gov.nih.nci.caarray.common.data.fileupload2
Class HybridizationFileUploadGroupData

java.lang.Object
  extended by gov.nih.nci.caarray.common.data.fileupload2.SerializableFileUploadDataBean
      extended by gov.nih.nci.caarray.common.data.fileupload2.FileUploadGroupData
          extended by gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
All Implemented Interfaces:
java.io.Serializable

public class HybridizationFileUploadGroupData
extends FileUploadGroupData

This class represents a group of files that are parsed to one or more bioassays. The files added will be parsed as a measured or derived bioassay. depending on their fileType's fileCategory attribute. All other files are simply stored. An instance of this class is intended to be constructed at the server side which knows what the file type(s) are available and expected given some parameters such as the name of a microaarray data analysis software. The client code then populates the instance with data files to be parsed or stored and forwards the instance to the upload and parsing process.

Author:
TranP
See Also:
Serialized Form

Field Summary
 
Fields inherited from class gov.nih.nci.caarray.common.data.fileupload2.FileUploadGroupData
acceptableFileTypes_
 
Fields inherited from class gov.nih.nci.caarray.common.data.fileupload2.SerializableFileUploadDataBean
id_
 
Constructor Summary
HybridizationFileUploadGroupData(HybridizationFileType[] fileTypes)
           
 
Method Summary
 void addFile(java.lang.String fileName, HybridizationFileType fileType, java.lang.String originalFileName, java.lang.String validatorCode, java.lang.String userId)
           
 boolean addFileByGuessingType(java.lang.String fileName, java.lang.String originalFileName, java.lang.String validatorCode, java.lang.String userId)
          Adds a file which type is to be discovered based on its original file's extension or the zipped version's extension.
 HybridizationFileType[] getAcceptableFileTypes()
          Gets the file types with which this instance is constructed.
 ArrayGroupData getArrayGroup()
           
 LabeledExtractDesc getChannelOneExtract()
           
 FactorValueData[] getChannelOneFactorValues()
           
 LabeledExtractDesc getChannelOneSpikedControl()
           
 LabeledExtractDesc getChannelTwoExtract()
           
 FactorValueData[] getChannelTwoFactorValues()
           
 LabeledExtractDesc getChannelTwoSpikedControl()
           
 ExperimentDesc getExperiment()
           
 ProtocolApplicationData getFeatureExtractionProtocolApplication()
           
 HybridizationFileType getFileTypeByGuessing(java.lang.String fileName)
           
 HybridizationFileUploadEntryData[] getFileUploadEntries()
           
 HybridizationFileUploadEntryData[] getFileUploadEntries(FileType searchFileType)
           
 ProtocolApplicationData getHybridizationProtocolApplication()
           
 ProtocolApplicationData getImageAcquisitionProtocolApplication()
           
 java.lang.String[] getNonParseableFiles()
           
 void setArrayGroup(ArrayGroupData arrayGroup)
           
 void setChannelOneExtract(LabeledExtractDesc channelOneExtract)
           
 void setChannelOneFactorValues(FactorValueData[] factorValues)
           
 void setChannelOneSpikedControl(LabeledExtractDesc channelOneSpikedControl)
           
 void setChannelTwoExtract(LabeledExtractDesc channelTwoExtract)
           
 void setChannelTwoFactorValues(FactorValueData[] factorValues)
           
 void setChannelTwoSpikedControl(LabeledExtractDesc channelTwoSpikedControl)
           
 void setExperiment(ExperimentDesc experiment)
           
 void setFeatureExtractionProtocolApplication(ProtocolApplicationData featureExtractionProtocolApplication)
           
 void setFileUploadEntries(HybridizationFileUploadEntryData[] fileUploadEntries)
           
 void setHybridizationProtocolApplication(ProtocolApplicationData hybridizationProtocolApplication)
           
 void setImageAcquisitionProtocolApplication(ProtocolApplicationData imageAcquisitionProtocolApplication)
           
 
Methods inherited from class gov.nih.nci.caarray.common.data.fileupload2.FileUploadGroupData
findFileTypeOther, getParsingEndDate, getParsingStartDate, getParsingSucceeded, guessFileType, setParsingEndDate, setParsingStartDate, setParsingSucceeded
 
Methods inherited from class gov.nih.nci.caarray.common.data.fileupload2.SerializableFileUploadDataBean
getId, setId, toString
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

HybridizationFileUploadGroupData

public HybridizationFileUploadGroupData(HybridizationFileType[] fileTypes)
Parameters:
fileTypes - - An array of fileTypes.
Method Detail

getFileUploadEntries

public HybridizationFileUploadEntryData[] getFileUploadEntries(FileType searchFileType)

getFileUploadEntries

public HybridizationFileUploadEntryData[] getFileUploadEntries()
Returns:
Returns the fileUploadEntries.

setFileUploadEntries

public void setFileUploadEntries(HybridizationFileUploadEntryData[] fileUploadEntries)
Parameters:
fileUploadEntries - The fileUploadEntries to set.

getAcceptableFileTypes

public HybridizationFileType[] getAcceptableFileTypes()
Gets the file types with which this instance is constructed. The measured bioassay type is the first one in the array.

