Uses of Class
org.forester.phylogeny.data.Sequence

Packages that use Sequence

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

Uses of Sequence in org.forester.io.parsers.phyloxml

Methods in org.forester.io.parsers.phyloxml that return types with arguments of type Sequence

Modifier and Type	Method	Description
static java.util.Map<java.lang.String,Sequence>	PhyloXmlHandler.getSequenceMapByIdForPhylogeny(Phylogeny ph)

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

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

Modifier and Type	Method	Description
Sequence	SequenceParser.parse(XmlElement element)

Uses of Sequence in org.forester.phylogeny

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

Modifier and Type	Method	Description
java.util.Collection<Sequence>	Phylogeny.getSequenceRelationQueries()

Method parameters in org.forester.phylogeny with type arguments of type Sequence

Modifier and Type	Method	Description
void	Phylogeny.setSequenceRelationQueries(java.util.Collection<Sequence> sequencesByName)

Uses of Sequence in org.forester.phylogeny.data

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

Modifier and Type	Method	Description
Sequence	SequenceRelation.getRef0()
Sequence	SequenceRelation.getRef1()
Sequence	NodeData.getSequence()	Convenience method -- always returns the first Sequence.
Sequence	NodeData.getSequence(int index)

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

Modifier and Type	Method	Description
java.util.List<Sequence>	NodeData.getSequences()

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

Modifier and Type	Method	Description
void	NodeData.addSequence(Sequence sequence)
int	Sequence.compareTo(Sequence o)
void	SequenceRelation.setRef0(Sequence ref0)
void	SequenceRelation.setRef1(Sequence ref1)
void	NodeData.setSequence(int index, Sequence sequence)
void	NodeData.setSequence(Sequence sequence)	Convenience method -- always sets the first Sequence.