteryx.phylogeny.data that return PhylogenyData

Modifier and Type	Method and Description
PhylogenyData	RenderableVector.copy()
PhylogenyData	RenderableMsaSequence.copy()
PhylogenyData	RenderableDomainArchitecture.copy()

Methods in org.forester.archaeopteryx.phylogeny.data with parameters of type PhylogenyData

Modifier and Type	Method and Description
boolean	RenderableVector.isEqual(PhylogenyData data)
boolean	RenderableMsaSequence.isEqual(PhylogenyData data)
boolean	RenderableDomainArchitecture.isEqual(PhylogenyData data)

Uses of PhylogenyData in org.forester.go

Subinterfaces of PhylogenyData in org.forester.go

Modifier and Type	Interface and Description
interface	GoTerm

Classes in org.forester.go that implement PhylogenyData

Modifier and Type	Class and Description
class	BasicGoTerm

Methods in org.forester.go that return PhylogenyData

Modifier and Type	Method and Description
PhylogenyData	BasicGoTerm.copy() Makes a shallow copy.

Methods in org.forester.go with parameters of type PhylogenyData

Modifier and Type	Method and Description
boolean	BasicGoTerm.isEqual(PhylogenyData go_term)

Uses of PhylogenyData in org.forester.io.parsers.phyloxml.data

Methods in org.forester.io.parsers.phyloxml.data that return PhylogenyData

Modifier and Type	Method and Description
PhylogenyData	PropertyParser.parse(XmlElement element)
PhylogenyData	DistributionParser.parse(XmlElement element)
PhylogenyData	AnnotationParser.parse(XmlElement element)
PhylogenyData	EventParser.parse(XmlElement element)
PhylogenyData	PolygonParser.parse(XmlElement element)
PhylogenyData	ColorParser.parse(XmlElement element)
PhylogenyData	ReferenceParser.parse(XmlElement element)
PhylogenyData	ConfidenceParser.parse(XmlElement element)
PhylogenyData	PhylogenyDataPhyloXmlParser.parse(XmlElement element)
PhylogenyData	UriParser.parse(XmlElement element)
PhylogenyData	PointParser.parse(XmlElement element)
PhylogenyData	IdentifierParser.parse(XmlElement element)
PhylogenyData	DateParser.parse(XmlElement element)
PhylogenyData	BranchWidthParser.parse(XmlElement element)
PhylogenyData	AccessionParser.parse(XmlElement element)
PhylogenyData	BinaryCharactersParser.parse(XmlElement element)

Uses of PhylogenyData in org.forester.phylogeny

Methods in org.forester.phylogeny that return PhylogenyData

Modifier and Type	Method and Description
PhylogenyData	PhylogenyBranch.getData()

Uses of PhylogenyData in org.forester.phylogeny.data

Classes in org.forester.phylogeny.data that implement PhylogenyData

Modifier and Type	Class and Description
class	Accession
class	Annotation
class	BinaryCharacters
class	BranchColor
class	BranchData
class	BranchWidth
class	Confidence
class	Date
class	Distribution
class	DomainArchitecture
class	Event
class	Identifier
class	NodeData
class	NodeVisualData
class	Point
class	Polygon
class	PropertiesMap
class	Property
class	ProteinDomain
class	Reference
class	Sequence
class	SequenceRelation
class	Taxonomy
class	Uri

Methods in org.forester.phylogeny.data that return PhylogenyData

Modifier and Type	Method and Description
PhylogenyData	BranchData.copy()
PhylogenyData	Confidence.copy()
PhylogenyData	Accession.copy()
PhylogenyData	Identifier.copy()
PhylogenyData	Sequence.copy() Not a deep copy.
PhylogenyData	Taxonomy.copy()
PhylogenyData	SequenceRelation.copy()
PhylogenyData	PropertiesMap.copy()
PhylogenyData	PhylogenyData.copy() Creates a new PhylogenyData object with identical values as this PhylogenyData.
PhylogenyData	Reference.copy()
PhylogenyData	NodeData.copy()
PhylogenyData	Polygon.copy()
PhylogenyData	Event.copy()
PhylogenyData	BranchWidth.copy()
PhylogenyData	Distribution.copy()
PhylogenyData	Point.copy()
PhylogenyData	DomainArchitecture.copy()
PhylogenyData	BinaryCharacters.copy()
PhylogenyData	Uri.copy()
PhylogenyData	Property.copy()
PhylogenyData	BranchColor.copy()
PhylogenyData	NodeVisualData.copy()
PhylogenyData	Date.copy()
PhylogenyData	Annotation.copy()
PhylogenyData	ProteinDomain.copy()

Methods in org.forester.phylogeny.data that return types with arguments of type PhylogenyData

Modifier and Type	Method and Description
static ArrayList<PhylogenyData>	PhylogenyDataUtil.copy(ArrayList<PhylogenyData> list) Creates a deep copy of ArrayList of PhylogenyData objects.

Methods in org.forester.phylogeny.data with parameters of type PhylogenyData

Modifier and Type	Method and Description
boolean	BranchData.isEqual(PhylogenyData data)
boolean	Confidence.isEqual(PhylogenyData confidence)
boolean	Accession.isEqual(PhylogenyData data)
boolean	Identifier.isEqual(PhylogenyData data)
boolean	Sequence.isEqual(PhylogenyData data)
boolean	Taxonomy.isEqual(PhylogenyData data) If this and taxonomy 'data' has an identifier, comparison will be based on that.
boolean	SequenceRelation.isEqual(PhylogenyData data)
boolean	PropertiesMap.isEqual(PhylogenyData data)
boolean	PhylogenyData.isEqual(PhylogenyData data) Compares this PhylogenyData to PhylogenyData data.
boolean	Reference.isEqual(PhylogenyData data)
boolean	NodeData.isEqual(PhylogenyData data)
boolean	Polygon.isEqual(PhylogenyData data)
boolean	Event.isEqual(PhylogenyData event)
boolean	BranchWidth.isEqual(PhylogenyData data)
boolean	Distribution.isEqual(PhylogenyData data)
boolean	Point.isEqual(PhylogenyData point)
boolean	DomainArchitecture.isEqual(PhylogenyData domain_architecture) Returns true if the names and the order of the domains match (domain and linker lengths are ignored).
boolean	BinaryCharacters.isEqual(PhylogenyData data)
boolean	Uri.isEqual(PhylogenyData data)
boolean	Property.isEqual(PhylogenyData data)
boolean	BranchColor.isEqual(PhylogenyData data)
boolean	NodeVisualData.isEqual(PhylogenyData data)
boolean	Date.isEqual(PhylogenyData data)
boolean	Annotation.isEqual(PhylogenyData data)
boolean	ProteinDomain.isEqual(PhylogenyData protein_domain)

Method parameters in org.forester.phylogeny.data with type arguments of type PhylogenyData

Modifier and Type	Method and Description
static ArrayList<PhylogenyData>	PhylogenyDataUtil.copy(ArrayList<PhylogenyData> list) Creates a deep copy of ArrayList of PhylogenyData objects.

Constructor parameters in org.forester.phylogeny.data with type arguments of type PhylogenyData

Constructor and Description
DomainArchitecture(List<PhylogenyData> domains, int total_length)