A B C D E F G H I J L M N O P R S T V W X Z

A

AngleBias - class org.cybertory.MSS.AngleBias.
Provides a bias in the calculation of radius in a particular direction for vertices of a randomly generated polygon.
AngleBias(float, float, float) - Constructor for class org.cybertory.MSS.AngleBias
 
ArgsExternalDataFactory - class org.cybertory.MSS.ArgsExternalDataFactory.
An implementation of ExternalDataFactory that gets its data from the java command line.
ArgsExternalDataFactory(HashMap, String) - Constructor for class org.cybertory.MSS.ArgsExternalDataFactory
 
accept(File) - Method in class org.cybertory.MSS.FileExtensionFilter
 
accept(File) - Method in class org.cybertory.MSS.PatternFileFilter
 
accept(File) - Method in class org.cybertory.MSS.XMLChooser.XMLFilter
 
actionPerformed(ActionEvent) - Method in class org.cybertory.MSS.ExternalDataPanel
 
actionPerformed(ActionEvent) - Method in class org.cybertory.MSS.MSSGUI
 
addAngleBias(AngleBias) - Method in class org.cybertory.MSS.PolygonFactory
 
addExternalDataFactory(ExternalDataFactory) - Method in class org.cybertory.MSS.ImagesRequest
 
addSchemaCommonParams(Element, String) - Static method in class org.cybertory.MSS.X_CommonScanSaveParams
 
addZonesGridLocations(Point[]) - Method in class org.cybertory.MSS.GridMaLayout
 
allowBackwardRef() - Method in class org.cybertory.MSS.XMLHandler
Allow multiple elements for this data type ?
allowBackwardRef() - Method in class org.cybertory.MSS.XMLHandlerArray
Allow data in the "defs" section, with later backward references ?
allowBackwardRef() - Method in class org.cybertory.MSS.XMLHandlerAtomic
Allow multiple elements for this data type ?
allowBackwardRef() - Method in class org.cybertory.MSS.XMLHandlerStd
 
allowBackwardRef() - Method in class org.cybertory.MSS.XMLHandlerSuper
 
allowMultiple() - Method in class org.cybertory.MSS.XMLHandler
 
allowMultiple() - Method in class org.cybertory.MSS.XMLHandlerArray
 
allowMultiple() - Method in class org.cybertory.MSS.XMLHandlerAtomic
 
allowMultiple() - Method in class org.cybertory.MSS.XMLHandlerStd
Allow data in the "defs" section, with later backward references ?
allowMultiple() - Method in class org.cybertory.MSS.XMLHandlerSuper
 
alternateElement(String, boolean) - Static method in class org.cybertory.MSS.XMLHandler
Create the element for either "ext_*" or "ref_*" with given parse label.

B

BooleanArrayer - class org.cybertory.MSS.BooleanArrayer.
Class creates a 'boolean' array from an array of type Object (that is actually filled with Boolean).
BooleanArrayer() - Constructor for class org.cybertory.MSS.BooleanArrayer
 
ByteArrayer - class org.cybertory.MSS.ByteArrayer.
Class creates a 'byte' array from an array of type Object (that is actually filled with Byte).
ByteArrayer() - Constructor for class org.cybertory.MSS.ByteArrayer
 

C

ChooserPanel - class org.cybertory.MSS.ChooserPanel.
Used in the GUI interface for the MSS.
ChooserPanel(String, ListItem[], ListSelectionListener) - Constructor for class org.cybertory.MSS.ChooserPanel
 
CircleFeatureShapeFactory - class org.cybertory.MSS.CircleFeatureShapeFactory.
A flavor of FeatureShapeFactory that produces circular features, including support for the variability of location, size, and shape.
CircleFeatureShapeFactory() - Constructor for class org.cybertory.MSS.CircleFeatureShapeFactory
Constructor; variability can be added by CircleFeatureShapeFactory.setVariability(java.util.Random, float, float, int, boolean, org.cybertory.MSS.AngleBias[]).
CommonScanSaveParams - class org.cybertory.MSS.CommonScanSaveParams.
A class to contain parameters that are common to implementations of ScanSaveType.
CommonScanSaveParams(String, String, File) - Constructor for class org.cybertory.MSS.CommonScanSaveParams
 
CommonScanSaveParams(String, String) - Constructor for class org.cybertory.MSS.CommonScanSaveParams
 
Constant2OpDesc - class org.cybertory.MSS.Constant2OpDesc.
An alternate implementation of functionality in the 'constant' operation.
Constant2OpDesc() - Constructor for class org.cybertory.MSS.Constant2OpDesc
 
Constant3OpDesc - class org.cybertory.MSS.Constant3OpDesc.
An alternate implementation of functionality in the 'constant' operation.
Constant3OpDesc() - Constructor for class org.cybertory.MSS.Constant3OpDesc
 
ConvertToFloatOpDesc - class org.cybertory.MSS.ConvertToFloatOpDesc.
This class is designed to be useable in with PendingRenderedOp / PendingParameterBlockJAI.
ConvertToFloatOpDesc() - Constructor for class org.cybertory.MSS.ConvertToFloatOpDesc
 
CybertoryMark - class org.cybertory.MSS.CybertoryMark.
Encapsulates the image for a "CYBERTORY.ORG" marker to be placed in the upper left corner of the microarray image scan.
CybertoryMark() - Constructor for class org.cybertory.MSS.CybertoryMark
 
cacheObject(String, Object) - Method in class org.cybertory.MSS.XMLAltData
 
calc(float, Random) - Method in class org.cybertory.MSS.PolynomialNoiseTerm
 
calcValue(double, double) - Method in class org.cybertory.MSS.GradientFunction
 
calcValue(double, double) - Method in class org.cybertory.MSS.SimpleFunction
 
canInstantiate(Class) - Static method in class org.cybertory.MSS.XMLHandlerAtomic
 
cause - Variable in class org.cybertory.MSS.XMLFormatException
 
coerceNumChannels(int) - Method in class org.cybertory.MSS.RawIntensitiesRecord
 
col - Variable in class org.cybertory.MSS.FeatureCharacteristics
 
col - Variable in class org.cybertory.MSS.RawIntensitiesRecord
 
commonParams - Variable in class org.cybertory.MSS.ScanSaveType
 
compareTo(Object) - Method in class org.cybertory.MSS.RawIntensitiesRecord
 
compareTo(Object) - Method in class org.cybertory.MSS.XMLHandler
To implement Comparable
computeRect(PlanarImage[], WritableRaster, Rectangle) - Method in class org.cybertory.MSS.PointModifyFunctionOpDesc.PointModifyFunctionOp
Method required for RenderedOp
context - Variable in class org.cybertory.MSS.XMLParseException
 
create(ParameterBlock, RenderingHints) - Method in class org.cybertory.MSS.Constant2OpDesc
 
create(ParameterBlock, RenderingHints) - Method in class org.cybertory.MSS.Constant3OpDesc
 
create(ParameterBlock, RenderingHints) - Method in class org.cybertory.MSS.ConvertToFloatOpDesc
Method needed for implementation of RenderedImageFactory
create(ParameterBlock, RenderingHints) - Method in class org.cybertory.MSS.DirtOpDesc
 
create(ParameterBlock, RenderingHints) - Method in class org.cybertory.MSS.FeaturesImageOpDesc
Method needed for implementation of RenderedImageFactory
create(ParameterBlock, RenderingHints) - Method in class org.cybertory.MSS.FirstNonzeroOpDesc
 
create(ParameterBlock, RenderingHints) - Method in class org.cybertory.MSS.GBlurOpDesc
 
create(ParameterBlock, RenderingHints) - Method in class org.cybertory.MSS.ImageFunction2OpDesc
 
create(ParameterBlock, RenderingHints) - Method in class org.cybertory.MSS.PointModifyFunctionOpDesc
 
create(ParameterBlock, RenderingHints) - Method in class org.cybertory.MSS.TiltOpDesc
 
create(ParameterBlock, RenderingHints) - Method in class org.cybertory.MSS.ZoneFeaturesImageOpDesc
Method needed for implementation of RenderedImageFactory
createFeatureShape(float, Point2D) - Method in class org.cybertory.MSS.CircleFeatureShapeFactory
Generate a specific shape, given the design location of a feature.
createFeatureShape(float) - Method in class org.cybertory.MSS.CircleFeatureShapeFactory
Generate a specific shape, centered at 0,0.
createFeatureShape(float, Point2D) - Method in interface org.cybertory.MSS.FeatureShapeFactory
Generates a shape for the feature at the given location.
createFeatureShape(float, Point2D) - Method in class org.cybertory.MSS.SquareFeatureShapeFactory
Generates a shape for the feature at the given location.
createFile(RenderedOp, String) - Method in class org.cybertory.MSS.FloatTiff
 
createFile(RenderedOp, String) - Method in class org.cybertory.MSS.GrayscaleTiffs
Create grayscale tiff image(s) from the working microarray image, one image file for each channel of the experiment.
createFile(RenderedOp, String) - Method in class org.cybertory.MSS.Jpeg
 
createFile(RenderedOp, String) - Method in class org.cybertory.MSS.ScanSaveType
 
createPolygon() - Method in class org.cybertory.MSS.PolygonFactory
Creates a polygon with the default radius (which must have been set up with a previous call to PolygonFactory.setDefaultRadius(float).
createPolygon(float) - Method in class org.cybertory.MSS.PolygonFactory
Creates a polygon with the specified (approximate) radius.
createPolygonPolar() - Method in class org.cybertory.MSS.PolygonFactory
 
createPolygonPolar(float) - Method in class org.cybertory.MSS.PolygonFactory
 
createTexture(Shape, int) - Method in interface org.cybertory.MSS.FeatureTexture
 
createTexture(Shape, int) - Method in class org.cybertory.MSS.FeatureTextureConst
 
createTexture(Shape, int) - Method in class org.cybertory.MSS.FeatureTextureDonut
 
createTexture(Shape, int) - Method in class org.cybertory.MSS.FeatureTextureFunction
 

D

DatException - exception org.cybertory.MSS.DatException.
Exception for use in parsing flat file data.
DatException(String, Throwable) - Constructor for class org.cybertory.MSS.DatException
 
DatException(String) - Constructor for class org.cybertory.MSS.DatException
 
DatMissingColumn - exception org.cybertory.MSS.DatMissingColumn.
An exception for when flat file data is missing a required column.
DatMissingColumn() - Constructor for class org.cybertory.MSS.DatMissingColumn
 
DataListItem - class org.cybertory.MSS.DataListItem.
 