Returns:

addFile

public void addFile(java.lang.String fileName,
                    HybridizationFileType fileType,
                    java.lang.String originalFileName,
                    java.lang.String validatorCode,
                    java.lang.String userId)
Parameters:
fileName -
fileType - - If null, the file is assumed to be "other" file and will be simply stored but not parsed.

addFileByGuessingType

public boolean addFileByGuessingType(java.lang.String fileName,
                                     java.lang.String originalFileName,
                                     java.lang.String validatorCode,
                                     java.lang.String userId)
Adds a file which type is to be discovered based on its original file's extension or the zipped version's extension. For efficiency, the upload mechanism would create a zip file for each of the files being uploaded and create the zip file name like this:

Original file name: HG-U133B-1.CHP

Created zip file name: HG-U133B-1_CHP.ZIP

In the example, if the specified file's extension ends with the pattern CHP and _CHP.ZIP case-insensitive the specified file is added. Otherwise, false is returned.

Although non-parseable/stored-only files are accepted, there must a type defined for them.

Parameters:
fileName -
Returns:

getFileTypeByGuessing

public HybridizationFileType getFileTypeByGuessing(java.lang.String fileName)

getNonParseableFiles

public java.lang.String[] getNonParseableFiles()

getChannelOneExtract

public LabeledExtractDesc getChannelOneExtract()
Returns:
Returns the channelOneExtract.

setChannelOneExtract

public void setChannelOneExtract(LabeledExtractDesc channelOneExtract)
Parameters:
channelOneExtract - The channelOneExtract to set.

getChannelOneSpikedControl

public LabeledExtractDesc getChannelOneSpikedControl()
Returns:
Returns the channelOneSpikedControl.

setChannelOneSpikedControl

public void setChannelOneSpikedControl(LabeledExtractDesc channelOneSpikedControl)
Parameters:
channelOneSpikedControl - The channelOneSpikedControl to set.

getChannelTwoExtract

public LabeledExtractDesc getChannelTwoExtract()
Returns:
Returns the channelTwoExtract.

setChannelTwoExtract

public void setChannelTwoExtract(LabeledExtractDesc channelTwoExtract)
Parameters:
channelTwoExtract - The channelTwoExtract to set.

getChannelTwoSpikedControl

public LabeledExtractDesc getChannelTwoSpikedControl()
Returns:
Returns the channelTwoSpikedControl.

setChannelTwoSpikedControl

public void setChannelTwoSpikedControl(LabeledExtractDesc channelTwoSpikedControl)
Parameters:
channelTwoSpikedControl - The channelTwoSpikedControl to set.

getExperiment

public ExperimentDesc getExperiment()
Returns:
Returns the experiment.

setExperiment

public void setExperiment(ExperimentDesc experiment)
Parameters:
experiment - The experiment to set.

getFeatureExtractionProtocolApplication

public ProtocolApplicationData getFeatureExtractionProtocolApplication()
Returns:
Returns the featureExtractionProtocolApplication.

setFeatureExtractionProtocolApplication

public void setFeatureExtractionProtocolApplication(ProtocolApplicationData featureExtractionProtocolApplication)
Parameters:
featureExtractionProtocolApplication - The featureExtractionProtocolApplication to set.

getHybridizationProtocolApplication

public ProtocolApplicationData getHybridizationProtocolApplication()
Returns:
Returns the hybridizationProtocolApplication.

setHybridizationProtocolApplication

public void setHybridizationProtocolApplication(ProtocolApplicationData hybridizationProtocolApplication)
Parameters:
hybridizationProtocolApplication - The hybridizationProtocolApplication to set.

getImageAcquisitionProtocolApplication

public ProtocolApplicationData getImageAcquisitionProtocolApplication()
Returns:
Returns the imageAcquisitionProtocolApplication.

setImageAcquisitionProtocolApplication

public void setImageAcquisitionProtocolApplication(ProtocolApplicationData imageAcquisitionProtocolApplication)
Parameters:
imageAcquisitionProtocolApplication - The imageAcquisitionProtocolApplication to set.

getArrayGroup

public ArrayGroupData getArrayGroup()
Returns:
Returns the arrayGroup.

setArrayGroup

public void setArrayGroup(ArrayGroupData arrayGroup)
Parameters:
arrayGroup - The arrayGroup to set.

getChannelOneFactorValues

public FactorValueData[] getChannelOneFactorValues()
Returns:
Returns the channelOneFactorValues.

setChannelOneFactorValues

public void setChannelOneFactorValues(FactorValueData[] factorValues)
Parameters:
channelOneFactorValues - The channelOneFactorValues to set.

getChannelTwoFactorValues

public FactorValueData[] getChannelTwoFactorValues()
Returns:
Returns the channelTwoFactorValues.

setChannelTwoFactorValues

public void setChannelTwoFactorValues(FactorValueData[] factorValues)
Parameters:
factorValues - The channelTwoFactorValues to set.