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A
- ArrayDesign - class org.biomage.ArrayDesign.ArrayDesign.
- Describes the design of an gene expression layout.
- ArrayDesign() - Constructor for class org.biomage.ArrayDesign.ArrayDesign
- Default constructor.
- ArrayDesign(Attributes) - Constructor for class org.biomage.ArrayDesign.ArrayDesign
- Attribute constructor.
- ArrayDesign_package - class org.biomage.ArrayDesign.ArrayDesign_package.
- Describes a microarray design that can be printed and then, in the case of gene expression, hybridized.
- ArrayDesign_package() - Constructor for class org.biomage.ArrayDesign.ArrayDesign_package
- Default constructor.
- ArrayDesign_package(Attributes) - Constructor for class org.biomage.ArrayDesign.ArrayDesign_package
- Attribute constructor.
- ArrayDesign_package.ArrayDesign_list - class org.biomage.ArrayDesign.ArrayDesign_package.ArrayDesign_list.
- Inner list class for holding multiple entries for attribute arrayDesign_list.
- ArrayDesign_package.ArrayDesign_list() - Constructor for class org.biomage.ArrayDesign.ArrayDesign_package.ArrayDesign_list
- ArrayDesign_package.CompositeGroup_list - class org.biomage.ArrayDesign.ArrayDesign_package.CompositeGroup_list.
- Inner list class for holding multiple entries for attribute compositeGroup_list.
- ArrayDesign_package.CompositeGroup_list() - Constructor for class org.biomage.ArrayDesign.ArrayDesign_package.CompositeGroup_list
- ArrayDesign_package.DesignElementGroup_list - class org.biomage.ArrayDesign.ArrayDesign_package.DesignElementGroup_list.
- Inner list class for holding multiple entries for attribute designElementGroup_list.
- ArrayDesign_package.DesignElementGroup_list() - Constructor for class org.biomage.ArrayDesign.ArrayDesign_package.DesignElementGroup_list
- ArrayDesign_package.PhysicalArrayDesign_list - class org.biomage.ArrayDesign.ArrayDesign_package.PhysicalArrayDesign_list.
- Inner list class for holding multiple entries for attribute physicalArrayDesign_list.
- ArrayDesign_package.PhysicalArrayDesign_list() - Constructor for class org.biomage.ArrayDesign.ArrayDesign_package.PhysicalArrayDesign_list
- ArrayDesign_package.ReporterGroup_list - class org.biomage.ArrayDesign.ArrayDesign_package.ReporterGroup_list.
- Inner list class for holding multiple entries for attribute reporterGroup_list.
- ArrayDesign_package.ReporterGroup_list() - Constructor for class org.biomage.ArrayDesign.ArrayDesign_package.ReporterGroup_list
- addToArrayDesign_list(ArrayDesign) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to add ArrayDesign to ArrayDesign_list
- addToArrayDesign_list(int, ArrayDesign) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to add ArrayDesign at position to ArrayDesign_list
- addToCompositeGroup_list(CompositeGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to add CompositeGroup to CompositeGroup_list
- addToCompositeGroup_list(int, CompositeGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to add CompositeGroup at position to CompositeGroup_list
- addToCompositeGroups(CompositeGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to add CompositeGroup to CompositeGroups_list
- addToCompositeGroups(int, CompositeGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to add CompositeGroup at position to CompositeGroups_list
- addToCompositeSequences(CompositeSequence) - Method in class org.biomage.ArrayDesign.CompositeGroup
- Method to add CompositeSequence to CompositeSequences_list
- addToCompositeSequences(int, CompositeSequence) - Method in class org.biomage.ArrayDesign.CompositeGroup
- Method to add CompositeSequence at position to CompositeSequences_list
- addToDesignElementGroup_list(DesignElementGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to add DesignElementGroup to DesignElementGroup_list
- addToDesignElementGroup_list(int, DesignElementGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to add DesignElementGroup at position to DesignElementGroup_list
- addToDesignProviders(Contact) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to add Contact to DesignProviders_list
- addToDesignProviders(int, Contact) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to add Contact at position to DesignProviders_list