DataListItem(File) - Constructor for class org.cybertory.MSS.DataListItem
 
DirtOpDesc - class org.cybertory.MSS.DirtOpDesc.
Produce an image with random dirt specs.
DirtOpDesc() - Constructor for class org.cybertory.MSS.DirtOpDesc
 
DoubleArrayer - class org.cybertory.MSS.DoubleArrayer.
Class creates a 'double' array from an array of type Object (that is actually filled with Double).
DoubleArrayer() - Constructor for class org.cybertory.MSS.DoubleArrayer
 
defaultFilenameExtension - Static variable in class org.cybertory.MSS.FloatTiff
 
defaultFilenameExtension - Static variable in class org.cybertory.MSS.GrayscaleTiffs
 
defaultFilenameExtension - Static variable in class org.cybertory.MSS.Jpeg
 
defaultShapeFactory - Variable in class org.cybertory.MSS.FeaturesSpecs
 
defaultTexture - Variable in class org.cybertory.MSS.FeaturesSpecs
 

E

ExtDataFormatException - exception org.cybertory.MSS.ExtDataFormatException.
An exception for when external data is of the wrong format -- occurs while trying to parse a string.
ExtDataFormatException(String, String, Class) - Constructor for class org.cybertory.MSS.ExtDataFormatException
 
ExtensionLoadException - exception org.cybertory.MSS.ExtensionLoadException.
An exception for errors in loading extension classes.
ExtensionLoadException(String) - Constructor for class org.cybertory.MSS.ExtensionLoadException
 
ExtensionLoadException(String, Throwable) - Constructor for class org.cybertory.MSS.ExtensionLoadException
 
ExtensionsLoader - class org.cybertory.MSS.ExtensionsLoader.
A utility class for loading classes from a jar file.
ExtensionsLoader() - Constructor for class org.cybertory.MSS.ExtensionsLoader
 
ExternalDataException - exception org.cybertory.MSS.ExternalDataException.
An exception for any error related to fetching external data.
ExternalDataException(String, Throwable) - Constructor for class org.cybertory.MSS.ExternalDataException
 
ExternalDataException(String) - Constructor for class org.cybertory.MSS.ExternalDataException
 
ExternalDataException(Throwable) - Constructor for class org.cybertory.MSS.ExternalDataException
 
ExternalDataFactory - interface org.cybertory.MSS.ExternalDataFactory.
The interface for classes that return external data objects given their key (name).
ExternalDataFactoryImpl - class org.cybertory.MSS.ExternalDataFactoryImpl.
An implementation of ExternalDataFactory that gets its data from the java command line.
ExternalDataFactoryImpl(Map) - Constructor for class org.cybertory.MSS.ExternalDataFactoryImpl
 
ExternalDataFactoryImpl() - Constructor for class org.cybertory.MSS.ExternalDataFactoryImpl
 
ExternalDataFilter - class org.cybertory.MSS.ExternalDataFilter.
 
ExternalDataFilter() - Constructor for class org.cybertory.MSS.ExternalDataFilter
 
ExternalDataPanel - class org.cybertory.MSS.ExternalDataPanel.
 
ExternalDataPanel(String[], Hashtable) - Constructor for class org.cybertory.MSS.ExternalDataPanel
 
ExternalDataPanel.LabeledTextField - class org.cybertory.MSS.ExternalDataPanel.LabeledTextField.
 
ExternalDataPanel.LabeledTextField(String) - Constructor for class org.cybertory.MSS.ExternalDataPanel.LabeledTextField
 
ExternalDataPanel.LabeledTextField(String, String) - Constructor for class org.cybertory.MSS.ExternalDataPanel.LabeledTextField
 
enumElem(String) - Static method in class org.cybertory.MSS.X_IntensitiesFileReader
 
errorString() - Method in class org.cybertory.MSS.DataListItem
 
errorString() - Method in interface org.cybertory.MSS.ListItem
 
errorString() - Method in class org.cybertory.MSS.PropertiesListItem
 
externalKeys() - Method in class org.cybertory.MSS.PropertiesListItem
 
extractChildren(Element, Filter, boolean) - Method in class org.cybertory.MSS.XMLHandler
 

F

FImageLayout - class org.cybertory.MSS.FImageLayout.
Subset of ImageLayout, but with float values instead of int values.
FImageLayout(PendingRenderedOp) - Constructor for class org.cybertory.MSS.FImageLayout
 
FImageLayout(RenderedImage) - Constructor for class org.cybertory.MSS.FImageLayout
 
FImageLayout(ImageLayout) - Constructor for class org.cybertory.MSS.FImageLayout
 
FImageLayout(float, float, float, float) - Constructor for class org.cybertory.MSS.FImageLayout
 
FeatureCharacteristics - class org.cybertory.MSS.FeatureCharacteristics.
This class is a vehicle by which to override defaults for a particular feature, specifically the FeatureShapeFactory and the FeatureTexture.
FeatureCharacteristics(int, int, FeatureShapeFactory, FeatureTexture) - Constructor for class org.cybertory.MSS.FeatureCharacteristics
 
FeatureShapeFactory - interface org.cybertory.MSS.FeatureShapeFactory.
This interface is for classes that determine the shape of a feature on the image, given the location of the center of the feature.
FeatureTexture - interface org.cybertory.MSS.FeatureTexture.
A means of altering the default uniform filling in of features.
FeatureTextureConst - class org.cybertory.MSS.FeatureTextureConst.
An implementation of FeatureTexture that wraps a constant image.
FeatureTextureConst(RenderedImage) - Constructor for class org.cybertory.MSS.FeatureTextureConst
 
FeatureTextureDonut - class org.cybertory.MSS.FeatureTextureDonut.
This class paints a shape as an outer donut ring of one color and the inside of the ring as another color.
FeatureTextureDonut(float, float) - Constructor for class org.cybertory.MSS.FeatureTextureDonut
Constructor
FeatureTextureFunction - class org.cybertory.MSS.FeatureTextureFunction.
A FeatureTexture that is derived from an ImageFunction object.
FeatureTextureFunction(ImageFunction) - Constructor for class org.cybertory.MSS.FeatureTextureFunction
 
FeatureTextureFunction(ImageFunction, float) - Constructor for class org.cybertory.MSS.FeatureTextureFunction
 
FeaturesImageOpDesc - class org.cybertory.MSS.FeaturesImageOpDesc.
An operation for creating the aspect of the image including features specific painting.
FeaturesImageOpDesc() - Constructor for class org.cybertory.MSS.FeaturesImageOpDesc
 
FeaturesIntensities - interface org.cybertory.MSS.FeaturesIntensities.
An interface for classes that serve up pixel intensities for zones.
FeaturesIntensitiesImpl - class org.cybertory.MSS.FeaturesIntensitiesImpl.
A standard implmentation of FeaturesIntensities that uses a constant multiple dimension array of pixel values.
FeaturesIntensitiesImpl(RawIntensitiesData) - Constructor for class org.cybertory.MSS.FeaturesIntensitiesImpl
 
FeaturesIntensitiesImpl(float[][][][]) - Constructor for class org.cybertory.MSS.FeaturesIntensitiesImpl
 
FeaturesSpecs - class org.cybertory.MSS.FeaturesSpecs.
This class encapsulates general features specifications.
FeaturesSpecs(float, float, float, FeatureShapeFactory, FeatureTexture) - Constructor for class org.cybertory.MSS.FeaturesSpecs
 
FileExtensionFilter - class org.cybertory.MSS.FileExtensionFilter.
 
FileExtensionFilter(String) - Constructor for class org.cybertory.MSS.FileExtensionFilter
 
FirstNonzeroOpDesc - class org.cybertory.MSS.FirstNonzeroOpDesc.
An operation for Gaussian blur.
FirstNonzeroOpDesc() - Constructor for class org.cybertory.MSS.FirstNonzeroOpDesc
 
FloatArrayer - class org.cybertory.MSS.FloatArrayer.
Class creates a 'float' array from an array of type Object (that is actually filled with Float).
FloatArrayer() - Constructor for class org.cybertory.MSS.FloatArrayer
 
FloatSampleModel - class org.cybertory.MSS.FloatSampleModel.
A SampleModel implementation for float pixels.
FloatSampleModel(int, int, int) - Constructor for class org.cybertory.MSS.FloatSampleModel
 
FloatTiff - class org.cybertory.MSS.FloatTiff.
An image file format that stores all channels as floats in one file.
FloatTiff(CommonScanSaveParams) - Constructor for class org.cybertory.MSS.FloatTiff
 
factory - Variable in class org.cybertory.MSS.FeatureCharacteristics
 
featureCellSizeX - Variable in class org.cybertory.MSS.FeaturesSpecs
 
featureCellSizeY - Variable in class org.cybertory.MSS.FeaturesSpecs
 
featureCharacteristics - Variable in class org.cybertory.MSS.ZoneCharacteristics
 
featureSize - Variable in class org.cybertory.MSS.FeaturesSpecs
 
filenameExtension - Variable in class org.cybertory.MSS.CommonScanSaveParams
 
filenameSuffix - Variable in class org.cybertory.MSS.CommonScanSaveParams
 
formatContext() - Method in class org.cybertory.MSS.XMLParseException
 

G

GBlurOpDesc - class org.cybertory.MSS.GBlurOpDesc.
An operation for Gaussian blur.
GBlurOpDesc() - Constructor for class org.cybertory.MSS.GBlurOpDesc
 
GradientFunction - class org.cybertory.MSS.GradientFunction.
This function assumes the target image has an origin of (0,0) and a lower left corner of (1,1).
GradientFunction(double, double, double) - Constructor for class org.cybertory.MSS.GradientFunction
 
GrayscaleTiffs - class org.cybertory.MSS.GrayscaleTiffs.
An image file save type that stores one channel per file, with integers for pixel values.
GrayscaleTiffs(CommonScanSaveParams, int) - Constructor for class org.cybertory.MSS.GrayscaleTiffs
 
GrayscaleTiffs(CommonScanSaveParams) - Constructor for class org.cybertory.MSS.GrayscaleTiffs
 
GridFeaturesIntensities - class org.cybertory.MSS.GridFeaturesIntensities.
For microarrays where all zones are the same size, located on a regular grid (evenly spaced metarows and metacols).
GridFeaturesIntensities(float[][][][], int, int, int, int, Point[]) - Constructor for class org.cybertory.MSS.GridFeaturesIntensities
 
GridFeaturesIntensities(float[][][][][], int, int) - Constructor for class org.cybertory.MSS.GridFeaturesIntensities
 
