Serialized Form
Package gov.nih.nci.caarray.common.data.array |
id_
long id_
manufacturingProtocolApplication_
ProtocolApplicationData manufacturingProtocolApplication_
desc_
ArrayGroupDesc desc_
arrays_
ArrayData[] arrays_
numArrays_
int numArrays_
arrayGroupBarCode_
java.lang.String arrayGroupBarCode_
substrateType_
VocabData substrateType_
arrayGroupSpacingX_
float arrayGroupSpacingX_
arrayGroupSpacingY_
float arrayGroupSpacingY_
arrayWidth_
float arrayWidth_
arrayLength_
float arrayLength_
arrayOrientationMark_
java.lang.String arrayOrientationMark_
arrayOrientationMarkPosition_
java.lang.String arrayOrientationMarkPosition_
arrayGroupDescription_
java.lang.String arrayGroupDescription_
visibility_
long visibility_
isEditable
boolean isEditable
id_
long id_
groupName_
java.lang.String groupName_
manufactureDate_
java.util.Date manufactureDate_
arrayDesign_
ArrayDesignData arrayDesign_
arrayManufacturers_
java.util.ArrayList<E> arrayManufacturers_
securedElement_
SecuredElementData securedElement_
protectionGroups_
ProtectionGroupData[] protectionGroups_
arrayNameArrayDesignName
java.lang.String arrayNameArrayDesignName
arrayDesignId_
long arrayDesignId_
freeText_
java.lang.String freeText_
substrateType_
VocabData substrateType_
manufacturingProtocolId_
long manufacturingProtocolId_
manufacturerId_
long manufacturerId_
startManufactureDate_
java.util.Date startManufactureDate_
endManufactureDate_
java.util.Date endManufactureDate_
groupName_
java.lang.String groupName_
visibility_
ProtectionGroupData visibility_
Package gov.nih.nci.caarray.common.data.arraydesign |
desc_
ArrayDesignDesc desc_
reporterFileType_
java.lang.String reporterFileType_
reporterFileLocation_
java.lang.String reporterFileLocation_
additionalReporterFileLocation_
java.lang.String additionalReporterFileLocation_
version_
java.lang.String version_
surfaceType_
VocabData surfaceType_
substrateType_
VocabData substrateType_
technologyType_
VocabData technologyType_
attachmentType_
VocabData attachmentType_
strandType_
VocabData strandType_
species_
VocabData species_
description_
java.lang.String description_
numberOfFeatures_
int numberOfFeatures_
providedByAffymetrix_
boolean providedByAffymetrix_
isEditable
boolean isEditable
id_
long id_
identifier_
java.lang.String identifier_
name_
java.lang.String name_
securedElement_
SecuredElementData securedElement_
protectionGroups_
ProtectionGroupData[] protectionGroups_
arrayDesignId_
long arrayDesignId_
identifier_
java.lang.String identifier_
attachmentType_
VocabData attachmentType_
freeText_
java.lang.String freeText_
name_
java.lang.String name_
speciesType_
VocabData speciesType_
strandType_
VocabData strandType_
substrateType_
VocabData substrateType_
surfaceType_
VocabData surfaceType_
technologyType_
VocabData technologyType_
visibility_
ProtectionGroupData visibility_
providerId_
long providerId_
designProviderRoles_
java.util.ArrayList<E> designProviderRoles_
protocolApplications_
java.util.ArrayList<E> protocolApplications_
mageIdentifier
java.lang.String mageIdentifier
desc_
CompositeGroupDesc desc_
compositeSequences_
java.util.Vector<E> compositeSequences_
securedElement_
SecuredElementData securedElement_
protectionGroups_
ProtectionGroupData[] protectionGroups_
name_
java.lang.String name_
id_
long id_
species_
VocabData species_
visibilitys_
long[] visibilitys_
freeText_
java.lang.String freeText_
name_
java.lang.String name_
compositegroupid_
long compositegroupid_
species_
VocabData species_
visibility_
ProtectionGroupData visibility_
role_
VocabData role_
contact_
ContactData contact_
desc_
FeatureGroupDesc desc_
securedElement_
SecuredElementData securedElement_
protectionGroups_
ProtectionGroupData[] protectionGroups_
id_
long id_
name_
java.lang.String name_
species_
VocabData species_
technologyType_
VocabData technologyType_
featureShape_
VocabData featureShape_
distanceUnit_
java.lang.String distanceUnit_
featureWidth_
double featureWidth_
featureLength_
double featureLength_
featureHeight_
double featureHeight_
visibilitys_
long[] visibilitys_
manufacturer_
OrganizationDesc manufacturer_
featuregroupid_
long featuregroupid_
name_
java.lang.String name_
species_
VocabData species_
technologyType_
VocabData technologyType_
featureShape_
VocabData featureShape_
distanceUnit_
java.lang.String distanceUnit_
featureWidth_
double featureWidth_
featureLength_
double featureLength_
featureHeight_
double featureHeight_
visibility_
ProtectionGroupData visibility_
desc_
ReporterGroupDesc desc_
securedElement_
SecuredElementData securedElement_
protectionGroups_
ProtectionGroupData[] protectionGroups_
name_
java.lang.String name_
species_
VocabData species_
id_
long id_
visibilitys_
long[] visibilitys_
name_
java.lang.String name_
species_
VocabData species_
reportergroupid_
long reportergroupid_
visibility_
ProtectionGroupData visibility_
Package gov.nih.nci.caarray.common.data.biomaterial |
action_
VocabData action_
protocolTypes_
java.util.ArrayList<E> protocolTypes_
desc_
BioMaterialDesc desc_
isEditable
boolean isEditable
protectionGroups_
ProtectionGroupData[] protectionGroups_
id_
long id_
name_
java.lang.String name_
description_
java.lang.String description_
materialType_
VocabData materialType_
species_
VocabData species_
parents_
java.util.ArrayList<E> parents_
isEditable
boolean isEditable
biomaterialId
long biomaterialId
materialType_
VocabData materialType_
species_
VocabData species_
sampleType_
VocabData sampleType_
provider_
VocabData provider_
biosourceType_
VocabData biosourceType_
freeText_
java.lang.String freeText_
bioMaterialName_
java.lang.String bioMaterialName_
visibility_
ProtectionGroupData visibility_
parentBioSampleId_
long parentBioSampleId_
parentBioSourceId_
long parentBioSourceId_
ignoreCopy
boolean ignoreCopy
treatments_
java.util.ArrayList<E> treatments_
characteristics_
java.util.ArrayList<E> characteristics_
bioSampleType_
VocabData bioSampleType_
mageIdentifier
java.lang.String mageIdentifier
provider
ContactData provider
bioSourceType_
VocabData bioSourceType_
provider_
ContactData provider_
mageIdentifier
java.lang.String mageIdentifier
compound_
VocabData compound_
measurement_
MeasurementData measurement_
label_
VocabData label_
label_
VocabData label_
mageIdentifier
java.lang.String mageIdentifier
measurement_
MeasurementData measurement_
id_
long id_
treatmentType_
VocabData treatmentType_
treatmentOrder_
java.lang.Integer treatmentOrder_
measurement_
MeasurementData measurement_
protocolApplication_
ProtocolApplicationData protocolApplication_
compoundMeasurements_
java.util.ArrayList<E> compoundMeasurements_
treatmentAction_
java.lang.String treatmentAction_
Package gov.nih.nci.caarray.common.data.contact |
phone_
java.lang.String phone_
tollFreePhone_
java.lang.String tollFreePhone_
fax_
java.lang.String fax_
desc_
OrganizationDesc desc_
email_
java.lang.String email_
mageIdentifier
java.lang.String mageIdentifier
id_
long id_
name_
java.lang.String name_
address_
java.lang.String address_
URI_
java.lang.String URI_
organizationName_
java.lang.String organizationName_
address_
java.lang.String address_
desc_
PersonDesc desc_
organization_
OrganizationData organization_
URI_
java.lang.String URI_
mageIdentifier
java.lang.String mageIdentifier
email_
java.lang.String email_
firstName_
java.lang.String firstName_
id_
long id_
lastName_
java.lang.String lastName_
midInitials_
java.lang.String midInitials_
firstName_
java.lang.String firstName_
lastName_
java.lang.String lastName_
organizationName_
java.lang.String organizationName_
Package gov.nih.nci.caarray.common.data.designelement |
desc_
CompositeSequenceDesc desc_
securedElement_
SecuredElementData securedElement_
protectionGroups_
ProtectionGroupData[] protectionGroups_
name_
java.lang.String name_
id_
long id_
Package gov.nih.nci.caarray.common.data.experiment |
id_
long id_
location_
java.lang.String location_
protocolApplication_
ProtocolApplicationData protocolApplication_
experiment_
ExperimentDesc experiment_
id_
long id_
name_
java.lang.String name_
value_
java.lang.String value_
source_
java.lang.String source_
id_
long id_
description_
java.lang.String description_
location_
java.lang.String location_
experiment_
ExperimentDesc experiment_
id_
long id_
type_
VocabData type_
name_
java.lang.String name_
scale_
VocabData scale_
factorValues_
java.util.ArrayList<E> factorValues_
desc_
ExperimentDesc desc_
isEditable
boolean isEditable
id_
long id_
securedElementId_
java.lang.String securedElementId_
identifier_
java.lang.String identifier_
name_
java.lang.String name_
description_
java.lang.String description_
completionDate_
java.util.Date completionDate_
species_
VocabData species_
types_
java.util.ArrayList<E> types_
experimentProviderRoles_
java.util.ArrayList<E> experimentProviderRoles_
numberOfHybridizations_
int numberOfHybridizations_
protectionGroups_
ProtectionGroupData[] protectionGroups_
archive_value
java.lang.String archive_value
sobject
java.lang.String sobject
sokey
java.lang.String sokey
serverURL
java.lang.String serverURL
destination
java.lang.String destination
endJumptoUrl
java.lang.String endJumptoUrl
files
java.lang.String files
actionCommand
java.lang.String actionCommand
role_
VocabData role_
contact_
ContactData contact_
id_
long id_
identifier_
java.lang.String identifier_
experimentName_
java.lang.String experimentName_
experimentType_
VocabData experimentType_
contact_
long contact_
species_
VocabData species_
freeText_
java.lang.String freeText_
visibility_
ProtectionGroupData visibility_
publications_
java.util.ArrayList<E> publications_
experimentalFactors_
java.util.ArrayList<E> experimentalFactors_
additionalQualifiers_
java.util.ArrayList<E> additionalQualifiers_
qualityControl_
QualityControlData qualityControl_
hybridizationFileUploads_
java.util.ArrayList<E> hybridizationFileUploads_
additionalUploadedFiles_
java.util.ArrayList<E> additionalUploadedFiles_
additionalDataProcessings_
java.util.ArrayList<E> additionalDataProcessings_
id_
long id_
value_
java.lang.String value_
name_
java.lang.String name_
id_
long id_
- Deprecated.
array_
ArrayData array_
- Deprecated.
arrayDesign
ArrayDesignDesc arrayDesign
- Deprecated.
experiment_
ExperimentDesc experiment_
- Deprecated.
arrayBatchName_
java.lang.String arrayBatchName_
- Deprecated.
arrayIdentifier_
java.lang.String arrayIdentifier_
- Deprecated.
hybridizationProtocolApplication_
ProtocolApplicationData hybridizationProtocolApplication_
- Deprecated.
imageAcquisitionProtocolApplication_
ProtocolApplicationData imageAcquisitionProtocolApplication_
- Deprecated.
featureExtractionProtocolApplication_
ProtocolApplicationData featureExtractionProtocolApplication_
- Deprecated.
uploadGroupName_
java.lang.String uploadGroupName_
- Deprecated.
numberOfChannels_
java.lang.Integer numberOfChannels_
- Deprecated.
factorValues_
java.util.ArrayList<E> factorValues_
- Deprecated.
extract_
LabeledExtractDesc extract_
- Deprecated.
spikedControl_
LabeledExtractDesc spikedControl_
- Deprecated.
celFileLocation_
java.lang.String celFileLocation_
- Deprecated.
expFileLocation_
java.lang.String expFileLocation_
- Deprecated.
txtFileLocation_
java.lang.String txtFileLocation_
- Deprecated.
chpFileLocation_
java.lang.String chpFileLocation_
- Deprecated.
channelTwoFactorValues_
java.util.ArrayList<E> channelTwoFactorValues_
- Deprecated.
channelTwoExtract_
LabeledExtractDesc channelTwoExtract_
- Deprecated.
channelTwoSpikedControl_
LabeledExtractDesc channelTwoSpikedControl_
- Deprecated.
gprFileLocation_
java.lang.String gprFileLocation_
- Deprecated.
gpsFileLocation_
java.lang.String gpsFileLocation_
- Deprecated.
gprFromSpotFileLocation_
java.lang.String gprFromSpotFileLocation_
- Deprecated.
hybridizationMappingType_
int hybridizationMappingType_
- Deprecated.
id_
long id_
publication_
java.lang.String publication_
pubMedId_
java.lang.String pubMedId_
pubMedLink_
java.lang.String pubMedLink_
title_
java.lang.String title_
publisher_
java.lang.String publisher_
editor_
java.lang.String editor_
year_
java.util.Date year_
volume_
java.lang.String volume_
issue_
java.lang.String issue_
pages_
java.lang.String pages_
URI_
java.lang.String URI_
authors_
java.lang.String authors_
id_
long id_
description_
java.lang.String description_
types_
VocabData[] types_
Package gov.nih.nci.caarray.common.data.fileupload2 |
fileParsingEntry_
ArrayDesignFileParsingEntryData fileParsingEntry_
arrayDesign_
ArrayDesignDesc arrayDesign_
fileUploadEntries_
java.util.ArrayList<E> fileUploadEntries_
uploadedFileData
UploadedFileData uploadedFileData
arrayDesignId
long arrayDesignId
fileEntryId
long fileEntryId
fileParsingEntryId
long fileParsingEntryId
fileGroupId
long fileGroupId
arrayDesignId
long arrayDesignId
fileEntryId
long fileEntryId
fileParsingEntryId
long fileParsingEntryId
fileGroupId
long fileGroupId
ojbConcreteClass
java.lang.String ojbConcreteClass
id
long id
fileTypeId
java.lang.String fileTypeId
fileName
java.lang.String fileName
uploadDate
java.util.Date uploadDate
caArrayDesignFileEntryData
CAArrayDesignFileUploadEntryData caArrayDesignFileEntryData
caFileUploadHistoryData
CAFileUploadHistoryData caFileUploadHistoryData
caMagemlFileEntryData
CAMagemlFileUploadEntryData caMagemlFileEntryData
status
java.lang.String status
statusDate
java.util.Date statusDate
validatorCode
java.lang.String validatorCode
userId
java.lang.String userId
originalFileName
java.lang.String originalFileName
id
long id
fileEntryId
long fileEntryId
status
java.lang.String status
statusDate
java.util.Date statusDate
description
java.lang.String description
fileEntryId
long fileEntryId
fileParsingEntryId
long fileParsingEntryId
contactId
long contactId
magellFileGroupId
long magellFileGroupId
name
java.lang.String name
version
java.lang.String version
description
java.lang.String description
contentType
java.lang.String contentType
msgToCurator
java.lang.String msgToCurator
parsingStartDate_
java.util.Date parsingStartDate_
parsingEndDate_
java.util.Date parsingEndDate_
parsingSucceeded_
java.lang.String parsingSucceeded_
failureDescription_
java.lang.String failureDescription_
ojbConcreteClass
java.lang.String ojbConcreteClass
id
java.lang.String id
creatingSoftware
java.lang.String creatingSoftware
creatingSoftwareVersion
java.lang.String creatingSoftwareVersion
fileExtension
java.lang.String fileExtension
fileZipExtension
java.lang.String fileZipExtension
fileCategory
java.lang.String fileCategory
required
java.lang.Boolean required
fileTypeMappings_
java.util.LinkedHashMap<K,V> fileTypeMappings_
serialVersionUID: -1999989794623791411L
fileType_
FileType fileType_
fileName_
java.lang.String fileName_
status_
java.lang.String status_
statusDate_
java.util.Date statusDate_
validatorCode_
java.lang.String validatorCode_
userId_
java.lang.String userId_
originalFileName_
java.lang.String originalFileName_
parsingStartDate_
java.util.Date parsingStartDate_
parsingEndDate_
java.util.Date parsingEndDate_
parsingSucceeded_
java.lang.String parsingSucceeded_
acceptableFileTypes_
java.util.ArrayList<E> acceptableFileTypes_
fileUploadEntry_
FileUploadEntryData fileUploadEntry_
status_
java.lang.String status_
statusDate_
java.util.Date statusDate_
description_
java.lang.String description_
fileUploadEntry_
long fileUploadEntry_
fileParsingEntry_
HybridizationFileParsingEntryData fileParsingEntry_
experiment_
ExperimentDesc experiment_
arrayGroup_
ArrayGroupData arrayGroup_
channelOneExtract_
LabeledExtractDesc channelOneExtract_
channelOneSpikedControl_
LabeledExtractDesc channelOneSpikedControl_
channelTwoExtract_
LabeledExtractDesc channelTwoExtract_
channelTwoSpikedControl_
LabeledExtractDesc channelTwoSpikedControl_
featureExtractionProtocolApplication_
ProtocolApplicationData featureExtractionProtocolApplication_
hybridizationProtocolApplication_
ProtocolApplicationData hybridizationProtocolApplication_
imageAcquisitionProtocolApplication_
ProtocolApplicationData imageAcquisitionProtocolApplication_
channelOneFactorValues_
java.util.ArrayList<E> channelOneFactorValues_
channelTwoFactorValues_
java.util.ArrayList<E> channelTwoFactorValues_
fileType_
HybridizationFileType fileType_
fileName_
java.lang.String fileName_
parsingStartDate_
java.util.Date parsingStartDate_
parsingEndDate_
java.util.Date parsingEndDate_
statusDate_
java.util.Date statusDate_
originalFileName_
java.lang.String originalFileName_
userId_
java.lang.String userId_
validatorCode_
java.lang.String validatorCode_
parsingSucceeded_
java.lang.String parsingSucceeded_
failureDescription
java.lang.String failureDescription
file2FileTypeMap_
java.util.LinkedHashMap<K,V> file2FileTypeMap_
experiment_
ExperimentDesc experiment_
arrayGroup_
ArrayGroupData arrayGroup_
channelOneExtract_
LabeledExtractDesc channelOneExtract_
channelOneSpikedControl_
LabeledExtractDesc channelOneSpikedControl_
channelTwoExtract_
LabeledExtractDesc channelTwoExtract_
channelTwoSpikedControl_
LabeledExtractDesc channelTwoSpikedControl_
featureExtractionProtocolApplication_
ProtocolApplicationData featureExtractionProtocolApplication_
hybridizationProtocolApplication_
ProtocolApplicationData hybridizationProtocolApplication_
imageAcquisitionProtocolApplication_
ProtocolApplicationData imageAcquisitionProtocolApplication_
channelOneFactorValues_
java.util.ArrayList<E> channelOneFactorValues_
channelTwoFactorValues_
java.util.ArrayList<E> channelTwoFactorValues_
fileUploadEntries_
java.util.ArrayList<E> fileUploadEntries_
name_
java.lang.String name_
version_
java.lang.String version_
description_
java.lang.String description_
contentType_
java.lang.String contentType_
contact_
PersonData contact_
msgToCurator_
java.lang.String msgToCurator_
name_
java.lang.String name_
version_
java.lang.String version_
description_
java.lang.String description_
contentType_
java.lang.String contentType_
contact_
long contact_
msgToCurator_
java.lang.String msgToCurator_
userId_
java.lang.String userId_
id_
long id_
id
long id
fileTypeId
java.lang.String fileTypeId
fileName
java.lang.String fileName
status