- addToFeatureGroups(FeatureGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to add FeatureGroup to FeatureGroups_list
- addToFeatureGroups(int, FeatureGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to add FeatureGroup at position to FeatureGroups_list
- addToFeatures(Feature) - Method in class org.biomage.ArrayDesign.FeatureGroup
- Method to add Feature to Features_list
- addToFeatures(int, Feature) - Method in class org.biomage.ArrayDesign.FeatureGroup
- Method to add Feature at position to Features_list
- addToPhysicalArrayDesign_list(PhysicalArrayDesign) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to add PhysicalArrayDesign to PhysicalArrayDesign_list
- addToPhysicalArrayDesign_list(int, PhysicalArrayDesign) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to add PhysicalArrayDesign at position to PhysicalArrayDesign_list
- addToProtocolApplications(ProtocolApplication) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to add ProtocolApplication to ProtocolApplications_list
- addToProtocolApplications(int, ProtocolApplication) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to add ProtocolApplication at position to ProtocolApplications_list
- addToReporterGroup_list(ReporterGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to add ReporterGroup to ReporterGroup_list
- addToReporterGroup_list(int, ReporterGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to add ReporterGroup at position to ReporterGroup_list
- addToReporterGroups(ReporterGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to add ReporterGroup to ReporterGroups_list
- addToReporterGroups(int, ReporterGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to add ReporterGroup at position to ReporterGroups_list
- addToReporters(Reporter) - Method in class org.biomage.ArrayDesign.ReporterGroup
- Method to add Reporter to Reporters_list
- addToReporters(int, Reporter) - Method in class org.biomage.ArrayDesign.ReporterGroup
- Method to add Reporter at position to Reporters_list
- addToTypes(OntologyEntry) - Method in class org.biomage.ArrayDesign.DesignElementGroup
- Method to add OntologyEntry to Types_list
- addToTypes(int, OntologyEntry) - Method in class org.biomage.ArrayDesign.DesignElementGroup
- Method to add OntologyEntry at position to Types_list
- addToZoneGroups(ZoneGroup) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
- Method to add ZoneGroup to ZoneGroups_list
- addToZoneGroups(int, ZoneGroup) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
- Method to add ZoneGroup at position to ZoneGroups_list
- addToZoneLocations(Zone) - Method in class org.biomage.ArrayDesign.ZoneGroup
- Method to add Zone to ZoneLocations_list
- addToZoneLocations(int, Zone) - Method in class org.biomage.ArrayDesign.ZoneGroup
- Method to add Zone at position to ZoneLocations_list
- arrayDesign_list - Variable in class org.biomage.ArrayDesign.ArrayDesign_package
- Describes the design of an gene expression layout.
C
- CompositeGroup - class org.biomage.ArrayDesign.CompositeGroup.
- Allows specification of the type of Composite Design Element.
- CompositeGroup() - Constructor for class org.biomage.ArrayDesign.CompositeGroup
- Default constructor.
- CompositeGroup(Attributes) - Constructor for class org.biomage.ArrayDesign.CompositeGroup
- Attribute constructor.
- column - Variable in class org.biomage.ArrayDesign.Zone
- column position in the ZoneGroup.
- compositeGroup_list - Variable in class org.biomage.ArrayDesign.ArrayDesign_package
- Allows specification of the type of Composite Design Element.
- compositeGroups - Variable in class org.biomage.ArrayDesign.ArrayDesign
- The grouping of like CompositeSequence together.
- compositeSequences - Variable in class org.biomage.ArrayDesign.CompositeGroup
- The compositeSequences that belong to this group.
D
- DesignElementGroup - class org.biomage.ArrayDesign.DesignElementGroup.
- The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained.
- DesignElementGroup() - Constructor for class org.biomage.ArrayDesign.DesignElementGroup
- Default constructor.
- DesignElementGroup(Attributes) - Constructor for class org.biomage.ArrayDesign.DesignElementGroup
- Attribute constructor.