GridMaLayout - class org.cybertory.MSS.GridMaLayout.
This class encapsulates the layout of a microarray with zones on a uniform grid, and where each zone has the same number of rows and columns.
GridMaLayout(int, int, int, int, float, float, float, float, float, float, float, float) - Constructor for class org.cybertory.MSS.GridMaLayout
 
genArray(Object[]) - Method in class org.cybertory.MSS.BooleanArrayer
 
genArray(Object[]) - Method in class org.cybertory.MSS.ByteArrayer
 
genArray(Object[]) - Method in class org.cybertory.MSS.DoubleArrayer
 
genArray(Object[]) - Method in class org.cybertory.MSS.FloatArrayer
 
genArray(Object[]) - Method in class org.cybertory.MSS.IntArrayer
 
genArray(Object[]) - Method in class org.cybertory.MSS.LongArrayer
 
genArray(Object[]) - Method in class org.cybertory.MSS.PrimitiveArrayer
 
genArray(Object[]) - Method in class org.cybertory.MSS.ShortArrayer
 
generateImages() - Method in class org.cybertory.MSS.ImagesRequest
 
getAllHandlers() - Static method in class org.cybertory.MSS.XMLHandler
 
getAltLabel(boolean, String) - Static method in class org.cybertory.MSS.XMLAltData
 
getArrayer(Class) - Static method in class org.cybertory.MSS.PrimitiveArrayer
 
getChildBoolean(Element, String) - Static method in class org.cybertory.MSS.XMLUtils
 
getChildBoolean(Element, String, boolean) - Static method in class org.cybertory.MSS.XMLUtils
 
getChildFloat(Element, String) - Static method in class org.cybertory.MSS.XMLUtils
 
getChildFloat(Element, String, float) - Static method in class org.cybertory.MSS.XMLUtils
 
getChildInteger(Element, String) - Static method in class org.cybertory.MSS.XMLUtils
 
getChildInteger(Element, String, int) - Static method in class org.cybertory.MSS.XMLUtils
 
getChildString(Element, String) - Static method in class org.cybertory.MSS.XMLUtils
 
getChildString(Element, String, String) - Static method in class org.cybertory.MSS.XMLUtils
 
getComment(Document) - Static method in class org.cybertory.MSS.XMLInspector
 
getData() - Method in class org.cybertory.MSS.IntensitiesFileReader
 
getData() - Method in interface org.cybertory.MSS.IntensitiesReader
 
getData() - Method in class org.cybertory.MSS.RawIntensitiesData
 
getDescription() - Method in class org.cybertory.MSS.DataListItem
 
getDescription() - Method in interface org.cybertory.MSS.ListItem
 
getDescription() - Method in class org.cybertory.MSS.PropertiesListItem
 
getDescription() - Method in class org.cybertory.MSS.XMLChooser.XMLFilter
 
getDimensions() - Method in class org.cybertory.MSS.GridMaLayout
 
getDimensions() - Method in interface org.cybertory.MSS.MaLayout
 
getDimensions() - Method in class org.cybertory.MSS.Packed2ZonesMaLayout
 
getDocComment(File) - Static method in class org.cybertory.MSS.XMLInspector
 
getDocument(File) - Static method in class org.cybertory.MSS.XMLInspector
 
getElements(double, double, double, double, int, int, int, double[], double[]) - Method in class org.cybertory.MSS.IFunctionFromName
 
getElements(float, float, float, float, int, int, int, float[], float[]) - Method in class org.cybertory.MSS.IFunctionFromName
 
getElements(double, double, double, double, int, int, int, double[], double[]) - Method in class org.cybertory.MSS.SimpleFunction
 
getElements(float, float, float, float, int, int, int, float[], float[]) - Method in class org.cybertory.MSS.SimpleFunction
 
getElements(double, double, double, double, int, int, int, double[], double[]) - Method in class org.cybertory.MSS.ZoneFeaturesImageOpDesc.CheckerboardFunction
 
getElements(float, float, float, float, int, int, int, float[], float[]) - Method in class org.cybertory.MSS.ZoneFeaturesImageOpDesc.CheckerboardFunction
 
getExternalData(String, Class) - Method in class org.cybertory.MSS.ArgsExternalDataFactory
Return a data object by key.
getExternalData(String, Class) - Method in interface org.cybertory.MSS.ExternalDataFactory
 
getExternalData(String, Class) - Method in class org.cybertory.MSS.ExternalDataFactoryImpl
Return a data object by key.
getHandledClasses(Class) - Static method in class org.cybertory.MSS.XMLHandler
Given a class (or interface), return its handled subclasses.
getHandler(Class) - Static method in class org.cybertory.MSS.XMLHandler
Return the handler instance associated with a handled data type.
getHandlersDefs() - Static method in class org.cybertory.MSS.XMLHandler
 
getHeight() - Method in class org.cybertory.MSS.FImageLayout
 
getHeight() - Method in class org.cybertory.MSS.GridMaLayout
 
getHeight() - Method in interface org.cybertory.MSS.MaLayout
Returns image height in pixels
getHeight() - Method in class org.cybertory.MSS.Packed2ZonesMaLayout
 
getImage(String) - Method in class org.cybertory.MSS.RImageFileLibrary
Retrieve an image from the library.
getImage(String) - Method in interface org.cybertory.MSS.RImageLibrary
 
getImageLayout() - Method in class org.cybertory.MSS.FImageLayout
 
getLayout() - Method in class org.cybertory.MSS.PendingRenderedOp
 
getMetaDimension() - Method in class org.cybertory.MSS.GridFeaturesIntensities
 
getMinX() - Method in class org.cybertory.MSS.FImageLayout
 
getMinY() - Method in class org.cybertory.MSS.FImageLayout
 
getModifiedCenter(Point2D) - Method in class org.cybertory.MSS.SpotterTipLocationEffects
 
getModifiedValue(float) - Method in class org.cybertory.MSS.PointModifyFunction
Override this method if the values for different channels are independent of each other.
getMultiple(float) - Method in class org.cybertory.MSS.AngleBias
Calculate the number to be multiplied by the vertex radius, given the angle of the vertex.
getMultiple(AngleBias[], float) - Static method in class org.cybertory.MSS.AngleBias
Calculate the number to be multiplied by the vertex radius, given the angle of the vertex and a list of angle biases.
getName() - Method in class org.cybertory.MSS.X_OperationJAI.X_JAIParam
 
getNormalized(int, float) - Method in class org.cybertory.MSS.RawIntensitiesRecord
 
getNumElements() - Method in class org.cybertory.MSS.IFunctionFromName
 
getNumElements() - Method in class org.cybertory.MSS.SimpleFunction
 
getNumElements() - Method in class org.cybertory.MSS.ZoneFeaturesImageOpDesc.CheckerboardFunction
 
getNumSources() - Method in class org.cybertory.MSS.Constant2OpDesc
 
getNumSources() - Method in class org.cybertory.MSS.Constant3OpDesc
 
getNumSources() - Method in class org.cybertory.MSS.ConvertToFloatOpDesc
 
getNumSources() - Method in class org.cybertory.MSS.DirtOpDesc
 
getNumSources() - Method in class org.cybertory.MSS.FeaturesImageOpDesc
 
getNumSources() - Method in class org.cybertory.MSS.ImageFunction2OpDesc
 
getNumSources() - Method in class org.cybertory.MSS.PointModifyFunctionOpDesc
 
getNumSources() - Method in class org.cybertory.MSS.TiltOpDesc
 
getNumZones() - Method in interface org.cybertory.MSS.FeaturesIntensities
 
getNumZones() - Method in class org.cybertory.MSS.FeaturesIntensitiesImpl
 
getNumZones() - Method in class org.cybertory.MSS.GridFeaturesIntensities
 
getNumZones() - Method in interface org.cybertory.MSS.ZonesInfo
 
getNumZones() - Method in class org.cybertory.MSS.ZonesInfoImpl
 
getOpNames() - Static method in class org.cybertory.MSS.X_PendingRenderedOp
 
getRenderingHints(int, int, int, int, int) - Static method in class org.cybertory.MSS.FloatSampleModel
 
getScaled(float) - Method in class org.cybertory.MSS.FImageLayout
 
getScaled(float) - Method in class org.cybertory.MSS.FeaturesSpecs
 
getScaled(float) - Method in class org.cybertory.MSS.GradientFunction
 
getScaled(float) - Method in class org.cybertory.MSS.GridMaLayout
 
getScaled(float) - Method in class org.cybertory.MSS.MaDimensions
 
getScaled(float) - Method in class org.cybertory.MSS.Packed2ZonesMaLayout
 
getScaled(float) - Method in class org.cybertory.MSS.PendingRenderedOp
Returns a scaled version of this object.
getScaled(float) - Method in interface org.cybertory.MSS.SelfScaler
 
getScaled(float) - Method in class org.cybertory.MSS.SpotterTipConst
 
getScaled(float) - Method in class org.cybertory.MSS.SpotterTipFunction
 
getScaled(float) - Method in class org.cybertory.MSS.SpotterTipLocationEffects
 
getScaled(float) - Method in class org.cybertory.MSS.ZoneCharacteristics
 
getScaled(float) - Method in class org.cybertory.MSS.ZonesInfoImpl
 
getScaledParameter(float, Object) - Method in interface org.cybertory.MSS.JAIParamScaler
 
getSelected() - Method in class org.cybertory.MSS.ChooserPanel
 
getSourceImageLayout(int) - Method in class org.cybertory.MSS.PendingParameterBlockJAI
Get the ImageLayout object that describes the source image.
getSpotterTipContact(Point2D, float) - Method in interface org.cybertory.MSS.SpotterTip
 
getSpotterTipContact(Point2D, float) - Method in class org.cybertory.MSS.SpotterTipConst
 
getSpotterTipContact(Point2D, float) - Method in class org.cybertory.MSS.SpotterTipFunction
 
getText() - Method in class org.cybertory.MSS.ExternalDataPanel.LabeledTextField
 
getTypeName(boolean) - Static method in class org.cybertory.MSS.XMLAltData
 
getWidth() - Method in class org.cybertory.MSS.FImageLayout
 
getWidth() - Method in class org.cybertory.MSS.GridMaLayout
 
getWidth() - Method in interface org.cybertory.MSS.MaLayout
Returns image width in pixels
getWidth() - Method in class org.cybertory.MSS.Packed2ZonesMaLayout
 
getXMLChildFilter(boolean) - Method in class org.cybertory.MSS.XMLHandler
 
getXMLChildFilter(String, boolean) - Method in class org.cybertory.MSS.XMLHandler
 
getXMLDoc() - Method in class org.cybertory.MSS.PropertiesListItem
 
getZoneCharacteristics(int) - Method in interface org.cybertory.MSS.ZonesInfo
 
getZoneCharacteristics(int) - Method in class org.cybertory.MSS.ZonesInfoImpl
 
getZoneDimension() - Method in class org.cybertory.MSS.GridFeaturesIntensities
 
getZoneIntensities(int) - Method in interface org.cybertory.MSS.ZonesInfo
 
getZoneIntensities(int) - Method in class org.cybertory.MSS.ZonesInfoImpl
 
getZoneLocation(int) - Method in class org.cybertory.MSS.GridMaLayout
 
getZoneLocation(int) - Method in interface org.cybertory.MSS.MaLayout
Get the location of a zone, given the index.
getZoneLocation(int) - Method in class org.cybertory.MSS.Packed2ZonesMaLayout
 
getZoneLocation(int) - Method in interface org.cybertory.MSS.ZonesInfo
 
getZoneLocation(int) - Method in class org.cybertory.MSS.ZonesInfoImpl
 
getZoneMetaCoordinate(int) - Method in class org.cybertory.MSS.GridFeaturesIntensities
 
getZoneMetaCoordinates() - Method in class org.cybertory.MSS.GridFeaturesIntensities
 

