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A
- addToBiologicalCharacteristics(BioSequence) - Method in class org.biomage.DesignElement.CompositeSequence
- Method to add BioSequence to BiologicalCharacteristics_list
- addToBiologicalCharacteristics(int, BioSequence) - Method in class org.biomage.DesignElement.CompositeSequence
- Method to add BioSequence at position to BiologicalCharacteristics_list
- addToCompositeCompositeMap_list(CompositeCompositeMap) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to add CompositeCompositeMap to CompositeCompositeMap_list
- addToCompositeCompositeMap_list(int, CompositeCompositeMap) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to add CompositeCompositeMap at position to CompositeCompositeMap_list
- addToCompositeCompositeMaps(CompositeCompositeMap) - Method in class org.biomage.DesignElement.CompositeSequence
- Method to add CompositeCompositeMap to CompositeCompositeMaps_list
- addToCompositeCompositeMaps(int, CompositeCompositeMap) - Method in class org.biomage.DesignElement.CompositeSequence
- Method to add CompositeCompositeMap at position to CompositeCompositeMaps_list
- addToCompositePositionSources(CompositePosition) - Method in class org.biomage.DesignElement.CompositeCompositeMap
- Method to add CompositePosition to CompositePositionSources_list
- addToCompositePositionSources(int, CompositePosition) - Method in class org.biomage.DesignElement.CompositeCompositeMap
- Method to add CompositePosition at position to CompositePositionSources_list
- addToCompositeSequence_list(CompositeSequence) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to add CompositeSequence to CompositeSequence_list
- addToCompositeSequence_list(int, CompositeSequence) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to add CompositeSequence at position to CompositeSequence_list
- addToControlFeatures(Feature) - Method in class org.biomage.DesignElement.Feature
- Method to add Feature to ControlFeatures_list
- addToControlFeatures(int, Feature) - Method in class org.biomage.DesignElement.Feature
- Method to add Feature at position to ControlFeatures_list
- addToControlledFeatures(Feature) - Method in class org.biomage.DesignElement.Feature
- Method to add Feature to ControlledFeatures_list
- addToControlledFeatures(int, Feature) - Method in class org.biomage.DesignElement.Feature
- Method to add Feature at position to ControlledFeatures_list
- addToDesignElement_list(DesignElement) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to add DesignElement to DesignElement_list
- addToDesignElement_list(int, DesignElement) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to add DesignElement at position to DesignElement_list
- addToFailTypes(OntologyEntry) - Method in class org.biomage.DesignElement.Reporter
- Method to add OntologyEntry to FailTypes_list
- addToFailTypes(int, OntologyEntry) - Method in class org.biomage.DesignElement.Reporter
- Method to add OntologyEntry at position to FailTypes_list
- addToFeatureInformationSources(FeatureInformation) - Method in class org.biomage.DesignElement.FeatureReporterMap
- Method to add FeatureInformation to FeatureInformationSources_list
- addToFeatureInformationSources(int, FeatureInformation) - Method in class org.biomage.DesignElement.FeatureReporterMap
- Method to add FeatureInformation at position to FeatureInformationSources_list
- addToFeatureReporterMap_list(FeatureReporterMap) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to add FeatureReporterMap to FeatureReporterMap_list
- addToFeatureReporterMap_list(int, FeatureReporterMap) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to add FeatureReporterMap at position to FeatureReporterMap_list
- addToFeatureReporterMaps(FeatureReporterMap) - Method in class org.biomage.DesignElement.Reporter
- Method to add FeatureReporterMap to FeatureReporterMaps_list
- addToFeatureReporterMaps(int, FeatureReporterMap) - Method in class org.biomage.DesignElement.Reporter
- Method to add FeatureReporterMap at position to FeatureReporterMaps_list
- addToImmobilizedCharacteristics(BioSequence) - Method in class org.biomage.DesignElement.Reporter
- Method to add BioSequence to ImmobilizedCharacteristics_list
- addToImmobilizedCharacteristics(int, BioSequence) - Method in class org.biomage.DesignElement.Reporter
- Method to add BioSequence at position to ImmobilizedCharacteristics_list
- addToMismatchInformation(MismatchInformation) - Method in class org.biomage.DesignElement.CompositePosition
- Method to add MismatchInformation to MismatchInformation_list
- addToMismatchInformation(int, MismatchInformation) - Method in class org.biomage.DesignElement.CompositePosition
- Method to add MismatchInformation at position to MismatchInformation_list
- addToMismatchInformation(MismatchInformation) - Method in class org.biomage.DesignElement.FeatureInformation
- Method to add MismatchInformation to MismatchInformation_list
- addToMismatchInformation(int, MismatchInformation) - Method in class org.biomage.DesignElement.FeatureInformation
- Method to add MismatchInformation at position to MismatchInformation_list
- addToMismatchInformation(MismatchInformation) - Method in class org.biomage.DesignElement.ReporterPosition
- Method to add MismatchInformation to MismatchInformation_list
- addToMismatchInformation(int, MismatchInformation) - Method in class org.biomage.DesignElement.ReporterPosition