- designElementGroup_list - Variable in class org.biomage.ArrayDesign.ArrayDesign_package
- The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained.
- designProviders - Variable in class org.biomage.ArrayDesign.ArrayDesign
- The primary contact for information on the array design
- distanceUnit - Variable in class org.biomage.ArrayDesign.FeatureGroup
- The unit for the feature measures.
- distanceUnit - Variable in class org.biomage.ArrayDesign.Zone
- Unit for the Zone attributes.
- distanceUnit - Variable in class org.biomage.ArrayDesign.ZoneGroup
- Unit for the ZoneGroup attributes.
- distanceUnit - Variable in class org.biomage.ArrayDesign.ZoneLayout
- Unit of the ZoneLayout attributes.
F
- FeatureGroup - class org.biomage.ArrayDesign.FeatureGroup.
- A collection of like features.
- FeatureGroup() - Constructor for class org.biomage.ArrayDesign.FeatureGroup
- Default constructor.
- FeatureGroup(Attributes) - Constructor for class org.biomage.ArrayDesign.FeatureGroup
- Attribute constructor.
- featureGroups - Variable in class org.biomage.ArrayDesign.ArrayDesign
- The grouping of like Features together.
- featureHeight - Variable in class org.biomage.ArrayDesign.FeatureGroup
- The height of the feature.
- featureLength - Variable in class org.biomage.ArrayDesign.FeatureGroup
- The length of the feature.
- featureShape - Variable in class org.biomage.ArrayDesign.FeatureGroup
- The expected shape of the feature on the array: circular, oval, square, etc.
- featureWidth - Variable in class org.biomage.ArrayDesign.FeatureGroup
- The width of the feature.
- features - Variable in class org.biomage.ArrayDesign.FeatureGroup
- The features that belong to this group.
G
- getArrayDesign_list() - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Get method for arrayDesign_list
- getColumn() - Method in class org.biomage.ArrayDesign.Zone
- Get method for column
- getCompositeGroup_list() - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Get method for compositeGroup_list
- getCompositeGroups() - Method in class org.biomage.ArrayDesign.ArrayDesign
- Get method for compositeGroups
- getCompositeSequences() - Method in class org.biomage.ArrayDesign.CompositeGroup
- Get method for compositeSequences
- getDesignElementGroup_list() - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Get method for designElementGroup_list
- getDesignProviders() - Method in class org.biomage.ArrayDesign.ArrayDesign
- Get method for designProviders
- getDistanceUnit() - Method in class org.biomage.ArrayDesign.FeatureGroup
- Get method for distanceUnit
- getDistanceUnit() - Method in class org.biomage.ArrayDesign.Zone
- Get method for distanceUnit
- getDistanceUnit() - Method in class org.biomage.ArrayDesign.ZoneGroup
- Get method for distanceUnit
- getDistanceUnit() - Method in class org.biomage.ArrayDesign.ZoneLayout
- Get method for distanceUnit
- getFeatureGroups() - Method in class org.biomage.ArrayDesign.ArrayDesign
- Get method for featureGroups
- getFeatureHeight() - Method in class org.biomage.ArrayDesign.FeatureGroup
- Get method for featureHeight
- getFeatureLength() - Method in class org.biomage.ArrayDesign.FeatureGroup
- Get method for featureLength
- getFeatureShape() - Method in class org.biomage.ArrayDesign.FeatureGroup
- Get method for featureShape
- getFeatureWidth() - Method in class org.biomage.ArrayDesign.FeatureGroup
- Get method for featureWidth
- getFeatures() - Method in class org.biomage.ArrayDesign.FeatureGroup
- Get method for features
- getFromArrayDesign_list(int) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to get ArrayDesign from ArrayDesign_list
- getFromCompositeGroup_list(int) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to get CompositeGroup from CompositeGroup_list
- getFromCompositeGroups(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to get CompositeGroup from CompositeGroups_list
- getFromCompositeSequences(int) - Method in class org.biomage.ArrayDesign.CompositeGroup
- Method to get CompositeSequence from CompositeSequences_list
- getFromDesignElementGroup_list(int) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to get DesignElementGroup from DesignElementGroup_list
- getFromDesignProviders(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to get Contact from DesignProviders_list