H

handledClass - Variable in class org.cybertory.MSS.XMLHandler
map of handlers keyed by short name for class
handledClass() - Method in class org.cybertory.MSS.XMLHandler
Return the Class object for the data type handled by this wrapper.
handlersReport(PrintStream) - Static method in class org.cybertory.MSS.XMLHandler
The Class whose data is parsed by this handler
height - Variable in class org.cybertory.MSS.MaDimensions
 
hide() - Method in class org.cybertory.MSS.X_OperationJAI.X_JAIParam
 

I

ID_Col - Static variable in class org.cybertory.MSS.IntensitiesFileReader
 
ID_Ignore - Static variable in class org.cybertory.MSS.IntensitiesFileReader
 
ID_Metacol - Static variable in class org.cybertory.MSS.IntensitiesFileReader
 
ID_Metarow - Static variable in class org.cybertory.MSS.IntensitiesFileReader
 
ID_Row - Static variable in class org.cybertory.MSS.IntensitiesFileReader
 
ID_ZoneIndex - Static variable in class org.cybertory.MSS.IntensitiesFileReader
 
IFunctionFromName - class org.cybertory.MSS.IFunctionFromName.
A class for ImageFunction implementations that are instantiated using a no-parameter constructor.
IFunctionFromName(String) - Constructor for class org.cybertory.MSS.IFunctionFromName
 
ImageFunction2OpDesc - class org.cybertory.MSS.ImageFunction2OpDesc.
An alternate implementation of functionality in the 'constant' operation.
ImageFunction2OpDesc() - Constructor for class org.cybertory.MSS.ImageFunction2OpDesc
 
ImagesRequest - class org.cybertory.MSS.ImagesRequest.
Microarray scan simulation (Image Generator class)
ImagesRequest(Document) - Constructor for class org.cybertory.MSS.ImagesRequest
 
IntArrayer - class org.cybertory.MSS.IntArrayer.
Class creates a 'int' array from an array of type Object (that is actually filled with Integer).
IntArrayer() - Constructor for class org.cybertory.MSS.IntArrayer
 
IntensitiesFileReader - class org.cybertory.MSS.IntensitiesFileReader.
A flexible class to read feature intensities data from a flat file.
IntensitiesFileReader(Reader) - Constructor for class org.cybertory.MSS.IntensitiesFileReader
 
IntensitiesFileReader(Reader, int[]) - Constructor for class org.cybertory.MSS.IntensitiesFileReader
 
IntensitiesFileReader(Reader, int[], Pattern, boolean) - Constructor for class org.cybertory.MSS.IntensitiesFileReader
 
IntensitiesReader - interface org.cybertory.MSS.IntensitiesReader.
An interface for reading RawIntensitiesRecord objects from a data source.
idFromString(String) - Static method in class org.cybertory.MSS.X_IntensitiesFileReader
 
image - Static variable in class org.cybertory.MSS.CybertoryMark
 
imagePath(String) - Method in class org.cybertory.MSS.ScanSaveType
 
imagePath(String, String) - Method in class org.cybertory.MSS.ScanSaveType
 
includesMetaCoords() - Method in class org.cybertory.MSS.IntensitiesFileReader
 
includesMetaCoords() - Method in interface org.cybertory.MSS.IntensitiesReader
 
includesZoneIndex() - Method in class org.cybertory.MSS.IntensitiesFileReader
 
includesZoneIndex() - Method in interface org.cybertory.MSS.IntensitiesReader
 
init() - Static method in class org.cybertory.MSS.Constant2OpDesc
 
init() - Static method in class org.cybertory.MSS.Constant3OpDesc
 
init() - Static method in class org.cybertory.MSS.ConvertToFloatOpDesc
 
init() - Static method in class org.cybertory.MSS.DirtOpDesc
 
init() - Static method in class org.cybertory.MSS.FeaturesImageOpDesc
 
init() - Static method in class org.cybertory.MSS.FirstNonzeroOpDesc
 
init() - Static method in class org.cybertory.MSS.GBlurOpDesc
 
init() - Static method in class org.cybertory.MSS.ImageFunction2OpDesc
 
init() - Static method in class org.cybertory.MSS.PointModifyFunctionOpDesc
 
init() - Static method in class org.cybertory.MSS.TiltOpDesc
 
init() - Static method in class org.cybertory.MSS.ZoneFeaturesImageOpDesc
 
instantiateBuiltinHandlers() - Static method in class org.cybertory.MSS.X_Builtins
 
intensities - Variable in class org.cybertory.MSS.RawIntensitiesRecord
 
intensitiesForZone(int) - Method in interface org.cybertory.MSS.FeaturesIntensities
 
intensitiesForZone(int) - Method in class org.cybertory.MSS.FeaturesIntensitiesImpl
 
intensitiesForZone(int) - Method in class org.cybertory.MSS.GridFeaturesIntensities
 
isAltElement(Element) - Static method in class org.cybertory.MSS.XMLAltData
 
isComplex() - Method in class org.cybertory.MSS.IFunctionFromName
 
isComplex() - Method in class org.cybertory.MSS.SimpleFunction
 
isComplex() - Method in class org.cybertory.MSS.ZoneFeaturesImageOpDesc.CheckerboardFunction
 
isValid() - Method in class org.cybertory.MSS.DataListItem
 
isValid() - Method in interface org.cybertory.MSS.ListItem
 
isValid() - Method in class org.cybertory.MSS.PropertiesListItem
 

J

JAIParamScaler - interface org.cybertory.MSS.JAIParamScaler.
This interface implements a means of scaling a JAI operation parameter to the actual pixel size.
Jpeg - class org.cybertory.MSS.Jpeg.
Save type for saving an image as a JPEG file.
Jpeg(CommonScanSaveParams, float) - Constructor for class org.cybertory.MSS.Jpeg
 

L

ListItem - interface org.cybertory.MSS.ListItem.
 
LongArrayer - class org.cybertory.MSS.LongArrayer.
Class creates a 'long' array from an array of type Object (that is actually filled with Long).
LongArrayer() - Constructor for class org.cybertory.MSS.LongArrayer
 
label - Variable in class org.cybertory.MSS.ExternalDataPanel.LabeledTextField
 
labelList() - Method in class org.cybertory.MSS.XMLChildFilter
 

M

MSSApp - class org.cybertory.MSS.MSSApp.
Microarray scan simulation application
MSSApp() - Constructor for class org.cybertory.MSS.MSSApp
 
MSSCommandLine - class org.cybertory.MSS.MSSCommandLine.
Microarray scan command line handler.
MSSCommandLine() - Constructor for class org.cybertory.MSS.MSSCommandLine
 
MSSGUI - class org.cybertory.MSS.MSSGUI.
Microarray scan simulation GUI interface
MSSGUI() - Constructor for class org.cybertory.MSS.MSSGUI
 
MaDimensions - class org.cybertory.MSS.MaDimensions.
A float equivalent to the Dimension class that is also a SelfScaler.
MaDimensions(float, float) - Constructor for class org.cybertory.MSS.MaDimensions
 
MaLayout - interface org.cybertory.MSS.MaLayout.
An interface for classes to specify the size of the microarray image and the locations of the zones.
main(String[]) - Static method in class org.cybertory.MSS.ChooserPanel
 
main(String[]) - Static method in class org.cybertory.MSS.MSSApp
 
main(String[]) - Static method in class org.cybertory.MSS.XMLChooser
 
main(String[]) - Static method in class org.cybertory.MSS.XMLInspector
 
manifestResolution(float) - Method in class org.cybertory.MSS.PendingParameterBlockJAI
This method applies the pixel size recursively to all parameters and image sources.
manifestResolution(float) - Method in class org.cybertory.MSS.PendingRenderedOp
This method invokes the application of pixel size.
markImage - Variable in class org.cybertory.MSS.SpotterTipContact
 
matches(Object) - Method in class org.cybertory.MSS.ExternalDataFilter
 
matches(Object) - Method in class org.cybertory.MSS.XMLChildFilter
 
metacol - Variable in class org.cybertory.MSS.RawIntensitiesRecord
 
metarow - Variable in class org.cybertory.MSS.RawIntensitiesRecord
 
miscInit() - Static method in class org.cybertory.MSS.X_Builtins
 
modifyValues(float[]) - Method in class org.cybertory.MSS.PointModifyFunction
Override this method if the values for different channels are not independent of each other.
modifyValues(float[]) - Method in class org.cybertory.MSS.PolynomialNoiseFunction
 

N

NumberOfChannels - class org.cybertory.MSS.NumberOfChannels.
Encapsulation of the number of channels to be in the image.
NumberOfChannels(int) - Constructor for class org.cybertory.MSS.NumberOfChannels
 
needsTypedef() - Method in class org.cybertory.MSS.XMLHandler
Allow data in the "defs" section, with later backward references ?
needsTypedef() - Method in class org.cybertory.MSS.XMLHandlerArray
Set up separate global typedef and always refer to it by type name ?
needsTypedef() - Method in class org.cybertory.MSS.XMLHandlerAtomic
Allow data in the "defs" section, with later backward references ?
needsTypedef() - Method in class org.cybertory.MSS.XMLHandlerStd
Allow multiple elements for this data type ?
needsTypedef() - Method in class org.cybertory.MSS.XMLHandlerSuper
 
numCols - Variable in class org.cybertory.MSS.GridFeaturesIntensities
 
numMetacols - Variable in class org.cybertory.MSS.GridFeaturesIntensities
 
numMetarows - Variable in class org.cybertory.MSS.GridFeaturesIntensities
 
numRows - Variable in class org.cybertory.MSS.GridFeaturesIntensities
 
numberOfChannels - Variable in class org.cybertory.MSS.NumberOfChannels
 
numberOfChannels - Variable in class org.cybertory.MSS.XMLAltData
 

O

OPERATION_NAME - Static variable in class org.cybertory.MSS.Constant2OpDesc
 
OPERATION_NAME - Static variable in class org.cybertory.MSS.Constant3OpDesc
 
OPERATION_NAME - Static variable in class org.cybertory.MSS.ConvertToFloatOpDesc
 
OPERATION_NAME - Static variable in class org.cybertory.MSS.DirtOpDesc
 
OPERATION_NAME - Static variable in class org.cybertory.MSS.FeaturesImageOpDesc
 
OPERATION_NAME - Static variable in class org.cybertory.MSS.FirstNonzeroOpDesc
 
OPERATION_NAME - Static variable in class org.cybertory.MSS.GBlurOpDesc
 
OPERATION_NAME - Static variable in class org.cybertory.MSS.ImageFunction2OpDesc
 
OPERATION_NAME - Static variable in class org.cybertory.MSS.PointModifyFunctionOpDesc
 
OPERATION_NAME - Static variable in class org.cybertory.MSS.TiltOpDesc
 
OPERATION_NAME - Static variable in class org.cybertory.MSS.ZoneFeaturesImageOpDesc
 
opName - Variable in class org.cybertory.MSS.X_OperationJAI
 
opSchema() - Method in class org.cybertory.MSS.X_OperationJAI
Generate the schema for this particular schema.
org.cybertory.MSS - package org.cybertory.MSS
 
outputDirectory - Variable in class org.cybertory.MSS.CommonScanSaveParams
 

P

Packed2ZonesMaLayout - class org.cybertory.MSS.Packed2ZonesMaLayout.
This class encapsulates the layout of a microarray with 2 zones overlapping to produce the effect of tight packing, such as in Agilent arrays.
Packed2ZonesMaLayout(int, int, int, int, float, float, float, float, float, float) - Constructor for class org.cybertory.MSS.Packed2ZonesMaLayout
 
PatternFileFilter - class org.cybertory.MSS.PatternFileFilter.
 
