com.biomatters.geneious.publicapi.plugin

Class AssemblerInput.ReferenceSequence

java.lang.Object

com.biomatters.geneious.publicapi.plugin.AssemblerInput.ReferenceSequence

Enclosing class:

AssemblerInput

public static class AssemblerInput.ReferenceSequence
extends Object

Represents a reference sequence in an assembly. Normally assembly algorithm implementations do not need to deal directly with this class. Instead they should use AssemblerInput.getNumberOfReferenceSequences() and AssemblerInput.getReferenceSequence(int, jebl.util.ProgressListener)

Constructor Summary

Constructors

Constructor and Description
AssemblerInput.ReferenceSequence(AnnotatedPluginDocument annotatedPluginDocument, int indexOfSequenceInDocument) Constructs a reference sequence.

Method Summary

Methods

Modifier and Type	Method and Description
int	getIndexOfSequenceInDocument() If the document returned from getSourceAnnotatedPluginDocument() is an alignment or sequence list, this method returns the index of the reference sequence in that document.
NucleotideSequenceDocument	getSequenceDocument(ProgressListener progressListener) Gets the SequenceDocument corresponding to this reference sequence, loading it from disk if necessary.
AnnotatedPluginDocument	getSourceAnnotatedPluginDocument() Gets the annotated plugin document that contains this reference sequence.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AssemblerInput.ReferenceSequence

public AssemblerInput.ReferenceSequence(AnnotatedPluginDocument annotatedPluginDocument,
                                int indexOfSequenceInDocument)

Constructs a reference sequence.

Parameters:

annotatedPluginDocument - the document containing the reference sequence. This may be either a stand-alone sequence, an alignment or a sequence list.

indexOfSequenceInDocument - if annotatedPluginDocument is either a sequence list of an alignment, this indicates the 0-based index of the reference sequence in that document. This should be -1 if the document is a stand-alone sequence

Method Detail

getSequenceDocument

public NucleotideSequenceDocument getSequenceDocument(ProgressListener progressListener)
                                               throws DocumentOperationException

Gets the SequenceDocument corresponding to this reference sequence, loading it from disk if necessary. This method can be very slow so should never be called from the swing thread.

Parameters:

progressListener - a progress listener to report progress to if the sequence needs to be loaded from disk.

Returns:

the SequenceDocument for this reference sequence. Will not be null.

Throws:

DocumentOperationException - if the sequence cannot be loaded.

getSourceAnnotatedPluginDocument

public AnnotatedPluginDocument getSourceAnnotatedPluginDocument()

Gets the annotated plugin document that contains this reference sequence. It could be either an alignment, a sequence list, or a stand-alone sequence.

Returns:

the annotated plugin document that contains this reference sequence.

getIndexOfSequenceInDocument

public int getIndexOfSequenceInDocument()

If the document returned from getSourceAnnotatedPluginDocument() is an alignment or sequence list, this method returns the index of the reference sequence in that document.

Returns:

the index of the reference sequence in the document returned from getSourceAnnotatedPluginDocument().

Since:

API 4.15 (Geneious 5.1.1)