- getFromFeatureGroups(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to get FeatureGroup from FeatureGroups_list
- getFromFeatures(int) - Method in class org.biomage.ArrayDesign.FeatureGroup
- Method to get Feature from Features_list
- getFromPhysicalArrayDesign_list(int) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to get PhysicalArrayDesign from PhysicalArrayDesign_list
- getFromProtocolApplications(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to get ProtocolApplication from ProtocolApplications_list
- getFromReporterGroup_list(int) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to get ReporterGroup from ReporterGroup_list
- getFromReporterGroups(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to get ReporterGroup from ReporterGroups_list
- getFromReporters(int) - Method in class org.biomage.ArrayDesign.ReporterGroup
- Method to get Reporter from Reporters_list
- getFromTypes(int) - Method in class org.biomage.ArrayDesign.DesignElementGroup
- Method to get OntologyEntry from Types_list
- getFromZoneGroups(int) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
- Method to get ZoneGroup from ZoneGroups_list
- getFromZoneLocations(int) - Method in class org.biomage.ArrayDesign.ZoneGroup
- Method to get Zone from ZoneLocations_list
- getLowerRightX() - Method in class org.biomage.ArrayDesign.Zone
- Get method for lowerRightX
- getLowerRightY() - Method in class org.biomage.ArrayDesign.Zone
- Get method for lowerRightY
- getNumFeaturesPerCol() - Method in class org.biomage.ArrayDesign.ZoneLayout
- Get method for numFeaturesPerCol
- getNumFeaturesPerRow() - Method in class org.biomage.ArrayDesign.ZoneLayout
- Get method for numFeaturesPerRow
- getNumberOfFeatures() - Method in class org.biomage.ArrayDesign.ArrayDesign
- Get method for numberOfFeatures
- getPhysicalArrayDesign_list() - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Get method for physicalArrayDesign_list
- getProtocolApplications() - Method in class org.biomage.ArrayDesign.ArrayDesign
- Get method for protocolApplications
- getReporterGroup_list() - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Get method for reporterGroup_list
- getReporterGroups() - Method in class org.biomage.ArrayDesign.ArrayDesign
- Get method for reporterGroups
- getReporters() - Method in class org.biomage.ArrayDesign.ReporterGroup
- Get method for reporters
- getRow() - Method in class org.biomage.ArrayDesign.Zone
- Get method for row
- getSpacingBetweenCols() - Method in class org.biomage.ArrayDesign.ZoneLayout
- Get method for spacingBetweenCols
- getSpacingBetweenRows() - Method in class org.biomage.ArrayDesign.ZoneLayout
- Get method for spacingBetweenRows
- getSpacingsBetweenZonesX() - Method in class org.biomage.ArrayDesign.ZoneGroup
- Get method for spacingsBetweenZonesX
- getSpacingsBetweenZonesY() - Method in class org.biomage.ArrayDesign.ZoneGroup
- Get method for spacingsBetweenZonesY
- getSpecies() - Method in class org.biomage.ArrayDesign.DesignElementGroup
- Get method for species
- getSurfaceType() - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
- Get method for surfaceType
- getTechnologyType() - Method in class org.biomage.ArrayDesign.FeatureGroup
- Get method for technologyType
- getTypes() - Method in class org.biomage.ArrayDesign.DesignElementGroup
- Get method for types
- getUpperLeftX() - Method in class org.biomage.ArrayDesign.Zone
- Get method for upperLeftX
- getUpperLeftY() - Method in class org.biomage.ArrayDesign.Zone
- Get method for upperLeftY
- getVersion() - Method in class org.biomage.ArrayDesign.ArrayDesign
- Get method for version
- getZoneGroups() - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
- Get method for zoneGroups
- getZoneLayout() - Method in class org.biomage.ArrayDesign.ZoneGroup
- Get method for zoneLayout
- getZoneLocations() - Method in class org.biomage.ArrayDesign.ZoneGroup
- Get method for zoneLocations
- getZonesPerX() - Method in class org.biomage.ArrayDesign.ZoneGroup
- Get method for zonesPerX
- getZonesPerY() - Method in class org.biomage.ArrayDesign.ZoneGroup
- Get method for zonesPerY
L
- lowerRightX - Variable in class org.biomage.ArrayDesign.Zone
- Boundary vertical lower right position relative to (0,0).
