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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.

A B C D F G I M N O P R S W X Y Z