PatternFileFilter(String[]) - Constructor for class org.cybertory.MSS.PatternFileFilter
 
PatternFileFilter(String) - Constructor for class org.cybertory.MSS.PatternFileFilter
 
PendingParameterBlockJAI - class org.cybertory.MSS.PendingParameterBlockJAI.
A version of ParameterBlockJAI that handles recursive scaling to pending pixel size of parameter and source images.
PendingParameterBlockJAI(String) - Constructor for class org.cybertory.MSS.PendingParameterBlockJAI
 
PendingRenderedOp - class org.cybertory.MSS.PendingRenderedOp.
This class is analogous to RenderedOp, but in addition it handles recursive application of pixel size.
PendingRenderedOp(PendingParameterBlockJAI) - Constructor for class org.cybertory.MSS.PendingRenderedOp
 
PendingRenderedOp(PendingParameterBlockJAI, RenderingHints) - Constructor for class org.cybertory.MSS.PendingRenderedOp
 
PointModifyFunction - class org.cybertory.MSS.PointModifyFunction.
In spirit, this class is an abstract class; subclasses must override either PointModifyFunction.modifyValues(float[]) or PointModifyFunction.getModifiedValue(float) methods.
PointModifyFunction() - Constructor for class org.cybertory.MSS.PointModifyFunction
 
PointModifyFunctionOpDesc - class org.cybertory.MSS.PointModifyFunctionOpDesc.
A JAI operation to modify pixel values, based upon a PointModifyFunction passed in.
PointModifyFunctionOpDesc() - Constructor for class org.cybertory.MSS.PointModifyFunctionOpDesc
 
PointModifyFunctionOpDesc.PointModifyFunctionOp - class org.cybertory.MSS.PointModifyFunctionOpDesc.PointModifyFunctionOp.
Custom JAI operation that adds Gaussian noise.
PointModifyFunctionOpDesc.PointModifyFunctionOp(RenderedImage, PointModifyFunction) - Constructor for class org.cybertory.MSS.PointModifyFunctionOpDesc.PointModifyFunctionOp
Constructor, called from RIF
PolygonFactory - class org.cybertory.MSS.PolygonFactory.
An object instance of PolygonFactory is a factory to create polygons of a specified degree of variability.
PolygonFactory(Random, float, float, int, float) - Constructor for class org.cybertory.MSS.PolygonFactory
Constructor: See class documentation for formulas to see how these parameters are used.
PolygonFactory(Random, int) - Constructor for class org.cybertory.MSS.PolygonFactory
Constructor with pre-packaged variability parameters.
PolynomialNoiseFunction - class org.cybertory.MSS.PolynomialNoiseFunction.
Custom JAI operation that adds noise as the sum of a series of specified terms of a polynomial formula, each being a normal distribution.
PolynomialNoiseFunction(Random, PolynomialNoiseTerm[]) - Constructor for class org.cybertory.MSS.PolynomialNoiseFunction
 
PolynomialNoiseFunction(Random, PolynomialNoiseTerm[], boolean) - Constructor for class org.cybertory.MSS.PolynomialNoiseFunction
Constructor, called from RIF
PolynomialNoiseTerm - class org.cybertory.MSS.PolynomialNoiseTerm.
Describes a term in a noise polynomial, used in PolynomialNoiseFunction.
PolynomialNoiseTerm(float, float) - Constructor for class org.cybertory.MSS.PolynomialNoiseTerm
 
PreserveAspectRatio - Static variable in class org.cybertory.MSS.ConvertToFloatOpDesc
 
PreserveSize - Static variable in class org.cybertory.MSS.ConvertToFloatOpDesc
 
PrimitiveArrayer - class org.cybertory.MSS.PrimitiveArrayer.
Base class for a series of classes to change arrays from objects to primitive types.
PrimitiveArrayer() - Constructor for class org.cybertory.MSS.PrimitiveArrayer
 
PropertiesListItem - class org.cybertory.MSS.PropertiesListItem.
 
PropertiesListItem(File, File) - Constructor for class org.cybertory.MSS.PropertiesListItem
 
parseAltElement(Element, Class) - Method in class org.cybertory.MSS.XMLAltData
 
parseChildren(Element, Filter, XMLAltData, boolean) - Method in class org.cybertory.MSS.XMLHandler
Parse zero or more children of the same data type.
parseCommonParams(Element, String, XMLAltData) - Static method in class org.cybertory.MSS.X_CommonScanSaveParams
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.XMLHandler
Given that the element already extracted from it's context, parse the data (whose type should match that of the handler).
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.XMLHandlerArray
Given that the element already extracted from it's context, parse the data (whose type should match that of the handler).
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.XMLHandlerAtomic
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.XMLHandlerStd
Given that the element already extracted from it's context, parse the data (whose type should match that of the handler).
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.XMLHandlerSuper
Given that the element already extracted from it's context, parse the data (whose type should match that of the handler).
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_AngleBias
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_BorderExtender
Given a jdom Element object (with children), construct a BorderExtender instance.
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_CircleFeatureShapeFactory
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_FImageLayout
Given a jdom Element object (with children), construct a FImageLayout instance.
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_FeatureCharacteristics
Given a jdom Element object (with children), construct a FeatureCharacteristics instance.
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_FeatureTextureConst
Given a jdom Element object (with children), construct a FeatureTextureConst instance.
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_FeatureTextureDonut
Given a jdom Element object (with children), construct a FeatureTextureDonut instance.
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_FeatureTextureFunction
Given a jdom Element object (with children), construct a FeatureTextureFunction instance.
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_FeaturesIntensitiesImpl
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_FeaturesSpecs
Given a jdom Element object (with children), construct a FeaturesSpecs instance.
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_File
Given a jdom Element object (with children), construct a FeaturesSpecs instance.
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_FloatTiff
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_GradientFunction
Given a jdom Element object (with children), construct a FeaturesSpecs instance.
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_GrayscaleTiffs
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_GridFeaturesIntensities
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_GridMaLayout
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_IFunctionFromName
Given a jdom Element object (with children), construct a FeaturesSpecs instance.
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_IntensitiesFileReader
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_Jpeg
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_MaDimensions
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_NumberOfChannels
Given a jdom Element object (with children), construct a NumberOfChannels instance.
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_Packed2ZonesMaLayout
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_PendingRenderedOp
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_PolynomialNoiseFunction
Given a jdom Element object (with children), construct a PolynomialNoiseFunction instance.
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_PolynomialNoiseTerm
Given a jdom Element object (with children), construct a PolynomialTerm instance.
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_Properties
Given a jdom Element object (with children), construct a FeaturesSpecs instance.
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_RImageFileLibrary
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_Random
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_RawIntensitiesData
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_RawIntensitiesRecord
Given a jdom Element object (with children), construct a FeaturesSpecs instance.
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_RenderedImage
Given a jdom Element object (with children), construct a RenderedImage instance.
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_Scan
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_Scanner
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_SpotterTipConst
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_SpotterTipFunction
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_SpotterTipLocationEffects
Given a jdom Element object (with children), construct a SpotterTipLocationEffects instance.
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_SquareFeatureShapeFactory
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_ZoneCharacteristics
 
parseElement(Element, XMLAltData) - Method in class org.cybertory.MSS.X_ZonesInfoImpl
 
parseOp(Element, XMLAltData) - Method in class org.cybertory.MSS.X_OperationJAI
 
parseParam(Element, XMLAltData) - Method in class org.cybertory.MSS.X_OperationJAI.X_JAIParam
 
parseRequest(Element, XMLAltData) - Static method in class org.cybertory.MSS.XMLHandler
 
parseXMLDocument(Document, ExternalDataFactory[]) - Static method in class org.cybertory.MSS.XMLHandler
Parse the entire XML document requesting microarray image scans.
processParams(String[]) - Static method in class org.cybertory.MSS.MSSCommandLine
 
propagateImageLayout(int) - Method in class org.cybertory.MSS.PendingRenderedOp
 
propertyChange(PropertyChangeEvent) - Method in class org.cybertory.MSS.XMLChooser.DescriptionPanel
 

R

RImageFileLibrary - class org.cybertory.MSS.RImageFileLibrary.
A library of image files, either in a directory or as specified in a hash containing a map to the image file locations.
RImageFileLibrary(HashMap) - Constructor for class org.cybertory.MSS.RImageFileLibrary
 
RImageFileLibrary(File) - Constructor for class org.cybertory.MSS.RImageFileLibrary
Initialize a library of all the files in the given directory.
RImageFileLibrary(File, String) - Constructor for class org.cybertory.MSS.RImageFileLibrary
Initialize a library of the files matching the given pattern string in the given directory.
RImageFileLibrary(File, String[]) - Constructor for class org.cybertory.MSS.RImageFileLibrary
Initialize a library of the files having one of the given list of extensions in the given directory.
RImageLibrary - interface org.cybertory.MSS.RImageLibrary.
An interface for classes to provide rendered image libraries.
RawIntensitiesData - class org.cybertory.MSS.RawIntensitiesData.
A wrapper for access to intensities data.
RawIntensitiesData(IntensitiesReader, int, int, float, boolean) - Constructor for class org.cybertory.MSS.RawIntensitiesData
 
RawIntensitiesData(IntensitiesReader, int, int, float) - Constructor for class org.cybertory.MSS.RawIntensitiesData
 
RawIntensitiesData(RawIntensitiesRecord[], int, int, float, boolean) - Constructor for class org.cybertory.MSS.RawIntensitiesData
 
RawIntensitiesRecord - class org.cybertory.MSS.RawIntensitiesRecord.
Encapsulates the raw intensities data for one feature as well as its location (indices) in the microarray grid.
RawIntensitiesRecord() - Constructor for class org.cybertory.MSS.RawIntensitiesRecord
 
readData() - Method in class org.cybertory.MSS.IntensitiesFileReader
 
registerBuiltinOperations() - Static method in class org.cybertory.MSS.X_Builtins
 
registerOperation(X_OperationJAI) - Static method in class org.cybertory.MSS.X_PendingRenderedOp
 
row - Variable in class org.cybertory.MSS.FeatureCharacteristics
 
row - Variable in class org.cybertory.MSS.RawIntensitiesRecord
 

S

Scan - class org.cybertory.MSS.Scan.
The top class in the hierarchy of data describing a simulated microarray scan.
Scan(PendingRenderedOp, Scanner, String, float) - Constructor for class org.cybertory.MSS.Scan
 
ScanSaveType - class org.cybertory.MSS.ScanSaveType.
Base class for image file save type.
ScanSaveType(CommonScanSaveParams) - Constructor for class org.cybertory.MSS.ScanSaveType
 
Scanner - class org.cybertory.MSS.Scanner.
Image scanner class, used by Scan class (which calls this class' Scanner.saveImages(org.cybertory.MSS.PendingRenderedOp, java.lang.String, float) method).
Scanner(ScanSaveType[], float) - Constructor for class org.cybertory.MSS.Scanner
Constructor
SelfScaler - interface org.cybertory.MSS.SelfScaler.
Interface for JAI operation parameters to implement to indicate they can scale themselves for pixel size.
ShortArrayer - class org.cybertory.MSS.ShortArrayer.
Class creates a 'short' array from an array of type Object (that is actually filled with Short).
ShortArrayer() - Constructor for class org.cybertory.MSS.ShortArrayer
 
SimpleFunction - class org.cybertory.MSS.SimpleFunction.
 