- Method to add MismatchInformation at position to MismatchInformation_list
- addToReporterCompositeMap_list(ReporterCompositeMap) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to add ReporterCompositeMap to ReporterCompositeMap_list
- addToReporterCompositeMap_list(int, ReporterCompositeMap) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to add ReporterCompositeMap at position to ReporterCompositeMap_list
- addToReporterCompositeMaps(ReporterCompositeMap) - Method in class org.biomage.DesignElement.CompositeSequence
- Method to add ReporterCompositeMap to ReporterCompositeMaps_list
- addToReporterCompositeMaps(int, ReporterCompositeMap) - Method in class org.biomage.DesignElement.CompositeSequence
- Method to add ReporterCompositeMap at position to ReporterCompositeMaps_list
- addToReporterPositionSources(ReporterPosition) - Method in class org.biomage.DesignElement.ReporterCompositeMap
- Method to add ReporterPosition to ReporterPositionSources_list
- addToReporterPositionSources(int, ReporterPosition) - Method in class org.biomage.DesignElement.ReporterCompositeMap
- Method to add ReporterPosition at position to ReporterPositionSources_list
- addToReporter_list(Reporter) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to add Reporter to Reporter_list
- addToReporter_list(int, Reporter) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to add Reporter at position to Reporter_list
B
- biologicalCharacteristics - Variable in class org.biomage.DesignElement.CompositeSequence
- The annotation on the BioSequence this CompositeSequence represents.
C
- CompositeCompositeMap - class org.biomage.DesignElement.CompositeCompositeMap.
- A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence.
- CompositeCompositeMap() - Constructor for class org.biomage.DesignElement.CompositeCompositeMap
- Default constructor.
- CompositeCompositeMap(Attributes) - Constructor for class org.biomage.DesignElement.CompositeCompositeMap
- Attribute constructor.
- CompositePosition - class org.biomage.DesignElement.CompositePosition.
- The location in the compositeSequence target's sequence to which a source compositeSequence maps.
- CompositePosition() - Constructor for class org.biomage.DesignElement.CompositePosition
- Default constructor.
- CompositePosition(Attributes) - Constructor for class org.biomage.DesignElement.CompositePosition
- Attribute constructor.
- CompositeSequence - class org.biomage.DesignElement.CompositeSequence.
- A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.
- CompositeSequence() - Constructor for class org.biomage.DesignElement.CompositeSequence
- Default constructor.
- CompositeSequence(Attributes) - Constructor for class org.biomage.DesignElement.CompositeSequence
- Attribute constructor.
- column - Variable in class org.biomage.DesignElement.FeatureLocation
- column position in the Zone.
- composite - Variable in class org.biomage.DesignElement.CompositePosition
- A source CompositeSequence that is part of a target CompositeSequence
- compositeCompositeMap_list - Variable in class org.biomage.DesignElement.DesignElement_package
- A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence.
- compositeCompositeMaps - Variable in class org.biomage.DesignElement.CompositeSequence
- A map to the compositeSequences that compose this CompositeSequence.
- compositePositionSources - Variable in class org.biomage.DesignElement.CompositeCompositeMap
- Association to the CompositeSequences that compose this CompositeSequence and where those CompositeSequences occur.
- compositeSequence - Variable in class org.biomage.DesignElement.CompositeCompositeMap
- A map to the compositeSequences that compose this CompositeSequence.
- compositeSequence - Variable in class org.biomage.DesignElement.ReporterCompositeMap
- A map to the reporters that compose this CompositeSequence.
- compositeSequence_list - Variable in class org.biomage.DesignElement.DesignElement_package
- A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.
- controlFeatures - Variable in class org.biomage.DesignElement.Feature
- Associates features with their control features.
- controlType - Variable in class org.biomage.DesignElement.DesignElement
- If the design element represents a control, the type of control it is (normalization, deletion, negative, positive, etc.)
- controlledFeatures - Variable in class org.biomage.DesignElement.Feature
- Associates features with their control features.
D
- DesignElement - class org.biomage.DesignElement.DesignElement.
- An element of an array.
- DesignElement() - Constructor for class org.biomage.DesignElement.DesignElement
- Default constructor.
- DesignElement(Attributes) - Constructor for class org.biomage.DesignElement.DesignElement
- Attribute constructor.
- DesignElement_package - class org.biomage.DesignElement.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.
- DesignElement_package() - Constructor for class org.biomage.DesignElement.DesignElement_package
- Default constructor.
- DesignElement_package(Attributes) - Constructor for class org.biomage.DesignElement.DesignElement_package
- Attribute constructor.
- DesignElement_package.CompositeCompositeMap_list - class org.biomage.DesignElement.DesignElement_package.CompositeCompositeMap_list.
- Inner list class for holding multiple entries for attribute compositeCompositeMap_list.