java.lang.String status
statusDate
java.util.Date statusDate
validatorCode
java.lang.String validatorCode
userId
java.lang.String userId
originalFileName
java.lang.String originalFileName
Package gov.nih.nci.caarray.common.data.measurement |
id_
long id_
value_
java.lang.String value_
unit_
UnitData unit_
type_
VocabData type_
name_
VocabData name_
Package gov.nih.nci.caarray.common.data.protocol |
hardware_
HardwareData hardware_
serialNumber_
java.lang.String serialNumber_
desc_
HardwareDesc desc_
URI_
java.lang.String URI_
parameters_
java.util.ArrayList<E> parameters_
softwares_
java.util.ArrayList<E> softwares_
isEditable
boolean isEditable
securedElement_
SecuredElementData securedElement_
protectionGroups_
ProtectionGroupData[] protectionGroups_
id_
long id_
visibilitys_
long[] visibilitys_
make_
java.lang.String make_
name_
java.lang.String name_
manufacturer_
OrganizationData manufacturer_
model_
java.lang.String model_
type_
VocabData type_
hardwareId_
long hardwareId_
model_
java.lang.String model_
make_
java.lang.String make_
name_
java.lang.String name_
manufacturerId_
long manufacturerId_
type_
VocabData type_
freeText_
java.lang.String freeText_
visibility_
ProtectionGroupData visibility_
id_
long id_
name_
java.lang.String name_
defaultValue_
MeasurementData defaultValue_
dataType_
VocabData dataType_
id_
long id_
parameterValues_
java.util.ArrayList<E> parameterValues_
id_
long id_
parameter_
ParameterData parameter_
value_
java.lang.String value_
protocol_
ProtocolData protocol_
performer_
PersonData performer_
activityDate_
java.util.Date activityDate_
softwareApplications_
java.util.ArrayList<E> softwareApplications_
hardwareApplications_
java.util.ArrayList<E> hardwareApplications_
activityDateAsString_
java.lang.String activityDateAsString_
desc_
ProtocolDesc desc_
identifier_
java.lang.String identifier_
description_
java.lang.String description_
hardwares_
java.util.Vector<E> hardwares_
softwares_
java.util.Vector<E> softwares_
parameters_
java.util.Vector<E> parameters_
URI_
java.lang.String URI_
mageIdentifier
java.lang.String mageIdentifier
isEditable
boolean isEditable
securedElement_
SecuredElementData securedElement_
protectionGroups_
ProtectionGroupData[] protectionGroups_
name_
java.lang.String name_
visibilitys_
long[] visibilitys_
id_
long id_
type_
VocabData type_
freeText_
java.lang.String freeText_
name_
java.lang.String name_
protocolId_
long protocolId_
type_
VocabData type_
softwareManufacturerId_
long softwareManufacturerId_
hardwareManufacturerId_
long hardwareManufacturerId_
visibility_
ProtectionGroupData visibility_
software_
SoftwareData software_
releaseDate_
java.util.Date releaseDate_
version_
java.lang.String version_
releaseDateAsString_
java.lang.String releaseDateAsString_
description_
java.lang.String description_
parameters_
java.util.ArrayList<E> parameters_
desc_
SoftwareDesc desc_
URI_
java.lang.String URI_
hardware_
HardwareDesc hardware_
softwares_
java.util.ArrayList<E> softwares_
isEditable
boolean isEditable
securedElement_
SecuredElementData securedElement_
protectionGroups_
ProtectionGroupData[] protectionGroups_
manufacturer_
OrganizationData manufacturer_
name_
java.lang.String name_
id_
long id_
type_
VocabData type_
visibilitys_
long[] visibilitys_
freeText_
java.lang.String freeText_
manufacturer_
java.lang.String manufacturer_
manufacturerId_
long manufacturerId_
name_
java.lang.String name_
releaseDate_
java.util.Date releaseDate_
softwareId_
long softwareId_
type_
VocabData type_
visibility_
ProtectionGroupData visibility_
Package gov.nih.nci.caarray.common.data.security |
name_
java.lang.String name_
description_
java.lang.String description_
protectionGroupId_
long protectionGroupId_
roleId
long roleId
roleName
java.lang.String roleName
roleDesc
java.lang.String roleDesc
applicationId
long applicationId
role_
RoleData role_
protectionGroups_
java.util.Vector<E> protectionGroups_
id_
long id_
name_
java.lang.String name_
objectId_
java.lang.String objectId_
name_
java.lang.String name_
description_
java.lang.String description_
ownerUserName_
java.lang.String ownerUserName_
protectionGroups_
ProtectionGroupData[] protectionGroups_
desc_
UserDesc desc_
title_
java.lang.String title_
phoneNumber_
java.lang.String phoneNumber_
email_
java.lang.String email_
organization_
java.lang.String organization_
dept_
java.lang.String dept_
location_
java.lang.String location_
loginName_
java.lang.String loginName_
lastName_
java.lang.String lastName_
firstName_
java.lang.String firstName_
userName_
java.lang.String userName_
roles_
java.util.Vector<E> roles_
Package gov.nih.nci.caarray.common.data.useradmin |
id
long id
groupName
java.lang.String groupName
description
java.lang.String description
largeElementCountFlag
java.lang.String largeElementCountFlag
updateDate
long updateDate
protectionGroupTypeId
long protectionGroupTypeId
users
java.util.Vector<E> users
role
java.lang.String role
groupName
java.lang.String groupName
id
java.lang.Long id
loginName
java.lang.String loginName
firstName
java.lang.String firstName
lastName
java.lang.String lastName
title
java.lang.String title
emailAddress
java.lang.String emailAddress
institutionName
java.lang.String institutionName
department
java.lang.String department
location
java.lang.String location
updateDate
java.lang.Long updateDate
startDate
java.lang.Long startDate
endDate
java.lang.Long endDate
isAdminUser
boolean isAdminUser
shouldBeAdminUser
boolean shouldBeAdminUser
role
java.lang.String role
status
java.lang.String status
userRoles
java.util.Vector<E> userRoles
allGroups
java.util.Collection<E> allGroups
groups
java.util.Vector<E> groups
phoneNumber
java.lang.String phoneNumber
password
java.lang.String password
userGroupData
java.util.Vector<E> userGroupData
id
long id
groupName
java.lang.String groupName
currentSelection
long currentSelection
role
java.lang.String role
id
java.lang.Long id
updateDate
java.lang.Long updateDate
roleId
java.lang.Long roleId
protectionGroupId
java.lang.Long protectionGroupId
userId
java.lang.Long userId
protectionElementId
java.lang.Long protectionElementId
protectionTypeId
java.lang.Long protectionTypeId
startDate
java.lang.Long startDate
endDate
java.lang.Long endDate
group
GroupData group
user
UserData user
loginName
java.lang.String loginName
firstName
java.lang.String firstName
lastName
java.lang.String lastName
institutionName
java.lang.String institutionName
emailAddress
java.lang.String emailAddress
roleSelection
int roleSelection
statusSelection
int statusSelection
Package gov.nih.nci.caarray.common.data.util |
creationDate_
java.util.Date creationDate_
pathName_
java.lang.String pathName_
size_
long size_
Package gov.nih.nci.caarray.common.data.vocab |
age_
java.lang.Integer age_
measurement_
VocabData measurement_
max_
java.lang.Integer max_
maxMeasurement_
VocabData maxMeasurement_
min_
java.lang.Integer min_
minMeasurement_
VocabData minMeasurement_
initialTimePoint_
VocabData initialTimePoint_
weight_
java.lang.Float weight_
weightMeasurement_
VocabData weightMeasurement_
height_
java.lang.Float height_
heightMeasurement_
VocabData heightMeasurement_
types_
java.util.ArrayList<E> types_
id_
long id_
category_
java.lang.String category_
name_
java.lang.String name_
version_
java.lang.String version_
userDefined_
boolean userDefined_
database_
DatabaseData database_
desc_
VocabDesc desc_
description_
java.lang.String description_
isEditable
boolean isEditable
id_
long id_
name_
java.lang.String name_
category_
java.lang.String category_
accessionNumber_
java.lang.String accessionNumber_
databaseReference_
java.lang.String databaseReference_
URI_
java.lang.String URI_
securedElement_
SecuredElementData securedElement_
name_
java.lang.String name_
databaseReference_
java.lang.String databaseReference_
accessionNumber_
java.lang.String accessionNumber_
category_
java.lang.String category_
includeAllSubCategories_
boolean includeAllSubCategories_
vocabId_
long vocabId_
userName_
java.lang.String userName_
Package gov.nih.nci.caarray.common.exception |
errorCode_
java.lang.String errorCode_
- The errorCode corresponds to the String message in the resource bundle
Package gov.nih.nci.caarray.services.array.ejb |
Package gov.nih.nci.caarray.services.arraydesign |
serialVersionUID: 5984882405977838443L
serialVersionUID: 2164143692840119460L
Package gov.nih.nci.caarray.services.arraydesign.ejb |
Package gov.nih.nci.caarray.services.arraydesign.loader |
serialVersionUID: 2297586445975630752L
caFileEntry
CAFileUploadEntry caFileEntry
username
java.lang.String username
serialVersionUID: 1L
Package gov.nih.nci.caarray.services.arraydesign.loader.affymetrix |
serialVersionUID: 5786747394362872165L
Package gov.nih.nci.caarray.services.arraydesign.loader.agilent |
serialVersionUID: 1003370171931726185L
Package gov.nih.nci.caarray.services.arraydesign.loader.genepix |
Package gov.nih.nci.caarray.services.arraydesign.loader.handler |
serialVersionUID: -3391277380299151472L
Package gov.nih.nci.caarray.services.arraydesign.loader.illumina |
serialVersionUID: -4582752762679694994L
Package gov.nih.nci.caarray.services.arraydesign.loader.imagene |
serialVersionUID: 1003370171931726185L
Package gov.nih.nci.caarray.services.arraydesign.loader.ucsf |
serialVersionUID: -8781404315438435762L
Package gov.nih.nci.caarray.services.bioassaydata |
serialVersionUID: 5440280342450437500L
bioAssay
BioAssay bioAssay
bioAssayData
BioAssayData bioAssayData
dataFile
java.io.File dataFile
sourceType
SourceType sourceType
array
Array array
username
java.lang.String username
newBioDataCube
boolean newBioDataCube
experiment
Experiment experiment
serialVersionUID: -2213097078438126860L
serialVersionUID: -6753131552372664841L
Package gov.nih.nci.caarray.services.bioassaydata.reader |
serialVersionUID: -538846822195287478L
Package gov.nih.nci.caarray.services.biomaterial.ejb |
Package gov.nih.nci.caarray.services.contact.ejb |
Package gov.nih.nci.caarray.services.exception |
sourceException
java.lang.Throwable sourceException
- The cause of this Exception.
sourceException
java.lang.Throwable sourceException
- The cause of this Exception.
Package gov.nih.nci.caarray.services.experiment.ejb |
serialVersionUID: -887818599562541L
idsToExperimentsForDeletion
java.util.Map<K,V> idsToExperimentsForDeletion
idsToHybridizationDeletionConfigurations
java.util.Map<K,V> idsToHybridizationDeletionConfigurations
username
java.lang.String username
password
java.lang.String password
authConf
java.lang.String authConf
hostname
java.lang.String hostname
port
int port
serialVersionUID: 6843872786525969757L
experimentId
long experimentId
filenamesToDatas
java.util.Map<K,V> filenamesToDatas
experimentData
ExperimentData experimentData
serialVersionUID: -971484719512285103L
messages
java.util.List<E> messages
Package gov.nih.nci.caarray.services.fileparse.mdb |
ejbContext
javax.ejb.MessageDrivenContext ejbContext
jndiContext
javax.naming.InitialContext jndiContext
ejbContext
javax.ejb.MessageDrivenContext ejbContext
jndiContext
javax.naming.InitialContext jndiContext
Package gov.nih.nci.caarray.services.fileparse2.mdb |
mdbCtx_
javax.ejb.MessageDrivenContext mdbCtx_
jndiContext
javax.naming.InitialContext jndiContext
mdbCtx_
javax.ejb.MessageDrivenContext mdbCtx_
jndiContext
javax.naming.InitialContext jndiContext
Package gov.nih.nci.caarray.services.fileparse2.parsers |
Package gov.nih.nci.caarray.services.fileupload |
arrayDesignDesc_
ArrayDesignDesc arrayDesignDesc_
uploadFile_
UploadFile uploadFile_
protectionGroups_
ProtectionGroupData[] protectionGroups_
owner_
java.lang.String owner_
bioAssayId
java.lang.Long bioAssayId
fileName
java.lang.String fileName
fileType
UploadFileTypes.MICROARRAY_FILE_TYPE fileType
softwareName
java.lang.String softwareName
experimentId_
java.lang.Long experimentId_
bioAssayFiles_
java.util.HashMap<K,V> bioAssayFiles_
nonBioAssayFiles_
java.util.ArrayList<E> nonBioAssayFiles_
owner_
java.lang.String owner_
protectionGroups_
ProtectionGroupData[] protectionGroups_
tempDirectory_
java.lang.String tempDirectory_
Package gov.nih.nci.caarray.services.fileupload2 |
fileUploadEntry
FileUploadEntry fileUploadEntry
arrayDesign
PhysicalArrayDesign arrayDesign
fileParsingEntry
ArrayDesignFileParsingEntry fileParsingEntry
fileUploadEntries
java.util.List<E> fileUploadEntries
arrayDesignId
java.lang.Long arrayDesignId
fileEntryId
java.lang.Long fileEntryId
fileParsingEntryId
java.lang.Long fileParsingEntryId
fileGroupId
java.lang.Long fileGroupId
fileParsingEntry
ArrayDesignFileParsingEntry fileParsingEntry
ojbConcreteClass
java.lang.String ojbConcreteClass
id
java.lang.Long id
fileTypeId
java.lang.String fileTypeId
fileName
java.lang.String fileName
caArrayDesignFileEntry
CAArrayDesignFileUploadEntry caArrayDesignFileEntry
caFileUploadHistory
CAFileUploadHistory caFileUploadHistory
caMagemlFileEntry
CAMagemlFileUploadEntry caMagemlFileEntry
status
java.lang.String status
statusDate
java.util.Date statusDate
validatorCode
java.lang.String validatorCode
userId
java.lang.String userId
originalFileName
java.lang.String originalFileName
id
java.lang.Long id
fileEntryId
java.lang.Long fileEntryId
status
java.lang.String status
statusDate
java.util.Date statusDate
description
java.lang.String description
fileEntryId
java.lang.Long fileEntryId
fileParsingEntryId
java.lang.Long fileParsingEntryId
contactId
java.lang.Long contactId
magellFileGroupId
java.lang.Long magellFileGroupId
name
java.lang.String name
version
java.lang.String version
description
java.lang.String description
contentType
java.lang.String contentType
msgToCurator
java.lang.String msgToCurator
ojbConcreteClass
java.lang.String ojbConcreteClass
parsingStartDate
java.util.Date parsingStartDate
parsingEndDate
java.util.Date parsingEndDate
parsingSucceeded
java.lang.String parsingSucceeded
failureDescription
java.lang.String failureDescription
ojbConcreteClass
java.lang.String ojbConcreteClass
fileType
FileType fileType
fileName
java.lang.String fileName
status
java.lang.String status
statusDate
java.util.Date statusDate
validatorCode
java.lang.String validatorCode
userId
java.lang.String userId
originalFileName
java.lang.String originalFileName
ojbConcreteClass
java.lang.String ojbConcreteClass
parsingStartDate
java.util.Date parsingStartDate
parsingEndDate
java.util.Date parsingEndDate
parsingSucceeded
java.lang.String parsingSucceeded
fileUploadEntry
FileUploadEntry fileUploadEntry
status
java.lang.String status
statusDate
java.util.Date statusDate
description
java.lang.String description
fileUploadEntry
FileUploadEntry fileUploadEntry
fileParsingEntry
HybridizationFileParsingEntry fileParsingEntry
experiment
Experiment experiment
channelOneExtract
LabeledExtract channelOneExtract
channelOneSpikedControl
LabeledExtract channelOneSpikedControl
channelTwoExtract
LabeledExtract channelTwoExtract
channelTwoSpikedControl
LabeledExtract channelTwoSpikedControl
channelOneFactorValues
java.util.List<E> channelOneFactorValues
channelTwoFactorValues
java.util.List<E> channelTwoFactorValues
measuredBioAssay
MeasuredBioAssay measuredBioAssay
derivedBioAssay
DerivedBioAssay derivedBioAssay
fileUploadEntries
java.util.List<E> fileUploadEntries
fileUploadEntry
FileUploadEntry fileUploadEntry
name
java.lang.String name
version
java.lang.String version
description
java.lang.String description
contentType
java.lang.String contentType
msgToCurator
java.lang.String msgToCurator
contact
Person contact
id
long id
Package gov.nih.nci.caarray.services.fileupload2.ejb |
Package gov.nih.nci.caarray.services.fileupload2.mdb |
serialVersionUID: 3632908452772996870L
messageDrivenContext
javax.ejb.MessageDrivenContext messageDrivenContext
Package gov.nih.nci.caarray.services.hybridization |
serialVersionUID: -6910414834644372520L
serialVersionUID: -9051098553615891425L
fileUploadEntries
HybridizationFileUploadEntry[] fileUploadEntries
username
java.lang.String username
Package gov.nih.nci.caarray.services.hybridization.ejb |
serialVersionUID: -75923324000366449L
dataFile
java.io.File dataFile
problems
java.util.List<E> problems
warnings
java.util.List<E> warnings
canRepair
boolean canRepair
needsRepair
boolean needsRepair
canReload
boolean canReload
username
java.lang.String username
password
java.lang.String password
authConf
java.lang.String authConf
hostname
java.lang.String hostname
port
int port
fileTypes
java.util.List<E> fileTypes
statuses
java.util.List<E> statuses
repair
boolean repair
reload
boolean reload
minutesToRun
int minutesToRun
maxFilesToProcess
int maxFilesToProcess
experimentIds
java.util.List<E> experimentIds
arrayDesignNames
java.util.List<E> arrayDesignNames
transactionTimeoutMinutes
int transactionTimeoutMinutes
serialVersionUID: -827591905547974310L
successful
boolean successful
dataFile
java.io.File dataFile
errorMessage
java.lang.String errorMessage
serialVersionUID: 5665773104514322885L
Package gov.nih.nci.caarray.services.mageml |
objectId_
java.lang.Long objectId_
objectType_
java.lang.Integer objectType_
pathName_
java.lang.String pathName_
zip_
boolean zip_
Package gov.nih.nci.caarray.services.mageml.ejb |
Package gov.nih.nci.caarray.services.mageml.mdb |
ejbContext
javax.ejb.MessageDrivenContext ejbContext
jndiContext
javax.naming.InitialContext jndiContext
Package gov.nih.nci.caarray.services.protocol.ejb |
Package gov.nih.nci.caarray.services.security |
name
java.lang.String name
-
Package gov.nih.nci.caarray.services.security.db |
Package gov.nih.nci.caarray.services.security.ejb |
Package gov.nih.nci.caarray.services.security.mageom.mdb |
maxAttempts_
long maxAttempts_
waitTime_
long waitTime_
updater_
SecuredElementIdUpdater updater_
orphanHandler_
SecuredElementOrphanHandler orphanHandler_
serialVersionUID: 1234567890L
_className
java.lang.String _className
- The class name of the newly inserted SecuredElement
_id
java.lang.String _id
- The id of the newly inserted SecuredElement
_attempts
int _attempts
- Number of times this message has been queued.
_waitTime
long _waitTime
- The time this message waited befor being requeued.