SimpleFunction() - Constructor for class org.cybertory.MSS.SimpleFunction
 
SizeToFit - Static variable in class org.cybertory.MSS.ConvertToFloatOpDesc
 
SpotterTip - interface org.cybertory.MSS.SpotterTip.
A SpotterTip encapsulates tip effects for a zone.
SpotterTipConst - class org.cybertory.MSS.SpotterTipConst.
An implementation of SpotterTip that uses a constant image.
SpotterTipConst(RenderedImage) - Constructor for class org.cybertory.MSS.SpotterTipConst
 
SpotterTipConst(RenderedImage, float) - Constructor for class org.cybertory.MSS.SpotterTipConst
 
SpotterTipContact - class org.cybertory.MSS.SpotterTipContact.
A struct-like class that encapsulates data about the contact point of a spotter tip.
SpotterTipContact(Point2D, RenderedImage) - Constructor for class org.cybertory.MSS.SpotterTipContact
 
SpotterTipFunction - class org.cybertory.MSS.SpotterTipFunction.
An implementation of SpotterTip that uses an ImageFunction.
SpotterTipFunction(ImageFunction) - Constructor for class org.cybertory.MSS.SpotterTipFunction
 
SpotterTipLocationEffects - class org.cybertory.MSS.SpotterTipLocationEffects.
The encapsulation of parameters that effect the location of the spotter tip center.
SpotterTipLocationEffects(float, float, float) - Constructor for class org.cybertory.MSS.SpotterTipLocationEffects
 
SquareFeatureShapeFactory - class org.cybertory.MSS.SquareFeatureShapeFactory.
This interface is for classes that determine the shape of a feature on the image, given the location of the center of the feature.
SquareFeatureShapeFactory() - Constructor for class org.cybertory.MSS.SquareFeatureShapeFactory
 
saveImages() - Method in class org.cybertory.MSS.Scan
 
saveImages(PendingRenderedOp, String, float) - Method in class org.cybertory.MSS.Scanner
 
saveTemp(RenderedImage, String) - Static method in class org.cybertory.MSS.Tiffer
 
saveTemp(RenderedImage, String, float, int) - Static method in class org.cybertory.MSS.Tiffer
 
schemaDocument() - Static method in class org.cybertory.MSS.XMLHandler
Return a JDOM Document for the entire schema of the XML for generating images.
schemaInContext(boolean, boolean) - Method in class org.cybertory.MSS.XMLHandler
 
schemaInContext(boolean, boolean, String) - Method in class org.cybertory.MSS.XMLHandler
Return an element for a particular context
schemaInContext(String, boolean, boolean) - Method in class org.cybertory.MSS.XMLHandler
 
schemaInContext(String, boolean, boolean, String) - Method in class org.cybertory.MSS.XMLHandler
Return an element for a particular context
schemaParam() - Method in class org.cybertory.MSS.X_OperationJAI.X_JAIParam
 
schemaTypedef(boolean) - Static method in class org.cybertory.MSS.XMLAltData
 
schemaTypedef() - Method in class org.cybertory.MSS.XMLHandler
Generate Schema type definition for the class (using JDOM).
schemaTypedef() - Method in class org.cybertory.MSS.XMLHandlerAtomic
Generate Schema type definition for the class (using JDOM).
schemaTypedef() - Method in class org.cybertory.MSS.XMLHandlerStd
Generate Schema type definition for the class (using JDOM).
schemaTypedef() - Method in class org.cybertory.MSS.XMLHandlerSuper
Generate Schema type definition for the class (using JDOM).
schemaTypedef() - Method in class org.cybertory.MSS.X_AngleBias
 
schemaTypedef() - Method in class org.cybertory.MSS.X_BorderExtender
Produces an 'xsd:element' component of an XML schema for the BorderExtender.
schemaTypedef() - Method in class org.cybertory.MSS.X_CircleFeatureShapeFactory
 
schemaTypedef() - Method in class org.cybertory.MSS.X_FImageLayout
Produces an 'xsd:element' component of an XML schema for the FImageLayout.
schemaTypedef() - Method in class org.cybertory.MSS.X_FeatureCharacteristics
Produces an 'xsd:element' component of an XML schema for the FeatureCharacteristics.
schemaTypedef() - Method in class org.cybertory.MSS.X_FeatureTextureConst
Produces an 'xsd:element' component of an XML schema for the FeatureTextureConst.
schemaTypedef() - Method in class org.cybertory.MSS.X_FeatureTextureDonut
Produces an 'xsd:element' component of an XML schema for the FeatureTextureDonut.
schemaTypedef() - Method in class org.cybertory.MSS.X_FeatureTextureFunction
Produces an 'xsd:element' component of an XML schema for the FeatureTextureFunction.
schemaTypedef() - Method in class org.cybertory.MSS.X_FeaturesIntensitiesImpl
From somewhere, we have to get the number of rows,cols.
schemaTypedef() - Method in class org.cybertory.MSS.X_FeaturesSpecs
Produces an 'xsd:element' component of an XML schema for the FeaturesSpecs.
schemaTypedef() - Method in class org.cybertory.MSS.X_File
Produces an 'xsd:element' component of an XML schema for the FeaturesSpecs.
schemaTypedef() - Method in class org.cybertory.MSS.X_FloatTiff
 
schemaTypedef() - Method in class org.cybertory.MSS.X_GradientFunction
Produces an 'xsd:element' component of an XML schema for the GradientFunction.
schemaTypedef() - Method in class org.cybertory.MSS.X_GrayscaleTiffs
 
schemaTypedef() - Method in class org.cybertory.MSS.X_GridFeaturesIntensities
From somewhere, we have to get the number of metarows,metarows as well as the number of rows,cols.
schemaTypedef() - Method in class org.cybertory.MSS.X_GridMaLayout
 
schemaTypedef() - Method in class org.cybertory.MSS.X_IFunctionFromName
Produces an 'xsd:element' component of an XML schema for the FeaturesSpecs.
schemaTypedef() - Method in class org.cybertory.MSS.X_IntensitiesFileReader
 
schemaTypedef() - Method in class org.cybertory.MSS.X_Jpeg
 
schemaTypedef() - Method in class org.cybertory.MSS.X_MaDimensions
 
schemaTypedef() - Method in class org.cybertory.MSS.X_NumberOfChannels
Produces an 'xsd:element' component of an XML schema for the NumberOfChannels.
schemaTypedef() - Method in class org.cybertory.MSS.X_Packed2ZonesMaLayout
 
schemaTypedef() - Method in class org.cybertory.MSS.X_PendingRenderedOp
Generate the schema as a choice of elements, each element for one operation (PendingRenderedOp instance).
schemaTypedef() - Method in class org.cybertory.MSS.X_PolynomialNoiseFunction
Produces an 'xsd:element' component of an XML schema for the PolynomialNoiseFunction.
schemaTypedef() - Method in class org.cybertory.MSS.X_PolynomialNoiseTerm
Produces an 'xsd:element' component of an XML schema for the PolynomialTerm.
schemaTypedef() - Method in class org.cybertory.MSS.X_Properties
Produces an 'xsd:element' component of an XML schema for the FeaturesSpecs.
schemaTypedef() - Method in class org.cybertory.MSS.X_RImageFileLibrary
 
schemaTypedef() - Method in class org.cybertory.MSS.X_Random
 
schemaTypedef() - Method in class org.cybertory.MSS.X_RawIntensitiesData
 
schemaTypedef() - Method in class org.cybertory.MSS.X_RawIntensitiesRecord
Produces an 'xsd:element' component of an XML schema for the FeaturesSpecs.
schemaTypedef() - Method in class org.cybertory.MSS.X_RenderedImage
Produces an 'xsd:element' component of an XML schema for the RenderedImage.
schemaTypedef() - Method in class org.cybertory.MSS.X_Scan
 
schemaTypedef() - Method in class org.cybertory.MSS.X_Scanner
 
schemaTypedef() - Method in class org.cybertory.MSS.X_SpotterTipConst
 
schemaTypedef() - Method in class org.cybertory.MSS.X_SpotterTipFunction
 
schemaTypedef() - Method in class org.cybertory.MSS.X_SpotterTipLocationEffects
Produces an 'xsd:element' component of an XML schema for the SpotterTipLocationEffects.
schemaTypedef() - Method in class org.cybertory.MSS.X_SquareFeatureShapeFactory
 
schemaTypedef() - Method in class org.cybertory.MSS.X_ZoneCharacteristics
 
schemaTypedef() - Method in class org.cybertory.MSS.X_ZonesInfoImpl
 
setAllowExternalData(boolean) - Method in class org.cybertory.MSS.X_OperationJAI.X_JAIParam
 
setAllowExternalData(String, boolean) - Method in class org.cybertory.MSS.X_OperationJAI
 
setBlur(int, float) - Method in class org.cybertory.MSS.Scanner
 
setCommentLinePattern(Pattern) - Method in class org.cybertory.MSS.IntensitiesFileReader
 
setDefaultRadius(float) - Method in class org.cybertory.MSS.PolygonFactory
Set up a default radius for use with calls to the PolygonFactory.createPolygon() without a radius parameter.
setDefaultValue(Object) - Method in class org.cybertory.MSS.X_OperationJAI.X_JAIParam
 
setDefaultValue(String, Object) - Method in class org.cybertory.MSS.X_OperationJAI
 
setHide(boolean) - Method in class org.cybertory.MSS.X_OperationJAI.X_JAIParam
 
setHide(String, boolean) - Method in class org.cybertory.MSS.X_OperationJAI
 
setImageLayout(FImageLayout) - Method in class org.cybertory.MSS.PendingRenderedOp
 
setIncludeCybertoryMark(boolean) - Method in class org.cybertory.MSS.Scanner
 
setLocationEffects(SpotterTipLocationEffects) - Method in class org.cybertory.MSS.SpotterTipConst
 
setLocationEffects(SpotterTipLocationEffects) - Method in class org.cybertory.MSS.SpotterTipFunction
 
setNoiseFunction(PointModifyFunction) - Method in class org.cybertory.MSS.Scanner
 