- DesignElement_package.CompositeCompositeMap_list() - Constructor for class org.biomage.DesignElement.DesignElement_package.CompositeCompositeMap_list
- DesignElement_package.CompositeSequence_list - class org.biomage.DesignElement.DesignElement_package.CompositeSequence_list.
- Inner list class for holding multiple entries for attribute compositeSequence_list.
- DesignElement_package.CompositeSequence_list() - Constructor for class org.biomage.DesignElement.DesignElement_package.CompositeSequence_list
- DesignElement_package.DesignElement_list - class org.biomage.DesignElement.DesignElement_package.DesignElement_list.
- Inner list class for holding multiple entries for attribute designElement_list.
- DesignElement_package.DesignElement_list() - Constructor for class org.biomage.DesignElement.DesignElement_package.DesignElement_list
- DesignElement_package.FeatureReporterMap_list - class org.biomage.DesignElement.DesignElement_package.FeatureReporterMap_list.
- Inner list class for holding multiple entries for attribute featureReporterMap_list.
- DesignElement_package.FeatureReporterMap_list() - Constructor for class org.biomage.DesignElement.DesignElement_package.FeatureReporterMap_list
- DesignElement_package.ReporterCompositeMap_list - class org.biomage.DesignElement.DesignElement_package.ReporterCompositeMap_list.
- Inner list class for holding multiple entries for attribute reporterCompositeMap_list.
- DesignElement_package.ReporterCompositeMap_list() - Constructor for class org.biomage.DesignElement.DesignElement_package.ReporterCompositeMap_list
- DesignElement_package.Reporter_list - class org.biomage.DesignElement.DesignElement_package.Reporter_list.
- Inner list class for holding multiple entries for attribute reporter_list.
- DesignElement_package.Reporter_list() - Constructor for class org.biomage.DesignElement.DesignElement_package.Reporter_list
- designElement_list - Variable in class org.biomage.DesignElement.DesignElement_package
- An element of an array.
- distanceUnit - Variable in class org.biomage.DesignElement.Position
- The units of the x, y positions.
F
- Feature - class org.biomage.DesignElement.Feature.
- An intended position on an array.
- Feature() - Constructor for class org.biomage.DesignElement.Feature
- Default constructor.
- Feature(Attributes) - Constructor for class org.biomage.DesignElement.Feature
- Attribute constructor.
- FeatureInformation - class org.biomage.DesignElement.FeatureInformation.
- As part of the map information, allows the association of one or more differences in the BioMaterial on a feature from the BioMaterial of the Reporter.
- FeatureInformation() - Constructor for class org.biomage.DesignElement.FeatureInformation
- Default constructor.
- FeatureInformation(Attributes) - Constructor for class org.biomage.DesignElement.FeatureInformation
- Attribute constructor.
- FeatureLocation - class org.biomage.DesignElement.FeatureLocation.
- Specifies where a feature is located relative to a grid.
- FeatureLocation() - Constructor for class org.biomage.DesignElement.FeatureLocation
- Default constructor.
- FeatureLocation(Attributes) - Constructor for class org.biomage.DesignElement.FeatureLocation
- Attribute constructor.
- FeatureReporterMap - class org.biomage.DesignElement.FeatureReporterMap.
- A FeatureReporterMap is the description of how source features are transformed into a target reporter.
- FeatureReporterMap() - Constructor for class org.biomage.DesignElement.FeatureReporterMap
- Default constructor.
- FeatureReporterMap(Attributes) - Constructor for class org.biomage.DesignElement.FeatureReporterMap
- Attribute constructor.
- failTypes - Variable in class org.biomage.DesignElement.Reporter
- 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.)
- feature - Variable in class org.biomage.DesignElement.FeatureInformation
- The feature the FeatureInformation is supplying information for.
- featureGroup - Variable in class org.biomage.DesignElement.Feature
- The features that belong to this group.
- featureInformationSources - Variable in class org.biomage.DesignElement.FeatureReporterMap
- Typically, the features on an array that are manufactured with this reporter's BioSequence.
- featureLocation - Variable in class org.biomage.DesignElement.Feature
- Location of this feature relative to a grid.
- featureReporterMap_list - Variable in class org.biomage.DesignElement.DesignElement_package
- A FeatureReporterMap is the description of how source features are transformed into a target reporter.
- featureReporterMaps - Variable in class org.biomage.DesignElement.Reporter
- Associates features with their reporter.
