Package ca.corefacility.bioinformatics.irida.service.util.impl

Class BioJavaSequenceFileUtilitiesImpl

java.lang.Object

ca.corefacility.bioinformatics.irida.service.util.impl.BioJavaSequenceFileUtilitiesImpl

All Implemented Interfaces:

SequenceFileUtilities

@Component
public class BioJavaSequenceFileUtilitiesImpl
extends java.lang.Object
implements SequenceFileUtilities

Sequence file utilities class using BioJava for calculation

Constructor Summary

Constructors

Constructor	Description
BioJavaSequenceFileUtilitiesImpl()

Method Summary

Modifier and Type	Method	Description
java.lang.Long	countSequenceFileLengthInBases(java.nio.file.Path file)	Calculate the length of a sequence file in bases

Methods inherited from class java.lang.Object

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

Constructor Detail

BioJavaSequenceFileUtilitiesImpl

public BioJavaSequenceFileUtilitiesImpl()

Method Detail

countSequenceFileLengthInBases

public java.lang.Long countSequenceFileLengthInBases(java.nio.file.Path file)
                                              throws UnsupportedReferenceFileContentError

Calculate the length of a sequence file in bases

Specified by:

countSequenceFileLengthInBases in interface SequenceFileUtilities

Parameters:

file - The reference file object to calculate

Returns:

The number of bases in the file

Throws:

UnsupportedReferenceFileContentError - When the file content is *not* DNA (ambiguous IUPAC bases, protein, etc.)