Package ca.corefacility.bioinformatics.irida.ria.web.services

Class UISequenceFileService

java.lang.Object

ca.corefacility.bioinformatics.irida.ria.web.services.UISequenceFileService

@Component
public class UISequenceFileService
extends java.lang.Object

UI Service for handling requests related to SequenceFiles

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	IMG_DUPLICATION_LEVEL
static java.lang.String	IMG_PERBASE
static java.lang.String	IMG_PERSEQUENCE
static java.lang.String[]	qcFileTypes

Constructor Summary

Constructors

Constructor	Description
UISequenceFileService(AnalysisService analysisService, SequencingObjectService sequencingObjectService)

Method Summary

Modifier and Type	Method	Description
void	downloadSequenceFile(java.lang.Long sequencingObjectId, java.lang.Long sequenceFileId, javax.servlet.http.HttpServletResponse response)	Download the sequence file
FastQCImagesResponse	getFastQCCharts(java.lang.Long sequencingObjectId, java.lang.Long sequenceFileId)	Gets the fastqc charts for the file.
FastQCDetailsResponse	getFastQCDetails(java.lang.Long sequencingObjectId, java.lang.Long sequenceFileId)	Gets the details for the sequence file

Methods inherited from class java.lang.Object

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

Field Detail

IMG_PERBASE

public static final java.lang.String IMG_PERBASE

See Also:

Constant Field Values

IMG_PERSEQUENCE

public static final java.lang.String IMG_PERSEQUENCE

See Also:

Constant Field Values

IMG_DUPLICATION_LEVEL

public static final java.lang.String IMG_DUPLICATION_LEVEL

See Also:

Constant Field Values

qcFileTypes

public static final java.lang.String[] qcFileTypes

Constructor Detail

UISequenceFileService

@Autowired
public UISequenceFileService(AnalysisService analysisService,
                             SequencingObjectService sequencingObjectService)

Method Detail

getFastQCDetails

public FastQCDetailsResponse getFastQCDetails(java.lang.Long sequencingObjectId,
                                              java.lang.Long sequenceFileId)

Gets the details for the sequence file

Parameters:

sequencingObjectId - ID for the SequencingObject

sequenceFileId - Id for the SequenceFile

Returns:

FastQCDetailsResponse dto which contains the sequencing object, sequence file, and the fastqc result.

getFastQCCharts

public FastQCImagesResponse getFastQCCharts(java.lang.Long sequencingObjectId,
                                            java.lang.Long sequenceFileId)
                                     throws java.io.IOException

Gets the fastqc charts for the file.

Parameters:

sequencingObjectId - ID for the SequencingObject

sequenceFileId - Id for the SequenceFile

Returns:

FastQCImagesResponse dto which has the byte arrays for the images as well as the fastqc version

Throws:

java.io.IOException - if entity is not found

downloadSequenceFile

public void downloadSequenceFile(java.lang.Long sequencingObjectId,
                                 java.lang.Long sequenceFileId,
                                 javax.servlet.http.HttpServletResponse response)
                          throws java.io.IOException

Download the sequence file

Parameters:

sequencingObjectId - ID for the SequencingObject

sequenceFileId - Id for the SequenceFile

response - HTTP response object

Throws:

java.io.IOException - if file is not found