Package gov.nih.nci.caarray.services.test |
Package gov.nih.nci.caarray.services.test.ejb |
Package gov.nih.nci.caarray.services.useradmin.ejb |
Package gov.nih.nci.caarray.services.util |
serialVersionUID: 1234567890L
securedElementId
java.lang.String securedElementId
isEditable
boolean isEditable
securedElementClassName
java.lang.String securedElementClassName
id
java.lang.Object id
Package gov.nih.nci.caarray.services.util.cache |
Package gov.nih.nci.caarray.services.util.dataconverter.assembler |
Package gov.nih.nci.caarray.services.util.db |
Package gov.nih.nci.caarray.services.util.file |
log_
org.apache.commons.logging.Log log_
log_
org.apache.commons.logging.Log log_
log_
org.apache.commons.logging.Log log_
log_
org.apache.commons.logging.Log log_
Package gov.nih.nci.caarray.services.util.fileuploadapplet |
selectedFileNameMap_
java.util.TreeMap<K,V> selectedFileNameMap_
- TreeMap with key = fileName, value = PlatformFile
Package gov.nih.nci.caarray.services.util.httpfileuploadapplet |
pattern
java.lang.String[] pattern
INSTRUCTION
java.lang.String INSTRUCTION
SUMMARY
java.lang.String SUMMARY
SUCCESS
java.lang.String SUCCESS
FAILURE
java.lang.String FAILURE
TIMEBYTES
java.lang.String TIMEBYTES
chooseLst
java.awt.List chooseLst
selectedLst
java.awt.List selectedLst
dataBt
javax.swing.JButton dataBt
otherBt
javax.swing.JButton otherBt
removeBt
javax.swing.JButton removeBt
removeAllBt
javax.swing.JButton removeAllBt
uploadBt
javax.swing.JButton uploadBt
stopBt
javax.swing.JButton stopBt
helpBt
javax.swing.JButton helpBt
doneBt
javax.swing.JButton doneBt
selectAllBt
javax.swing.JButton selectAllBt
deSelectAllBt
javax.swing.JButton deSelectAllBt
progressBar
javax.swing.JProgressBar progressBar
driveLabel
javax.swing.JLabel driveLabel
selectedFiles
javax.swing.JLabel selectedFiles
uploadFileName
javax.swing.JLabel uploadFileName
currentDir
java.io.File currentDir
files
java.lang.String[] files
dateFormatter
java.text.DateFormat dateFormatter
cDirLabel
javax.swing.JLabel cDirLabel
directoryDisplayLabel
javax.swing.JLabel directoryDisplayLabel
driveChoice
java.awt.Choice driveChoice
selectedFileVec
java.util.Vector<E> selectedFileVec
uFile
HttpUploadFile uFile
up
HttpUploadParameters up
thread
HttpFileUploadThread thread
timer
javax.swing.Timer timer
resultWindow
HttpFileUploadApplet.ResultFrame resultWindow
helpWindow
HttpFileUploadApplet.HelpFrame helpWindow
extensions
java.lang.String[] extensions
module
java.lang.String module
isSingleFile
boolean isSingleFile
close
javax.swing.JButton close
helpLabel
javax.swing.JLabel helpLabel
helpText
javax.swing.JTextArea helpText
helpPane
javax.swing.JScrollPane helpPane
contentPane
java.awt.Container contentPane
close
javax.swing.JButton close
successLabel
javax.swing.JLabel successLabel
failLabel
javax.swing.JLabel failLabel
timeLabel
javax.swing.JLabel timeLabel
successText
javax.swing.JTextArea successText
failText
javax.swing.JTextArea failText
timeText
javax.swing.JTextArea timeText
successPane
javax.swing.JScrollPane successPane
failPane
javax.swing.JScrollPane failPane
contentPane
java.awt.Container contentPane
contentPane
javax.swing.JPanel contentPane
duplicatedFileList
java.awt.List duplicatedFileList
overwriteBt
javax.swing.JButton overwriteBt
message
javax.swing.JLabel message
cancelBt
javax.swing.JButton cancelBt
directory
java.lang.String directory
noteLb
javax.swing.JLabel noteLb
jLabel1
javax.swing.JLabel jLabel1
emptyLb
javax.swing.JLabel emptyLb
selectAllBt
javax.swing.JButton selectAllBt
gridBagLayout1
java.awt.GridBagLayout gridBagLayout1
cList
java.util.ArrayList<E> cList
Package gov.nih.nci.caarray.services.util.jms |
id
java.lang.Long id
waitTime
java.lang.Long waitTime
queueName
java.lang.String queueName
data
byte[] data
hostIP
java.lang.String hostIP
Package gov.nih.nci.caarray.services.util.netcdf |
Package gov.nih.nci.caarray.services.util.ojb |
Package gov.nih.nci.caarray.services.util.ojb.conversions |
serialVersionUID: 8346405256667832336L
Package gov.nih.nci.caarray.services.util.parse |
Package gov.nih.nci.caarray.services.util.transaction |
serialVersionUID: 191544618098222917L
Package gov.nih.nci.caarray.services.vocab.ejb |
Package gov.nih.nci.caarray.ui.arraydesign |
action
java.lang.String action
arrayId
long arrayId
manufactureDate
java.lang.String manufactureDate
arrayName
java.lang.String arrayName
barcode
java.lang.String barcode
arrayDesignId
long arrayDesignId
arrayDesigns
java.util.Collection<E> arrayDesigns
substrateType
long substrateType
substrateTypes
java.util.Collection<E> substrateTypes
manufacturers
java.util.Collection<E> manufacturers
selectedManufacturers
java.lang.String[] selectedManufacturers
width
java.lang.String width
length
java.lang.String length
orientationMark
java.lang.String orientationMark
orientationMarkPosition
java.lang.String orientationMarkPosition
orientationMarkPositions
java.util.Collection<E> orientationMarkPositions
visibilitys
java.util.Collection<E> visibilitys
selectedVisibilitys
java.lang.String[] selectedVisibilitys
description
java.lang.String description
protocols
java.util.Collection<E> protocols
protocolId
long protocolId
reason
java.lang.String reason
fileId
long fileId
expId
long expId
isEditable
boolean isEditable
arrayDesignName
java.lang.String arrayDesignName
substrateTypeName
java.lang.String substrateTypeName
manufacturerName
java.lang.String manufacturerName
numberCopies
long numberCopies
mode
java.lang.String mode
selectedVisibilityNames
java.lang.String[] selectedVisibilityNames
selectedVisibilityIds
java.lang.String[] selectedVisibilityIds
providerId
long providerId
providerType
long providerType
providers_
java.util.Collection<E> providers_
providersOrgs_
java.util.Collection<E> providersOrgs_
roleId
long roleId
roles
java.util.Collection<E> roles
protocolId
long protocolId
protocols
java.util.Collection<E> protocols
mode_
java.lang.String mode_
uploadFile
boolean uploadFile
arrayDesignId
long arrayDesignId
attachmentTypeId_
long attachmentTypeId_
- Attachment Type ID
attachmentTypeName_
java.lang.String attachmentTypeName_
attachmentTypes_
java.util.Collection<E> attachmentTypes_
- Attachment Types
description_
java.lang.String description_
uploadTypeId
int uploadTypeId
uploadTypes_
java.util.Collection<E> uploadTypes_
reporterTypeId_
int reporterTypeId_
reporterTypes_
java.util.Collection<E> reporterTypes_
fileAdditional_
CustomFormFile fileAdditional_
fileGAL_
CustomFormFile fileGAL_
- Full path to Definition File
fileMAGE_
CustomFormFile fileMAGE_
- Full path to Annotation File
identifier_
java.lang.String identifier_
name_
java.lang.String name_
- Array Design Name
selectedVisibilitys_
java.lang.String[] selectedVisibilitys_
speciesTypeId_
long speciesTypeId_
- Species Type ID
speciesTypes_
java.util.Collection<E> speciesTypes_
- Species Types
strandTypeId_
long strandTypeId_
- Strand Type ID
strandTypes_
java.util.Collection<E> strandTypes_
- Strand Types
substrateTypeId_
long substrateTypeId_
- Substrate Type ID
substrateTypes_
java.util.Collection<E> substrateTypes_
- SubStrate Types
surfaceTypeId_
long surfaceTypeId_
- surface Type ID
surfaceTypes_
java.util.Collection<E> surfaceTypes_
- Surface Types
technologyTypeId_
long technologyTypeId_
- Technology Type ID
technologyTypes_
java.util.Collection<E> technologyTypes_
- Technology Types
version_
java.lang.String version_
- Array Version
visibilitys_
java.util.Collection<E> visibilitys_
speciesTypeName_
java.lang.String speciesTypeName_
strandTypeName_
java.lang.String strandTypeName_
substrateTypeName_
java.lang.String substrateTypeName_
surfaceTypeName_
java.lang.String surfaceTypeName_
technologyTypeName_
java.lang.String technologyTypeName_
mode_
java.lang.String mode_
numberOfFeatures_
int numberOfFeatures_
protocolApplicationId_
long protocolApplicationId_
protocolApplication_
ProtocolApplicationData protocolApplication_
protocolApplications_
ProtocolApplicationData[] protocolApplications_
providerId_
long providerId_
providers_
DesignProviderRoleData[] providers_
reporterFileLocation_
java.lang.String reporterFileLocation_
additionalReporterFileLocation_
java.lang.String additionalReporterFileLocation_
galFileLocation_
java.lang.String galFileLocation_
mageFileLocation_
java.lang.String mageFileLocation_
reporterTypeId_
int reporterTypeId_
reporterTypeName_
java.lang.String reporterTypeName_
reporterTypes_
java.util.Collection<E> reporterTypes_
uploadTypeId_
int uploadTypeId_
uploadTypeName_
java.lang.String uploadTypeName_
uploadTypes_
java.util.Collection<E> uploadTypes_
providedByAffymetrix
boolean providedByAffymetrix
arrayDesignFile
ArrayDesignUploadedFileData arrayDesignFile
uploadFile
boolean uploadFile
arrayDesignFileToken
java.lang.String arrayDesignFileToken
mageIdentifier
java.lang.String mageIdentifier
isEditable
boolean isEditable
arrayDesignFileUploadEntryData
ArrayDesignFileUploadEntryData arrayDesignFileUploadEntryData
freeText_
java.lang.String freeText_
- free search text
searchResults_
java.util.Collection<E> searchResults_
visibilityId_
long visibilityId_
providerId
long providerId
providers_
java.util.Collection<E> providers_
providersOrgs_
java.util.Collection<E> providersOrgs_
mode
java.lang.String mode
arrayDesignName
java.lang.String arrayDesignName
substrateTypeName
java.lang.String substrateTypeName
manufacturerName
java.lang.String manufacturerName
orientationMarkPositionName
java.lang.String orientationMarkPositionName
protocolApplications_
ProtocolApplicationData[] protocolApplications_
searchResults
java.util.Collection<E> searchResults
manufacturerId
long manufacturerId
visibilityId
long visibilityId
manufactureDateStart
java.lang.String manufactureDateStart
manufactureDateEnd
java.lang.String manufactureDateEnd
Package gov.nih.nci.caarray.ui.biomaterial |
back_
java.lang.String back_
mode_
java.lang.String mode_
biomaterialId_
long biomaterialId_
materialTypeId_
long materialTypeId_
materialTypeName_
java.lang.String materialTypeName_
materialTypes_
java.util.Collection<E> materialTypes_
taxonType_
long taxonType_
taxonTypes_
java.util.Collection<E> taxonTypes_
visibilitys_
java.util.Collection<E> visibilitys_
charList_
java.util.Collection<E> charList_
biomaterialCharacteristics_
VocabData[] biomaterialCharacteristics_
ageTypes_
java.lang.String[] ageTypes_
ageUnits_
java.util.Collection<E> ageUnits_
age_
int age_
ageUnitName_
java.lang.String ageUnitName_
ageUnitId_
long ageUnitId_
ageMax_
int ageMax_
ageMaxUnitName_
java.lang.String ageMaxUnitName_
ageMaxUnitId_
long ageMaxUnitId_
ageMin_
int ageMin_
ageMinUnitName_
java.lang.String ageMinUnitName_
ageMinUnitId_
long ageMinUnitId_
allele_
java.lang.String allele_
initialTimePoints_
java.util.Collection<E> initialTimePoints_
initialTimePointName_
java.lang.String initialTimePointName_
initialTimePointId_
long initialTimePointId_
bedding_
java.lang.String bedding_
clinicalHistory_
java.lang.String clinicalHistory_
familyHistory_
java.lang.String familyHistory_
generation_
java.lang.String generation_
geographicLocation_
java.lang.String geographicLocation_
host_
java.lang.String host_
pathogenTest_
java.lang.String pathogenTest_
environmentalHistoryDesign_
java.lang.String environmentalHistoryDesign_
atmosphere_
java.lang.String atmosphere_
barrierFacility_
java.lang.String barrierFacility_
humidity_
java.lang.String humidity_
light_
java.lang.String light_
nutrients_
java.lang.String nutrients_
populationDensity_
java.lang.String populationDensity_
temperature_
java.lang.String temperature_
water_
java.lang.String water_
biometricWeightUnits_
java.util.Collection<E> biometricWeightUnits_
biometricWeight_
float biometricWeight_
biometricWeightUnitName_
java.lang.String biometricWeightUnitName_
biometricWeightUnitId_
long biometricWeightUnitId_
biometricHeightUnits_
java.util.Collection<E> biometricHeightUnits_
biometricHeight_
float biometricHeight_
biometricHeightUnitName_
java.lang.String biometricHeightUnitName_
biometricHeightUnitId_
long biometricHeightUnitId_
cellLine_
java.lang.String cellLine_
cellLineId_
long cellLineId_
cellLines_
java.util.Collection<E> cellLines_
cellType_
java.lang.String cellType_
cellTypeId_
long cellTypeId_
cellTypes_
java.util.Collection<E> cellTypes_
chromosomalAberrationTypeId_
long chromosomalAberrationTypeId_
chromosomalAberrationTypes_
java.util.Collection<E> chromosomalAberrationTypes_
chromosomalAberrations_
java.util.Collection<E> chromosomalAberrations_
chromosomalAberrationDescription_
java.lang.String chromosomalAberrationDescription_
clinicalTest_
java.lang.String clinicalTest_
clinicalTreatment_
java.lang.String clinicalTreatment_
developmentalStage_
java.lang.String developmentalStage_
developmentalStageId_
long developmentalStageId_
developmentalStages_
java.util.Collection<E> developmentalStages_
diseaseLocation_
java.lang.String diseaseLocation_
diseaseLocationId_
long diseaseLocationId_
diseaseLocations_
java.util.Collection<E> diseaseLocations_
diseaseStage_
java.lang.String diseaseStage_
diseaseStageId
long[] diseaseStageId
diseaseStages_
java.util.Collection<E> diseaseStages_
diseaseState
java.lang.String diseaseState
diseaseStateId
long diseaseStateId
diseaseStates
java.util.Collection<E> diseaseStates
geneticModificationId_
long geneticModificationId_
geneticModificationName_
java.lang.String geneticModificationName_
geneticModifications_
java.util.Collection<E> geneticModifications_
geneticModificationDescription_
java.lang.String geneticModificationDescription_
genotype_
java.lang.String genotype_
histology_
java.lang.String histology_
individual_
java.lang.String individual_
organismPart_
java.lang.String organismPart_
organismPartId_
long organismPartId_
organismParts_
java.util.Collection<E> organismParts_
organismStatus_
java.lang.String organismStatus_
organismStatusId_
long organismStatusId_
organismStatuses_
java.util.Collection<E> organismStatuses_
ploidy_
java.lang.String ploidy_
ploidyId_
long ploidyId_
ploidys_
java.util.Collection<E> ploidys_
phenotype_
java.lang.String phenotype_
sex_
java.lang.String sex_
sexId_
long sexId_
sexTypes_
java.util.Collection<E> sexTypes_
media_
java.lang.String media_
mediaId_
long mediaId_
mediaTypes_
java.util.Collection<E> mediaTypes_
strainOrLine_
java.lang.String strainOrLine_
strainOrLineId_
long strainOrLineId_
strainOrLines_
java.util.Collection<E> strainOrLines_
tumorGrading_
java.lang.String tumorGrading_
tumorGradingId_
long tumorGradingId_
tumorGradings_
java.util.Collection<E> tumorGradings_
targetedCellType_
java.lang.String targetedCellType_
targetedCellTypeId_
long targetedCellTypeId_
targetedCellTypes_
java.util.Collection<E> targetedCellTypes_
selectedCharacteristics_
java.util.ArrayList<E> selectedCharacteristics_
isEditable
boolean isEditable
allCharacteristics_
java.util.Collection<E> allCharacteristics_
object_
java.lang.String object_
returnFwd_
java.lang.String returnFwd_
error_
java.lang.String error_
ageOrRange_
java.lang.String ageOrRange_
reason
java.lang.String reason
fileId
long fileId
expId
long expId
labelId
long labelId
description_
java.lang.String description_
selectedVisibilitys_
java.lang.String[] selectedVisibilitys_
newTypeName_
java.lang.String newTypeName_
newTaxonTypeName_
java.lang.String newTaxonTypeName_
newMaterialTypeName_
java.lang.String newMaterialTypeName_
isCancel_
java.lang.String isCancel_
reason
java.lang.String reason
fileId
long fileId
expId
long expId
labelId
long labelId
biosourceName
java.lang.String biosourceName
biosourceType
long biosourceType
biosourceTypes
java.util.Collection<E> biosourceTypes
provider
long provider
providers
java.util.Collection<E> providers
selectedVisibilitys_
java.lang.String[] selectedVisibilitys_
visibilitys_
java.util.Collection<E> visibilitys_
description
java.lang.String description
visibility
java.util.Collection<E> visibility
materialTypeName
java.lang.String materialTypeName
taxonName
java.lang.String taxonName
providerName
java.lang.String providerName
biosourceTypeName
java.lang.String biosourceTypeName
reason
java.lang.String reason
fileId
long fileId
expId
long expId
labelId
long labelId
mageIdentifier
java.lang.String mageIdentifier
freeText
java.lang.String freeText
visibilityId
long visibilityId
searchResults_
java.util.Collection<E> searchResults_
labeledExtractName_
java.lang.String labeledExtractName_
labeledExtractID_
long labeledExtractID_
error_
java.lang.String error_
biosampleId_
long biosampleId_
biosamples_
java.util.Collection<E> biosamples_
label_
long label_
labels_
java.util.Collection<E> labels_
amount_
java.lang.String amount_
amountUnit_
long amountUnit_
units_
java.util.Collection<E> units_
newLabel_
java.lang.String newLabel_
errors_
java.lang.String errors_
protocolApplication_
ProtocolApplicationData protocolApplication_
reason
java.lang.String reason
fileId
long fileId
expId
long expId
description
java.lang.String description
parents
java.util.Collection<E> parents
labelName_
java.lang.String labelName_
isEditable
boolean isEditable
mageIdentifier
java.lang.String mageIdentifier
visibilityId
long visibilityId
freeText
java.lang.String freeText
sampleId
long sampleId
searchResults_
java.util.Collection<E> searchResults_
outputName
java.lang.String outputName
outputDesc
java.lang.String outputDesc
biomaterials
java.util.Collection<E> biomaterials
selectedBiomaterials
java.lang.String[] selectedBiomaterials
mode
java.lang.String mode
measurementValue
java.lang.String measurementValue
measurementUnits
java.util.Collection<E> measurementUnits
measurementUnit
long measurementUnit
measurementUnitTypes
java.util.Collection<E> measurementUnitTypes
measurementUnitType
long measurementUnitType
sampleName
java.lang.String sampleName
sampleType
long sampleType
sampleTypes
java.util.Collection<E> sampleTypes
sourceBiomaterials
java.util.Collection<E> sourceBiomaterials
treatmentAction
java.lang.String treatmentAction
biomaterialId
long biomaterialId
creationDescription
java.lang.String creationDescription
description
java.lang.String description
id
long id
parentBiomaterials
java.util.Collection<E> parentBiomaterials
sampleName
java.lang.String sampleName
sampleType
long sampleType
sampleTypeName
java.lang.String sampleTypeName
sampleTypes
java.util.Collection<E> sampleTypes
sourceBiomaterials
java.util.Collection<E> sourceBiomaterials
treatmentEvents
java.util.ArrayList<E> treatmentEvents
compoundMData
CompoundMeasurementData[] compoundMData
biomaterialCharacteristics
VocabData[] biomaterialCharacteristics
treatmentNumber
int treatmentNumber
back
java.lang.String back
treatmentEventId
long treatmentEventId
mode
java.lang.String mode
individualTreatmentId
java.lang.String individualTreatmentId
reason
java.lang.String reason
fileId
long fileId
expId
long expId
labelId
long labelId
requestAction
java.lang.String requestAction
mageIdentifier
java.lang.String mageIdentifier
isEditable
boolean isEditable
sampleName
java.lang.String sampleName
speciesTypeId
long speciesTypeId
speciesTypes
java.util.Collection<E> speciesTypes
materialTypeId
long materialTypeId
materialTypes
java.util.Collection<E> materialTypes
biosourceId
long biosourceId
biosources
java.util.Collection<E> biosources
visibilityId
long visibilityId
visibilitys
java.util.Collection<E> visibilitys
searchResults_
java.util.Collection<E> searchResults_
biomaterialCharacteristics
VocabData[] biomaterialCharacteristics
description
java.lang.String description
creationDescription
java.lang.String creationDescription
selectedVisibilities
java.util.Collection<E> selectedVisibilities
sourceBiomaterialId
long sourceBiomaterialId
sourceBiomaterialName
java.lang.String sourceBiomaterialName
resultingBiomaterialTypeId
long resultingBiomaterialTypeId
biomaterialId
long biomaterialId
resultingName
java.lang.String resultingName
resultingBiomaterialTypeName
java.lang.String resultingBiomaterialTypeName
measurementUnitTypes
java.util.Collection<E> measurementUnitTypes
measurementUnits
java.util.Collection<E> measurementUnits
treatments
TreatmentEvent[] treatments
parentBiomaterials
java.util.Collection<E> parentBiomaterials
treatmentTypes
java.util.Collection<E> treatmentTypes
treatmentAction
java.lang.String treatmentAction
mode
java.lang.String mode
treatmentEvents
java.util.ArrayList<E> treatmentEvents
reason
java.lang.String reason
fileId
long fileId
expId
long expId
labelId
long labelId
biomaterials
java.util.Collection<E> biomaterials
selectedBiomaterial
long selectedBiomaterial
selectedBiomaterialName
java.lang.String selectedBiomaterialName
numberSamples
long numberSamples
splitAction
java.lang.String splitAction
outputName1
java.lang.String outputName1
outputDesc1
java.lang.String outputDesc1
outputName2
java.lang.String outputName2
outputDesc2
java.lang.String outputDesc2
mode
java.lang.String mode
measurementUnitTypes
java.util.Collection<E> measurementUnitTypes
measurementValue1
java.lang.String measurementValue1
measurementUnits1
java.util.Collection<E> measurementUnits1
measurementUnit1
long measurementUnit1
measurementUnitType1
long measurementUnitType1
measurementValue2
java.lang.String measurementValue2
measurementUnits2
java.util.Collection<E> measurementUnits2
measurementUnit2
long measurementUnit2
measurementUnitType2
long measurementUnitType2
creationDescription
java.lang.String creationDescription
measurementValue
java.lang.String measurementValue
treatmentType
long treatmentType
treatmentTypeName
java.lang.String treatmentTypeName
measurementType
long measurementType
measurementTypeName
java.lang.String measurementTypeName
measurementUnit
long measurementUnit
measurementUnitName
java.lang.String measurementUnitName
treatmentOrder
long treatmentOrder
protocolApplication
ProtocolApplicationData protocolApplication
protocolVisibility
java.util.Collection<E> protocolVisibility
deleteLabel
java.lang.String deleteLabel
treatmentAction
java.lang.String treatmentAction
compoundMData
CompoundMeasurementData[] compoundMData
sourceBiomaterialId
long sourceBiomaterialId
sourceBiomaterialName
java.lang.String sourceBiomaterialName
resultingDescription
java.lang.String resultingDescription
resultingName
java.lang.String resultingName
resultingBiomaterialType
long resultingBiomaterialType
resultingBiomaterialTypeName
java.lang.String resultingBiomaterialTypeName
treatmentAction
java.lang.String treatmentAction
mode
java.lang.String mode
measurementUnitTypes
java.util.Collection<E> measurementUnitTypes
measurementUnits
java.util.Collection<E> measurementUnits
treatments
TreatmentEvent[] treatments
treatmentTypes
java.util.Collection<E> treatmentTypes
newMaterialTypeName
java.lang.String newMaterialTypeName
treatmentType
long treatmentType
treatmentOrder
long treatmentOrder
measurementValue
java.lang.String measurementValue
measurementUnitType
long measurementUnitType
measurementUnit
long measurementUnit
protocols
java.util.Collection<E> protocols
treatmentTypeName
java.lang.String treatmentTypeName
log_
org.apache.commons.logging.Log log_
