Package com.biomatters.geneious.publicapi.plugin

Class SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment

java.lang.Object

com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment

Enclosing class:

SequenceAnnotationGenerator.AnnotationGeneratorResult

public static final class SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment
extends java.lang.Object

An immutable class representing an insertion, deletion, or replacement of residues or bases in a sequence.

Constructor Summary

Constructors

Constructor	Description
ResidueAdjustment(int firstResidueToReplaceInclusive, int lastResidueToReplaceExclusive, java.lang.String newResidues)	Construct a new insertion, deletion, or replacement of residues or bases in a sequence.
ResidueAdjustment(ImmutableSequence newSequence)	Replaces the entire sequence with a new sequence.

Method Summary

Modifier and Type	Method	Description
int	getFirstResidueToReplaceInclusive()	Get the 0-based first residue to replace or delete.
int	getLastResidueToReplaceExclusive()	Get the 0-based index (exclusive) of the last residue to delete or replace.
java.lang.String	getNewResidues()	Get the new residues to insert to the residues to replace the existing residues with.
ImmutableSequence	getNewSequence()	Gets a new sequence to replace the entire old sequence.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

ResidueAdjustment

public ResidueAdjustment(int firstResidueToReplaceInclusive,
                         int lastResidueToReplaceExclusive,
                         java.lang.String newResidues)

Construct a new insertion, deletion, or replacement of residues or bases in a sequence. For example:

• ResidueAdjustment(0,0,"GA") represents an insertion of residues "GA" at the beginning of the sequence.
• ResidueAdjustment(0,3,"") represents a deletion of the first 3 residues of the sequence.
• ResidueAdjustment(1,2,"GA") represents a replacement of the 2nd residue in the sequence with "GA"

Parameters:

firstResidueToReplaceInclusive - 0-based index of the first residue to delete or replace. In the case of an insertion, this is the index of the residue to insert immediately prior to.

lastResidueToReplaceExclusive - 0-based index (exclusive) of the last residue to delete or replace. In the case of an insertion, this should be equal to firstResidueToReplaceInclusive

newResidues - the new residues to insert to the residues to replace the existing residues with. In the case of a deletion, this should be an empty string.

ResidueAdjustment

public ResidueAdjustment(ImmutableSequence newSequence)

Replaces the entire sequence with a new sequence. This may only be done if the original sequence was also an ImmutableSequence

Parameters:

newSequence - the new sequence to replace the old one

Since:

API 4.40 (Geneious 5.4.0)

Method Detail

getFirstResidueToReplaceInclusive

public int getFirstResidueToReplaceInclusive()

Get the 0-based first residue to replace or delete. In the case of an insertion, this is the index of the residue to insert immediately prior to.

Returns:

the 0-based first residue to replace or delete. In the case of an insertion, this is the index of the residue to insert immediately prior to.

getLastResidueToReplaceExclusive

public int getLastResidueToReplaceExclusive()

Get the 0-based index (exclusive) of the last residue to delete or replace. In the case of an insertion, this should be equal to getFirstResidueToReplaceInclusive().

Returns:

the 0-based index (exclusive) of the last residue to delete or replace. In the case of an insertion, this should be equal to getFirstResidueToReplaceInclusive().

getNewResidues

public java.lang.String getNewResidues()

Get the new residues to insert to the residues to replace the existing residues with. In the case of a deletion, this should be an empty string.

Returns:

the new residues to insert to the residues to replace the existing residues with. In the case of a deletion, this should be an empty string.

getNewSequence

public ImmutableSequence getNewSequence()

Gets a new sequence to replace the entire old sequence. This must only return a non-null value if the original sequence was an ImmutableSequence

Returns:

a new sequence to replace the old sequence. This method may return null, in which case getNewResidues() should be used instead.

Since:

API 4.40 (Geneious 5.4.0)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object