G
- getBiologicalCharacteristics() - Method in class org.biomage.DesignElement.CompositeSequence
- Get method for biologicalCharacteristics
- getColumn() - Method in class org.biomage.DesignElement.FeatureLocation
- Get method for column
- getComposite() - Method in class org.biomage.DesignElement.CompositePosition
- Get method for composite
- getCompositeCompositeMap_list() - Method in class org.biomage.DesignElement.DesignElement_package
- Get method for compositeCompositeMap_list
- getCompositeCompositeMaps() - Method in class org.biomage.DesignElement.CompositeSequence
- Get method for compositeCompositeMaps
- getCompositePositionSources() - Method in class org.biomage.DesignElement.CompositeCompositeMap
- Get method for compositePositionSources
- getCompositeSequence() - Method in class org.biomage.DesignElement.CompositeCompositeMap
- Get method for compositeSequence
- getCompositeSequence() - Method in class org.biomage.DesignElement.ReporterCompositeMap
- Get method for compositeSequence
- getCompositeSequence_list() - Method in class org.biomage.DesignElement.DesignElement_package
- Get method for compositeSequence_list
- getControlFeatures() - Method in class org.biomage.DesignElement.Feature
- Get method for controlFeatures
- getControlType() - Method in class org.biomage.DesignElement.DesignElement
- Get method for controlType
- getControlledFeatures() - Method in class org.biomage.DesignElement.Feature
- Get method for controlledFeatures
- getDesignElement_list() - Method in class org.biomage.DesignElement.DesignElement_package
- Get method for designElement_list
- getDistanceUnit() - Method in class org.biomage.DesignElement.Position
- Get method for distanceUnit
- getFailTypes() - Method in class org.biomage.DesignElement.Reporter
- Get method for failTypes
- getFeature() - Method in class org.biomage.DesignElement.FeatureInformation
- Get method for feature
- getFeatureGroup() - Method in class org.biomage.DesignElement.Feature
- Get method for featureGroup
- getFeatureInformationSources() - Method in class org.biomage.DesignElement.FeatureReporterMap
- Get method for featureInformationSources
- getFeatureLocation() - Method in class org.biomage.DesignElement.Feature
- Get method for featureLocation
- getFeatureReporterMap_list() - Method in class org.biomage.DesignElement.DesignElement_package
- Get method for featureReporterMap_list
- getFeatureReporterMaps() - Method in class org.biomage.DesignElement.Reporter
- Get method for featureReporterMaps
- getFromBiologicalCharacteristics(int) - Method in class org.biomage.DesignElement.CompositeSequence
- Method to get BioSequence from BiologicalCharacteristics_list
- getFromCompositeCompositeMap_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to get CompositeCompositeMap from CompositeCompositeMap_list
- getFromCompositeCompositeMaps(int) - Method in class org.biomage.DesignElement.CompositeSequence
- Method to get CompositeCompositeMap from CompositeCompositeMaps_list
- getFromCompositePositionSources(int) - Method in class org.biomage.DesignElement.CompositeCompositeMap
- Method to get CompositePosition from CompositePositionSources_list
- getFromCompositeSequence_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to get CompositeSequence from CompositeSequence_list
- getFromControlFeatures(int) - Method in class org.biomage.DesignElement.Feature
- Method to get Feature from ControlFeatures_list
- getFromControlledFeatures(int) - Method in class org.biomage.DesignElement.Feature
- Method to get Feature from ControlledFeatures_list
- getFromDesignElement_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to get DesignElement from DesignElement_list
- getFromFailTypes(int) - Method in class org.biomage.DesignElement.Reporter
- Method to get OntologyEntry from FailTypes_list
- getFromFeatureInformationSources(int) - Method in class org.biomage.DesignElement.FeatureReporterMap
- Method to get FeatureInformation from FeatureInformationSources_list
- getFromFeatureReporterMap_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to get FeatureReporterMap from FeatureReporterMap_list
- getFromFeatureReporterMaps(int) - Method in class org.biomage.DesignElement.Reporter
- Method to get FeatureReporterMap from FeatureReporterMaps_list
- getFromImmobilizedCharacteristics(int) - Method in class org.biomage.DesignElement.Reporter
- Method to get BioSequence from ImmobilizedCharacteristics_list
- getFromMismatchInformation(int) - Method in class org.biomage.DesignElement.CompositePosition
- Method to get MismatchInformation from MismatchInformation_list
- getFromMismatchInformation(int) - Method in class org.biomage.DesignElement.FeatureInformation
- Method to get MismatchInformation from MismatchInformation_list
- getFromMismatchInformation(int) - Method in class org.biomage.DesignElement.ReporterPosition
- Method to get MismatchInformation from MismatchInformation_list
- getFromReporterCompositeMap_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to get ReporterCompositeMap from ReporterCompositeMap_list
- getFromReporterCompositeMaps(int) - Method in class org.biomage.DesignElement.CompositeSequence
- Method to get ReporterCompositeMap from ReporterCompositeMaps_list
