Uses of Class
org.forester.phylogeny.data.Sequence
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Packages that use Sequence Package Description org.forester.io.parsers.phyloxml org.forester.io.parsers.phyloxml.data org.forester.phylogeny org.forester.phylogeny.data -
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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)
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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)
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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)
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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.
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