Uses of Interface
org.forester.phylogeny.data.PhylogenyData
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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 -
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Uses of PhylogenyData in org.forester.archaeopteryx.phylogeny.data
Subinterfaces of PhylogenyData in org.forester.archaeopteryx.phylogeny.data Modifier and Type Interface Description interface
RenderablePhylogenyData
Classes in org.forester.archaeopteryx.phylogeny.data that implement PhylogenyData Modifier and Type Class Description class
RenderableDomainArchitecture
class
RenderableMsaSequence
class
RenderableVector
Methods in org.forester.archaeopteryx.phylogeny.data that return PhylogenyData Modifier and Type Method Description PhylogenyData
RenderableDomainArchitecture. copy()
PhylogenyData
RenderableMsaSequence. copy()
PhylogenyData
RenderableVector. copy()
Methods in org.forester.archaeopteryx.phylogeny.data with parameters of type PhylogenyData Modifier and Type Method Description boolean
RenderableDomainArchitecture. isEqual(PhylogenyData data)
boolean
RenderableMsaSequence. isEqual(PhylogenyData data)
boolean
RenderableVector. isEqual(PhylogenyData data)
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Uses of PhylogenyData in org.forester.go
Subinterfaces of PhylogenyData in org.forester.go Modifier and Type Interface Description interface
GoTerm
Classes in org.forester.go that implement PhylogenyData Modifier and Type Class Description class
BasicGoTerm
Methods in org.forester.go that return PhylogenyData Modifier and Type Method Description PhylogenyData
BasicGoTerm. copy()
Makes a shallow copy.Methods in org.forester.go with parameters of type PhylogenyData Modifier and Type Method Description boolean
BasicGoTerm. isEqual(PhylogenyData go_term)
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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 Description PhylogenyData
AccessionParser. parse(XmlElement element)
PhylogenyData
AnnotationParser. parse(XmlElement element)
PhylogenyData
BinaryCharactersParser. parse(XmlElement element)
PhylogenyData
BranchWidthParser. parse(XmlElement element)
PhylogenyData
ColorParser. parse(XmlElement element)
PhylogenyData
ConfidenceParser. parse(XmlElement element)
PhylogenyData
DateParser. parse(XmlElement element)
PhylogenyData
DistributionParser. parse(XmlElement element)
PhylogenyData
EventParser. parse(XmlElement element)
PhylogenyData
IdentifierParser. parse(XmlElement element)
PhylogenyData
PhylogenyDataPhyloXmlParser. parse(XmlElement element)
PhylogenyData
PointParser. parse(XmlElement element)
PhylogenyData
PolygonParser. parse(XmlElement element)
PhylogenyData
PropertyParser. parse(XmlElement element)
PhylogenyData
ReferenceParser. parse(XmlElement element)
PhylogenyData
UriParser. parse(XmlElement element)
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Uses of PhylogenyData in org.forester.phylogeny
Methods in org.forester.phylogeny that return PhylogenyData Modifier and Type Method Description PhylogenyData
PhylogenyBranch. getData()
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Uses of PhylogenyData in org.forester.phylogeny.data
Classes in org.forester.phylogeny.data that implement PhylogenyData Modifier and Type Class 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 Description PhylogenyData
Accession. copy()
PhylogenyData
Annotation. copy()
PhylogenyData
BinaryCharacters. copy()
PhylogenyData
BranchColor. copy()
PhylogenyData
BranchData. copy()
PhylogenyData
BranchWidth. copy()
PhylogenyData
Confidence. copy()
PhylogenyData
Date. copy()
PhylogenyData
Distribution. copy()
PhylogenyData
DomainArchitecture. copy()
PhylogenyData
Event. copy()
PhylogenyData
Identifier. copy()
PhylogenyData
NodeData. copy()
PhylogenyData
NodeVisualData. copy()
PhylogenyData
PhylogenyData. copy()
Creates a new PhylogenyData object with identical values as this PhylogenyData.PhylogenyData
Point. copy()
PhylogenyData
Polygon. copy()
PhylogenyData
PropertiesMap. copy()
PhylogenyData
Property. copy()
PhylogenyData
ProteinDomain. copy()
PhylogenyData
Reference. copy()
PhylogenyData
Sequence. copy()
Not a deep copy.PhylogenyData
SequenceRelation. copy()
PhylogenyData
Taxonomy. copy()
PhylogenyData
Uri. copy()
Methods in org.forester.phylogeny.data that return types with arguments of type PhylogenyData Modifier and Type Method Description static java.util.ArrayList<PhylogenyData>
PhylogenyDataUtil. copy(java.util.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 Description boolean
Accession. isEqual(PhylogenyData data)
boolean
Annotation. isEqual(PhylogenyData data)
boolean
BinaryCharacters. isEqual(PhylogenyData data)
boolean
BranchColor. isEqual(PhylogenyData data)
boolean
BranchData. isEqual(PhylogenyData data)
boolean
BranchWidth. isEqual(PhylogenyData data)
boolean
Confidence. isEqual(PhylogenyData confidence)
boolean
Date. isEqual(PhylogenyData data)
boolean
Distribution. isEqual(PhylogenyData data)
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
Event. isEqual(PhylogenyData event)
boolean
Identifier. isEqual(PhylogenyData data)
boolean
NodeData. isEqual(PhylogenyData data)
boolean
NodeVisualData. isEqual(PhylogenyData data)
boolean
PhylogenyData. isEqual(PhylogenyData data)
Compares this PhylogenyData to PhylogenyData data.boolean
Point. isEqual(PhylogenyData point)
boolean
Polygon. isEqual(PhylogenyData data)
boolean
PropertiesMap. isEqual(PhylogenyData data)
boolean
Property. isEqual(PhylogenyData data)
boolean
ProteinDomain. isEqual(PhylogenyData protein_domain)
boolean
Reference. isEqual(PhylogenyData data)
boolean
Sequence. isEqual(PhylogenyData data)
boolean
SequenceRelation. isEqual(PhylogenyData data)
boolean
Taxonomy. isEqual(PhylogenyData data)
If this and taxonomy 'data' has an identifier, comparison will be based on that.boolean
Uri. isEqual(PhylogenyData data)
Method parameters in org.forester.phylogeny.data with type arguments of type PhylogenyData Modifier and Type Method Description static java.util.ArrayList<PhylogenyData>
PhylogenyDataUtil. copy(java.util.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 Description DomainArchitecture(java.util.List<PhylogenyData> domains, int total_length)
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