com.biomatters.geneious.publicapi.plugin

Class AlignmentOperation

java.lang.Object

com.biomatters.geneious.publicapi.plugin.AlignmentOperation

public abstract class AlignmentOperation
extends Object

A convenience class to enable plugins to contain alignment operations which do not need to concern themselves with:

• The type of documents that have been selected (sequence documents, sequence list documents, or alignment documents)
• Reordering and reversing of the sequences
• Whether the alignment is local or global
• Referenced documents
• Bases/residues unsupported by the underlying algorithm

If a plugin wants to handle these itself, it could implement itself as a DocumentOperation instead, but that is not recommended.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AlignmentOperation.InputProperties Represents the properties of the input to an AlignmentOperation

Constructor Summary

Constructors

Constructor and Description
AlignmentOperation()

Method Summary

Methods

Modifier and Type	Method and Description
abstract List<CharSequence>	align(SequenceDocument.Alphabet alphabet, List<CharSequence> sequences, Options options, ProgressListener progressListener) Align the given sequences
boolean	canRunOnGeneiousServer() Returns true if this operation supports being run on a GeneiousServer.
boolean	canRunOnLocalGeneious()
String	getAlignmentOptionsDescription(List<CharSequence> alignedSequences, Options options) Deprecated. this functionality is now supplied by operation history
String	getDescription()
Options	getGeneralOptions() Gets some Options that work for this operation when invoked on any type and number of input sequences
String	getHelp()
Icons	getIcons()
abstract String	getName()
Options	getOptions(AlignmentOperation.InputProperties inputProperties) A more powerful alternative to getOptions(com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument.Alphabet, boolean, boolean) that may provide the properties of the input to the operation.
Options	getOptions(SequenceDocument.Alphabet alphabet, boolean pairwise, boolean isSingleAlignment) Get the options appropriate for aligning these sequences
Double	getScore(List<CharSequence> alignedSequences, Options options) Used as score parameter when constructing the result alignment, see DefaultAlignmentDocument.DefaultAlignmentDocument(SequenceDocument[], List, String, Double, String)
abstract String	getSupportedCharacters(SequenceDocument.Alphabet alphabet) Get the characters that are supported by this alignment operation.
abstract double	getTabPosition()
String	getUniqueIdPrefix()
abstract boolean	isProOnly()
boolean	isRefine(Options options)
boolean	preserveSequenceOrder(Options options)
abstract boolean	supportsAlphabet(SequenceDocument.Alphabet alphabet)

Methods inherited from class java.lang.Object

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

Constructor Detail

AlignmentOperation

public AlignmentOperation()

Method Detail

getName

public abstract String getName()

Returns:

human-readable name for this operation

getUniqueIdPrefix

public String getUniqueIdPrefix()

Returns:

prefix for the unique ID of all operations created from this class. See DocumentOperation.getUniqueId()

getDescription

public String getDescription()

Returns:

description of what the operations created from this class. See DocumentOperation.getActionOptions()

getIcons

public Icons getIcons()

Returns:

icons for these operations. See DocumentOperation.getActionOptions()

getTabPosition

public abstract double getTabPosition()

Returns:

A position between 0 and 1 indicating where in the alignment menu this operation appears. See GeneiousActionOptions.setMainMenuLocation(com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions.MainMenu, double)}

getHelp

public String getHelp()

Returns:

help for these operations. See DocumentOperation.getHelp()

supportsAlphabet

public abstract boolean supportsAlphabet(SequenceDocument.Alphabet alphabet)

Parameters:

alphabet -

Returns:

true iff alignments can be performed on sequences of this alphabet

getOptions

public Options getOptions(SequenceDocument.Alphabet alphabet,
                 boolean pairwise,
                 boolean isSingleAlignment)
                   throws DocumentOperationException

Get the options appropriate for aligning these sequences

Parameters:

alphabet - alphabet of the sequences

pairwise - true iff there are only two (unique) sequences

isSingleAlignment - iff the only selected document is an alignment

Returns:

the alignment options

Throws:

DocumentOperationException - if obtaining the options for this operation is unsuccessful for any reason

getGeneralOptions

public Options getGeneralOptions()
                          throws DocumentOperationException

Gets some Options that work for this operation when invoked on any type and number of input sequences

Throws:

DocumentOperationException - if this operation doesn't support general options.

