Package ca.corefacility.bioinformatics.irida.model.workflow.analysis

Class AnalysisFastQC

java.lang.Object

ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC

All Implemented Interfaces:

IridaThing, Timestamped<java.lang.Long>

@Entity
public class AnalysisFastQC
extends Analysis

Specific implementation of Analysis for storing properties created by FastQC.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	AnalysisFastQC.AnalysisFastQCBuilder	Builder for creating instances of AnalysisFastQC.

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AnalysisFastQC()	Required for hibernate, should not be used anywhere else, so private.
	AnalysisFastQC(AnalysisFastQC.AnalysisFastQCBuilder builder)

Method Summary

Modifier and Type	Method	Description
static AnalysisFastQC.AnalysisFastQCBuilder	builder()	get an AnalysisFastQCBuilder
byte[]	getDuplicationLevelChart()	Line chartshowing duplication-level as a PNG-formatted image in a byte array.
java.lang.String	getEncoding()
java.lang.String	getFastqcVersion()
java.lang.String	getFileType()
java.lang.Integer	getFilteredSequences()
java.lang.Short	getGcContent()
java.lang.Integer	getMaxLength()
java.lang.Integer	getMinLength()
java.util.Set<OverrepresentedSequence>	getOverrepresentedSequences()
byte[]	getPerBaseQualityScoreChart()	Box and whisker plot showing per-base quality scores as a PNG-formatted image in a byte array.
byte[]	getPerSequenceQualityScoreChart()	Line chartshowing per-sequence quality scores as a PNG-formatted image in a byte array.
java.lang.Long	getTotalBases()
java.lang.Integer	getTotalSequences()

Methods inherited from class ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis

equals, getAdditionalProperties, getAnalysisOutputFile, getAnalysisOutputFileNames, getAnalysisOutputFiles, getAnalysisOutputFilesMap, getAnalysisType, getCreatedDate, getDescription, getExecutionManagerAnalysisId, getId, getLabel, hashCode, setAnalysisType, setId, toString

Methods inherited from class ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel

add, add, getLink, getLinks, getRemoteStatus, getSelfHref, hasLink, hasLinks, removeLinks, setRemoteStatus

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface ca.corefacility.bioinformatics.irida.model.IridaThing

getIdentifier, setLabel

Constructor Detail

AnalysisFastQC

protected AnalysisFastQC()

Required for hibernate, should not be used anywhere else, so private.

AnalysisFastQC

public AnalysisFastQC(AnalysisFastQC.AnalysisFastQCBuilder builder)

Method Detail

builder

public static AnalysisFastQC.AnalysisFastQCBuilder builder()

get an AnalysisFastQCBuilder

Returns:

an AnalysisFastQCBuilder

getPerBaseQualityScoreChart

public byte[] getPerBaseQualityScoreChart()
                                   throws java.io.IOException

Box and whisker plot showing per-base quality scores as a PNG-formatted image in a byte array.

Returns:

a PNG-formatted byte array for per-base quality score.

Throws:

java.io.IOException - if the file does not exist

getPerSequenceQualityScoreChart

public byte[] getPerSequenceQualityScoreChart()
                                       throws java.io.IOException

Line chartshowing per-sequence quality scores as a PNG-formatted image in a byte array.

Returns:

a PNG-formatted byte array for per-sequence quality score.

Throws:

java.io.IOException - if the file does not exist

getDuplicationLevelChart

public byte[] getDuplicationLevelChart()
                                throws java.io.IOException

Line chartshowing duplication-level as a PNG-formatted image in a byte array.

Returns:

a PNG-formatted byte array for duplication levels.

Throws:

java.io.IOException - if the file does not exist

getFastqcVersion

public java.lang.String getFastqcVersion()

getFileType

public java.lang.String getFileType()

getEncoding

public java.lang.String getEncoding()

getTotalSequences

public java.lang.Integer getTotalSequences()

getFilteredSequences

public java.lang.Integer getFilteredSequences()

getMinLength

public java.lang.Integer getMinLength()

getMaxLength

public java.lang.Integer getMaxLength()

getGcContent

public java.lang.Short getGcContent()

getTotalBases

public java.lang.Long getTotalBases()

getOverrepresentedSequences

public java.util.Set<OverrepresentedSequence> getOverrepresentedSequences()