biomaterials
java.util.Collection<E> biomaterials
creationDescription
java.lang.String creationDescription
mode
java.lang.String mode
resultingBiomaterialType
long resultingBiomaterialType
resultingBiomaterialTypeName
java.lang.String resultingBiomaterialTypeName
resultingDescription
java.lang.String resultingDescription
resultingName
java.lang.String resultingName
sourceBiomaterialId
long sourceBiomaterialId
sourceBiomaterialName
java.lang.String sourceBiomaterialName
treatmentAction
java.lang.String treatmentAction
treatmentEvents
java.util.ArrayList<E> treatmentEvents
treatmentTypeName
java.lang.String treatmentTypeName
treatmentOrder
int treatmentOrder
submitted
java.lang.String submitted
biomaterials
java.util.Collection<E> biomaterials
compoundID_
long compoundID_
creationDescription
java.lang.String creationDescription
compounds
java.util.Collection<E> compounds
materialTypes
java.util.Collection<E> materialTypes
measurementUnit
long measurementUnit
compoundmeasurementUnit
long compoundmeasurementUnit
measurementUnits
java.util.Collection<E> measurementUnits
compoundmeasurementUnits
java.util.Collection<E> compoundmeasurementUnits
measurementUnitType
long measurementUnitType
compoundmeasurementUnitType
long compoundmeasurementUnitType
measurementUnitTypes
java.util.Collection<E> measurementUnitTypes
compoundmeasurementUnitTypes
java.util.Collection<E> compoundmeasurementUnitTypes
otherUnitType
int otherUnitType
otherCompoundUnitType
int otherCompoundUnitType
otherUnitTypeName
java.lang.String otherUnitTypeName
otherCompoundUnitTypeName
java.lang.String otherCompoundUnitTypeName
otherUnit
java.lang.String otherUnit
otherCompoundUnit
java.lang.String otherCompoundUnit
measurementValue
java.lang.String measurementValue
compoundmeasurementValue
java.lang.String compoundmeasurementValue
mode
java.lang.String mode
protocolApplication
ProtocolApplicationData protocolApplication
protocolVisibility
java.util.Collection<E> protocolVisibility
resultingBiomaterialType
long resultingBiomaterialType
resultingBiomaterialTypeName
java.lang.String resultingBiomaterialTypeName
resultingDescription
java.lang.String resultingDescription
resultingName
java.lang.String resultingName
sourceBiomaterialId
long sourceBiomaterialId
sourceBiomaterialName
java.lang.String sourceBiomaterialName
treatmentAction
java.lang.String treatmentAction
treatmentEvents
java.util.ArrayList<E> treatmentEvents
treatmentOrder
int treatmentOrder
treatmentType
long treatmentType
treatmentTypeName
java.lang.String treatmentTypeName
treatmentTypes
java.util.Collection<E> treatmentTypes
log_
org.apache.commons.logging.Log log_
protocolId
long protocolId
valid
boolean valid
compoundOrder
int compoundOrder
eventOrder
int eventOrder
deleteAction
java.lang.String deleteAction
compoundMeasurements
java.util.Collection<E> compoundMeasurements
log_
org.apache.commons.logging.Log log_
compounds
java.util.Collection<E> compounds
measurementUnits
java.util.Collection<E> measurementUnits
measurementUnitTypes
java.util.Collection<E> measurementUnitTypes
compoundmeasurementUnits
java.util.Collection<E> compoundmeasurementUnits
treatmentEvents
java.util.ArrayList<E> treatmentEvents
treatmentTypes
java.util.Collection<E> treatmentTypes
compoundMeasurements
java.util.List<E> compoundMeasurements
protocolApplication
ProtocolApplicationData protocolApplication
measurementUnit
long measurementUnit
compoundmeasurementUnit
long compoundmeasurementUnit
measurementUnitType
long measurementUnitType
compoundmeasurementUnitType
long compoundmeasurementUnitType
compoundData
CompoundMeasurementData compoundData
compoundModifyUnits
java.util.Collection<E> compoundModifyUnits
otherCompoundModifyUnitTypeName
java.lang.String otherCompoundModifyUnitTypeName
otherCompoundModifyUnit
java.lang.String otherCompoundModifyUnit
modifyUnit
long modifyUnit
modifyUnitType
long modifyUnitType
modifyUnitValue
java.lang.String modifyUnitValue
otherUnitTypeName
java.lang.String otherUnitTypeName
otherCompoundUnitTypeName
java.lang.String otherCompoundUnitTypeName
otherUnit
java.lang.String otherUnit
otherCompoundUnit
java.lang.String otherCompoundUnit
measurementValue
java.lang.String measurementValue
compoundmeasurementValue
java.lang.String compoundmeasurementValue
mode
java.lang.String mode
compoundId
long compoundId
sourceBiomaterialId
long sourceBiomaterialId
treatmentId
long treatmentId
treatmentOrder
int treatmentOrder
treatmentType
long treatmentType
treatmentTypeName
java.lang.String treatmentTypeName
compoundOrder
int compoundOrder
eventOrder
int eventOrder
protocolId
long protocolId
sourceBiomaterialName
java.lang.String sourceBiomaterialName
resultingName
java.lang.String resultingName
resultingBiomaterialTypeName
java.lang.String resultingBiomaterialTypeName
resultingDescription
java.lang.String resultingDescription
action
java.lang.String action
isNew
boolean isNew
reason
java.lang.String reason
fileId
long fileId
expId
long expId
labelId
long labelId
Package gov.nih.nci.caarray.ui.contact |
id
long id
name
java.lang.String name
middleInitials
java.lang.String middleInitials
address
java.lang.String address
city
java.lang.String city
state
java.lang.String state
zip
java.lang.String zip
country
java.lang.String country
phoneNumber
java.lang.String phoneNumber
faxNumber
java.lang.String faxNumber
email
java.lang.String email
url
java.lang.String url
affiliation
long affiliation
back
java.lang.String back
mode
java.lang.String mode
orgAddress
java.lang.String orgAddress
results
java.util.Collection<E> results
nameSearch
java.lang.String nameSearch
results
java.util.Collection<E> results
firstNameSearch
java.lang.String firstNameSearch
lastNameSearch
java.lang.String lastNameSearch
address
java.lang.String address
affiliationId
long affiliationId
affiliations
java.util.Collection<E> affiliations
email
java.lang.String email
faxNumber
java.lang.String faxNumber
firstName
java.lang.String firstName
id
long id
lastName
java.lang.String lastName
middleInitial
java.lang.String middleInitial
phoneNumber
java.lang.String phoneNumber
url
java.lang.String url
back
java.lang.String back
mode
java.lang.String mode
id
long id
firstName
java.lang.String firstName
lastName
java.lang.String lastName
name
java.lang.String name
middleInitials
java.lang.String middleInitials
address
java.lang.String address
city
java.lang.String city
state
java.lang.String state
zip
java.lang.String zip
country
java.lang.String country
phoneNumber
java.lang.String phoneNumber
faxNumber
java.lang.String faxNumber
email
java.lang.String email
url
java.lang.String url
affiliation
long affiliation
affiliationName
java.lang.String affiliationName
firstNameSearch
java.lang.String firstNameSearch
lastNameSearch
java.lang.String lastNameSearch
mageIdentifier
java.lang.String mageIdentifier
Package gov.nih.nci.caarray.ui.core |
uploadURL
java.lang.String uploadURL
- The destination url to which the uploading files will be
sent and saved.
notifyURL
java.lang.String notifyURL
- The destination url to which server is notified for the next step
process.
defaultURL
java.lang.String defaultURL
- The default url to go when user presses the done button to
end the uploading process.
id
java.lang.String id
- The String variable that holds the key to the hybridization annotation
data for this upload operation,that is stored in a static cache
on the server side.
archiveValue
java.lang.String archiveValue
- The String variable holding the value for HttpFileUploadpplet archive
jar file path. default to nothing.
sid
java.lang.String sid
- The session id for session identification.
module
java.lang.String module
- The string token to indicate where the
applet is invoked, so set the applet to
perform required function.
tunnelURL
java.lang.String tunnelURL
- The URL from which the existing file names
are fetched to the applet to ensure the same
file names are handled. Works together with
the module token.
permissibleFileExtension
java.lang.String permissibleFileExtension
- The concatenated file extension permissible
to the module.
fileData
HybridizationFileUploadGroupData fileData
- The data object that gathers all the hybridization annotation
data through many jsp pages.
caFileEntryData
CAFileUploadEntryData caFileEntryData
timeStamp
java.lang.String timeStamp
fileList
java.util.List<E> fileList
- The container object that is the place for all meta data for
the uploaded files. Valid data type: HttpUploadedFileData.
isStopped
boolean isStopped
- The boolean flag. Set to true when user requests a stop action.
Otherwise it is false. Default value is false.
type
java.lang.String type
- The type means Data or Other user set at the time files are selected.
filePath
java.lang.String filePath
- The absolute file path of the uploaded file on the
client machine, before it was zipped.
fileName
java.lang.String fileName
- The zip file name for the uploaded file, based on zip file naming convention
for the application such as hybData_gpr.zip from
hybData.gpr.
userId
java.lang.String userId
- The sumbitters userId for the uploaded file,.
originalFileName
java.lang.String originalFileName
- The original file name for the uploaded file,
hybData.gpr.
validatorCode
java.lang.String validatorCode
- The validatorCode validation for the for the uploaded file.
fileExtension
java.lang.String fileExtension
- The original file's extension that is preserved in the zipped file
file name.
id
java.lang.String id
- It is actually the key to access cached data about this upload operation.
Package gov.nih.nci.caarray.ui.experiment |
experimentTypeID_
long[] experimentTypeID_
experimentSearchTypeID_
long experimentSearchTypeID_
experimentTypes_
java.util.Collection<E> experimentTypes_
visibility_
java.lang.String[] visibility_
visibilities_
java.util.Collection<E> visibilities_
principalInvestigator_
java.lang.String principalInvestigator_
investigators_
java.util.Collection<E> investigators_
species_
long species_
speciesLists_
java.util.Collection<E> speciesLists_
isEditable
boolean isEditable
hybridizationGroupName
java.lang.String hybridizationGroupName
log_
org.apache.commons.logging.Log log_
ID_
long ID_
expId
java.lang.String expId
method
java.lang.String method
experimentTitle_
java.lang.String experimentTitle_
experimentCompleteDate_
java.lang.String experimentCompleteDate_
otherExperimentType_
java.lang.String otherExperimentType_
description_
java.lang.String description_
contactor_
java.lang.String contactor_
numberOfFactor_
java.lang.String numberOfFactor_
factorTypes_
java.util.Collection<E> factorTypes_
factorNames_
java.lang.String[] factorNames_
fTypes_
java.lang.String[] fTypes_
scaleTypes_
java.util.Collection<E> scaleTypes_
scales_
java.lang.String[] scales_
levels_
java.lang.String[] levels_
experimentType_
java.lang.String[] experimentType_
visibility_
java.lang.String[] visibility_
investigatorID_
long investigatorID_
contactID_
long contactID_
experimentFactorData_
java.util.Collection<E> experimentFactorData_
factorValue_
java.lang.String[] factorValue_
factorID
long factorID
factorValueID
long factorValueID
factorName_
java.lang.String factorName_
experimentFactorTypeID_
long experimentFactorTypeID_
experimentFactorScaleID_
long experimentFactorScaleID_
pubMedID_
java.lang.String pubMedID_
pubMedLink_
java.lang.String pubMedLink_
publicationTitle_
java.lang.String publicationTitle_
publicationAuthor_
java.lang.String publicationAuthor_
publication_
java.lang.String publication_
publisher_
java.lang.String publisher_
publicationEditor_
java.lang.String publicationEditor_
publishYear_
java.lang.String publishYear_
publicationVolume_
java.lang.String publicationVolume_
publicationIssue_
java.lang.String publicationIssue_
publicationPage_
java.lang.String publicationPage_
publicationURI_
java.lang.String publicationURI_
publicationData_
java.util.Collection<E> publicationData_
publicationDataID_
long publicationDataID_
buttonName_
java.lang.String buttonName_
qualityControlData_
QualityControlData qualityControlData_
qualityControlTypeList_
java.util.Collection<E> qualityControlTypeList_
qualityControlDescription_
java.lang.String qualityControlDescription_
selectedQualityControlType_
java.lang.String[] selectedQualityControlType_
additionalQualifierData_
java.util.Collection<E> additionalQualifierData_
additionalQualifierName_
java.lang.String additionalQualifierName_
additionalQualifierSource_
java.lang.String additionalQualifierSource_
additionalQualifierValue_
java.lang.String additionalQualifierValue_
additionalQualifierDataID_
long additionalQualifierDataID_
additionalDataProcessData_
java.util.Collection<E> additionalDataProcessData_
additionalUploadedFileData_
java.util.Collection<E> additionalUploadedFileData_
additionalUploadFile_
CustomFormFile additionalUploadFile_
additionalUploadFileDesc_
java.lang.String additionalUploadFileDesc_
additionalDataProcessingFile_
CustomFormFile additionalDataProcessingFile_
applyProtocolID_
long applyProtocolID_
applyProtocol_
java.util.Collection<E> applyProtocol_
selectedVisibilityNames_
java.lang.String[] selectedVisibilityNames_
hybridizationData_
java.util.Collection<E> hybridizationData_
arrayDesign_
java.util.Collection<E> arrayDesign_
manufacture_
java.util.Collection<E> manufacture_
manufactureID_
long manufactureID_
numberOfHybridization_
int numberOfHybridization_
arrayDesignID_
long arrayDesignID_
hybridizationProtocols_
java.util.Collection<E> hybridizationProtocols_
hybridizationProtocolID_
long hybridizationProtocolID_
imageProtocols_
java.util.Collection<E> imageProtocols_
imageProtocolID_
long imageProtocolID_
imageProtocolData_
ProtocolData imageProtocolData_
featureProtocols_
java.util.Collection<E> featureProtocols_
featureProtocolID_
long featureProtocolID_
hybridizationProtocolData_
ProtocolData hybridizationProtocolData_
hybridizationActivityDate_
java.lang.String hybridizationActivityDate_
hybridizationParameters_
java.lang.String[] hybridizationParameters_
imageActivateDate_
java.lang.String imageActivateDate_
imageParameters_
java.lang.String[] imageParameters_
featureProtocolData_
ProtocolData featureProtocolData_
performerID_
long performerID_
performers_
java.util.Collection<E> performers_
featureParameters_
java.lang.String[] featureParameters_
featureActivateDate_
java.lang.String featureActivateDate_
arrayDesignName_
java.lang.String arrayDesignName_
numberOfChannels_
int numberOfChannels_
hybridizationProtocolName_
java.lang.String hybridizationProtocolName_
imageProtocolName_
java.lang.String imageProtocolName_
featureProtocolName_
java.lang.String featureProtocolName_
arrayBatch_
java.lang.String[] arrayBatch_
arrayIdentifier_
long[] arrayIdentifier_
arrayIdentifiers_
java.util.Collection<E> arrayIdentifiers_
extract_
java.util.Collection<E> extract_
extractID_
long[] extractID_
spikedControls_
java.util.Collection<E> spikedControls_
spikedControlID_
long[] spikedControlID_
hybridizationFactors_
java.util.Collection<E> hybridizationFactors_
hybridizationFactorValues_
java.lang.String[] hybridizationFactorValues_
additionalDataApplyProtocolData_
ProtocolData additionalDataApplyProtocolData_
dataProcessURI_
java.lang.String dataProcessURI_
dataProcessProtocolDescription_
java.lang.String dataProcessProtocolDescription_
dataProcessSoftwareReleaseDate_
java.lang.String[] dataProcessSoftwareReleaseDate_
dataProcessSoftwareVersion_
java.lang.String[] dataProcessSoftwareVersion_
dataProcessSoftwareParameters_
java.lang.String[] dataProcessSoftwareParameters_
magemlFileLocation_
java.lang.String magemlFileLocation_
hybridizationProtocol
ProtocolApplicationData[] hybridizationProtocol
featureProtocol
ProtocolApplicationData[] featureProtocol
imageProtocol
ProtocolApplicationData[] imageProtocol
fileMAGEML_
CustomFormFile fileMAGEML_
hybridizations
Hybridization[] hybridizations
dataProcessProtocolParameters_
java.lang.String[] dataProcessProtocolParameters_
dataProcessHardwareSerialNumber_
java.lang.String[] dataProcessHardwareSerialNumber_
dataProcessHardwareParameters_
java.lang.String[] dataProcessHardwareParameters_
dataProcessProtocolPerformers_
java.util.Collection<E> dataProcessProtocolPerformers_
protocolPerformerID_
long protocolPerformerID_
protocolActivityDate_
java.lang.String protocolActivityDate_
additionalDataProcessDownloadPath_
java.lang.String additionalDataProcessDownloadPath_
isFactorEmpty
java.lang.String isFactorEmpty
curatorMessage_
java.lang.String curatorMessage_
isCancel
java.lang.String isCancel
additionalFileUploadCancel
java.lang.String additionalFileUploadCancel
validate
java.lang.String validate
publicationCancel
java.lang.String publicationCancel
previous
java.lang.String previous
experimentMAGEMLData_
FileData experimentMAGEMLData_
identifier_
java.lang.String identifier_
batchFileName
java.lang.String batchFileName
dArrayDesign
long dArrayDesign
dFactorNameID
long dFactorNameID
dFactorValueID
long dFactorValueID
batchFileResults
java.util.Collection<E> batchFileResults
chp_file_exist
java.lang.String chp_file_exist
cel_file_exist
java.lang.String cel_file_exist
exp_file_exist
java.lang.String exp_file_exist
txt_file_exist
java.lang.String txt_file_exist
gpr_file_exist
java.lang.String gpr_file_exist
gps_file_exist
java.lang.String gps_file_exist
other_file_exist
java.lang.String other_file_exist
fileType
java.lang.String fileType
from
java.lang.String from
isExperimentOwnedByCurrentUser
boolean isExperimentOwnedByCurrentUser
serialVersionUID: -6826827990796989631L
ID_
long ID_
experimentName_
java.lang.String experimentName_
freeText_
java.lang.String freeText_
mode_
java.lang.String mode_
searchResults_
java.util.Collection<E> searchResults_
visibility_
long visibility_
identifier_
java.lang.String identifier_
log_
org.apache.commons.logging.Log log_
id_
long id_
expId
java.lang.String expId
method
java.lang.String method
mode
java.lang.String mode
experimentTitle_
java.lang.String experimentTitle_
experimentCompleteDate_
java.lang.String experimentCompleteDate_
description_
java.lang.String description_
experimentType_
java.lang.String experimentType_
visibility_
java.lang.String visibility_
identifier_
java.lang.String identifier_
fileGroupId
java.lang.String fileGroupId
arrayBatchName
java.lang.String arrayBatchName
fileName
java.lang.String fileName
originalFileName
java.lang.String originalFileName
arrayDesignName
java.lang.String arrayDesignName
numberOfChannels
java.lang.String numberOfChannels
hybridizationProtocolName
java.lang.String hybridizationProtocolName
imageProtocolName
java.lang.String imageProtocolName
featureProtocolName
java.lang.String featureProtocolName
arrayIdentifier
java.lang.String arrayIdentifier
arrayIdentifierId
long arrayIdentifierId
channelOne
LabeledExtractDesc channelOne
channelOneSpike
LabeledExtractDesc channelOneSpike
channelTwo
LabeledExtractDesc channelTwo
channelTwoSpike
LabeledExtractDesc channelTwoSpike
channelId
long channelId
factorLevelChOne
FactorDropDownData[] factorLevelChOne
factorLevelChTwo
FactorDropDownData[] factorLevelChTwo
factorForChannelOne
long[] factorForChannelOne
factorForChannelTwo
long[] factorForChannelTwo
fileList
java.util.Collection<E> fileList
annotationId
int annotationId
multipleIds
java.lang.String[] multipleIds
isEditable
boolean isEditable
log_
org.apache.commons.logging.Log log_
id_
long id_
expId
java.lang.String expId
method
java.lang.String method
fileGroupId
java.lang.String fileGroupId
factorForChannelOne
long[] factorForChannelOne
factorForChannelTwo
long[] factorForChannelTwo
method
java.lang.String method
id
java.lang.String id
hybridizationId
java.lang.String hybridizationId
hybridizationGroupName
java.lang.String hybridizationGroupName
arrayDesignName
java.lang.String arrayDesignName
numberOfChannels
java.lang.String numberOfChannels
numberOfHybridization
java.lang.String numberOfHybridization
hybridizationProtocolName
java.lang.String hybridizationProtocolName
imageProtocolName
java.lang.String imageProtocolName
featureProtocolName
java.lang.String featureProtocolName
validate
java.lang.String validate
hybridizations
Hybridization[] hybridizations
arrayIdentifier
long[] arrayIdentifier
arrayIdentifiers
java.util.Collection<E> arrayIdentifiers
arrayGroupTemplateName
java.lang.String arrayGroupTemplateName
log
org.apache.commons.logging.Log log
ID
long ID
method
java.lang.String method
arrayDesign
java.util.Collection<E> arrayDesign
fileMappingType
java.util.Collection<E> fileMappingType
arrayDesignID
long arrayDesignID
hybridizationProtocolID
long hybridizationProtocolID
imageProtocolID
long imageProtocolID
featureProtocolID
long featureProtocolID
hybridizationProtocols
java.util.Collection<E> hybridizationProtocols
imageProtocols
java.util.Collection<E> imageProtocols
featureProtocols
java.util.Collection<E> featureProtocols
hybridizationProtocolData
ProtocolData hybridizationProtocolData
imageProtocolData
ProtocolData imageProtocolData
featureProtocolData
ProtocolData featureProtocolData
performers
java.util.Collection<E> performers
numberOfChannels
int numberOfChannels
arrayDesignName
java.lang.String arrayDesignName
hybridizationProtocolName
java.lang.String hybridizationProtocolName
imageProtocolName
java.lang.String imageProtocolName
featureProtocolName
java.lang.String featureProtocolName
arrayBatch
java.lang.String arrayBatch
arrayIdentifier
long arrayIdentifier
arrayIdentifiers
java.util.Collection<E> arrayIdentifiers
extractID
long extractID
extractIDCh2
long extractIDCh2
spikedControlID
long spikedControlID
spikedControlIDCh2
long spikedControlIDCh2
hybridizationProtocol
ProtocolApplicationData[] hybridizationProtocol
featureProtocol
ProtocolApplicationData[] featureProtocol
imageProtocol
ProtocolApplicationData[] imageProtocol
hybridization
Hybridization hybridization
fileType
int fileType
fileTypeName
java.lang.String fileTypeName
contentPane
javax.swing.JPanel contentPane
chooseLst
java.awt.List chooseLst
selectedLst
java.awt.List selectedLst
dataBt
javax.swing.JButton dataBt
otherBt
javax.swing.JButton otherBt
removeBt
javax.swing.JButton removeBt
removeAllBt
javax.swing.JButton removeAllBt
uploadBt
javax.swing.JButton uploadBt
selectAllBt
javax.swing.JButton selectAllBt
deSelectAllBt
javax.swing.JButton deSelectAllBt
progressBar
javax.swing.JProgressBar progressBar
driveLabel
javax.swing.JLabel driveLabel
selectedFiles
javax.swing.JLabel selectedFiles
uploadFileName
javax.swing.JLabel uploadFileName
currentDir
java.io.File currentDir
files
java.lang.String[] files
dateFormatter
java.text.DateFormat dateFormatter
cDirLabel
javax.swing.JLabel cDirLabel
directoryDisplayLabel
javax.swing.JLabel directoryDisplayLabel
driveChoice
java.awt.Choice driveChoice
selectedFileVec
java.util.Vector<E> selectedFileVec
uFile
gov.nih.nci.caarray.ui.experiment.UploadFile uFile
Package gov.nih.nci.caarray.ui.experiment.data |
uploadURL
java.lang.String uploadURL
- The destination url to which the uploading files will be
sent and saved.