setNumberOfChannels(int) - Method in class org.cybertory.MSS.PendingRenderedOp
Configure the number of channels for the output.
setOutputDir(File) - Method in class org.cybertory.MSS.Scanner
Set the output directory for the tiff/jpeg images -- defaults to the user's current directory.
setParameterDivideToScale(String) - Method in class org.cybertory.MSS.PendingParameterBlockJAI
A call to this method sets it up so that the given named parameter is divided by the pixel size when it becomes available.
setParameterScaler(String, JAIParamScaler) - Method in class org.cybertory.MSS.PendingParameterBlockJAI
Assign a JAIParamScaler to scale a particular parameter when the pixel size is known.
setPixelSizeParamName(String) - Method in class org.cybertory.MSS.PendingParameterBlockJAI
This sets the specified parameter (by name) to be set to the pixel size once its known.
setRandom(Random) - Method in class org.cybertory.MSS.SpotterTipLocationEffects
 
setRequired(boolean) - Method in class org.cybertory.MSS.X_OperationJAI.X_JAIParam
 
setRequired(String, boolean) - Method in class org.cybertory.MSS.X_OperationJAI
 
setSkipBlack(boolean) - Method in class org.cybertory.MSS.PointModifyFunctionOpDesc.PointModifyFunctionOp
 
setUniformZoneCharacteristics(ZoneCharacteristics) - Method in class org.cybertory.MSS.ZonesInfoImpl
 
setVariability(Random, float, float, int, boolean, AngleBias[]) - Method in class org.cybertory.MSS.CircleFeatureShapeFactory
Add variability factors to the shape generation.
setZoneCharacteristics(int, ZoneCharacteristics) - Method in class org.cybertory.MSS.ZonesInfoImpl
 
setZoneIndex(int) - Method in class org.cybertory.MSS.ZoneCharacteristics
 
setZonesCharacteristics(ZoneCharacteristics[]) - Method in class org.cybertory.MSS.ZonesInfoImpl
 
shortName() - Method in class org.cybertory.MSS.DataListItem
 
sort(RawIntensitiesRecord[]) - Static method in class org.cybertory.MSS.RawIntensitiesRecord
 

T

Tiffer - class org.cybertory.MSS.Tiffer.
 
Tiffer() - Constructor for class org.cybertory.MSS.Tiffer
 
TiltOpDesc - class org.cybertory.MSS.TiltOpDesc.
Tilt : a JAI operation to rotate the entire image, gracefully dealing with edge effects.
TiltOpDesc() - Constructor for class org.cybertory.MSS.TiltOpDesc
 
texture - Variable in class org.cybertory.MSS.FeatureCharacteristics
 
tip - Variable in class org.cybertory.MSS.ZoneCharacteristics
 
tipCenter - Variable in class org.cybertory.MSS.SpotterTipContact
 
toLowerFirstChar(String) - Static method in class org.cybertory.MSS.XMLUtils
 
toString() - Method in class org.cybertory.MSS.DataListItem
 
toString() - Method in interface org.cybertory.MSS.ListItem
 
toString() - Method in class org.cybertory.MSS.PropertiesListItem
 
toString() - Method in class org.cybertory.MSS.XMLParseException
 
toUpperFirstChar(String) - Static method in class org.cybertory.MSS.XMLUtils
 
typeDescription() - Method in class org.cybertory.MSS.XMLHandler
 
typeDescription() - Method in class org.cybertory.MSS.X_AngleBias
 
typeDescription() - Method in class org.cybertory.MSS.X_BorderExtender
 
typeDescription() - Method in class org.cybertory.MSS.X_CircleFeatureShapeFactory
 
typeDescription() - Method in class org.cybertory.MSS.X_FImageLayout
 
typeDescription() - Method in class org.cybertory.MSS.X_FeatureCharacteristics
 
typeDescription() - Method in class org.cybertory.MSS.X_FeatureTextureConst
 
typeDescription() - Method in class org.cybertory.MSS.X_FeatureTextureFunction
 
typeDescription() - Method in class org.cybertory.MSS.X_FeaturesIntensitiesImpl
 
typeDescription() - Method in class org.cybertory.MSS.X_FeaturesSpecs
 
typeDescription() - Method in class org.cybertory.MSS.X_File
 
typeDescription() - Method in class org.cybertory.MSS.X_FloatTiff
 
typeDescription() - Method in class org.cybertory.MSS.X_GradientFunction
 
typeDescription() - Method in class org.cybertory.MSS.X_GrayscaleTiffs
 
typeDescription() - Method in class org.cybertory.MSS.X_GridFeaturesIntensities
 
typeDescription() - Method in class org.cybertory.MSS.X_GridMaLayout
 
typeDescription() - Method in class org.cybertory.MSS.X_IFunctionFromName
 
typeDescription() - Method in class org.cybertory.MSS.X_IntensitiesFileReader
 
typeDescription() - Method in class org.cybertory.MSS.X_Jpeg
 
typeDescription() - Method in class org.cybertory.MSS.X_MaDimensions
 
typeDescription() - Method in class org.cybertory.MSS.X_NumberOfChannels
 
typeDescription() - Method in class org.cybertory.MSS.X_Packed2ZonesMaLayout
 
typeDescription() - Method in class org.cybertory.MSS.X_PendingRenderedOp
 
typeDescription() - Method in class org.cybertory.MSS.X_PolynomialNoiseFunction
 
typeDescription() - Method in class org.cybertory.MSS.X_PolynomialNoiseTerm
 
typeDescription() - Method in class org.cybertory.MSS.X_Properties
 
typeDescription() - Method in class org.cybertory.MSS.X_RImageFileLibrary
 
typeDescription() - Method in class org.cybertory.MSS.X_Random
 
typeDescription() - Method in class org.cybertory.MSS.X_RawIntensitiesData
 
typeDescription() - Method in class org.cybertory.MSS.X_RawIntensitiesRecord
 
typeDescription() - Method in class org.cybertory.MSS.X_RenderedImage
 
typeDescription() - Method in class org.cybertory.MSS.X_Scan
 
typeDescription() - Method in class org.cybertory.MSS.X_Scanner
 
typeDescription() - Method in class org.cybertory.MSS.X_SpotterTipConst
 
typeDescription() - Method in class org.cybertory.MSS.X_SpotterTipFunction
 
typeDescription() - Method in class org.cybertory.MSS.X_SpotterTipLocationEffects
 
typeDescription() - Method in class org.cybertory.MSS.X_SquareFeatureShapeFactory
 
typeDescription() - Method in class org.cybertory.MSS.X_ZoneCharacteristics
 
typeDescription() - Method in class org.cybertory.MSS.X_ZonesInfoImpl
 
typeName - Variable in class org.cybertory.MSS.XMLUnhandledTypeException
 

V

validateParameters(String, ParameterBlock, StringBuffer) - Method in class org.cybertory.MSS.Constant2OpDesc
 
validateParameters(String, ParameterBlock, StringBuffer) - Method in class org.cybertory.MSS.Constant3OpDesc
 
validateParameters(String, ParameterBlock, StringBuffer) - Method in class org.cybertory.MSS.GBlurOpDesc
 
validateParameters(String, ParameterBlock, StringBuffer) - Method in class org.cybertory.MSS.ImageFunction2OpDesc
 
validateParameters(String, ParameterBlock, StringBuffer) - Method in class org.cybertory.MSS.TiltOpDesc
 
validateSources(String, ParameterBlock, StringBuffer) - Method in class org.cybertory.MSS.Constant2OpDesc
 
validateSources(String, ParameterBlock, StringBuffer) - Method in class org.cybertory.MSS.Constant3OpDesc
 
validateSources(String, ParameterBlock, StringBuffer) - Method in class org.cybertory.MSS.DirtOpDesc
 
validateSources(String, ParameterBlock, StringBuffer) - Method in class org.cybertory.MSS.GBlurOpDesc
 
validateSources(String, ParameterBlock, StringBuffer) - Method in class org.cybertory.MSS.ImageFunction2OpDesc
 
validateSources(String, ParameterBlock, StringBuffer) - Method in class org.cybertory.MSS.TiltOpDesc
 
valueChanged(ListSelectionEvent) - Method in class org.cybertory.MSS.ChooserPanel
 
valueChanged(ListSelectionEvent) - Method in class org.cybertory.MSS.MSSGUI
Enable the Accept button IFF both a properties file and a data file are selected.

W

width - Variable in class org.cybertory.MSS.MaDimensions
 

X

XMLAltData - class org.cybertory.MSS.XMLAltData.
Encapsulation of the handling of external and forward cached objects for access while parsing the XML.
XMLAltData(ExternalDataFactory[]) - Constructor for class org.cybertory.MSS.XMLAltData
 
XMLAltData(ExternalDataFactory[], int) - Constructor for class org.cybertory.MSS.XMLAltData
 
XMLChildFilter - class org.cybertory.MSS.XMLChildFilter.
Encapsulate the selection of appropriate child elements in XML parsing.
XMLChildFilter(String[], boolean, boolean) - Constructor for class org.cybertory.MSS.XMLChildFilter
 
XMLChildFilter(String, boolean, boolean) - Constructor for class org.cybertory.MSS.XMLChildFilter
 
XMLChooser - class org.cybertory.MSS.XMLChooser.
 
XMLChooser() - Constructor for class org.cybertory.MSS.XMLChooser
 
XMLChooser(File) - Constructor for class org.cybertory.MSS.XMLChooser
 
XMLChooser.DescriptionPanel - class org.cybertory.MSS.XMLChooser.DescriptionPanel.
 
XMLChooser.DescriptionPanel() - Constructor for class org.cybertory.MSS.XMLChooser.DescriptionPanel
 
XMLChooser.XMLFilter - class org.cybertory.MSS.XMLChooser.XMLFilter.
 
XMLChooser.XMLFilter() - Constructor for class org.cybertory.MSS.XMLChooser.XMLFilter
 
XMLFormatException - exception org.cybertory.MSS.XMLFormatException.
Exception for errors in XML format.
XMLFormatException(Element, Exception) - Constructor for class org.cybertory.MSS.XMLFormatException
 
XMLHandler - class org.cybertory.MSS.XMLHandler.
The base class for code associated with handled data types, including functionality for generating XML Schema and parsing the corresponding XML data.
XMLHandler(Class) - Constructor for class org.cybertory.MSS.XMLHandler
Constructor (never accessed by user code since abstract).
XMLHandlerArray - class org.cybertory.MSS.XMLHandlerArray.
This class is to handle arrays of non-atomic types.
XMLHandlerArray(Class, XMLHandler) - Constructor for class org.cybertory.MSS.XMLHandlerArray
Constructor, should only be called from XMLHandler.getHandler(java.lang.Class) so as to control the propagation of instances of handlers.
XMLHandlerAtomic - class org.cybertory.MSS.XMLHandlerAtomic.
One class that can serve for XMLHandler instances for all of: primitive types (int, float, boolean, etc.) and their object equivalents (Integer, Float, ...
XMLHandlerAtomic(Class) - Constructor for class org.cybertory.MSS.XMLHandlerAtomic
 
XMLHandlerStd - class org.cybertory.MSS.XMLHandlerStd.
The base class for most custom handler extensions.
XMLHandlerStd(Class, boolean) - Constructor for class org.cybertory.MSS.XMLHandlerStd
 
XMLHandlerStd(Class) - Constructor for class org.cybertory.MSS.XMLHandlerStd
 
XMLHandlerSuper - class org.cybertory.MSS.XMLHandlerSuper.
Class for automatic generation of XML handlers for super classes of the custom handlers.
XMLHandlerSuper(Class) - Constructor for class org.cybertory.MSS.XMLHandlerSuper
 
XMLInspector - class org.cybertory.MSS.XMLInspector.
 
