Uses of Class
com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk
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Packages that use SequenceListOnDisk 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 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. -
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Uses of SequenceListOnDisk in com.biomatters.geneious.publicapi.documents.sequence
Methods in com.biomatters.geneious.publicapi.documents.sequence that return SequenceListOnDisk Modifier and Type Method Description static <T extends SequenceDocument>
SequenceListOnDisk<T>SequenceListOnDisk. create(java.util.List<T> sequences, boolean tryCompressingSequences, jebl.util.ProgressListener progressListener)
Creates a new SequenceListOnDisk from an existing list of ungapped sequences.static <T extends SequenceDocument>
SequenceListOnDisk<T>SequenceListOnDisk. createInterlaced(SequenceListOnDisk<T> sequences1, SequenceListOnDisk<T> sequences2, jebl.util.ProgressListener progressListener)
Creates a new SequenceListOnDisk by interlacing a pair of existing SequenceListOnDisks.static SequenceListOnDisk
SequenceListOnDisk. fromXml(org.jdom.Element element)
Recreates a SequenceListOnDisk from XML returned fromtoXML(String)
SequenceListOnDisk<T>
SequenceListOnDisk.Builder. getSequenceList()
Gets the result returned from a previous call totoSequenceList
.SequenceListOnDisk<SequenceDocument>
SequenceListOnDisk.AlignmentData. getSequences()
Gets the sequences for this dataSequenceListOnDisk<T>
SequenceListOnDisk.Builder. toSequenceList(jebl.util.ProgressListener progressListener)
Creates a SequenceListOnDisk from this builder.Methods in com.biomatters.geneious.publicapi.documents.sequence with parameters of type SequenceListOnDisk Modifier and Type Method Description static <T extends SequenceDocument>
SequenceListOnDisk<T>SequenceListOnDisk. createInterlaced(SequenceListOnDisk<T> sequences1, SequenceListOnDisk<T> sequences2, jebl.util.ProgressListener progressListener)
Creates a new SequenceListOnDisk by interlacing a pair of existing SequenceListOnDisks. -
Uses of SequenceListOnDisk in com.biomatters.geneious.publicapi.implementations
Methods in com.biomatters.geneious.publicapi.implementations with parameters of type SequenceListOnDisk Modifier and Type Method Description EndGapsManager
EndGapsManager.Builder. toEndGapsManager(SequenceListOnDisk<? extends SequenceDocument> associatedSequences)
Creates anEndGapsManager
from this builderConstructors in com.biomatters.geneious.publicapi.implementations with parameters of type SequenceListOnDisk Constructor Description EndGapsManager(org.jdom.Element element, SequenceListOnDisk<SequenceDocument> associatedSequences)
Recreates an EndGapsManager from XML.
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