gov.nih.nci.caarray.common.data.fileupload2
Class HybridizationFileUploadGroupData
java.lang.Object
gov.nih.nci.caarray.common.data.fileupload2.SerializableFileUploadDataBean
gov.nih.nci.caarray.common.data.fileupload2.FileUploadGroupData
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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
HybridizationFileUploadGroupData
public HybridizationFileUploadGroupData(HybridizationFileType[] fileTypes)
- Parameters:
fileTypes
- - An array of fileTypes.
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.