notifyURL
java.lang.String notifyURL
- The destination url to which server is notified for the next step
process.
defaultURL
java.lang.String defaultURL
- The default url to go when user presses the done button to
end the uploading process.
id
java.lang.String id
- The String variable that holds the key to the hybridization annotation
data for this upload operation,that is stored in a static cache
on the server side.
archiveValue
java.lang.String archiveValue
- The String variable holding the value for HttpFileUploadpplet archive
jar file path. default to nothing.
sid
java.lang.String sid
- The session id for session identification.
module
java.lang.String module
- The string token to indicate where the
applet is invoked, so set the applet to
perform required function.
tunnelURL
java.lang.String tunnelURL
- The URL from which the existing file names
are fetched to the applet to ensure the same
file names are handled. Works together with
the module token.
permissibleFileExtension
java.lang.String permissibleFileExtension
- The concatenated file extension permissible
to the module.
fileData
HybridizationFileUploadGroupData fileData
- The data object that gathers all the hybridization annotation
data through many jsp pages.
fileArrayDesignData
ArrayDesignFileUploadGroupData fileArrayDesignData
fileList
java.util.List<E> fileList
- The container object that is the place for all meta data for
the uploaded files. Valid data type: HttpUploadedFileData.
isStopped
boolean isStopped
- The boolean flag. Set to true when user requests a stop action.
Otherwise it is false. Default value is false.
type
java.lang.String type
- The type means Data or Other user set at the time files are selected.
filePath
java.lang.String filePath
- The absolute file path of the uploaded file on the
client machine, before it was zipped.
fileName
java.lang.String fileName
- The zip file name for the uploaded file, based on zip file naming convention
for the application such as hybData_gpr.zip from
hybData.gpr.
userId
java.lang.String userId
- The sumbitters userId for the uploaded file,.
originalFileName
java.lang.String originalFileName
- The original file name for the uploaded file,
hybData.gpr.
validatorCode
java.lang.String validatorCode
- The validatorCode validation for the for the uploaded file.
fileExtension
java.lang.String fileExtension
- The original file's extension that is preserved in the zipped file
file name.
id
java.lang.String id
- It is actually the key to access cached data about this upload operation.
Package gov.nih.nci.caarray.ui.login |
log
org.apache.commons.logging.Log log
userName
java.lang.String userName
password
java.lang.String password
log
org.apache.commons.logging.Log log
affiliation
java.lang.String affiliation
firstName
java.lang.String firstName
middleInitial
java.lang.String middleInitial
lastName
java.lang.String lastName
address1
java.lang.String address1
address2
java.lang.String address2
city
java.lang.String city
state
java.lang.String state
zip
java.lang.String zip
country
java.lang.String country
phone
java.lang.String phone
email
java.lang.String email
Package gov.nih.nci.caarray.ui.ontology |
accessionNumber
java.lang.String accessionNumber
back
java.lang.String back
databaseId
long databaseId
databaseName
java.lang.String databaseName
databases
DatabaseData[] databases
databaseVersion
java.lang.String databaseVersion
description
java.lang.String description
error
java.lang.String error
id
long id
log_
org.apache.commons.logging.Log log_
mode
java.lang.String mode
name
java.lang.String name
searchResults
java.util.Collection<E> searchResults
URI
java.lang.String URI
nameAndDatabase
java.lang.String nameAndDatabase
log_
org.apache.commons.logging.Log log_
cultivarOrEcotype
java.lang.String cultivarOrEcotype
Package gov.nih.nci.caarray.ui.protocol |
visibilitys_
java.util.Collection<E> visibilitys_
selectedVisibilitys_
java.lang.String[] selectedVisibilitys_
back
java.lang.String back
newTypeName_
java.lang.String newTypeName_
URI_
java.lang.String URI_
mode_
java.lang.String mode_
hardwareId_
long hardwareId_
hardwareTypeId_
long hardwareTypeId_
hardwareTypeName_
java.lang.String hardwareTypeName_
hardwareTypes_
java.util.Collection<E> hardwareTypes_
hardwareModel_
java.lang.String hardwareModel_
hardwareName_
java.lang.String hardwareName_
hardwareMake_
java.lang.String hardwareMake_
hardwareManufacturerId_
long hardwareManufacturerId_
hardwareManufacturerName_
java.lang.String hardwareManufacturerName_
hardwareManufacturers_
java.util.Collection<E> hardwareManufacturers_
isEditable
boolean isEditable
error_
java.lang.String error_
log_
org.apache.commons.logging.Log log_
id
long id
visibility
java.util.Collection<E> visibility
parameters
java.util.Collection<E> parameters
back
java.lang.String back
URI_
java.lang.String URI_
newSoftwareId
long newSoftwareId
allSoftware
java.util.Collection<E> allSoftware
associatedSoftware
SoftwareDesc[] associatedSoftware
freeText_
java.lang.String freeText_
visibilityId_
long visibilityId_
visibilityName_
java.lang.String visibilityName_
visibilitys_
java.util.Collection<E> visibilitys_
searchResults_
java.util.Collection<E> searchResults_
back
java.lang.String back
dataType_
java.lang.String dataType_
dataTypeId_
long dataTypeId_
dataTypes_
java.util.Collection<E> dataTypes_
defaultValue
java.lang.String defaultValue
name
java.lang.String name
object
java.lang.String object
objectId
long objectId
parameterId
long parameterId
unitNames_
java.util.Collection<E> unitNames_
unitNameId_
long unitNameId_
unitOtherId_
long unitOtherId_
unitTypeOther_
java.lang.String unitTypeOther_
unitNameOther_
java.lang.String unitNameOther_
unitTypes_
java.util.Collection<E> unitTypes_
unitTypeId_
long unitTypeId_
mode_
java.lang.String mode_
id
long id
description
java.lang.String description
selectedVisibilitys_
java.lang.String[] selectedVisibilitys_
visibilitys_
java.util.Collection<E> visibilitys_
back
java.lang.String back
newTypeName_
java.lang.String newTypeName_
cancelURI
java.lang.String cancelURI
id
long id
cancel
java.lang.String cancel
parameters_
java.util.Collection<E> parameters_
parameterValues_
java.lang.String[] parameterValues_
performerId_
long performerId_
performers_
java.util.Collection<E> performers_
activityDate_
java.lang.String activityDate_
description_
java.lang.String description_
protocolType_
java.lang.String protocolType_
protocolId_
long protocolId_
protocols_
java.util.Collection<E> protocols_
protocolsApp_
ProtocolApplicationData[] protocolsApp_
mode_
java.lang.String mode_
applyMode_
java.lang.String applyMode_
button
java.lang.String button
reason
java.lang.String reason
fileId
long fileId
expId
long expId
originalProtocolsApp
ProtocolApplicationData originalProtocolsApp
originalProtocolId
long originalProtocolId
mode_
java.lang.String mode_
isEditable
boolean isEditable
protocolId_
long protocolId_
name_
java.lang.String name_
protocolTypeId_
long protocolTypeId_
protocolTypeName_
java.lang.String protocolTypeName_
protocolTypes_
java.util.Collection<E> protocolTypes_
error_
java.lang.String error_
description_
java.lang.String description_
URI_
java.lang.String URI_
id
long id
description
java.lang.String description
visibility_
java.util.Collection<E> visibility_
parameters
java.util.Collection<E> parameters
back_
java.lang.String back_
hardware
java.util.Collection<E> hardware
software
java.util.Collection<E> software
allHardware
java.util.Collection<E> allHardware
allSoftware
java.util.Collection<E> allSoftware
newHardwareId
long newHardwareId
newSoftwareId
long newSoftwareId
mageIdentifier
java.lang.String mageIdentifier
freeText_
java.lang.String freeText_
visibilityId_
long visibilityId_
visibilityName_
java.lang.String visibilityName_
visibilitys_
java.util.Collection<E> visibilitys_
searchResults_
java.util.Collection<E> searchResults_
visibilitys_
java.util.Collection<E> visibilitys_
selectedVisibilitys_
java.lang.String[] selectedVisibilitys_
back
java.lang.String back
newTypeName_
java.lang.String newTypeName_
URI_
java.lang.String URI_
mode_
java.lang.String mode_
softwareId_
long softwareId_
name_
java.lang.String name_
softwareTypeId_
long softwareTypeId_
softwareTypeName_
java.lang.String softwareTypeName_
softwareTypes_
java.util.Collection<E> softwareTypes_
releaseDate_
java.lang.String releaseDate_
softwareManufacturerId_
long softwareManufacturerId_
softwareManufacturerName_
java.lang.String softwareManufacturerName_
softwareManufacturers_
java.util.Collection<E> softwareManufacturers_
error_
java.lang.String error_
isEditable
boolean isEditable
log_
org.apache.commons.logging.Log log_
id
long id
visibility
java.util.Collection<E> visibility
parameters
java.util.Collection<E> parameters
back
java.lang.String back
URI_
java.lang.String URI_
hardwareID
long hardwareID
subSoftwareID
long subSoftwareID
allHardware
java.util.Collection<E> allHardware
allSoftware
java.util.Collection<E> allSoftware
associatedSoftware
java.util.Collection<E> associatedSoftware
associatedHardware
HardwareDesc associatedHardware
freeText_
java.lang.String freeText_
visibilityId_
long visibilityId_
visibilityName_
java.lang.String visibilityName_
visibilitys_
java.util.Collection<E> visibilitys_
searchResults_
java.util.Collection<E> searchResults_
Package gov.nih.nci.caarray.ui.useradmin |
id
long id
groupName
java.lang.String groupName
description
java.lang.String description
largeElementCountFlag
java.lang.String largeElementCountFlag
updateDate
long updateDate
protectionGroupTypeId
long protectionGroupTypeId
back
java.lang.String back
mode
java.lang.String mode
id
long id
groupName
java.lang.String groupName
description
java.lang.String description
largeElementCountFlag
java.lang.String largeElementCountFlag
updateDate
long updateDate
protectionGroupTypeId
long protectionGroupTypeId
results
java.util.Collection<E> results
groupNameSearch
java.lang.String groupNameSearch
id
long id
loginName
java.lang.String loginName
firstName
java.lang.String firstName
lastName
java.lang.String lastName
title
java.lang.String title
emailAddress
java.lang.String emailAddress
institutionName
java.lang.String institutionName
department
java.lang.String department
location
java.lang.String location
updateDate
java.lang.String updateDate
startDate
java.lang.String startDate
endDate
java.lang.String endDate
status
java.lang.String status
back
java.lang.String back
mode
java.lang.String mode
isAdminUser
boolean isAdminUser
phoneNumber
java.lang.String phoneNumber
pwd
java.lang.String pwd
confirmPassword
java.lang.String confirmPassword
userRoles
java.util.Vector<E> userRoles
id
long id
loginName
java.lang.String loginName
firstName
java.lang.String firstName
lastName
java.lang.String lastName
title
java.lang.String title
emailAddress
java.lang.String emailAddress
institutionName
java.lang.String institutionName
department
java.lang.String department
location
java.lang.String location
updateDate
java.lang.String updateDate
startDate
java.lang.String startDate
endDate
java.lang.String endDate
status
java.lang.String status
isAdminUser
boolean isAdminUser
role
java.lang.String role
userRoles
java.util.Vector<E> userRoles
groups
java.util.Collection<E> groups
phoneNumber
java.lang.String phoneNumber
password
java.lang.String password
id
long id
loginName
java.lang.String loginName
firstName
java.lang.String firstName
lastName
java.lang.String lastName
groups
java.util.Vector<E> groups
assignedGroups
java.util.Vector<E> assignedGroups
groupIds
java.lang.String[] groupIds
results
java.util.Collection<E> results
firstNameSearch
java.lang.String firstNameSearch
lastNameSearch
java.lang.String lastNameSearch
loginNameSearch
java.lang.String loginNameSearch
institutionSearch
java.lang.String institutionSearch
emailSearch
java.lang.String emailSearch
userRoleSelection
int userRoleSelection
userRoleCollection
java.util.Vector<E> userRoleCollection
userStatusSelection
int userStatusSelection
userStatusCollection
java.util.Vector<E> userStatusCollection
Package org.biomage.Array |
arrayIdentifier
java.lang.String arrayIdentifier
- An identifying string, e.g. a barcode.
arrayXOrigin
java.lang.Float arrayXOrigin
- This can indicate the x position on a slide, chip, etc. of the
first Feature and is usually specified relative to the fiducial.
arrayYOrigin
java.lang.Float arrayYOrigin
- This can indicate the y position on a slide, chip, etc. of the
first Feature and is usually specified relative to the fiducial.
originRelativeTo
java.lang.String originRelativeTo
- What the array origin is relative to, e.g. upper left corner,
fiducial, etc.
arrayDesign
ArrayDesign arrayDesign
- The association of a physical array with its array design.
information
ArrayManufacture information
- Association between the manufactured array and the information on
that manufacture.
arrayGroup
ArrayGroup arrayGroup
- Association between an ArrayGroup and its Arrays, typically the
ArrayGroup will represent a slide and the Arrays will be the
manufactured so that they may be hybridized separately on that
slide.
arrayManufactureDeviations
java.util.List<E> arrayManufactureDeviations
- Association to classes to describe deviations from the
ArrayDesign.
arrayGroup_list
Array_package.ArrayGroup_list arrayGroup_list
- An array package is a physical platform that contains one or more
arrays that are separately addressable (e.g. several arrays that can
be hybridized on a single microscope slide) or a virtual grouping
together of arrays.