Since:

API 4.700 (Geneious 7.0.0)

getOptions

public Options getOptions(AlignmentOperation.InputProperties inputProperties)
                   throws DocumentOperationException

A more powerful alternative to getOptions(com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument.Alphabet, boolean, boolean) that may provide the properties of the input to the operation. These may include properties such as the location the operation is run and the alphabet of the input sequences.

Operations that have Options that need to change state depending on which GeneiousService the operation is run on should implement this method and register a listener on the results of AlignmentOperation.InputProperties.getLocationOptions() by calling OperationLocationOptions.addLocationChangedListener(com.biomatters.geneious.publicapi.plugin.OperationLocationOptions.LocationChangedListener)

Parameters:

inputProperties - properties of the input to the AlignmentOperation. See AlignmentOperation.InputProperties

Returns:

the alignment options

Throws:

DocumentOperationException - if obtaining the options for this operation is unsuccessful for any reason

Since:

API 4.15 (Geneious 5.1.1)

align

public abstract List<CharSequence> align(SequenceDocument.Alphabet alphabet,
                       List<CharSequence> sequences,
                       Options options,
                       ProgressListener progressListener)
                                  throws DocumentOperationException

Align the given sequences

Parameters:

alphabet - alphabet of the sequences

sequences - sequences to align

options - options for aligning these sequences

progressListener - used to report progress on the alignment

Returns:

the aligned sequence strings. The returned sequences must be the same as the input sequences except for the introduction of gaps and optionally reverse complementing in the case of nucleotide sequences. For local alignment, the sequences must be in the same order as the input sequences. For global alignment these do not have to be in the same order as the ones passed in.

Throws:

DocumentOperationException - if there is a problem or the user cancels the alignment

getAlignmentOptionsDescription

public String getAlignmentOptionsDescription(List<CharSequence> alignedSequences,
                                    Options options)
                                      throws DocumentOperationException

Deprecated. this functionality is now supplied by operation history

Used as alignmentOptions parameter when constructing the result alignment, see DefaultAlignmentDocument.DefaultAlignmentDocument(SequenceDocument[], List, String, Double, String)

Parameters:

alignedSequences - aligned sequences

options - options used to align the sequences

Returns:

the alignment options as a string

Throws:

DocumentOperationException

getSupportedCharacters

public abstract String getSupportedCharacters(SequenceDocument.Alphabet alphabet)

Get the characters that are supported by this alignment operation. Other characters will be converted to 'N' in the case of nucleotide sequences and 'X' in the case of protein sequences before {com.biomatters.geneious.publicapi.plugin.AlignmentOperation@link align(SequenceDocument.Alphabet, List, Options, ProgressListener)}

Parameters:

alphabet - alphabet to get the characters for

Returns:

characters that are supported or null to indicate that all characters are supported. The default implementation returns

getScore

public Double getScore(List<CharSequence> alignedSequences,
              Options options)

Used as score parameter when constructing the result alignment, see DefaultAlignmentDocument.DefaultAlignmentDocument(SequenceDocument[], List, String, Double, String)

Parameters:

alignedSequences - aligned sequences

options - options used to align the sequences

Returns:

the score as a Double or null for no score (the default implementation returns null)

isRefine

public boolean isRefine(Options options)

Parameters:

options - options used to align the sequences

Returns:

true iff we are refining an existing alignment rather than aligning the sequences passed in

preserveSequenceOrder

public boolean preserveSequenceOrder(Options options)

Parameters:

options - options used to align the sequences

Returns:

true iff the generated alignment should preserve the original order of the sequences.

isProOnly

public abstract boolean isProOnly()

Returns:

true iff the alignment method requires an active license

canRunOnLocalGeneious

public boolean canRunOnLocalGeneious()

Returns:

true if this operation supports being run on the current computer.

Since:

API 4.15 (Geneious 5.1.1)

canRunOnGeneiousServer

public boolean canRunOnGeneiousServer()

Returns true if this operation supports being run on a GeneiousServer. If this returns true then the user is presented with the option of running the operation on their local computer or on a connected GeneiousServer.

Operations should only return true if the following is true, otherwise undesired behavior may occur.

• The state of the Options returned from its various getOptions() methods can be completely restored by calling Options.valuesFromXML(org.jdom.Element) with the element obtained from Options.valuesToXML(String).
• All results are returned through the DocumentOperation.OperationCallback or as an element in the return list.
• The operation does not access any GeneiousServices directly.

Returns:

true if the operation can be run on a remote GeneiousServer

Since:

API 4.15 (Geneious 5.1.1)