- getFromReporterPositionSources(int) - Method in class org.biomage.DesignElement.ReporterCompositeMap
- Method to get ReporterPosition from ReporterPositionSources_list
- getFromReporter_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to get Reporter from Reporter_list
- getImmobilizedCharacteristics() - Method in class org.biomage.DesignElement.Reporter
- Get method for immobilizedCharacteristics
- getMismatchInformation() - Method in class org.biomage.DesignElement.CompositePosition
- Get method for mismatchInformation
- getMismatchInformation() - Method in class org.biomage.DesignElement.FeatureInformation
- Get method for mismatchInformation
- getMismatchInformation() - Method in class org.biomage.DesignElement.ReporterPosition
- Get method for mismatchInformation
- getNewSequence() - Method in class org.biomage.DesignElement.MismatchInformation
- Get method for newSequence
- getPosition() - Method in class org.biomage.DesignElement.Feature
- Get method for position
- getReplacedLength() - Method in class org.biomage.DesignElement.MismatchInformation
- Get method for replacedLength
- getReporter() - Method in class org.biomage.DesignElement.FeatureReporterMap
- Get method for reporter
- getReporter() - Method in class org.biomage.DesignElement.ReporterPosition
- Get method for reporter
- getReporterCompositeMap_list() - Method in class org.biomage.DesignElement.DesignElement_package
- Get method for reporterCompositeMap_list
- getReporterCompositeMaps() - Method in class org.biomage.DesignElement.CompositeSequence
- Get method for reporterCompositeMaps
- getReporterPositionSources() - Method in class org.biomage.DesignElement.ReporterCompositeMap
- Get method for reporterPositionSources
- getReporter_list() - Method in class org.biomage.DesignElement.DesignElement_package
- Get method for reporter_list
- getRow() - Method in class org.biomage.DesignElement.FeatureLocation
- Get method for row
- getStartCoord() - Method in class org.biomage.DesignElement.MismatchInformation
- Get method for startCoord
- getWarningType() - Method in class org.biomage.DesignElement.Reporter
- Get method for warningType
- getX() - Method in class org.biomage.DesignElement.Position
- Get method for x
- getY() - Method in class org.biomage.DesignElement.Position
- Get method for y
- getZone() - Method in class org.biomage.DesignElement.Feature
- Get method for zone
I
- immobilizedCharacteristics - Variable in class org.biomage.DesignElement.Reporter
- The sequence annotation on the BioMaterial this reporter represents.
M
- MismatchInformation - class org.biomage.DesignElement.MismatchInformation.
- Describes how a reporter varies from its ReporterCharacteristics sequence(s) or how a Feature varies from its Reporter sequence.
- MismatchInformation() - Constructor for class org.biomage.DesignElement.MismatchInformation
- Default constructor.
- MismatchInformation(Attributes) - Constructor for class org.biomage.DesignElement.MismatchInformation
- Attribute constructor.
- mismatchInformation - Variable in class org.biomage.DesignElement.CompositePosition
- Differences in how the contained compositeSequence matches its target compositeSequence's sequence.
- mismatchInformation - Variable in class org.biomage.DesignElement.FeatureInformation
- 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.
- mismatchInformation - Variable in class org.biomage.DesignElement.ReporterPosition
- Differences in how the reporter matches its compositeSequence's sequence.
N
- newSequence - Variable in class org.biomage.DesignElement.MismatchInformation
- The sequence that replaces the specified sequence starting at start_coord.
O
- org.biomage.DesignElement - package org.biomage.DesignElement
P
- Position - class org.biomage.DesignElement.Position.
- Specifies a position on an array.
- Position() - Constructor for class org.biomage.DesignElement.Position
- Default constructor.
- Position(Attributes) - Constructor for class org.biomage.DesignElement.Position
- Attribute constructor.
- position - Variable in class org.biomage.DesignElement.Feature
- The position of the feature on the array, relative to the top, left corner.
R
- Reporter - class org.biomage.DesignElement.Reporter.
- A Design Element that represents some biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.
- Reporter() - Constructor for class org.biomage.DesignElement.Reporter
- Default constructor.
- Reporter(Attributes) - Constructor for class org.biomage.DesignElement.Reporter
- Attribute constructor.
- ReporterCompositeMap - class org.biomage.DesignElement.ReporterCompositeMap.
- A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences.
- ReporterCompositeMap() - Constructor for class org.biomage.DesignElement.ReporterCompositeMap
- Default constructor.
- ReporterCompositeMap(Attributes) - Constructor for class org.biomage.DesignElement.ReporterCompositeMap
- Attribute constructor.
- ReporterPosition - class org.biomage.DesignElement.ReporterPosition.
- The location in the composite target's sequence to which a source reporter maps.
- ReporterPosition() - Constructor for class org.biomage.DesignElement.ReporterPosition
- Default constructor.
- ReporterPosition(Attributes) - Constructor for class org.biomage.DesignElement.ReporterPosition
- Attribute constructor.