The array package that has been manufactured has information about
where certain artifacts about the array are located for scanning and
feature extraction purposes.
array_list
Array_package.Array_list array_list
- The physical substrate along with its features and their
annotation
arrayManufacture_list
Array_package.ArrayManufacture_list arrayManufacture_list
- Describes the process by which arrays are produced.
barcode
java.lang.String barcode
- Identifier for the ArrayGroup.
arraySpacingX
java.lang.Float arraySpacingX
- If there exist more than one array on a slide or a chip, then the
spacing between the arrays is useful so that scanning / feature
extraction software can crop images representing 1 unique bioassay.
arraySpacingY
java.lang.Float arraySpacingY
- If there exist more than one array on a slide or a chip, then the
spacing between the arrays is useful so that scanning / feature
extraction software can crop images representing 1 unique bioassay.
numArrays
java.lang.Integer numArrays
- This attribute defines the number of arrays on a chip or a slide.
orientationMark
java.lang.String orientationMark
- For a human to determine where the top left side of the array is,
such as a barcode or frosted side of the glass, etc.
orientationMarkPosition
ArrayGroup.OrientationMarkPosition orientationMarkPosition
- One of top, bottom, left or right.
width
java.lang.Float width
- The width of the platform
length
java.lang.Float length
- The length of the platform.
fiducials
java.util.List<E> fiducials
- Association to the marks on the Array for alignment for the
scanner.
arrays
java.util.List<E> arrays
- Association between an ArrayGroup and its Arrays, typically the
ArrayGroup will represent a slide and the Arrays will be the
manufactured so that they may be hybridized separately on that
slide.
substrateType
OntologyEntry substrateType
- Commonly, arrays will be spotted on 1x3 glass microscope slides
but there is nothing that says this must be the case. This
association is for scanners to inform them on the possible different
formats of slides that can contain arrays.
distanceUnit
DistanceUnit distanceUnit
- The unit of the measurement attributes.
value
int value
name
java.lang.String name
nameToValue
java.util.HashMap<K,V> nameToValue
valueToName
java.util.HashMap<K,V> valueToName
top
int top
bottom
int bottom
left
int left
right
int right
VALID_POSITIONS
java.util.ArrayList<E> VALID_POSITIONS
manufacturingDate
java.util.Date manufacturingDate
- The date the arrays were manufactured
tolerance
java.lang.Float tolerance
- The allowable error of a feature printed to its intended
position.
arrays
java.util.List<E> arrays
- Association between the manufactured array and the information on
that manufacture.
arrayManufacturers
java.util.List<E> arrayManufacturers
- The person or organization to contact for information concerning
the ArrayManufacture.
qualityControlStatistics
java.util.List<E> qualityControlStatistics
- Information on the quality of the ArrayManufacture.
featureLIMSs
java.util.List<E> featureLIMSs
- Information on the manufacture of the features.
protocolApplications
java.util.List<E> protocolApplications
- The protocols followed in the manufacturing of the arrays.
adjustments
java.util.List<E> adjustments
- Descriptions of how a Zone has been printed differently than
specified in the ArrayDesign.
featureDefects
java.util.List<E> featureDefects
- Description on features who are manufactured in a different
location than specified in the ArrayDesign.
defectType
OntologyEntry defectType
- Indicates the type of defect (e.g. a missing feature or a moved
feature).
positionDelta
PositionDelta positionDelta
- How the feature deviates in position from the ArrayDesign.
feature
Feature feature
- The feature that was manufactured defectively.
fiducialType
OntologyEntry fiducialType
- A descriptive string that indicates the type of a fiducial (e.g.
the chrome border on an Affymetrix array, a laser ablation mark).
distanceUnit
DistanceUnit distanceUnit
- The units the fiducial is measured in.
position
Position position
- The position, relative to the upper left corner, of the fiducial
ojbConcreteClass
java.lang.String ojbConcreteClass
quality
java.lang.String quality
- A brief description of the quality of the array manufacture
process.
feature
Feature feature
- The feature whose LIMS information is being described.
bioMaterial
BioMaterial bioMaterial
- The BioMaterial used for the feature.
identifierLIMS
DatabaseEntry identifierLIMS
- Association to a LIMS data source for further information on the
manufacturing process.
bioMaterialPlateIdentifier
java.lang.String bioMaterialPlateIdentifier
- The plate from which a biomaterial was obtained.
bioMaterialPlateRow
java.lang.String bioMaterialPlateRow
- The plate row from which a biomaterial was obtained. Specified
by a letter.
bioMaterialPlateCol
java.lang.String bioMaterialPlateCol
- The plate column from which a biomaterial was obtained.
Specified by a number.
deltaX
java.lang.Float deltaX
- Deviation from the y coordinate of this feature's position.
deltaY
java.lang.Float deltaY
- Deviation from the y coordinate of this feature's position.
distanceUnit
DistanceUnit distanceUnit
- The unit for the attributes.
defectType
OntologyEntry defectType
- Indicates the type of defect (e.g. a missing zone or a moved
zone).
positionDelta
PositionDelta positionDelta
- How the zone deviates in position from the ArrayDesign.
zone
Zone zone
- Reference to the Zone that was misprinted.
Package org.biomage.ArrayDesign |
ojbConcreteClass
java.lang.String ojbConcreteClass
reporterFileLocation
java.lang.String reporterFileLocation
reporterFileType
java.lang.String reporterFileType
additionalReporterFileLocation
java.lang.String additionalReporterFileLocation
deleted
boolean deleted
version
java.lang.String version
- The version of this design.
numberOfFeatures
java.lang.Integer numberOfFeatures
- The number of features for this array
protocolApplications
java.util.List<E> protocolApplications
- Describes the application of any protocols, such as the
methodology used to pick oligos, in the design of the array.
featureGroups
java.util.List<E> featureGroups
- The grouping of like Features together. Typically for a physical
array design, this will be a single grouping of features whose type
might be PCR Product or Oligo. If more than one technology type
occurs on the array, such as the mixing of Cloned BioMaterial and
Oligos, then there would be multiple FeatureGroups to segregate the
technology types.
reporterGroups
java.util.List<E> reporterGroups
- The grouping of like Reporter together. If more than one
technology type occurs on the array, such as the mixing of Cloned
BioMaterial and Oligos, then there would be multiple ReporterGroups
to segregate the technology types.
compositeGroups
java.util.List<E> compositeGroups
- The grouping of like CompositeSequence together. If more than
one technology type occurs on the array, such as the mixing of
Cloned BioMaterial and Oligos, then there would be multiple
CompositeGroups to segregate the technology types.
designProviderRoles
java.util.List<E> designProviderRoles
- The providers of the ArrayDesign that have a role which describes
how he/she contributes the ArrayDesign, e.g. investigator, primary contact,
etc.
reporterGroup_list
ArrayDesign_package.ReporterGroup_list reporterGroup_list
- Allows specification of the type of Reporter Design Element.
compositeGroup_list
ArrayDesign_package.CompositeGroup_list compositeGroup_list
- Allows specification of the type of Composite Design Element.
arrayDesign_list
ArrayDesign_package.ArrayDesign_list arrayDesign_list
- Describes the design of an gene expression layout. In some cases
this might be virtual and, for instance, represent the output from
analysis software at the composite level without reporters or
features.
compositeSequences
java.util.List<E> compositeSequences
- The compositeSequences that belong to this group.
ojbConcreteClass
java.lang.String ojbConcreteClass
types
java.util.List<E> types
- The specific type of a feature, reporter, or composite. A
composite type might be a gene while a reporter type might be a cDNA
clone or an oligo.
species
OntologyEntry species
- The organism from which the biosequences of this group are from.
contact
Contact contact
role
OntologyEntry role
featureWidth
java.lang.Float featureWidth
- The width of the feature.
featureLength
java.lang.Float featureLength
- The length of the feature.
featureHeight
java.lang.Float featureHeight
- The height of the feature.
technologyType
OntologyEntry technologyType
- The technology type of this design. By specifying a technology
type, higher level analysis can use appropriate algorithms to
compare the results from multiple arrays. The technology type may
be spotted cDNA or in situ photolithography.
featureShape
OntologyEntry featureShape
- The expected shape of the feature on the array: circular, oval,
square, etc.
distanceUnit
DistanceUnit distanceUnit
- The unit for the feature measures.
features
java.util.List<E> features
- The features that belong to this group.
surfaceType
OntologyEntry surfaceType
- The type of surface from a controlled vocabulary that would
include terms such as non-absorptive, absorptive, etc.
zoneGroups
java.util.List<E> zoneGroups
- In the case where the array design is specified by one or more
zones, allows specifying where those zones are located.
reporters
java.util.List<E> reporters
- The reporters that belong to this group.
row
java.lang.Integer row
- row position in the ZoneGroup
column
java.lang.Integer column
- column position in the ZoneGroup.
upperLeftX
java.lang.Float upperLeftX
- Boundary vertical upper left position relative to (0,0).
upperLeftY
java.lang.Float upperLeftY
- Boundary horizontal upper left position relative to (0,0).
lowerRightX
java.lang.Float lowerRightX
- Boundary vertical lower right position relative to (0,0).
lowerRightY
java.lang.Float lowerRightY
- Boundary horizontal lower right position relative to (0,0).
distanceUnit
DistanceUnit distanceUnit
- Unit for the Zone attributes.
spacingsBetweenZonesX
java.lang.Float spacingsBetweenZonesX
- Spacing between zones, if applicable.
spacingsBetweenZonesY
java.lang.Float spacingsBetweenZonesY
- Spacing between zones, if applicable.
zonesPerX
java.lang.Integer zonesPerX
- The number of zones on the x-axis.
zonesPerY
java.lang.Integer zonesPerY
- The number of zones on the y-axis.
distanceUnit
DistanceUnit distanceUnit
- Unit for the ZoneGroup attributes.
zoneLayout
ZoneLayout zoneLayout
- Describes the rectangular layout of features in the array design.
zoneLocations
java.util.List<E> zoneLocations
- Describes the location of different zones within the array
design.
numFeaturesPerRow
java.lang.Integer numFeaturesPerRow
- The number of features from left to right.
numFeaturesPerCol
java.lang.Integer numFeaturesPerCol
- The number of features from top to bottom of the grid.
spacingBetweenRows
java.lang.Float spacingBetweenRows
- Spacing between the rows.
spacingBetweenCols
java.lang.Float spacingBetweenCols
- Spacing between the columns.
distanceUnit
DistanceUnit distanceUnit
- Unit of the ZoneLayout attributes.
Package org.biomage.AuditAndSecurity |
date
java.util.Date date
- The date of a change.
action
Audit.Action action
- Indicates whether an action is a creation or a modification.
performer
Contact performer
- The contact for creating or changing the instance referred to by
the Audit.
value
int value
name
java.lang.String name
nameToValue
java.util.HashMap<K,V> nameToValue
valueToName
java.util.HashMap<K,V> valueToName
creation
int creation
modification
int modification
contact_list
AuditAndSecurity_package.Contact_list contact_list
- A contact is either a person or an organization.
securityGroup_list
AuditAndSecurity_package.SecurityGroup_list securityGroup_list
- Groups contacts together based on their security privileges.
security_list
AuditAndSecurity_package.Security_list security_list
- Permission information for an object as to ownership, write and
read permissions.
URI
java.lang.String URI
address
java.lang.String address
phone
java.lang.String phone
tollFreePhone
java.lang.String tollFreePhone
email
java.lang.String email
fax
java.lang.String fax
roles
java.util.List<E> roles
- The roles (lab equipment sales, contractor, etc.) the contact fills.
parent
Organization parent
- The containing organization (the university or business which a
lab belongs to, etc.)
lastName
java.lang.String lastName
firstName
java.lang.String firstName
midInitials
java.lang.String midInitials
affiliation
Organization affiliation
- The organization a person belongs to.
owner
java.util.List<E> owner
- The owner of the security rights.
securityGroups
java.util.List<E> securityGroups
- Specifies which security groups have permission to view the
associated object.
members
java.util.List<E> members
- The members of the Security Group.
loginName
java.lang.String loginName
firstName
java.lang.String firstName
lastName
java.lang.String lastName
emailAddress
java.lang.String emailAddress
institutionName
java.lang.String institutionName
Package org.biomage.BioAssay |
ojbConcreteClass
java.lang.String ojbConcreteClass
channels
java.util.List<E> channels
- Channels can be non-null for all subclasses. For instance,
collapsing across replicate features will create a DerivedBioAssay
that will potentially reference channels.
bioAssayFactorValues
java.util.List<E> bioAssayFactorValues
- The values that this BioAssay is associated with for the
experiment.
deleted
boolean deleted
- caARRAY-specific marker for a DELETED BioAssay. tranp.
channel_list
BioAssay_package.Channel_list channel_list
- A channel represents an independent acquisition scheme for the
ImageAcquisition event, typically a wavelength.
bioAssay_list
BioAssay_package.BioAssay_list bioAssay_list
- An abstract class which represents both physical and
computational groupings of arrays and biomaterials.
ojbConcreteClass
java.lang.String ojbConcreteClass
sourceBioMaterialMeasurements
java.util.List<E> sourceBioMaterialMeasurements
- The BioSample and its amount used in the BioAssayCreation event.
array
Array array
- The array used in the BioAssayCreation event.
physicalBioAssayTarget
PhysicalBioAssay physicalBioAssayTarget
- The association between the BioAssayCreation event (typically
Hybridization) and the PhysicalBioAssay and its annotation of this
event.
ojbConcreteClass
java.lang.String ojbConcreteClass
physicalBioAssay
PhysicalBioAssay physicalBioAssay
- The set of treatments undergone by this PhysicalBioAssay.
target
PhysicalBioAssay target
- The PhysicalBioAssay that was treated.
labels
java.util.List<E> labels
- The compound used to label the extract.
type
OntologyEntry type
- The derivation type, for instance collapsed spot replicate,
ratio, averaged intensity, bioassay replicates, etc.
derivedBioAssayData
java.util.List<E> derivedBioAssayData
- The data associated with the DerivedBioAssay.
derivedBioAssayMap
java.util.List<E> derivedBioAssayMap
- The DerivedBioAssay that is produced by the sources of the
BioAssayMap.
physicalBioAssaySource
PhysicalBioAssay physicalBioAssaySource
- The PhysicalBioAssay used in the FeatureExtraction event.
measuredBioAssayTarget
MeasuredBioAssay measuredBioAssayTarget
- The association between the MeasuredBioAssay and the
FeatureExtraction Event.
URI
java.lang.String URI
- The file location in which an image may be found.
channels
java.util.List<E> channels
- The channels captured in this image.
format
OntologyEntry format
- The file format of the image typically a TIF or a JPEG.
images
java.util.List<E> images
- The images produced by the ImageAcquisition event.
featureExtraction
FeatureExtraction featureExtraction
- The association between the MeasuredBioAssay and the
FeatureExtraction Event.
measuredBioAssayData
java.util.List<E> measuredBioAssayData
- The data associated with the MeasuredBioAssay.
physicalBioAssayData
java.util.List<E> physicalBioAssayData
- The Images associated with this PhysicalBioAssay by
ImageAcquisition.
bioAssayCreation
BioAssayCreation bioAssayCreation
- The association between the BioAssayCreation event (typically
Hybridization) and the PhysicalBioAssay and its annotation of this
event.
bioAssayTreatments
java.util.List<E> bioAssayTreatments
- The set of treatments undergone by this PhysicalBioAssay.
Package org.biomage.BioAssayData |
ojbConcreteClass
java.lang.String ojbConcreteClass
summaryStatistics
java.util.List<E> summaryStatistics
- Statistics on the Quality of the BioAssayData.
bioAssayDimension
BioAssayDimension bioAssayDimension
- The BioAssays of the BioAssayData.
designElementDimension
DesignElementDimension designElementDimension
- The DesignElements of the BioAssayData.
quantitationTypeDimension
QuantitationTypeDimension quantitationTypeDimension
- The QuantitationTypes of the BioAssayData.
bioDataValues
BioDataValues bioDataValues
- The data values of the BioAssayData.
bioAssayDimension_list
BioAssayData_package.BioAssayDimension_list bioAssayDimension_list
- An ordered list of bioAssays.
designElementDimension_list
BioAssayData_package.DesignElementDimension_list designElementDimension_list
- An ordered list of designElements. It will be realized as one of
its three subclasses.
quantitationTypeDimension_list
BioAssayData_package.QuantitationTypeDimension_list quantitationTypeDimension_list
- An ordered list of quantitationTypes.
bioAssayMap_list
BioAssayData_package.BioAssayMap_list bioAssayMap_list
- The BioAssayMap is the description of how source
MeasuredBioAssays and/or DerivedBioAssays are manipulated
(mathematically) to produce DerivedBioAssays.
quantitationTypeMap_list
BioAssayData_package.QuantitationTypeMap_list quantitationTypeMap_list
- A QuantitationTypeMap is the description of how source
QuantitationTypes are mathematically transformed into a target
QuantitationType.
bioAssayData_list
BioAssayData_package.BioAssayData_list bioAssayData_list
- Represents the dataset created when the BioAssays are created.
BioAssayData is the entry point to the values. Because the actual
values are represented by a different object, BioDataValues, which
can be memory intensive, the annotation of the transformation can be
gotten separate from the data.
bioAssays
java.util.List<E> bioAssays
- The BioAssays for this Dimension
bioAssayMapTarget
DerivedBioAssay bioAssayMapTarget
- The DerivedBioAssay that is produced by the sources of the
BioAssayMap.
sourceBioAssays
java.util.List<E> sourceBioAssays
- The sources of the BioAssayMap that are used to produce a target
DerivedBioAssay.
bioAssayMaps
java.util.List<E> bioAssayMaps
- The maps for the BioAssays.
bioAssay
BioAssay bioAssay
- The BioAssay associated with the value of the BioAssayDatum.
designElementTuples
HasDesignElementTuples.DesignElementTuples_list designElementTuples
- DesignElement with the QuantitationTypes and their values for
this BioAssay
order
BioDataCube.Order order
- The order to expect the dimension. The enumeration uses the
first letter of the three dimensions to represent the six possible
orderings.
dataInternal
DataInternal dataInternal
- Transformed class to associate white spaced delimited data to the
BioAssayDataCube
dataExternal
DataExternal dataExternal
- Transformed class to associate external data to the
BioAssayDataCube
sourceType
SourceType sourceType
- Indicates the type of data file (or DataInternal) where the cube
originated. Note that this is a caArray extension to the MAGE model.
value
int value
name
java.lang.String name
nameToValue
java.util.HashMap<K,V> nameToValue
valueToName
java.util.HashMap<K,V> valueToName
BDQ
int BDQ
BQD
int BQD
DBQ
int DBQ
DQB
int DQB
QBD
int QBD
QDB
int QDB
bioAssayTuples
HasBioAssayTupleData.BioAssayTuples_list bioAssayTuples
- Each BioAssayTuple contains the the Data for a BioAssay.
ojbConcreteClass
java.lang.String ojbConcreteClass
compositeSequences
java.util.List<E> compositeSequences
- The CompositeSequences for this Dimension.
dataFormat
java.lang.String dataFormat
- The format of the external file, whitespace delimited, tab
delimited, netcdf, etc...
dataFormatInfoURI
java.lang.String dataFormatInfoURI
- Location for documentation on the data format
filenameURI
java.lang.String filenameURI
- The name and location of the file containing the external data
pcData
PCData pcData
- The tab delimited data.
value
java.lang.Object value
- Value for the BioAssay, DesignElement and QuantitationType
specified by the parent tuple elements.
producerTransformation
Transformation producerTransformation
- The association between the DerivedBioAssayData and the
Transformation event that produced it.
ojbConcreteClass
java.lang.String ojbConcreteClass
ojbConcreteClass
java.lang.String ojbConcreteClass
designElementMaps
java.util.List<E> designElementMaps
- The maps for the DesignElements.
designElement
DesignElement designElement
- The DesignElement associated with the value of the BioAssayDatum.
quantitationTypeTuples
HasQuantitationTypeTuples.QuantitationTypeTuples_list quantitationTypeTuples
- A QuantitationType and the value associated with it
containedFeatures
java.util.List<E> containedFeatures
- The features for this dimension.
quantitationTypes
java.util.List<E> quantitationTypes
- The QuantitationTypes for this Dimension.
targetQuantitationType
QuantitationType targetQuantitationType
- The QuantitationType whose value will be produced from the values
of the source QuantitationType according to the Protocol.
sourcesQuantitationType
java.util.List<E> sourcesQuantitationType
- The QuantitationType sources for values for the transformation.
quantitationTypeMaps
java.util.List<E> quantitationTypeMaps
- The maps for the QuantitationTypes.
quantitationType
QuantitationType quantitationType
- The QuantitationType associated with the value of the
BioAssayDatum.
datum
Datum datum
- The value to associate with the Quantitation Type.
reporters
java.util.List<E> reporters
- The reporters for this dimension.
bioAssayDataSources
java.util.List<E> bioAssayDataSources
- The BioAssayData sources that the Transformation event uses to
produce the target DerivedBioAssayData.
derivedBioAssayDataTarget
DerivedBioAssayData derivedBioAssayDataTarget
- The association between the DerivedBioAssayData and the
Transformation event that produced it.
quantitationTypeMapping
QuantitationTypeMapping quantitationTypeMapping
- The collection of mappings for the QuantitationTypes.
designElementMapping
DesignElementMapping designElementMapping
- The collection of mappings for the DesignElements.
bioAssayMapping
BioAssayMapping bioAssayMapping
- The collection of mappings for the BioAssays.
Package org.biomage.BioEvent |
protocolApplications
java.util.List<E> protocolApplications
- The applied protocols to the BioEvent.
Package org.biomage.BioMaterial |
action
OntologyEntry action
protocolTypes
java.util.List<E> protocolTypes
ojbConcreteClass
java.lang.String ojbConcreteClass
imported
boolean imported
- caARRAY internal flag to indicate if this BioMaterial is imported. This
should only be set to TRUE by MAGEML importer and not be changed afterwards.
copied
java.lang.Boolean copied
- caARRAY internal flag to indicate if this BioMaterial is generated by copy of existing biomaterial.
