Uses of Class
com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
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Packages that use DefaultAlignmentDocument Package Description com.biomatters.geneious.publicapi.documents.sequence Provides interfaces specifying the types ofsequence
andalignment
documents in Geneious, together with concrete classes used by sequence documents such asSequenceAnnotation
andSequenceCharSequence
.com.biomatters.geneious.publicapi.documents.types Provides interfaces specifying the types of documents available in Geneious.com.biomatters.geneious.publicapi.implementations Provides implementations for many of the document interfaces defined in the package com.biomatters.geneious.publicapi.documents.types together with some utility classes for dealing with some of these document types.com.biomatters.geneious.publicapi.utilities Provides various utility methods and classes, none of which are necessary for creating a plugin, but many plugins implentations will find these methods useful. -
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Uses of DefaultAlignmentDocument in com.biomatters.geneious.publicapi.documents.sequence
Methods in com.biomatters.geneious.publicapi.documents.sequence that return DefaultAlignmentDocument Modifier and Type Method Description DefaultAlignmentDocument
SequenceListOnDisk.Builder. toAlignmentDocument(jebl.util.ProgressListener progressListener)
Creates an Alignment document from this builder. -
Uses of DefaultAlignmentDocument in com.biomatters.geneious.publicapi.documents.types
Subclasses of DefaultAlignmentDocument in com.biomatters.geneious.publicapi.documents.types Modifier and Type Class Description class
PhylogenyDocument
A document containing an alignment and one or more trees whose tips are the sequences (i.e. -
Uses of DefaultAlignmentDocument in com.biomatters.geneious.publicapi.implementations
Subclasses of DefaultAlignmentDocument in com.biomatters.geneious.publicapi.implementations Modifier and Type Class Description class
DefaultPhylogenyDocument
An implementation of a Phylogeny document.Methods in com.biomatters.geneious.publicapi.implementations that return DefaultAlignmentDocument Modifier and Type Method Description static DefaultAlignmentDocument
DefaultAlignmentDocument. fromJeblAlignment(jebl.evolution.alignments.Alignment alignment)
Converts the given JEBL alignment into a DefaultAlignmentDocument.static DefaultAlignmentDocument
SequenceExtractionUtilities. reverseComplement(SequenceAlignmentDocument alignmentToReverse, jebl.util.ProgressListener progressListener)
Creates a new alignment that is the reverse complement of the given alignment.static DefaultAlignmentDocument
SequenceExtractionUtilities. withoutAnnotations(SequenceAlignmentDocument alignment, jebl.util.ProgressListener progressListener)
Creates a new alignment that is the same as the given alignment, but without annotations Any documents referenced by the original alignment will not be referenced in the new alignment (because references always preserve annotations) -
Uses of DefaultAlignmentDocument in com.biomatters.geneious.publicapi.utilities
Methods in com.biomatters.geneious.publicapi.utilities that return DefaultAlignmentDocument Modifier and Type Method Description static DefaultAlignmentDocument
SequenceUtilities. alignmentFromJeblSequences(java.lang.String name, java.util.List<jebl.evolution.sequences.Sequence> jeblSequences)
Converts the given alignment of Jebl sequences into a DefaultAlignmentDocument
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