Package com.biomatters.geneious.publicapi.documents.sequence

Class SequenceAlignmentDocument.ReferencedSequence

java.lang.Object

com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument.ReferencedSequence

Enclosing class:

SequenceAlignmentDocument

public static final class SequenceAlignmentDocument.ReferencedSequence
extends java.lang.Object

Represents a reference to the original document that a sequence in this alignment was aligned from. Usually this is a reference to an AnnotatedPluginDocument containing a SequenceDocument. However, the referenced AnnotatedPluginDocument may instead contain a SequenceListDocument if the alignment was built from a sequence list document or a SequenceAlignmentDocument if the alignment was built using the consensus alignment builder.

Constructor Summary

Constructors

Constructor	Description
ReferencedSequence(AnnotatedPluginDocument referencedDocument)	Construct a reference to a document that is a SequenceDocument.
ReferencedSequence(AnnotatedPluginDocument referencedDocument, int indexInSequenceListDocument)

Method Summary

Modifier and Type	Method	Description
boolean	equals(java.lang.Object o)
static java.util.List<SequenceAlignmentDocument.ReferencedSequence>	forSequenceDocuments(AnnotatedPluginDocument... documents)	Creates a list of ReferencedSequence, with 1 entry in the list for each given document (each of which must be a SequenceDocument) or null.
int	getIndexInSequenceListDocument()	If getReferencedDocument() is a SequenceListDocument then this method returns the index of the referenced sequence in that SequenceListDocument
AnnotatedPluginDocument	getReferencedDocument()	Gets the document a sequence in the alignment was built from.
static SequenceDocument	getSequenceDocument(SequenceAlignmentDocument.ReferencedSequence referencedSequence, SequenceDocument.Alphabet alphabet)	Get the sequence document referenced by a ReferencedSequence (if it references a SequenceDocument or SequenceListDocument)
SequenceDocument	getSequenceDocument(SequenceDocument.Alphabet alphabet)	Get the sequence document referenced by this ReferencedSequence (if it references a SequenceDocument or SequenceListDocument)
int	hashCode()
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

ReferencedSequence

public ReferencedSequence(AnnotatedPluginDocument referencedDocument,
                          int indexInSequenceListDocument)

Parameters:

referencedDocument - the document to reference. Must not be null.

indexInSequenceListDocument - if the referenced document is a SequenceListDocument then this must be the index of the referenced sequence in that SequenceListDocument. Or -1 if the referenced document is not a SequenceListDocument.

ReferencedSequence

public ReferencedSequence(AnnotatedPluginDocument referencedDocument)

Construct a reference to a document that is a SequenceDocument. (it must not be a SequenceListDocument). This is equivalent to calling ReferencedSequence(referencedDocument,-1)

Parameters:

referencedDocument - the document to referenc,de

Method Detail

getReferencedDocument

public AnnotatedPluginDocument getReferencedDocument()

Gets the document a sequence in the alignment was built from.

Usually this AnnotatedPluginDocument contains a SequenceDocument. However, the AnnotatedPluginDocument may instead contain a SequenceListDocument if the alignment was built from a sequence list document or a SequenceAlignmentDocument if the alignment was built using the consensus alignment builder.

Returns:

The referenced document. Will never be null.

getIndexInSequenceListDocument

public int getIndexInSequenceListDocument()

If getReferencedDocument() is a SequenceListDocument then this method returns the index of the referenced sequence in that SequenceListDocument

Returns:

the index of the referenced sequence in that SequenceListDocument or -1 if the referenced document is not a SequenceListDocument.

forSequenceDocuments

public static java.util.List<SequenceAlignmentDocument.ReferencedSequence> forSequenceDocuments(AnnotatedPluginDocument... documents)

Creates a list of ReferencedSequence, with 1 entry in the list for each given document (each of which must be a SequenceDocument) or null.

Parameters:

documents - the documents to create a list refering to.

Returns:

a list of ReferencedSequence where each entry in the list is null iff the corresponding entry in documents was null

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getSequenceDocument

public SequenceDocument getSequenceDocument(SequenceDocument.Alphabet alphabet)
                                     throws com.biomatters.geneious.publicapi.plugin.DocumentOperationException

Get the sequence document referenced by this ReferencedSequence (if it references a SequenceDocument or SequenceListDocument)

Parameters:

alphabet - alphabet of the sequence. Never null

Returns:

the sequence document or null if this references something other than a sequenceDocument or sequenceListDocument

Throws:

com.biomatters.geneious.publicapi.plugin.DocumentOperationException - if the referenced sequence document could not be loaded

getSequenceDocument

public static SequenceDocument getSequenceDocument(SequenceAlignmentDocument.ReferencedSequence referencedSequence,
                                                   SequenceDocument.Alphabet alphabet)
                                            throws com.biomatters.geneious.publicapi.plugin.DocumentOperationException

Get the sequence document referenced by a ReferencedSequence (if it references a SequenceDocument or SequenceListDocument)

Parameters:

alphabet - alphabet of the sequence. Never null

referencedSequence - the referenced sequence to get the sequence document from. Can be null

Returns:

the sequence document or null if the referencedSequence passed in was null or if it references something other than a sequenceDocument or sequenceListDocument

Throws:

com.biomatters.geneious.publicapi.plugin.DocumentOperationException - if the referenced document could not be loaded