This should only be set to TRUE when adding the biomaterial by copy of Labeledextract/Biomaterial
and not be changed afterwards. This would allow to query biomaterial and ignore the ones generated
by copy.
qualityControlStatistics
java.util.List<E> qualityControlStatistics
- Measures of the quality of the BioMaterial.
characteristics
java.util.List<E> characteristics
- Innate properties of the biosource, such as genotype, cultivar,
tissue type, cell type, ploidy, etc.
materialType
OntologyEntry materialType
- The type of material used, i.e. rna, dna, lipid, phosphoprotein,
etc.
treatments
java.util.List<E> treatments
- This association is one way from BioMaterial to Treatment. From
this a BioMaterial can discover the amount and type of BioMaterial
that was part of the treatment that produced it.
topLevelBioMaterials
java.util.List<E> topLevelBioMaterials
- This association is one way from BioMaterial to it top most parent
biomaterial. From this, a biomaterial can discover its topm parent
biosource and the associated securedelementID. This relation is added
for caArray to efficiently discover the parent bioseource and associated
secured element id.
compound_list
BioMaterial_package.Compound_list compound_list
- A Compound can be a simple compound such as SDS (sodium dodecyl
sulfate). It may also be made of other Compounds in proportions
using CompoundMeasurements to enumerate the Compounds and their
amounts such as LB (Luria Broth) Media.
bioMaterial_list
BioMaterial_package.BioMaterial_list bioMaterial_list
- BioMaterial is an abstract class that represents the important
substances such as cells, tissues, DNA, proteins, etc...
Biomaterials can be related to other biomaterial through a directed
acyclic graph (represented by treatment(s)).
bioMaterial
BioMaterial bioMaterial
- A source BioMaterial for a treatment.
measurement
Measurement measurement
- The amount of the BioMaterial.
type
OntologyEntry type
- The Type attribute describes the role the BioSample holds in the
treatment hierarchy. This type can be an extract.
sourceContact
java.util.List<E> sourceContact
- The BioSource's source is the provider of the biological material
(a cell line, strain, etc...). This could be the ATTC (American
Tissue Type Collection).
isSolvent
java.lang.Boolean isSolvent
- A Compound may be a special case Solvent.
compoundIndices
java.util.List<E> compoundIndices
- Indices into common Compound Indices, such as the Merck Index,
for this Compound.
componentCompounds
java.util.List<E> componentCompounds
- The Compounds and their amounts used to create this Compound.
externalLIMS
DatabaseEntry externalLIMS
- Reference to an entry in an external LIMS data source.
compound
Compound compound
- A Compound to be used to create another Compound.
measurement
Measurement measurement
- The amount of the Compound.
labels
java.util.List<E> labels
- Compound used to label the extract.
order
java.lang.Integer order
- The chronological order in which a treatment occurred (in
relation to other treatments). More than one treatment can have the
same chronological order indicating that they happened (or were
caused to happen) simultaneously.
action
OntologyEntry action
- The event that occurred (e.g. grow, wait, add, etc...). The
actions should be a recommended vocabulary
actionMeasurement
Measurement actionMeasurement
- Measures events like duration, centrifuge speed, etc.
compoundMeasurements
java.util.List<E> compoundMeasurements
- The compounds and their amounts used in the treatment.
sourceBioMaterialMeasurements
java.util.List<E> sourceBioMaterialMeasurements
- The BioMaterials and the amounts used in the treatment
Package org.biomage.BioSequence |
length
java.lang.Integer length
- The number of residues in the biosequence.
isApproximateLength
java.lang.Boolean isApproximateLength
- If length not positively known will be true
isCircular
java.lang.Boolean isCircular
- Indicates if the BioSequence is circular in nature.
sequence
java.lang.String sequence
- The actual components of the sequence, for instance, for DNA a
string consisting of A,T,C and G.
The attribute is optional and instead of specified here, can be
found through the DatabaseEntry.
sequenceDatabases
java.util.List<E> sequenceDatabases
- References an entry in a species database, like GenBank, UniGene,
etc.
ontologyEntries
java.util.List<E> ontologyEntries
- Ontology entries referring to common values associated with
BioSequences, such as gene names, go ids, etc.
polymerType
OntologyEntry polymerType
- A choice of protein, RNA, or DNA.
type
OntologyEntry type
- The type of biosequence, i.e. gene, exon, UniGene cluster,
fragment, BAC, EST, etc.
species
OntologyEntry species
- The organism from which this sequence was obtained.
seqFeatures
java.util.List<E> seqFeatures
- Association to annotations for subsequences. Corresponds to the
GenBank Frame Table.
bioSequence_list
BioSequence_package.BioSequence_list bioSequence_list
- A BioSequence is a representation of a DNA, RNA, or protein
sequence. It can be represented by a Clone, Gene, or the sequence.
basis
SeqFeature.Basis basis
- How the evidence for a SeqFeature was determined.
regions
java.util.List<E> regions
- Association to classes that describe the location with the
sequence of the SeqFeature.
value
int value
name
java.lang.String name
nameToValue
java.util.HashMap<K,V> nameToValue
valueToName
java.util.HashMap<K,V> valueToName
experimental
int experimental
computational
int computational
both
int both
unknown
int unknown
NA
int NA
strandType
java.lang.String strandType
- Indicates the direction and/or type of the SeqFeature, i.e.
whether it is in the 5' or 3' direction, is double stranded, etc.
subregions
java.util.List<E> subregions
- Regions within the SeqFeature.
coordinate
SequencePosition coordinate
- At which base pairs or amino acid this SeqFeature begins and
ends.
ojbConcreteClass
java.lang.String ojbConcreteClass
start
java.lang.Integer start
- The location of the base, for nucleotides, that the SeqFeature
starts.
end
java.lang.Integer end
- The location of the base, for nucleotides, that the SeqFeature
ends.
title
java.lang.String title
authors
java.lang.String authors
publication
java.lang.String publication
publisher
java.lang.String publisher
editor
java.lang.String editor
year
java.util.Date year
volume
java.lang.String volume
issue
java.lang.String issue
pages
java.lang.String pages
URI
java.lang.String URI
parameters
java.util.List<E> parameters
- Criteria that can be used to look up the reference in a
repository.
accessions
java.util.List<E> accessions
- References in publications, eg Medline and PubMed, for this
BibliographicReference.
Package org.biomage.Common |
descriptions
java.util.List<E> descriptions
- Free hand text descriptions. Makes available the associations of
Description to an instance of Describable.
auditTrail
java.util.List<E> auditTrail
- A list of Audit instances that track changes to the instance of
Describable.
security
Security security
- Information on the security for the instance of the class.
id
long id
securedElementId
java.lang.String securedElementId
editable
boolean editable
propertySets
java.util.List<E> propertySets
- Allows specification of name/value pairs. Meant to primarily
help in-house, pipeline processing of instances by providing a place
for values that aren't part of the specification proper.
identifier
java.lang.String identifier
- An identifier is an unambiguous string that is unique within the
scope (i.e. a document, a set of related documents, or a repository)
of its use.
name
java.lang.String name
- The potentially ambiguous common identifier.
name
java.lang.String name
identifier
java.lang.String identifier
auditAndSecurity_package
AuditAndSecurity_package auditAndSecurity_package
- Specifies classes that allow tracking of changes and information
on user permissions to view the data and annotation.
description_package
Description_package description_package
- The classes in this package allow a variety of references to
third party annotation and direct annotation by the experimenter.
measurement_package
Measurement_package measurement_package
- The classes of this package provide utility information on the
quantities of other classes to each other.
bQS_package
BQS_package bQS_package
- Allows a reference to an article, book or other publication to be
specified for searching repositories.
bioEvent_package
BioEvent_package bioEvent_package
- An abstract class representing an event that takes sources of
some type to produce a target of some type. Each of the realized
subclasses determines the type of the sources and the target. The
association to a protocol application allows specification of how
the event was performed.
protocol_package
Protocol_package protocol_package
- Provides a relatively immutable class, Protocol, that can
describe a generic laboratory procedure or analysis algorithm, for
example, and an instance class, ProtocolApplication, which can
describe the actual application of a protocol. The
ProtocolApplication provides values for the replaceable parameters
of the Protocol and, through the Description association of
Describable, any variation from the Protocol.
bioMaterial_package
BioMaterial_package bioMaterial_package
- The classes in this package describe how a BioSource is treated
to obtain the BioMaterial (typically a LabeledExtract) that is used
by a BioAssayCreation in combination with an Array to produce a
PhysicalBioAssay. A set of treatments are typically linear in time
but can form a Directed Acyclic Graph.
bioSequence_package
BioSequence_package bioSequence_package
- Describes a known gene or sequence. BioAssays typically seek to
identify what BioSequences are expressed in a BioMaterial after
treatments, the expression level measured from the association
between the BioMaterial and the Array. The Array's Features
typically provide known locations for this association to occur.
Most often, the Reporter and CompositeSequence are known and the
presence or absence of a particular BioSequence in the BioMaterial
is based on whether there as been an association to the
DesignElement targeted for it. Some other experiments may not know
the DesignElement's target but can discover it with known properties
of the BioSequences in the BioMaterial.
designElement_package
DesignElement_package designElement_package
- The classes of this package are the contained classes of the
ArrayDesign and describe through the DesignElements what is intended
to be at each location of the Array. The Feature describes an
intended location on the Array, the Reporter the Oligo, Clone, PCR
Product that is on a Feature and the CompositeSequence which
combines Reporters or CompositeSequences into what the child
DesignElements are meant to represent biologically, e.g. a Gene,
Exon, SpliceVariant, etc.
arrayDesign_package
ArrayDesign_package arrayDesign_package
- Describes a microarray design that can be printed and then, in
the case of gene expression, hybridized. An array design consists
of several features (also called spots) in which reporter sequences
are placed. Many features may have the same reporter replicated and
a reporter may be specified in one or more array designs.
The nature of the reporter's biosequence placed on a spot will
depend on the technology. Two well-known technologies differ
significantly-spotter arrays draw material from a well and place a
spot on the array whereas in situ oligo arrays are created through
the synthesis of many, short (~20-100mer) nucleotide sequences onto
the features.
Reporters can be grouped together into CompositeSequences, typically
representing a gene or one or more splice variants in gene
expression experiments.
There are then two distinct ways that DesignElements are grouped.
The one described in the ArrayDesign package by FeatureGroup,
ReporterGroup and CompositeGroup is by technology type, that is, one
might want to segregate the controls to a Group and all the
non-controls to another. Or if PCR Product and Oligos are both
used on an array they would likely be in different groups. The
grouping described in the DesignElement package by the mappings
relates the Features to the Reporter, the Reporters to
CompositeSequence, and at higher levels, CompositeSequences to
CompositeSequence.
array_package
Array_package array_package
- Describes the process of creating arrays from array designs.
Includes information on how arrays are grouped together, if
relevant, how an array deviates from its array design both in layout
and per feature and potentially contains references to LIMS data
that might contain more detail on the BioMaterial used to create the
reporters.
bioAssay_package
BioAssay_package bioAssay_package
- Provides classes that contain information and annotation on the
event of joining an Array with a BioMaterial preparation, the
acquisition of images and the extraction of data on a per feature
basis from those images. The derived classes of BioAssay represent
the base PhysicalBioAssays which lead to the production of Images,
the MeasuredBioAssay which is associated with the set of
quantitations produced by FeatureExtraction, and DerivedBioAssay
(see BioAssayData package) which groups together BioAssays that have
been analyzed together to produce further refinement of the
quantitations.
The design of this package and the related BioAssayData package was
driven by the following query considerations and the desire to
return as little data as necessary to satisfy a query. Often, the
first set of queries for experiments below the Experiment level will
want to discover the why of an experiment and this is captured in
the BioAssay class through its FactorValue, BioEvent and Description
associations. This separates it from the data but allows an
overview of the experiment hierarchy. The BioAssayData class
association to BioDataValues is optional only to allow queries on
them to discover the how of the experiment through the association
to the transformation and mappings of the three BioAssayData
dimensions and the protocols used. Once a researcher, for instance,
has narrowed down the experiments of interest then the actual data,
represented by the BioDataValues, can be downloaded. Because these
data can be in the hundreds of megabytes to gigabytes range, it was
considered desirable to be able to return information and annotation
on the experiment without the data.
quantitationType_package
QuantitationType_package quantitationType_package
- This Package defines the classes for quantitations, such as
measured and derived signal, error, and pvalue. The subclasses of
StandardQuantitationType will be the best fit from FeatureExtraction
or Transformation Protocol for the values obtained. Other values
can be specified using SpecializedQuantitationType.
bioAssayData_package
BioAssayData_package bioAssayData_package
- The classes defined here provide data and the information and
annotation on the derivation of that data. Some of the scenarios
that might occur are the following.
FeatureExtraction of a single PhysicalBioAssay produces
MeasuredBioAssayData that has a single BioAssay on the
BioAssayDimension, typically the Features described in the
ArrayDesign on the DesignElementDimension, and the Quantitations
associated with the application of a FeatureExtraction protocol on
the QuantitationDimension.
An error model transformation might be applied that doesn't change
the BioAssayDimension or the DesignElementDimension but likely
changes the QuantitationDimension. A transformation on replicate
Reporters or CompositeSequences might be applied on the single
BioAssay that would change the DesignElementDimension and the
QuantitationDimension both. Replicate and Control BioAssays might
be added to the BioAssayDimension and a transformation could change
the BioAssayDimension and the QuantitationDimension but not change
the DesignElementDimension to produce a new DerivedBioAssayData. Or
some combination of the above transformations could be performed at
once to change all three dimensions.
Because the classes derive from Describable, the Experimenter can
provide as much detail at each level of the class hierarchy as
desired.
experiment_package
Experiment_package experiment_package
- Represents the container for a hierarchical grouping of
BioAssays. Can have the end results of Clustering Analysis
specified and, through the ExperimentDesign, a description and
annotation of the overall design of the experiment and what it was
to show.
higherLevelAnalysis_package
HigherLevelAnalysis_package higherLevelAnalysis_package
- Describes the results of performing analysis on the result of the
BioAssayData from an Experiment.
modelToClass
org.biomage.Common.MAGEJava.ModelNameToClassMap modelToClass
- Instantiate the ModelNameToClassMap
id
long id
- caARRAY-specific identifier
name
java.lang.String name
- The name of the key.
value
java.lang.String value
- The value of the name.
type
java.lang.String type
- The type of the key.
propertySets
java.util.List<E> propertySets
- Allows nested specification of name/value pairs
Package org.biomage.Description |
category
java.lang.String category
- caARRAY-specific attribute to categorize the appropriate database type
that should be used for which ontologies. tranp 08/12/04
userDefined
boolean userDefined
- caARRAY-specific attribute to indicate if this database entry represents
a public database.
version
java.lang.String version
- The version for which a DatabaseReference applies.
URI
java.lang.String URI
- The location of the Database.
contacts
java.util.List<E> contacts
- Information on the contacts for the database
accession
java.lang.String accession
- The identifier used to look up the record.
accessionVersion
java.lang.String accessionVersion
- The appropriate version of the accession (if applicable).
URI
java.lang.String URI
- The location of the record.
type
OntologyEntry type
- The type of record (e.g. a protein in SwissProt, or a yeast
strain in SGD).
database
Database database
- Reference to the database where the DataEntry instance can be
found.
text
java.lang.String text
- The description.
URI
java.lang.String URI
- A reference to the location and type of an outside resource.
externalReference
ExternalReference externalReference
- Specifies where the described instance was originally obtained
from.
annotations
java.util.List<E> annotations
- Allows specification of ontology entries related to the instance
being described.
databaseReferences
java.util.List<E> databaseReferences
- References to entries in databases.
bibliographicReferences
java.util.List<E> bibliographicReferences
- References to existing literature.
database_list
Description_package.Database_list database_list
- An address to a repository.
exportedFromServer
java.lang.String exportedFromServer
- The originating server for the object, a network address or
common name.
exportedFromDB
java.lang.String exportedFromDB
- Name of the database, if applicable, that the object was exported
from.
exportID
java.lang.String exportID
- The identifier of the object at the originating source.
exportName
java.lang.String exportName
- The name of the object at the originating source.
category
java.lang.String category
- The category to which this entry belongs.
value
java.lang.String value
- The value for this entry in this category.
description
java.lang.String description
- The description of the meaning for this entry.
ontologyReference
DatabaseEntry ontologyReference
- Many ontology entries will not yet have formalized ontologies.
In those cases, they will not have a database reference to the
ontology.
In the future it is highly encouraged that these ontologies be
developed and ontologyEntry be subclassed from DatabaseReference.
associations
java.util.List<E> associations
- Allows an instance of an OntologyEntry to be further qualified.
Package org.biomage.Description.Ontology |
measurement
OntologyEntry measurement
ageValue
OntologyEntry ageValue
minMeasurement
OntologyEntry minMeasurement
minValue
OntologyEntry minValue
maxMeasurement
OntologyEntry maxMeasurement
maxValue
OntologyEntry maxValue
initialTimePoint
OntologyEntry initialTimePoint
ojbConcreteClass
java.lang.String ojbConcreteClass
weight
OntologyEntry weight
weightMeasurement
OntologyEntry weightMeasurement
height
OntologyEntry height
heightMeasurement
OntologyEntry heightMeasurement
types
java.util.List<E> types
Package org.biomage.DesignElement |
compositeSequence
CompositeSequence compositeSequence
- A map to the compositeSequences that compose this
CompositeSequence.
compositePositionSources
java.util.List<E> compositePositionSources
- Association to the CompositeSequences that compose this
CompositeSequence and where those CompositeSequences occur.
composite
CompositeSequence composite
- A source CompositeSequence that is part of a target
CompositeSequence
mismatchInformation
java.util.List<E> mismatchInformation
- Differences in how the contained compositeSequence matches its
target compositeSequence's sequence.
biologicalCharacteristics
java.util.List<E> biologicalCharacteristics
- The annotation on the BioSequence this CompositeSequence
represents. Typically the sequences will be a Genes, Exons, or
SpliceVariants.
reporterCompositeMaps
java.util.List<E> reporterCompositeMaps
- A map to the reporters that compose this CompositeSequence.
compositeCompositeMaps
java.util.List<E> compositeCompositeMaps
- A map to the compositeSequences that compose this
CompositeSequence.
controlType
OntologyEntry controlType
- If the design element represents a control, the type of control
it is (normalization, deletion, negative, positive, etc.)
compositeSequence_list
DesignElement_package.CompositeSequence_list compositeSequence_list
- A collection of Reporter or CompositeSequence Design Elements,
annotated through the association to BioSequence.
reporter_list
DesignElement_package.Reporter_list reporter_list
- A Design Element that represents some biological material (clone,
oligo, etc.) on an array which will report on some biosequence or
biosequences. The derived data from the measured data of its
Features represents the presence or absence of the biosequence or
biosequences it is reporting on in the BioAssay.
Reporters are Identifiable and several Features on the same array
can be mapped to the same reporter as can Features from a different
ArrayDesign. The granularity of the Reporters independence is
dependent on the technology and the intent of the ArrayDesign.
Oligos using mature technologies can in general be assumed to be
safely replicated on many features where as with PCR Products there
might be the desire for quality assurence to make reporters one to
one with features and use the mappings to CompositeSequences for
replication purposes.
compositeCompositeMap_list
DesignElement_package.CompositeCompositeMap_list compositeCompositeMap_list
- A CompositeCompositeMap is the description of how source
CompositeSequences are transformed into a target CompositeSequence.