- lowerRightY - Variable in class org.biomage.ArrayDesign.Zone
- Boundary horizontal lower right position relative to (0,0).
N
- numFeaturesPerCol - Variable in class org.biomage.ArrayDesign.ZoneLayout
- The number of features from top to bottom of the grid.
- numFeaturesPerRow - Variable in class org.biomage.ArrayDesign.ZoneLayout
- The number of features from left to right.
- numberOfFeatures - Variable in class org.biomage.ArrayDesign.ArrayDesign
- The number of features for this array
O
- org.biomage.ArrayDesign - package org.biomage.ArrayDesign
P
- PhysicalArrayDesign - class org.biomage.ArrayDesign.PhysicalArrayDesign.
- A design that is expected to be used to manufacture physical arrays.
- PhysicalArrayDesign() - Constructor for class org.biomage.ArrayDesign.PhysicalArrayDesign
- Default constructor.
- PhysicalArrayDesign(Attributes) - Constructor for class org.biomage.ArrayDesign.PhysicalArrayDesign
- Attribute constructor.
- physicalArrayDesign_list - Variable in class org.biomage.ArrayDesign.ArrayDesign_package
- A design that is expected to be used to manufacture physical arrays.
- protocolApplications - Variable in class org.biomage.ArrayDesign.ArrayDesign
- Describes the application of any protocols, such as the methodology used to pick oligos, in the design of the array.
R
- ReporterGroup - class org.biomage.ArrayDesign.ReporterGroup.
- Allows specification of the type of Reporter Design Element.
- ReporterGroup() - Constructor for class org.biomage.ArrayDesign.ReporterGroup
- Default constructor.
- ReporterGroup(Attributes) - Constructor for class org.biomage.ArrayDesign.ReporterGroup
- Attribute constructor.
- removeElementAtFromArrayDesign_list(int) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to remove by position from ArrayDesign_list
- removeElementAtFromCompositeGroup_list(int) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to remove by position from CompositeGroup_list
- removeElementAtFromCompositeGroups(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to remove by position from CompositeGroups_list
- removeElementAtFromCompositeSequences(int) - Method in class org.biomage.ArrayDesign.CompositeGroup
- Method to remove by position from CompositeSequences_list
- removeElementAtFromDesignElementGroup_list(int) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to remove by position from DesignElementGroup_list
- removeElementAtFromDesignProviders(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to remove by position from DesignProviders_list
- removeElementAtFromFeatureGroups(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to remove by position from FeatureGroups_list
- removeElementAtFromFeatures(int) - Method in class org.biomage.ArrayDesign.FeatureGroup
- Method to remove by position from Features_list
- removeElementAtFromPhysicalArrayDesign_list(int) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to remove by position from PhysicalArrayDesign_list
- removeElementAtFromProtocolApplications(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to remove by position from ProtocolApplications_list
- removeElementAtFromReporterGroup_list(int) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to remove by position from ReporterGroup_list
- removeElementAtFromReporterGroups(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to remove by position from ReporterGroups_list
- removeElementAtFromReporters(int) - Method in class org.biomage.ArrayDesign.ReporterGroup
- Method to remove by position from Reporters_list
- removeElementAtFromTypes(int) - Method in class org.biomage.ArrayDesign.DesignElementGroup
- Method to remove by position from Types_list
- removeElementAtFromZoneGroups(int) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
- Method to remove by position from ZoneGroups_list
- removeElementAtFromZoneLocations(int) - Method in class org.biomage.ArrayDesign.ZoneGroup
- Method to remove by position from ZoneLocations_list
- removeFromArrayDesign_list(ArrayDesign) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to remove first ArrayDesign from ArrayDesign_list