- removeElementAtFromBiologicalCharacteristics(int) - Method in class org.biomage.DesignElement.CompositeSequence
- Method to remove by position from BiologicalCharacteristics_list
- removeElementAtFromCompositeCompositeMap_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to remove by position from CompositeCompositeMap_list
- removeElementAtFromCompositeCompositeMaps(int) - Method in class org.biomage.DesignElement.CompositeSequence
- Method to remove by position from CompositeCompositeMaps_list
- removeElementAtFromCompositePositionSources(int) - Method in class org.biomage.DesignElement.CompositeCompositeMap
- Method to remove by position from CompositePositionSources_list
- removeElementAtFromCompositeSequence_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to remove by position from CompositeSequence_list
- removeElementAtFromControlFeatures(int) - Method in class org.biomage.DesignElement.Feature
- Method to remove by position from ControlFeatures_list
- removeElementAtFromControlledFeatures(int) - Method in class org.biomage.DesignElement.Feature
- Method to remove by position from ControlledFeatures_list
- removeElementAtFromDesignElement_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to remove by position from DesignElement_list
- removeElementAtFromFailTypes(int) - Method in class org.biomage.DesignElement.Reporter
- Method to remove by position from FailTypes_list
- removeElementAtFromFeatureInformationSources(int) - Method in class org.biomage.DesignElement.FeatureReporterMap
- Method to remove by position from FeatureInformationSources_list
- removeElementAtFromFeatureReporterMap_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to remove by position from FeatureReporterMap_list
- removeElementAtFromFeatureReporterMaps(int) - Method in class org.biomage.DesignElement.Reporter
- Method to remove by position from FeatureReporterMaps_list
- removeElementAtFromImmobilizedCharacteristics(int) - Method in class org.biomage.DesignElement.Reporter
- Method to remove by position from ImmobilizedCharacteristics_list
- removeElementAtFromMismatchInformation(int) - Method in class org.biomage.DesignElement.CompositePosition
- Method to remove by position from MismatchInformation_list
- removeElementAtFromMismatchInformation(int) - Method in class org.biomage.DesignElement.FeatureInformation
- Method to remove by position from MismatchInformation_list
- removeElementAtFromMismatchInformation(int) - Method in class org.biomage.DesignElement.ReporterPosition
- Method to remove by position from MismatchInformation_list
- removeElementAtFromReporterCompositeMap_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to remove by position from ReporterCompositeMap_list
- removeElementAtFromReporterCompositeMaps(int) - Method in class org.biomage.DesignElement.CompositeSequence
- Method to remove by position from ReporterCompositeMaps_list
- removeElementAtFromReporterPositionSources(int) - Method in class org.biomage.DesignElement.ReporterCompositeMap
- Method to remove by position from ReporterPositionSources_list
- removeElementAtFromReporter_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to remove by position from Reporter_list
- removeFromBiologicalCharacteristics(BioSequence) - Method in class org.biomage.DesignElement.CompositeSequence
- Method to remove first BioSequence from BiologicalCharacteristics_list
- removeFromCompositeCompositeMap_list(CompositeCompositeMap) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to remove first CompositeCompositeMap from CompositeCompositeMap_list
- removeFromCompositeCompositeMaps(CompositeCompositeMap) - Method in class org.biomage.DesignElement.CompositeSequence
- Method to remove first CompositeCompositeMap from CompositeCompositeMaps_list
- removeFromCompositePositionSources(CompositePosition) - Method in class org.biomage.DesignElement.CompositeCompositeMap
- Method to remove first CompositePosition from CompositePositionSources_list
- removeFromCompositeSequence_list(CompositeSequence) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to remove first CompositeSequence from CompositeSequence_list
- removeFromControlFeatures(Feature) - Method in class org.biomage.DesignElement.Feature
- Method to remove first Feature from ControlFeatures_list
- removeFromControlledFeatures(Feature) - Method in class org.biomage.DesignElement.Feature
- Method to remove first Feature from ControlledFeatures_list
- removeFromDesignElement_list(DesignElement) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to remove first DesignElement from DesignElement_list
- removeFromFailTypes(OntologyEntry) - Method in class org.biomage.DesignElement.Reporter
- Method to remove first OntologyEntry from FailTypes_list
- removeFromFeatureInformationSources(FeatureInformation) - Method in class org.biomage.DesignElement.FeatureReporterMap
- Method to remove first FeatureInformation from FeatureInformationSources_list
- removeFromFeatureReporterMap_list(FeatureReporterMap) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to remove first FeatureReporterMap from FeatureReporterMap_list
- removeFromFeatureReporterMaps(FeatureReporterMap) - Method in class org.biomage.DesignElement.Reporter
- Method to remove first FeatureReporterMap from FeatureReporterMaps_list
- removeFromImmobilizedCharacteristics(BioSequence) - Method in class org.biomage.DesignElement.Reporter
- Method to remove first BioSequence from ImmobilizedCharacteristics_list
- removeFromMismatchInformation(MismatchInformation) - Method in class org.biomage.DesignElement.CompositePosition
- Method to remove first MismatchInformation from MismatchInformation_list
- removeFromMismatchInformation(MismatchInformation) - Method in class org.biomage.DesignElement.FeatureInformation
- Method to remove first MismatchInformation from MismatchInformation_list
- removeFromMismatchInformation(MismatchInformation) - Method in class org.biomage.DesignElement.ReporterPosition
- Method to remove first MismatchInformation from MismatchInformation_list
- removeFromReporterCompositeMap_list(ReporterCompositeMap) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to remove first ReporterCompositeMap from ReporterCompositeMap_list
- removeFromReporterCompositeMaps(ReporterCompositeMap) - Method in class org.biomage.DesignElement.CompositeSequence
- Method to remove first ReporterCompositeMap from ReporterCompositeMaps_list
- removeFromReporterPositionSources(ReporterPosition) - Method in class org.biomage.DesignElement.ReporterCompositeMap
- Method to remove first ReporterPosition from ReporterPositionSources_list
- removeFromReporter_list(Reporter) - Method in class org.biomage.DesignElement.DesignElement_package
- Method to remove first Reporter from Reporter_list
- replacedLength - Variable in class org.biomage.DesignElement.MismatchInformation
- Length of the original sequence that is replaced.