For instance, several CompositeSequences could represent different
sequence regions for a Gene and could be mapped to different
CompositeSequences, each representing a different splice variant for
that Gene.
reporterCompositeMap_list
DesignElement_package.ReporterCompositeMap_list reporterCompositeMap_list
- A ReporterCompositeMap is the description of how source Reporters
are transformed into a target CompositeSequences. For instance,
several reporters that tile across a section of a chromosome could
be mapped to a CompositeSequence.
featureReporterMap_list
DesignElement_package.FeatureReporterMap_list featureReporterMap_list
- A FeatureReporterMap is the description of how source features
are transformed into a target reporter. These would map replicate
features for a reporter to the reporter.
controlFeatures
java.util.List<E> controlFeatures
- Associates features with their control features.
controlledFeatures
java.util.List<E> controlledFeatures
- Associates features with their control features.
position
Position position
- The position of the feature on the array, relative to the top,
left corner.
zone
Zone zone
- A reference to the zone this feature is in.
featureLocation
FeatureLocation featureLocation
- Location of this feature relative to a grid.
featureGroup
FeatureGroup featureGroup
- The features that belong to this group.
feature
Feature feature
- The feature the FeatureInformation is supplying information for.
mismatchInformation
java.util.List<E> mismatchInformation
- Differences in how the feature matches the reporter's sequence,
typical examples is the Affymetrix probe pair where one of the
features is printed with a mismatch to the other feature's perfect
match.
row
java.lang.Integer row
- row position in the Zone
column
java.lang.Integer column
- column position in the Zone.
reporter
Reporter reporter
- Associates features with their reporter.
featureInformationSources
java.util.List<E> featureInformationSources
- Typically, the features on an array that are manufactured with
this reporter's BioSequence.
startCoord
java.lang.Integer startCoord
- Offset into the sequence that the mismatch occurs.
newSequence
java.lang.String newSequence
- The sequence that replaces the specified sequence starting at
start_coord.
replacedLength
java.lang.Integer replacedLength
- Length of the original sequence that is replaced. A deletion is
specified when the length of the newSequence is less than the
replacedLength.
x
java.lang.Float x
- The horizontal distance from the upper left corner of the array.
y
java.lang.Float y
- The vertical distance from the upper left corner of the array.
distanceUnit
DistanceUnit distanceUnit
- The units of the x, y positions.
immobilizedCharacteristics
java.util.List<E> immobilizedCharacteristics
- The sequence annotation on the BioMaterial this reporter
represents. Typically the sequences will be an Oligo Sequence,
Clone or PCR Primer.
warningType
OntologyEntry warningType
- Similar to failType but indicates a warning rather than a
failure.
failTypes
java.util.List<E> failTypes
- If at some time the reporter is determined to be failed this
indicts the failure (doesn't report on what it was intended to
report on, etc.)
featureReporterMaps
java.util.List<E> featureReporterMaps
- Associates features with their reporter.
compositeSequence
CompositeSequence compositeSequence
- A map to the reporters that compose this CompositeSequence.
reporterPositionSources
java.util.List<E> reporterPositionSources
- Association to the reporters that compose this CompositeSequence
and where those reporters occur.
reporter
Reporter reporter
- A reporter that comprises part of a CompositeSequence.
mismatchInformation
java.util.List<E> mismatchInformation
- Differences in how the reporter matches its compositeSequence's
sequence.
Package org.biomage.Experiment |
id
long id
location
java.lang.String location
protocolApplication
ProtocolApplication protocolApplication
experiment
Experiment experiment
id
long id
description
java.lang.String description
location
java.lang.String location
experiment
Experiment experiment
providerRoles
java.util.List<E> providerRoles
- The providers of the Experiment that have a role which describes
how he/she contributes the experiment, e.g. investigator, primary contact,
etc.
analysisResults
java.util.List<E> analysisResults
- The results of analyzing the data, typically with a clustering
algorithm.
bioAssayData
java.util.List<E> bioAssayData
- The collection of BioAssayDatas for this Experiment.
bioAssays
java.util.List<E> bioAssays
- The collection of BioAssays for this Experiment.
experimentDesigns
java.util.List<E> experimentDesigns
- The association to the description and annotation of the
Experiment, along with the grouping of the top-level BioAssays.
deleted
boolean deleted
- caARRAY-specific marker if this Experiment is deleted.
experiment_list
Experiment_package.Experiment_list experiment_list
- The Experiment is the collection of all the BioAssays that are
related by the ExperimentDesign.
category
OntologyEntry category
- The category of an ExperimentalFactor could be biological (time,
[glucose]) or a methodological factor (differing cDNA preparation
protocols).
factorValues
java.util.List<E> factorValues
- The pairing of BioAssay FactorValues with the ExperimentDesign
ExperimentFactor.
annotations
java.util.List<E> annotations
- Allows describing additional information such as concentration of
Tamoxafin with a CASRegistry #.
types
java.util.List<E> types
- Classification of an experiment. For example 'normal vs.
diseased', 'treated vs. untreated', 'time course', 'tiling', etc.
topLevelBioAssays
java.util.List<E> topLevelBioAssays
- The organization of the BioAssays as specified by the
ExperimentDesign (TimeCourse, Dosage, etc.)
experimentalFactors
java.util.List<E> experimentalFactors
- The description of the factors (TimeCourse, Dosage, etc.) that
group the BioAssays.
qualityControlDescription
Description qualityControlDescription
- Description of the quality control aspects of the Experiment.
normalizationDescription
Description normalizationDescription
- Description of the normalization strategy of the Experiment.
replicateDescription
Description replicateDescription
- Description of the replicate strategy of the Experiment.
contact
Contact contact
role
OntologyEntry role
experimentalFactor
ExperimentalFactor experimentalFactor
- The pairing of BioAssay FactorValues with the ExperimentDesign
ExperimentFactor.
measurement
Measurement measurement
- The measured value for this factor.
value
OntologyEntry value
- Allows a more complex value to be specified for a FactorValue
than a simple Measurement.
id
long id
- Deprecated.
experiment
Experiment experiment
- Deprecated.
arrayIdentifier
java.lang.String arrayIdentifier
- Deprecated.
arrayBatchName
java.lang.String arrayBatchName
- Deprecated.
celFileLocation
java.lang.String celFileLocation
- Deprecated.
expFileLocation
java.lang.String expFileLocation
- Deprecated.
txtFileLocation
java.lang.String txtFileLocation
- Deprecated.
chpFileLocation
java.lang.String chpFileLocation
- Deprecated.
gprFileLocation
java.lang.String gprFileLocation
- Deprecated.
gpsFileLocation
java.lang.String gpsFileLocation
- Deprecated.
gprFromSpotFileLocation
java.lang.String gprFromSpotFileLocation
- Deprecated.
measuredBioAssay
MeasuredBioAssay measuredBioAssay
- Deprecated.
derivedBioAssay
DerivedBioAssay derivedBioAssay
- Deprecated.
uploadGroupName
java.lang.String uploadGroupName
- Deprecated.
extract
LabeledExtract extract
- Deprecated.
spikedControl
LabeledExtract spikedControl
- Deprecated.
factorValues
java.util.List<E> factorValues
- Deprecated.
channelTwoExtract
LabeledExtract channelTwoExtract
- Deprecated.
channelTwoSpikedControl
LabeledExtract channelTwoSpikedControl
- Deprecated.
channelTwoFactorValues
java.util.List<E> channelTwoFactorValues
- Deprecated.
Package org.biomage.HigherLevelAnalysis |
clusterBioAssayData
BioAssayData clusterBioAssayData
- The BioAssayData whose values were used by the cluster algorithm.
nodes
java.util.List<E> nodes
- The nodes of the cluster.
bioAssayDataCluster_list
HigherLevelAnalysis_package.BioAssayDataCluster_list bioAssayDataCluster_list
- A mathematical method of higher level analysis whereby
BioAssayData are grouped together into nodes.
nodes
java.util.List<E> nodes
- Nested nodes of the BioAssayDataCluster.
nodeContents
java.util.List<E> nodeContents
- The contents of the node, expressed as either a one, two or three
dimensional object.
nodeValue
java.util.List<E> nodeValue
- Values or measurements for this node that may be produced by the
clustering algorithm. Typical are distance values for the nodes.
bioAssayDimension
BioAssayDimension bioAssayDimension
- The relevant BioAssays for this NodeContents from the
BioAssayData.
designElementDimension
DesignElementDimension designElementDimension
- The relevant DesignElements for this NodeContents from the
BioAssayData.
quantitationDimension
QuantitationTypeDimension quantitationDimension
- The relevant QuantitationTypes for this NodeContents from the
BioAssayData.
name
java.lang.String name
- The name for this value.
value
java.lang.Object value
- The value for this NodeValue.
type
OntologyEntry type
- The type of value, distance, etc.
scale
OntologyEntry scale
- The scale (linear, log10, ln, etc.) of the value.
dataType
OntologyEntry dataType
- The data type of the any element.
Package org.biomage.Interface |
Package org.biomage.Measurement |
unitNameCV
ConcentrationUnit.UnitNameCV unitNameCV
value
int value
name
java.lang.String name
nameToValue
java.util.HashMap<K,V> nameToValue
valueToName
java.util.HashMap<K,V> valueToName
M
int M
mM
int mM
nM
int nM
uM
int uM
pM
int pM
fM
int fM
mg_per_mL
int mg_per_mL
mL_per_L
int mL_per_L
g_per_L
int g_per_L
gram_percent
int gram_percent
percent_vol_per_vol
int percent_vol_per_vol
percent_weight_per_vol
int percent_weight_per_vol
percent_weight_per_weight
int percent_weight_per_weight
other
int other
unitNameCV
DistanceUnit.UnitNameCV unitNameCV
value
int value
name
java.lang.String name
nameToValue
java.util.HashMap<K,V> nameToValue
valueToName
java.util.HashMap<K,V> valueToName
nm
int nm
um
int um
mm
int mm
cm
int cm
m
int m
A
int A
other
int other
unitNameCV
MassUnit.UnitNameCV unitNameCV
value
int value
name
java.lang.String name
nameToValue
java.util.HashMap<K,V> nameToValue
valueToName
java.util.HashMap<K,V> valueToName
kg
int kg
g
int g
mg
int mg
ug
int ug
ng
int ng
pg
int pg
fg
int fg
other
int other
type
Measurement.Type type
- The type of measurement, for instance if the measurement is five
feet, it can be either absolute (five feet tall) or change (five
feet further along).
value
java.lang.Object value
- The value of the measurement. kindCV (and otherKind) determine
with Unit the datatype of value.
kindCV
Measurement.KindCV kindCV
- One of the enumeration values to determine the controlled
vocabulary of the value.
otherKind
java.lang.String otherKind
- Name of the controlled vocabulary if it isn't one of the Unit
subclasses.
unit
Unit unit
- The Unit associated with the Measurement.
value
int value
name
java.lang.String name
nameToValue
java.util.HashMap<K,V> nameToValue
valueToName
java.util.HashMap<K,V> valueToName
time
int time
distance
int distance
temperature
int temperature
quantity
int quantity
mass
int mass
volume
int volume
concentration
int concentration
other
int other
value
int value
name
java.lang.String name
nameToValue
java.util.HashMap<K,V> nameToValue
valueToName
java.util.HashMap<K,V> valueToName
absolute
int absolute
change
int change
unitNameCV
QuantityUnit.UnitNameCV unitNameCV
value
int value
name
java.lang.String name
nameToValue
java.util.HashMap<K,V> nameToValue
valueToName
java.util.HashMap<K,V> valueToName
mol
int mol
amol
int amol
fmol
int fmol
pmol
int pmol
nmol
int nmol
umol
int umol
molecules
int molecules
other
int other
unitNameCV
TemperatureUnit.UnitNameCV unitNameCV
value
int value
name
java.lang.String name
nameToValue
java.util.HashMap<K,V> nameToValue
valueToName
java.util.HashMap<K,V> valueToName
degrees_C
int degrees_C
degrees_F
int degrees_F
K
int K
unitNameCV
TimeUnit.UnitNameCV unitNameCV
value
int value
name
java.lang.String name
nameToValue
java.util.HashMap<K,V> nameToValue
valueToName
java.util.HashMap<K,V> valueToName
years
int years
months
int months
weeks
int weeks
days
int days
hours
int hours
minutes
int minutes
seconds
int seconds
us
int us
ms
int ms
other
int other
ojbConcreteClass
java.lang.String ojbConcreteClass
unitName
java.lang.String unitName
- The name of the unit.
unitNameCV
VolumeUnit.UnitNameCV unitNameCV
value
int value
name
java.lang.String name
nameToValue
java.util.HashMap<K,V> nameToValue
valueToName
java.util.HashMap<K,V> valueToName
ml
int ml
cc
int cc
dl
int dl
L
int L
ul
int ul
nl
int nl
pl
int pl
fl
int fl
other
int other
Package org.biomage.Protocol |
model
java.lang.String model
- The model (number) of a piece of hardware.
make
java.lang.String make
- The make of the Hardware (its manufacturer).
type
OntologyEntry type
- The type of a piece of Hardware. Examples include: scanner, wash
station...
softwares
java.util.List<E> softwares
- Associates Hardware and Software together.
hardwareManufacturers
java.util.List<E> hardwareManufacturers
- Contact for information on the Hardware.
serialNumber
java.lang.String serialNumber
- Manufacturer's identifier for the Hardware.
hardware
Hardware hardware
- The underlying hardware.
defaultValue
Measurement defaultValue
- Allows the optional specification of a default values and the
unit for the Parameter
dataType
OntologyEntry dataType
- The type of data generated by the parameter i.e. Boolean, float,
etc...
URI
java.lang.String URI
- Where an instantiated Parameterizable is located.
parameterTypes
java.util.List<E> parameterTypes
- The description of the parameters for the Parameterizable class
instance.
parameterValues
java.util.List<E> parameterValues
- The parameter values for this Parameterizable Application.
value
java.lang.Object value
- The value of the parameter. Will have the datatype of its
associated Parameter.
parameterType
Parameter parameterType
- The parameter this value is for.
text
java.lang.String text
- The text description of the Protocol.
title
java.lang.String title
- The title of the Protocol
type
OntologyEntry type
- The type of a Protocol, a user should provide/use a recommended
vocabulary. Examples of types include: RNA extraction, array
washing, etc...
hardwares
java.util.List<E> hardwares
- Hardware used by this protocol.
softwares
java.util.List<E> softwares
- Software used by this Protocol.
hardware_list
Protocol_package.Hardware_list hardware_list
- Hardware represents the hardware used. Examples of Hardware
include: computers, scanners, wash stations etc...
software_list
Protocol_package.Software_list software_list
- Software represents the software used. Examples of Software
include: feature extraction software, clustering software, etc...
protocol_list
Protocol_package.Protocol_list protocol_list
- A Protocol is a parameterizable description of a method.
ProtocolApplication is used to specify the ParameterValues of it's
Protocol's Parameters.
activityDate
java.util.Date activityDate
- When the protocol was applied.
hardwareApplications
java.util.List<E> hardwareApplications
- The use of hardware for the application of the protocol.
softwareApplications
java.util.List<E> softwareApplications
- The use of software for the application of the protocol.
performers
java.util.List<E> performers
- The people who performed the protocol.
protocol
Protocol protocol
- The protocol that is being used.
type
OntologyEntry type
- The type of a piece of Software. Examples include: feature
extractor...
hardware
Hardware hardware
- Associates Hardware and Software together.
softwares
java.util.List<E> softwares
- Software packages this software uses, i.e. operating system, 3rd
party software packages, etc.
softwareManufacturers
java.util.List<E> softwareManufacturers
- Contact for information on the software.
version
java.lang.String version
- The version of the software.
releaseDate
java.util.Date releaseDate
- When the software was released.
software
Software software
- The underlying software.
Package org.biomage.QuantitationType |
targetQuantitationType
QuantitationType targetQuantitationType
- The association between a ConfidenceIndicator and the
QuantitationType its is an indicator for.
ojbConcreteClass
java.lang.String ojbConcreteClass
isBackground
java.lang.Boolean isBackground
- Indicates whether the quantitation has been measured from the
background or from the feature itself.
channel
Channel channel
- The optional channel associated with the QuantitationType.
scale
OntologyEntry scale
- Indication of how to interpret the value. From a suggested
vocabulary of {LINEAR | LN | LOG2 |LOG10 | FOLD_CHANGE | OTHER}
dataType
OntologyEntry dataType
- The specific type for the quantitations. From a controlled
vocabulary of {float, int, boolean, etc.}
confidenceIndicators
java.util.List<E> confidenceIndicators
- The association between a ConfidenceIndicator and the
QuantitationType its is an indicator for.
quantitationTypeMaps
java.util.List<E> quantitationTypeMaps
- The QuantitationType whose value will be produced from the values
of the source QuantitationType according to the Protocol.
quantitationType_list
QuantitationType_package.QuantitationType_list quantitationType_list
- A method for calculating a single datum of the matrix (e.g. raw
intensity, background, error).
Package org.biomage.tools.apps.annot |
arrayPage
ArrayPage arrayPage
arrayBtn
javax.swing.JButton arrayBtn
goBtn
javax.swing.JButton goBtn
fileMenu
javax.swing.JMenu fileMenu
pageMenu
javax.swing.JMenu pageMenu
helpMenu
javax.swing.JMenu helpMenu
menuBar
javax.swing.JMenuBar menuBar
aboutMI
javax.swing.JMenuItem aboutMI
arrayMI
javax.swing.JMenuItem arrayMI
exitMI
javax.swing.JMenuItem exitMI
helpMI
javax.swing.JMenuItem helpMI
newMI
javax.swing.JMenuItem newMI
openMI
javax.swing.JMenuItem openMI
saveMI
javax.swing.JMenuItem saveMI
saveAsMI
javax.swing.JMenuItem saveAsMI
topPanel
javax.swing.JPanel topPanel
toolBarPanel
javax.swing.JPanel toolBarPanel
pageSP
javax.swing.JScrollPane pageSP
logSP
javax.swing.JScrollPane logSP
splitPane
javax.swing.JSplitPane splitPane
cmdToolBar
javax.swing.JToolBar cmdToolBar
pageToolBar
javax.swing.JToolBar pageToolBar
toolBarSeperator
javax.swing.JToolBar[] toolBarSeperator
NUM_SEPERATOR
int NUM_SEPERATOR
pageShowed
boolean pageShowed
sizeX
int sizeX
sizeY
int sizeY
resetBtn
javax.swing.JButton resetBtn
facePanel
javax.swing.JPanel facePanel
guiSet
GuiSet guiSet
Package org.biomage.tools.apps.annot.pages |
blankLB
javax.swing.JLabel[] blankLB
urlLB
javax.swing.JLabel urlLB
addrLB
javax.swing.JLabel addrLB
spaceLB
javax.swing.JLabel spaceLB
zSpaceLB
javax.swing.JLabel zSpaceLB
xLB
javax.swing.JLabel xLB
yLB
javax.swing.JLabel yLB
zlRowLB
javax.swing.JLabel zlRowLB
zlColLB
javax.swing.JLabel zlColLB
zNumLB
javax.swing.JLabel zNumLB
zlNumLB
javax.swing.JLabel zlNumLB
arrayDesignPanel
javax.swing.JPanel arrayDesignPanel
manufacturerPanel
javax.swing.JPanel manufacturerPanel
zoneLayoutPanel
javax.swing.JPanel zoneLayoutPanel
zoneGroupPanel
javax.swing.JPanel zoneGroupPanel
urlTF
javax.swing.JTextField urlTF
addrTF
javax.swing.JTextField addrTF
zRowNumTF
javax.swing.JTextField zRowNumTF
zColNumTF
javax.swing.JTextField zColNumTF
zlRowNumTF
javax.swing.JTextField zlRowNumTF
zlColNumTF
javax.swing.JTextField zlColNumTF
rowSpaceTF
javax.swing.JTextField rowSpaceTF
colSpaceTF
javax.swing.JTextField colSpaceTF
zSpaceXTF
javax.swing.JTextField zSpaceXTF
zSpaceYTF
javax.swing.JTextField zSpaceYTF
guiSet
GuiSet guiSet
EMPTY_LABEL
int EMPTY_LABEL
validChecker
XMLConvertInputVerifier validChecker
guiSet
GuiSet guiSet
contactPanel
javax.swing.JPanel contactPanel
personPanel
javax.swing.JPanel personPanel
orgPanel
javax.swing.JPanel orgPanel
contactTypeLB
javax.swing.JLabel contactTypeLB
nameLB
javax.swing.JLabel nameLB
urlLB
javax.swing.JLabel urlLB
addrLB
javax.swing.JLabel addrLB
phoneLB
javax.swing.JLabel phoneLB
tollFreePhoneLB
javax.swing.JLabel tollFreePhoneLB
emailLB
javax.swing.JLabel emailLB
faxLB
javax.swing.JLabel faxLB
firstNameLB
javax.swing.JLabel firstNameLB
lastNameLB
javax.swing.JLabel lastNameLB
midInitialsLB
javax.swing.JLabel midInitialsLB
affiliationLB
javax.swing.JLabel affiliationLB
organizationLB
javax.swing.JLabel organizationLB
nameLI
javax.swing.JList nameLI
urlTF
javax.swing.JTextField urlTF
addrTF
javax.swing.JTextField addrTF
phoneTF
javax.swing.JTextField phoneTF
tollFreePhoneTF
javax.swing.JTextField tollFreePhoneTF
emailTF
javax.swing.JTextField emailTF
faxTF
javax.swing.JTextField faxTF
firstNameTF
javax.swing.JTextField firstNameTF
lastNameTF
javax.swing.JTextField lastNameTF
midInitialsTF
javax.swing.JTextField midInitialsTF
affiliationTF
javax.swing.JTextField affiliationTF
organizationTF
javax.swing.JTextField organizationTF
Package org.biomage.tools.generate_classes |
Package org.biomage.tools.helpers |
mgedOntologyClass
java.lang.String mgedOntologyClass
isInstantiable
boolean isInstantiable
MOEstack
java.util.ArrayList<E> MOEstack
isAssignable
boolean isAssignable
isAssigned
boolean isAssigned
assignableValues
java.util.ArrayList<E> assignableValues
mgedOntologyProperty
java.lang.String mgedOntologyProperty
propType
java.lang.String propType
Package org.biomage.tools.xmlutils |