- removeFromCompositeGroup_list(CompositeGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to remove first CompositeGroup from CompositeGroup_list
- removeFromCompositeGroups(CompositeGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to remove first CompositeGroup from CompositeGroups_list
- removeFromCompositeSequences(CompositeSequence) - Method in class org.biomage.ArrayDesign.CompositeGroup
- Method to remove first CompositeSequence from CompositeSequences_list
- removeFromDesignElementGroup_list(DesignElementGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to remove first DesignElementGroup from DesignElementGroup_list
- removeFromDesignProviders(Contact) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to remove first Contact from DesignProviders_list
- removeFromFeatureGroups(FeatureGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to remove first FeatureGroup from FeatureGroups_list
- removeFromFeatures(Feature) - Method in class org.biomage.ArrayDesign.FeatureGroup
- Method to remove first Feature from Features_list
- removeFromPhysicalArrayDesign_list(PhysicalArrayDesign) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to remove first PhysicalArrayDesign from PhysicalArrayDesign_list
- removeFromProtocolApplications(ProtocolApplication) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to remove first ProtocolApplication from ProtocolApplications_list
- removeFromReporterGroup_list(ReporterGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Method to remove first ReporterGroup from ReporterGroup_list
- removeFromReporterGroups(ReporterGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Method to remove first ReporterGroup from ReporterGroups_list
- removeFromReporters(Reporter) - Method in class org.biomage.ArrayDesign.ReporterGroup
- Method to remove first Reporter from Reporters_list
- removeFromTypes(OntologyEntry) - Method in class org.biomage.ArrayDesign.DesignElementGroup
- Method to remove first OntologyEntry from Types_list
- removeFromZoneGroups(ZoneGroup) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
- Method to remove first ZoneGroup from ZoneGroups_list
- removeFromZoneLocations(Zone) - Method in class org.biomage.ArrayDesign.ZoneGroup
- Method to remove first Zone from ZoneLocations_list
- reporterGroup_list - Variable in class org.biomage.ArrayDesign.ArrayDesign_package
- Allows specification of the type of Reporter Design Element.
- reporterGroups - Variable in class org.biomage.ArrayDesign.ArrayDesign
- The grouping of like Reporter together.
- reporters - Variable in class org.biomage.ArrayDesign.ReporterGroup
- The reporters that belong to this group.
- row - Variable in class org.biomage.ArrayDesign.Zone
- row position in the ZoneGroup
S
- setArrayDesign_list(ArrayDesign_package.ArrayDesign_list) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Set method for arrayDesign_list
- setColumn(int) - Method in class org.biomage.ArrayDesign.Zone
- Set method for column
- setCompositeGroup_list(ArrayDesign_package.CompositeGroup_list) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Set method for compositeGroup_list
- setCompositeGroups(HasCompositeGroups.CompositeGroups_list) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Set method for compositeGroups
- setCompositeSequences(HasCompositeSequences.CompositeSequences_list) - Method in class org.biomage.ArrayDesign.CompositeGroup
- Set method for compositeSequences
- setDesignElementGroup_list(ArrayDesign_package.DesignElementGroup_list) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Set method for designElementGroup_list
- setDesignProviders(HasDesignProviders.DesignProviders_list) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Set method for designProviders
- setDistanceUnit(DistanceUnit) - Method in class org.biomage.ArrayDesign.FeatureGroup
- Set method for distanceUnit
- setDistanceUnit(DistanceUnit) - Method in class org.biomage.ArrayDesign.Zone
- Set method for distanceUnit
- setDistanceUnit(DistanceUnit) - Method in class org.biomage.ArrayDesign.ZoneGroup
- Set method for distanceUnit