- reporter - Variable in class org.biomage.DesignElement.FeatureReporterMap
- Associates features with their reporter.
- reporter - Variable in class org.biomage.DesignElement.ReporterPosition
- A reporter that comprises part of a CompositeSequence.
- reporterCompositeMap_list - Variable in class org.biomage.DesignElement.DesignElement_package
- A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences.
- reporterCompositeMaps - Variable in class org.biomage.DesignElement.CompositeSequence
- A map to the reporters that compose this CompositeSequence.
- reporterPositionSources - Variable in class org.biomage.DesignElement.ReporterCompositeMap
- Association to the reporters that compose this CompositeSequence and where those reporters occur.
- reporter_list - Variable in class org.biomage.DesignElement.DesignElement_package
- A Design Element that represents some biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.
- row - Variable in class org.biomage.DesignElement.FeatureLocation
- row position in the Zone
S
- setBiologicalCharacteristics(HasBiologicalCharacteristics.BiologicalCharacteristics_list) - Method in class org.biomage.DesignElement.CompositeSequence
- Set method for biologicalCharacteristics
- setColumn(int) - Method in class org.biomage.DesignElement.FeatureLocation
- Set method for column
- setComposite(CompositeSequence) - Method in class org.biomage.DesignElement.CompositePosition
- Set method for composite
- setCompositeCompositeMap_list(DesignElement_package.CompositeCompositeMap_list) - Method in class org.biomage.DesignElement.DesignElement_package
- Set method for compositeCompositeMap_list
- setCompositeCompositeMaps(HasCompositeCompositeMaps.CompositeCompositeMaps_list) - Method in class org.biomage.DesignElement.CompositeSequence
- Set method for compositeCompositeMaps
- setCompositePositionSources(HasCompositePositionSources.CompositePositionSources_list) - Method in class org.biomage.DesignElement.CompositeCompositeMap
- Set method for compositePositionSources
- setCompositeSequence(CompositeSequence) - Method in class org.biomage.DesignElement.CompositeCompositeMap
- Set method for compositeSequence
- setCompositeSequence(CompositeSequence) - Method in class org.biomage.DesignElement.ReporterCompositeMap
- Set method for compositeSequence
- setCompositeSequence_list(DesignElement_package.CompositeSequence_list) - Method in class org.biomage.DesignElement.DesignElement_package
- Set method for compositeSequence_list
- setControlFeatures(HasControlFeatures.ControlFeatures_list) - Method in class org.biomage.DesignElement.Feature
- Set method for controlFeatures
- setControlType(OntologyEntry) - Method in class org.biomage.DesignElement.DesignElement
- Set method for controlType
- setControlledFeatures(HasControlledFeatures.ControlledFeatures_list) - Method in class org.biomage.DesignElement.Feature
- Set method for controlledFeatures
- setDesignElement_list(DesignElement_package.DesignElement_list) - Method in class org.biomage.DesignElement.DesignElement_package
- Set method for designElement_list
- setDistanceUnit(DistanceUnit) - Method in class org.biomage.DesignElement.Position
- Set method for distanceUnit
- setFailTypes(HasFailTypes.FailTypes_list) - Method in class org.biomage.DesignElement.Reporter
- Set method for failTypes
- setFeature(Feature) - Method in class org.biomage.DesignElement.FeatureInformation
- Set method for feature
- setFeatureGroup(FeatureGroup) - Method in class org.biomage.DesignElement.Feature
- Set method for featureGroup
- setFeatureInformationSources(HasFeatureInformationSources.FeatureInformationSources_list) - Method in class org.biomage.DesignElement.FeatureReporterMap
- Set method for featureInformationSources
- setFeatureLocation(FeatureLocation) - Method in class org.biomage.DesignElement.Feature
- Set method for featureLocation
- setFeatureReporterMap_list(DesignElement_package.FeatureReporterMap_list) - Method in class org.biomage.DesignElement.DesignElement_package
- Set method for featureReporterMap_list
- setFeatureReporterMaps(HasFeatureReporterMaps.FeatureReporterMaps_list) - Method in class org.biomage.DesignElement.Reporter
- Set method for featureReporterMaps
- setImmobilizedCharacteristics(HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list) - Method in class org.biomage.DesignElement.Reporter
- Set method for immobilizedCharacteristics
- setMismatchInformation(HasMismatchInformation.MismatchInformation_list) - Method in class org.biomage.DesignElement.CompositePosition
- Set method for mismatchInformation
- setMismatchInformation(HasMismatchInformation.MismatchInformation_list) - Method in class org.biomage.DesignElement.FeatureInformation
- Set method for mismatchInformation
- setMismatchInformation(HasMismatchInformation.MismatchInformation_list) - Method in class org.biomage.DesignElement.ReporterPosition
- Set method for mismatchInformation
- setNewSequence(String) - Method in class org.biomage.DesignElement.MismatchInformation
- Set method for newSequence
- setPosition(Position) - Method in class org.biomage.DesignElement.Feature
- Set method for position
- setReplacedLength(int) - Method in class org.biomage.DesignElement.MismatchInformation
- Set method for replacedLength
- setReporter(Reporter) - Method in class org.biomage.DesignElement.FeatureReporterMap
- Set method for reporter
- setReporter(Reporter) - Method in class org.biomage.DesignElement.ReporterPosition
- Set method for reporter
