com.biomatters.geneious.publicapi.plugin

Class Assembler

java.lang.Object

com.biomatters.geneious.publicapi.plugin.Assembler

public abstract class Assembler
extends Object

Allows the implementation of a read mapper, reference assembler or de novo assembler. A GeneiousPlugin can return 1 or more assembly algorithm implementations via GeneiousPlugin.getAssemblers().

The API documentation includes a sample implementation called ExampleAssembler

While these could be implemented as a DocumentOperation, the Assembler API simplifies the process.

Since:

API 4.14 (Geneious 5.1.0)

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Assembler.Callback Used for assembly algorithms to provide results back to Geneious.
static class	Assembler.ContigOutputSupport Used for indicating whether an assembly algorithm outputs contigs, consensus sequences, or both.
static class	Assembler.ReferenceSequenceSupport Used for indicating whether an assembly algorithm supports no reference sequence, a single reference sequence, or multiple reference sequences.

Field Summary

Fields

Modifier and Type	Field and Description
static String	DE_NOVO_UNIQUE_ID_SUFFIX If an assembly implementation supports both reference sequence and de novo assembly, its de novo assembler getUniqueId() should end with this.
static String	REFERENCE_UNIQUE_ID_SUFFIX If an assembly implementation supports both reference sequence and de novo assembly, its referenced assembler getUniqueId() should end with this.

Constructor Summary

Constructors

Constructor and Description
Assembler()

Method Summary

Methods

Modifier and Type	Method and Description
abstract void	assemble(Options options, AssemblerInput assemblyInput, ProgressListener progressListener, Assembler.Callback callback) Called to actually perform the assembly.
boolean	canRunOnGeneiousServer() Returns true if this operation supports being run on a GeneiousServer.
boolean	canRunOnLocalGeneious() Determine whether this assembly algorithm supports being run on the current computer.
abstract Assembler.ContigOutputSupport	getContigOutputSupport() Gets the type of data generated by this assembler.
abstract String	getName() Provides a short 1 or 2 word name for this algorithm.
abstract Options	getOptions(OperationLocationOptions locationOptions, AssemblerInput.Properties inputProperties) Gets some options to display to the user before performing assembly.
abstract Assembler.ReferenceSequenceSupport	getReferenceSequenceSupport() Gets whether or not this algorithm supports/requires assembling to a reference sequence and if so, whether it can assemble to multiple reference sequences.
abstract String	getUniqueId() Gets a unique id for this algorithm.
boolean	handlesTrimAnnotations() Returns true if this assembler handles trim annotations (SequenceAnnotation.TYPE_TRIMMED on input sequences and preserves them on generated contigs.
boolean	isProOnly() If true, this assembler will be always disabled when the user doesn't have an active license.
abstract boolean	providesUnusedReads() Returns true if this assembler can inform the Assembler.Callback about all reads that couldn't be assembled.
boolean	providesUsedReads() Returns true if this assembler can inform the Assembler.Callback about all reads that could be assembled.
boolean	providesUsedReadsIncludeMates() Returns true if this assembler can inform the Assembler.Callback about the mates of all reads that could be assembled.
boolean	supportsInputContigs() true if this assembly algorithm can accept contigs (SequenceAlignmentDocuments as input along with sequences.
boolean	supportsReferenceSequencesWithDuplicateNames()
boolean	supportsSingleInputContig() true if this assembly can accept single contigs as input and do some sort of fine tuning to improve the contig.

Methods inherited from class java.lang.Object

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

Field Detail

DE_NOVO_UNIQUE_ID_SUFFIX

public static final String DE_NOVO_UNIQUE_ID_SUFFIX

If an assembly implementation supports both reference sequence and de novo assembly, its de novo assembler getUniqueId() should end with this.

See Also:

Constant Field Values

REFERENCE_UNIQUE_ID_SUFFIX

public static final String REFERENCE_UNIQUE_ID_SUFFIX

If an assembly implementation supports both reference sequence and de novo assembly, its referenced assembler getUniqueId() should end with this.

See Also:

Constant Field Values

Constructor Detail

Assembler

public Assembler()

Method Detail

getUniqueId

public abstract String getUniqueId()

Gets a unique id for this algorithm. Since this must be unique, prefixing it with the fully qualified class name is recommended. Also see getReferenceSequenceSupport(). The Geneious assemblers have unique IDs "Geneious.deNovo" and "Geneious.reference".

Returns:

a unique id for this algorithm

See Also:

getReferenceSequenceSupport(), DE_NOVO_UNIQUE_ID_SUFFIX, REFERENCE_UNIQUE_ID_SUFFIX

getName

public abstract String getName()

Provides a short 1 or 2 word name for this algorithm.

Returns:

a short 1 or 2 word name for this algorithm.

getOptions

public abstract Options getOptions(OperationLocationOptions locationOptions,
                 AssemblerInput.Properties inputProperties)
                            throws DocumentOperationException

Gets some options to display to the user before performing assembly.

Parameters:

locationOptions - Used to control where the assembler is run. Will be null if the assembler can only be run locally. See OperationLocationOptions for more details.

inputProperties - some properties summarising the data to be assembled. If the user changes the reference sequence after the options are retrieved, the property values will change. The assembly implementation can request to be notified about this using AssemblerInput.Properties.addChangeListener(org.virion.jam.util.SimpleListener) @return some options to display to the user before performing assembly.

Returns:

options to display to the user for doing assembly.