- setDistanceUnit(DistanceUnit) - Method in class org.biomage.ArrayDesign.ZoneLayout
- Set method for distanceUnit
- setFeatureGroups(HasFeatureGroups.FeatureGroups_list) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Set method for featureGroups
- setFeatureHeight(float) - Method in class org.biomage.ArrayDesign.FeatureGroup
- Set method for featureHeight
- setFeatureLength(float) - Method in class org.biomage.ArrayDesign.FeatureGroup
- Set method for featureLength
- setFeatureShape(OntologyEntry) - Method in class org.biomage.ArrayDesign.FeatureGroup
- Set method for featureShape
- setFeatureWidth(float) - Method in class org.biomage.ArrayDesign.FeatureGroup
- Set method for featureWidth
- setFeatures(HasFeatures.Features_list) - Method in class org.biomage.ArrayDesign.FeatureGroup
- Set method for features
- setLowerRightX(float) - Method in class org.biomage.ArrayDesign.Zone
- Set method for lowerRightX
- setLowerRightY(float) - Method in class org.biomage.ArrayDesign.Zone
- Set method for lowerRightY
- setNumFeaturesPerCol(int) - Method in class org.biomage.ArrayDesign.ZoneLayout
- Set method for numFeaturesPerCol
- setNumFeaturesPerRow(int) - Method in class org.biomage.ArrayDesign.ZoneLayout
- Set method for numFeaturesPerRow
- setNumberOfFeatures(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Set method for numberOfFeatures
- setPhysicalArrayDesign_list(ArrayDesign_package.PhysicalArrayDesign_list) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Set method for physicalArrayDesign_list
- setProtocolApplications(HasProtocolApplications.ProtocolApplications_list) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Set method for protocolApplications
- setReporterGroup_list(ArrayDesign_package.ReporterGroup_list) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- Set method for reporterGroup_list
- setReporterGroups(HasReporterGroups.ReporterGroups_list) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Set method for reporterGroups
- setReporters(HasReporters.Reporters_list) - Method in class org.biomage.ArrayDesign.ReporterGroup
- Set method for reporters
- setRow(int) - Method in class org.biomage.ArrayDesign.Zone
- Set method for row
- setSpacingBetweenCols(float) - Method in class org.biomage.ArrayDesign.ZoneLayout
- Set method for spacingBetweenCols
- setSpacingBetweenRows(float) - Method in class org.biomage.ArrayDesign.ZoneLayout
- Set method for spacingBetweenRows
- setSpacingsBetweenZonesX(float) - Method in class org.biomage.ArrayDesign.ZoneGroup
- Set method for spacingsBetweenZonesX
- setSpacingsBetweenZonesY(float) - Method in class org.biomage.ArrayDesign.ZoneGroup
- Set method for spacingsBetweenZonesY
- setSpecies(OntologyEntry) - Method in class org.biomage.ArrayDesign.DesignElementGroup
- Set method for species
- setSurfaceType(OntologyEntry) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
- Set method for surfaceType
- setTechnologyType(OntologyEntry) - Method in class org.biomage.ArrayDesign.FeatureGroup
- Set method for technologyType
- setTypes(HasTypes.Types_list) - Method in class org.biomage.ArrayDesign.DesignElementGroup
- Set method for types
- setUpperLeftX(float) - Method in class org.biomage.ArrayDesign.Zone
- Set method for upperLeftX
- setUpperLeftY(float) - Method in class org.biomage.ArrayDesign.Zone
- Set method for upperLeftY
- setVersion(String) - Method in class org.biomage.ArrayDesign.ArrayDesign
- Set method for version
- setZoneGroups(HasZoneGroups.ZoneGroups_list) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
- Set method for zoneGroups
- setZoneLayout(ZoneLayout) - Method in class org.biomage.ArrayDesign.ZoneGroup
- Set method for zoneLayout
- setZoneLocations(HasZoneLocations.ZoneLocations_list) - Method in class org.biomage.ArrayDesign.ZoneGroup
- Set method for zoneLocations
- setZonesPerX(int) - Method in class org.biomage.ArrayDesign.ZoneGroup
- Set method for zonesPerX
- setZonesPerY(int) - Method in class org.biomage.ArrayDesign.ZoneGroup
- Set method for zonesPerY
- spacingBetweenCols - Variable in class org.biomage.ArrayDesign.ZoneLayout
- Spacing between the columns.