- setReporterCompositeMap_list(DesignElement_package.ReporterCompositeMap_list) - Method in class org.biomage.DesignElement.DesignElement_package
- Set method for reporterCompositeMap_list
- setReporterCompositeMaps(HasReporterCompositeMaps.ReporterCompositeMaps_list) - Method in class org.biomage.DesignElement.CompositeSequence
- Set method for reporterCompositeMaps
- setReporterPositionSources(HasReporterPositionSources.ReporterPositionSources_list) - Method in class org.biomage.DesignElement.ReporterCompositeMap
- Set method for reporterPositionSources
- setReporter_list(DesignElement_package.Reporter_list) - Method in class org.biomage.DesignElement.DesignElement_package
- Set method for reporter_list
- setRow(int) - Method in class org.biomage.DesignElement.FeatureLocation
- Set method for row
- setStartCoord(int) - Method in class org.biomage.DesignElement.MismatchInformation
- Set method for startCoord
- setWarningType(OntologyEntry) - Method in class org.biomage.DesignElement.Reporter
- Set method for warningType
- setX(float) - Method in class org.biomage.DesignElement.Position
- Set method for x
- setY(float) - Method in class org.biomage.DesignElement.Position
- Set method for y
- setZone(Zone) - Method in class org.biomage.DesignElement.Feature
- Set method for zone
- startCoord - Variable in class org.biomage.DesignElement.MismatchInformation
- Offset into the sequence that the mismatch occurs.
W
- warningType - Variable in class org.biomage.DesignElement.Reporter
- Similar to failType but indicates a warning rather than a failure.
- writeAssociations(Writer) - Method in class org.biomage.DesignElement.CompositeCompositeMap
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.DesignElement.CompositePosition
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.DesignElement.CompositeSequence
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.DesignElement.DesignElement
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.DesignElement.DesignElement_package
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.DesignElement.Feature
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.DesignElement.FeatureInformation
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.DesignElement.FeatureLocation
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.DesignElement.FeatureReporterMap
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.DesignElement.MismatchInformation
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.DesignElement.Position
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.DesignElement.Reporter
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.DesignElement.ReporterCompositeMap
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.DesignElement.ReporterPosition
- writeAssociations
- writeAttributes(Writer) - Method in class org.biomage.DesignElement.CompositeCompositeMap
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.DesignElement.CompositePosition
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.DesignElement.CompositeSequence
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.DesignElement.DesignElement
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.DesignElement.DesignElement_package
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.DesignElement.Feature
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.DesignElement.FeatureInformation
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.DesignElement.FeatureLocation
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.DesignElement.FeatureReporterMap
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.DesignElement.MismatchInformation
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.DesignElement.Position
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.DesignElement.Reporter
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.DesignElement.ReporterCompositeMap
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.DesignElement.ReporterPosition
- writeAttributes
- writeMAGEML(Writer) - Method in class org.biomage.DesignElement.CompositeCompositeMap
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.DesignElement.CompositePosition
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.DesignElement.CompositeSequence
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.DesignElement.DesignElement
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.DesignElement.DesignElement_package
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.DesignElement.Feature
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.DesignElement.FeatureInformation
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.DesignElement.FeatureLocation
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.DesignElement.FeatureReporterMap
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.DesignElement.MismatchInformation
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.DesignElement.Position
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.DesignElement.Reporter
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.DesignElement.ReporterCompositeMap
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.DesignElement.ReporterPosition
- writeMAGEML
X
- x - Variable in class org.biomage.DesignElement.Position
- The horizontal distance from the upper left corner of the array.
Y
- y - Variable in class org.biomage.DesignElement.Position
- The vertical distance from the upper left corner of the array.
Z
- zone - Variable in class org.biomage.DesignElement.Feature
- A reference to the zone this feature is in.
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