Throws:

DocumentOperationException - if this assembler doesn't support assembly on the given AssemblerInput.Properties

getReferenceSequenceSupport

public abstract Assembler.ReferenceSequenceSupport getReferenceSequenceSupport()

Gets whether or not this algorithm supports/requires assembling to a reference sequence and if so, whether it can assemble to multiple reference sequences. If an algorithm can support either reference assembly or de novo assembly, 2 different algorithm implementations must be created. In this case the 2 implementations should start with the same getUniqueId() prefix, and end with DE_NOVO_UNIQUE_ID_SUFFIX and REFERENCE_UNIQUE_ID_SUFFIX so that Geneious can recognize they are the same and provide appropriate options to the user.

Returns:

the type of reference sequences this assembler supports.

See Also:

getUniqueId()

supportsReferenceSequencesWithDuplicateNames

public boolean supportsReferenceSequencesWithDuplicateNames()

Returns:

false if AssemblerInput.getReferenceSequence(int, jebl.util.ProgressListener) throws a DocumentOperationException if there are duplicate reference sequence names. The default implementation returns false

Since:

API 4.710 (Geneious 7.1.0)

getContigOutputSupport

public abstract Assembler.ContigOutputSupport getContigOutputSupport()

Gets the type of data generated by this assembler. Some assemblers may generate just a consensus sequence (in which case they should return Assembler.ContigOutputSupport.ConsensusOnly

Returns:

the type of data generated by this assembler.

supportsInputContigs

public boolean supportsInputContigs()

true if this assembly algorithm can accept contigs (SequenceAlignmentDocuments as input along with sequences. If so, then Reads provided as input to the assembler may be contigs instead of single or paired sequences.

The default implementation returns false.

Returns:

true if this assembly algorithm can accept contigs (SequenceAlignmentDocuments as input along with sequences.

See Also:

supportsSingleInputContig()

supportsSingleInputContig

public boolean supportsSingleInputContig()

true if this assembly can accept single contigs as input and do some sort of fine tuning to improve the contig.

Returns:

true if this assembly can accept single contigs as input and do some sort of fine tuning to improve the contig.

Since:

API 4.30 (Geneious 5.3.0)

See Also:

supportsInputContigs()

providesUnusedReads

public abstract boolean providesUnusedReads()

Returns true if this assembler can inform the Assembler.Callback about all reads that couldn't be assembled. This controls whether the "Save unused reads" option will be enabled in the user interface. An assembler can query whether or not the user actually selected the setting using AssemblerInput.isSaveUnusedReads()

Returns:

true if this assembler will inform the Assembler.Callback about all reads that couldn't be assembled.

providesUsedReads

public boolean providesUsedReads()

Returns true if this assembler can inform the Assembler.Callback about all reads that could be assembled. This controls whether the "Save used reads" option (and associated "include mates" option if providesUsedReadsIncludeMates()) will be enabled in the user interface. An assembler can query whether or not the user actually selected the setting using AssemblerInput.isSaveUsedReads()

Returns:

true if this assembler will inform the Assembler.Callback about all reads that could be assembled.

Since:

API 4.50 (Geneious 5.5.0)

providesUsedReadsIncludeMates

public boolean providesUsedReadsIncludeMates()

Returns true if this assembler can inform the Assembler.Callback about the mates of all reads that could be assembled. This controls whether the "include mates" option (associated with the "Save used reads" option) will be enabled in the user interface. An assembler can query whether or not the user actually selected the setting using AssemblerInput.isSaveUsedReadsIncludeMates()

Returns:

true if this assembler will inform the Assembler.Callback about the mates of all reads that could be assembled.

Since:

API 4.50 (Geneious 5.5.0)

handlesTrimAnnotations

public boolean handlesTrimAnnotations()

Returns true if this assembler handles trim annotations (SequenceAnnotation.TYPE_TRIMMED on input sequences and preserves them on generated contigs. The default implementation returns false.

Returns:

true if this assembler handles trim annotations (SequenceAnnotation.TYPE_TRIMMED on input sequences and preserves them on generated contigs.

Since:

API 4.15 (Geneious 5.1.1)

assemble

public abstract void assemble(Options options,
            AssemblerInput assemblyInput,
            ProgressListener progressListener,
            Assembler.Callback callback)
                       throws DocumentOperationException

Called to actually perform the assembly. All generated contigs (and unused reads if supported) should be given to the callback. Note: The operation will be run in a non AWT thread. If you need to perform user interface interaction in addition to the options provided in the optionsPanel (for example prompting for user input) then you need to place this inside a ThreadUtilities.invokeAndWait() function call.

WARNING: Geneious may call this function multiple times simultaneously. Therefore, any implementation should not store its internal state within instance fields.

Parameters:

options - the options returned from getOptions(OperationLocationOptions, com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties)

assemblyInput - the input data to assemble.

progressListener - a progress listener to report progress to and to check for cancelling.

callback - the callback to add the results to. @throws DocumentOperationException if the operation can't be performed or is cancelled.

Throws:

DocumentOperationException - if something goes wrong during assembly.

canRunOnLocalGeneious

public boolean canRunOnLocalGeneious()

Determine whether this assembly algorithm supports being run on the current computer. For example the algorithm may only work on particular operating systems or only on Geneious server.

Returns:

true if this assembly algorithm supports being run on the current computer.

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

Returns:

true if the operation can be run on a remote GeneiousServer

See Also:

DocumentOperation.canRunOnGeneiousServer()

isProOnly

public boolean isProOnly()

If true, this assembler will be always disabled when the user doesn't have an active license. When disabled for this reason it will also have "(restricted)" appended to its name.

The default implementation returns true.

Returns:

whether this action requires an active license