Uses of Interface
com.biomatters.geneious.publicapi.documents.sequence.SequenceListDocument
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Packages that use SequenceListDocument 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.implementations.structure ProvidesMolecularStructureDocument
implementations for many commonly used 3D structure documents.com.biomatters.geneious.publicapi.plugin Provides theGeneiousPlugin
interface and plugin related interfaces. -
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Uses of SequenceListDocument in com.biomatters.geneious.publicapi.documents.sequence
Subinterfaces of SequenceListDocument in com.biomatters.geneious.publicapi.documents.sequence Modifier and Type Interface Description interface
EditableSequenceListDocument
ASequenceListDocument
that can have its internal lists of nucleotide and amino acid sequences reordered, added to, or removed from.interface
ExtendedEditableSequenceListDocument
Similar to anEditableSequenceListDocument
but also allows replacing sequences with new sequences or modifying the contents of individual sequencesClasses in com.biomatters.geneious.publicapi.documents.sequence that implement SequenceListDocument Modifier and Type Class Description class
DefaultSequenceListDocument
A default implementation of aSequenceListDocument
.Methods in com.biomatters.geneious.publicapi.documents.sequence with parameters of type SequenceListDocument Modifier and Type Method Description static DefaultSequenceListDocument
DefaultSequenceListDocument. createNewDocumentByTransformingSequences(SequenceListDocument sequenceListDocument, SequenceDocument.Alphabet alphabet, SequenceDocument.Transformer transformer, jebl.util.ProgressListener progressListener, boolean allowMultipleThreads)
Creates a new DefaultSequenceListDocument (whose sequences will be aSequenceListOnDisk
) by applying a transformation to each of the sequences in sequenceListDocument. -
Uses of SequenceListDocument in com.biomatters.geneious.publicapi.implementations.structure
Classes in com.biomatters.geneious.publicapi.implementations.structure that implement SequenceListDocument Modifier and Type Class Description class
PdbDocument
A PDB molecular structure document. -
Uses of SequenceListDocument in com.biomatters.geneious.publicapi.plugin
Fields in com.biomatters.geneious.publicapi.plugin with type parameters of type SequenceListDocument Modifier and Type Field Description static DocumentType<SequenceListDocument>
DocumentType. SEQUENCE_LIST_TYPE
Sequence list document type which matches either nucleotide or protein sequence lists.Methods in com.biomatters.geneious.publicapi.plugin with parameters of type SequenceListDocument Modifier and Type Method Description void
Assembler.Callback. addUnusedReads(SequenceListDocument unusedReads, jebl.util.ProgressListener progressListener)
Adds a list of reads that were not assembled.Constructors in com.biomatters.geneious.publicapi.plugin with parameters of type SequenceListDocument Constructor Description AssemblerInput(java.util.List<NucleotideSequenceDocument> referenceSequences, SequenceListDocument sequenceListDocument)
Constructs some assembly input from sequences that are all in memory.
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