- spacingBetweenRows - Variable in class org.biomage.ArrayDesign.ZoneLayout
- Spacing between the rows.
- spacingsBetweenZonesX - Variable in class org.biomage.ArrayDesign.ZoneGroup
- Spacing between zones, if applicable.
- spacingsBetweenZonesY - Variable in class org.biomage.ArrayDesign.ZoneGroup
- Spacing between zones, if applicable.
- species - Variable in class org.biomage.ArrayDesign.DesignElementGroup
- The organism from which the biosequences of this group are from.
- surfaceType - Variable in class org.biomage.ArrayDesign.PhysicalArrayDesign
- The type of surface from a controlled vocabulary that would include terms such as non-absorptive, absorptive, etc.
T
- technologyType - Variable in class org.biomage.ArrayDesign.FeatureGroup
- The technology type of this design.
- types - Variable in class org.biomage.ArrayDesign.DesignElementGroup
- The specific type of a feature, reporter, or composite.
U
- upperLeftX - Variable in class org.biomage.ArrayDesign.Zone
- Boundary vertical upper left position relative to (0,0).
- upperLeftY - Variable in class org.biomage.ArrayDesign.Zone
- Boundary horizontal upper left position relative to (0,0).
V
- version - Variable in class org.biomage.ArrayDesign.ArrayDesign
- The version of this design.
W
- writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.ArrayDesign
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.CompositeGroup
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.DesignElementGroup
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.FeatureGroup
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.ReporterGroup
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.Zone
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.ZoneGroup
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.ZoneLayout
- writeAssociations
- writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.ArrayDesign
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.CompositeGroup
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.DesignElementGroup
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.FeatureGroup
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.ReporterGroup
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.Zone
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.ZoneGroup
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.ZoneLayout
- writeAttributes
- writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.ArrayDesign
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.CompositeGroup
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.DesignElementGroup
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.FeatureGroup
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.ReporterGroup
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.Zone
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.ZoneGroup
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.ZoneLayout
- writeMAGEML
Z
- Zone - class org.biomage.ArrayDesign.Zone.
- Specifies the location of a zone on an array.
- Zone() - Constructor for class org.biomage.ArrayDesign.Zone
- Default constructor.
- Zone(Attributes) - Constructor for class org.biomage.ArrayDesign.Zone
- Attribute constructor.
- ZoneGroup - class org.biomage.ArrayDesign.ZoneGroup.
- Specifies a repeating area on an array.
- ZoneGroup() - Constructor for class org.biomage.ArrayDesign.ZoneGroup
- Default constructor.
- ZoneGroup(Attributes) - Constructor for class org.biomage.ArrayDesign.ZoneGroup
- Attribute constructor.
- ZoneLayout - class org.biomage.ArrayDesign.ZoneLayout.
- Specifies the layout of features in a rectangular grid.
- ZoneLayout() - Constructor for class org.biomage.ArrayDesign.ZoneLayout
- Default constructor.
- ZoneLayout(Attributes) - Constructor for class org.biomage.ArrayDesign.ZoneLayout
- Attribute constructor.
- zoneGroups - Variable in class org.biomage.ArrayDesign.PhysicalArrayDesign
- In the case where the array design is specified by one or more zones, allows specifying where those zones are located.
- zoneLayout - Variable in class org.biomage.ArrayDesign.ZoneGroup
- Describes the rectangular layout of features in the array design.
- zoneLocations - Variable in class org.biomage.ArrayDesign.ZoneGroup
- Describes the location of different zones within the array design.
- zonesPerX - Variable in class org.biomage.ArrayDesign.ZoneGroup
- The number of zones on the x-axis.
- zonesPerY - Variable in class org.biomage.ArrayDesign.ZoneGroup
- The number of zones on the y-axis.
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