Package com.biomatters.geneious.publicapi.plugin

Class AssemblerInput.Library

java.lang.Object

com.biomatters.geneious.publicapi.plugin.AssemblerInput.Library

Enclosing class:

AssemblerInput

public class AssemblerInput.Library
extends java.lang.Object

A library of reads to be assembled, represented as a single document in Geneious. These are obtained via AssemblerInput.getLibraries()

Since:

API 4.1000 (Geneious 10.0.0)

Method Summary

Modifier and Type	Method	Description
boolean	allSequencesHaveQuality()
java.util.List<java.io.File>	asFastqOrFastaFiles(java.io.File fileWithoutExtension, boolean compress, boolean asSingleFile, boolean replaceSpacesInSequenceNameWithUnderscores, jebl.util.ProgressListener progressListener)	Returns this library as a list of between one and three fasta or fastq files.
java.util.List<java.io.File>	asFastqOrFastaFiles(java.io.File fileWithoutExtension, boolean compress, jebl.util.ProgressListener progressListener)	Returns this library as a list of between one and three fasta or fastq files.
AssemblerInput.DataType	getDataType()
AssemblerInput.PairedDataType	getPairedDataType()

Methods inherited from class java.lang.Object

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

Method Detail

getDataType

public AssemblerInput.DataType getDataType()

Returns:

the data type of this library, using the assigned DocumentField.DATA_TYPE_FIELD if the user has specified one, or guessing if not.

getPairedDataType

public AssemblerInput.PairedDataType getPairedDataType()
                                                throws com.biomatters.geneious.publicapi.plugin.DocumentOperationException

Returns:

the paired data type of this library, using the assigned DocumentField.PAIRED_DATA_TYPE_FIELD if the user has specified one, or guessing if not. Even if a value is specified for DocumentField.PAIRED_DATA_TYPE_FIELD but the data has no pairs, then returns AssemblerInput.PairedDataType.Unpaired

Throws:

com.biomatters.geneious.publicapi.plugin.DocumentOperationException

allSequencesHaveQuality

public boolean allSequencesHaveQuality()

Returns:

true if all sequences in this library have quality data (i.e. fastq rather than fasta)

asFastqOrFastaFiles

public java.util.List<java.io.File> asFastqOrFastaFiles(java.io.File fileWithoutExtension,
                                                        boolean compress,
                                                        jebl.util.ProgressListener progressListener)
                                                 throws com.biomatters.geneious.publicapi.plugin.DocumentOperationException

Returns this library as a list of between one and three fasta or fastq files.

Equivalent to asFastqOrFastaFiles(fileWithoutExtension, compress, false, true, progressListener)

Parameters:

fileWithoutExtension - the name of the file to export to without an extension. The returned files will have additional text appended as well as an extension

Returns:

a single file if the reads are all unpaired. two files if the reads are all paired reads. three files if there are a mixture, in which case the first two files are the pairs and the third is the unpaired reads.

Throws:

com.biomatters.geneious.publicapi.plugin.DocumentOperationException

See Also:

asFastqOrFastaFiles(File, boolean, boolean, boolean, ProgressListener)

asFastqOrFastaFiles

public java.util.List<java.io.File> asFastqOrFastaFiles(java.io.File fileWithoutExtension,
                                                        boolean compress,
                                                        boolean asSingleFile,
                                                        boolean replaceSpacesInSequenceNameWithUnderscores,
                                                        jebl.util.ProgressListener progressListener)
                                                 throws com.biomatters.geneious.publicapi.plugin.DocumentOperationException

Returns this library as a list of between one and three fasta or fastq files.

Parameters:

fileWithoutExtension - the name of the file to export to without an extension. The returned files will have additional text appended as well as an extension

compress - true compress the data as gz

asSingleFile - true to always produce just a single file even if there are paired reads present. Both reads in a pair will always appear adjacent in the file produced.

replaceSpacesInSequenceNameWithUnderscores - replaces spaces in sequence names with underscores in the file contents.

Returns:

a single file if the reads are all unpaired or if asSingleFile is true. two files if the reads are all paired reads and asSingleFile is false. three files if there are a mixture, in which case the first two files are the pairs and the third is the unpaired reads and asSingleFile is false.

Throws:

com.biomatters.geneious.publicapi.plugin.DocumentOperationException - if there is a problem loading the libraries to create a merged library

Since:

API 4.202001 (Geneious 2020.0.1)