XMLInspector() - Constructor for class org.cybertory.MSS.XMLInspector
 
XMLMissingAltData - exception org.cybertory.MSS.XMLMissingAltData.
Exception for when alternate data (external or backward cached) is missing.
XMLMissingAltData(boolean, Element, String) - Constructor for class org.cybertory.MSS.XMLMissingAltData
 
XMLMissingElementException - exception org.cybertory.MSS.XMLMissingElementException.
Exception for a missing element while parsing XML.
XMLMissingElementException(Element, String) - Constructor for class org.cybertory.MSS.XMLMissingElementException
 
XMLParseException - exception org.cybertory.MSS.XMLParseException.
Exception for errors in parsing XML.
XMLParseException(String, Element) - Constructor for class org.cybertory.MSS.XMLParseException
 
XMLParseException(String, Element, Throwable) - Constructor for class org.cybertory.MSS.XMLParseException
 
XMLUnhandledTypeException - exception org.cybertory.MSS.XMLUnhandledTypeException.
Exception for when an unhandled data type occurs in the parameters for JAI operation.
XMLUnhandledTypeException(Class) - Constructor for class org.cybertory.MSS.XMLUnhandledTypeException
 
XMLUnhandledTypeException(String) - Constructor for class org.cybertory.MSS.XMLUnhandledTypeException
 
XMLUtils - class org.cybertory.MSS.XMLUtils.
General utilities for formatting and parsing XML.
XMLUtils() - Constructor for class org.cybertory.MSS.XMLUtils
 
X_AngleBias - class org.cybertory.MSS.X_AngleBias.
XML wrapper for AngleBias.
X_AngleBias() - Constructor for class org.cybertory.MSS.X_AngleBias
 
X_BorderExtender - class org.cybertory.MSS.X_BorderExtender.
XML wrapper for BorderExtender.
X_BorderExtender() - Constructor for class org.cybertory.MSS.X_BorderExtender
 
X_Builtins - class org.cybertory.MSS.X_Builtins.
Class to initialize various data types and JAI operations.
X_Builtins() - Constructor for class org.cybertory.MSS.X_Builtins
 
X_CircleFeatureShapeFactory - class org.cybertory.MSS.X_CircleFeatureShapeFactory.
XML wrapper for CircleFeatureShapeFactory.
X_CircleFeatureShapeFactory() - Constructor for class org.cybertory.MSS.X_CircleFeatureShapeFactory
 
X_CommonScanSaveParams - class org.cybertory.MSS.X_CommonScanSaveParams.
XML wrapper for CommonScanSaveParams.
X_CommonScanSaveParams() - Constructor for class org.cybertory.MSS.X_CommonScanSaveParams
 
X_FImageLayout - class org.cybertory.MSS.X_FImageLayout.
XML wrapper for FImageLayout.
X_FImageLayout() - Constructor for class org.cybertory.MSS.X_FImageLayout
 
X_FeatureCharacteristics - class org.cybertory.MSS.X_FeatureCharacteristics.
XML wrapper for FeatureCharacteristics.
X_FeatureCharacteristics() - Constructor for class org.cybertory.MSS.X_FeatureCharacteristics
 
X_FeatureTextureConst - class org.cybertory.MSS.X_FeatureTextureConst.
XML wrapper for FeatureTextureConst.
X_FeatureTextureConst() - Constructor for class org.cybertory.MSS.X_FeatureTextureConst
 
X_FeatureTextureDonut - class org.cybertory.MSS.X_FeatureTextureDonut.
 
X_FeatureTextureDonut() - Constructor for class org.cybertory.MSS.X_FeatureTextureDonut
 
X_FeatureTextureFunction - class org.cybertory.MSS.X_FeatureTextureFunction.
XML wrapper for FeatureTextureFunction.
X_FeatureTextureFunction() - Constructor for class org.cybertory.MSS.X_FeatureTextureFunction
 
X_FeaturesIntensitiesImpl - class org.cybertory.MSS.X_FeaturesIntensitiesImpl.
XML wrapper for FeaturesIntensitiesImpl.
X_FeaturesIntensitiesImpl() - Constructor for class org.cybertory.MSS.X_FeaturesIntensitiesImpl
 
X_FeaturesSpecs - class org.cybertory.MSS.X_FeaturesSpecs.
XML wrapper for FeaturesSpecs.
X_FeaturesSpecs() - Constructor for class org.cybertory.MSS.X_FeaturesSpecs
 
X_File - class org.cybertory.MSS.X_File.
XML wrapper for File.
X_File() - Constructor for class org.cybertory.MSS.X_File
 
X_FloatTiff - class org.cybertory.MSS.X_FloatTiff.
XML wrapper for FloatTiff.
X_FloatTiff() - Constructor for class org.cybertory.MSS.X_FloatTiff
 
X_GradientFunction - class org.cybertory.MSS.X_GradientFunction.
 
X_GradientFunction() - Constructor for class org.cybertory.MSS.X_GradientFunction
 
X_GrayscaleTiffs - class org.cybertory.MSS.X_GrayscaleTiffs.
XML wrapper for GrayscaleTiffs.
X_GrayscaleTiffs() - Constructor for class org.cybertory.MSS.X_GrayscaleTiffs
 
X_GridFeaturesIntensities - class org.cybertory.MSS.X_GridFeaturesIntensities.
XML wrapper for GridFeaturesIntensities.
X_GridFeaturesIntensities() - Constructor for class org.cybertory.MSS.X_GridFeaturesIntensities
 
X_GridMaLayout - class org.cybertory.MSS.X_GridMaLayout.
XML wrapper for GridMaLayout.
X_GridMaLayout() - Constructor for class org.cybertory.MSS.X_GridMaLayout
 
X_IFunctionFromName - class org.cybertory.MSS.X_IFunctionFromName.
XML wrapper for ImageFunction instantiated from a class name.
X_IFunctionFromName() - Constructor for class org.cybertory.MSS.X_IFunctionFromName
 
X_IntensitiesFileReader - class org.cybertory.MSS.X_IntensitiesFileReader.
XML wrapper for IntensitiesFileReader.
X_IntensitiesFileReader() - Constructor for class org.cybertory.MSS.X_IntensitiesFileReader
 
X_Jpeg - class org.cybertory.MSS.X_Jpeg.
XML wrapper for Jpeg.
X_Jpeg() - Constructor for class org.cybertory.MSS.X_Jpeg
 
X_MaDimensions - class org.cybertory.MSS.X_MaDimensions.
XML wrapper for MaDimensions.
X_MaDimensions() - Constructor for class org.cybertory.MSS.X_MaDimensions
 
X_NumberOfChannels - class org.cybertory.MSS.X_NumberOfChannels.
XML wrapper for NumberOfChannels.
X_NumberOfChannels() - Constructor for class org.cybertory.MSS.X_NumberOfChannels
 
X_OperationJAI - class org.cybertory.MSS.X_OperationJAI.
 
X_OperationJAI(OperationDescriptorImpl) - Constructor for class org.cybertory.MSS.X_OperationJAI
 
X_OperationJAI.X_JAIParam - class org.cybertory.MSS.X_OperationJAI.X_JAIParam.
This class encapsulates information about parameter to JAI operation.
X_OperationJAI.X_JAIParam(int, ParameterListDescriptor) - Constructor for class org.cybertory.MSS.X_OperationJAI.X_JAIParam
 
X_OperationJAI.X_JAIParam(String, Class, Object) - Constructor for class org.cybertory.MSS.X_OperationJAI.X_JAIParam
 
X_Packed2ZonesMaLayout - class org.cybertory.MSS.X_Packed2ZonesMaLayout.
XML wrapper for Packed2ZonesMaLayout.
X_Packed2ZonesMaLayout() - Constructor for class org.cybertory.MSS.X_Packed2ZonesMaLayout
 
X_PendingRenderedOp - class org.cybertory.MSS.X_PendingRenderedOp.
XML wrapper for PendingRenderedOp.
X_PendingRenderedOp() - Constructor for class org.cybertory.MSS.X_PendingRenderedOp
 
X_PolynomialNoiseFunction - class org.cybertory.MSS.X_PolynomialNoiseFunction.
XML wrapper for PolynomialNoiseFunction.
X_PolynomialNoiseFunction() - Constructor for class org.cybertory.MSS.X_PolynomialNoiseFunction
 
X_PolynomialNoiseTerm - class org.cybertory.MSS.X_PolynomialNoiseTerm.
XML wrapper for PolynomialTerm.
X_PolynomialNoiseTerm() - Constructor for class org.cybertory.MSS.X_PolynomialNoiseTerm
 
X_Properties - class org.cybertory.MSS.X_Properties.
XML wrapper for Properties.
X_Properties() - Constructor for class org.cybertory.MSS.X_Properties
 
X_RImageFileLibrary - class org.cybertory.MSS.X_RImageFileLibrary.
XML wrapper for RImageFileLibrary.
X_RImageFileLibrary() - Constructor for class org.cybertory.MSS.X_RImageFileLibrary
 
X_Random - class org.cybertory.MSS.X_Random.
XML wrapper for Random.
X_Random() - Constructor for class org.cybertory.MSS.X_Random
 
X_RawIntensitiesData - class org.cybertory.MSS.X_RawIntensitiesData.
XML wrapper for RawIntensitiesData.
X_RawIntensitiesData() - Constructor for class org.cybertory.MSS.X_RawIntensitiesData
 
X_RawIntensitiesRecord - class org.cybertory.MSS.X_RawIntensitiesRecord.
XML wrapper for RawIntensitiesRecord.
X_RawIntensitiesRecord() - Constructor for class org.cybertory.MSS.X_RawIntensitiesRecord
 
X_RenderedImage - class org.cybertory.MSS.X_RenderedImage.
XML wrapper for RenderedImage.
X_RenderedImage() - Constructor for class org.cybertory.MSS.X_RenderedImage
 
X_Scan - class org.cybertory.MSS.X_Scan.
XML wrapper for Scan.
X_Scan() - Constructor for class org.cybertory.MSS.X_Scan
 
X_Scanner - class org.cybertory.MSS.X_Scanner.
XML wrapper for Scanner.
X_Scanner() - Constructor for class org.cybertory.MSS.X_Scanner
 
X_SpotterTipConst - class org.cybertory.MSS.X_SpotterTipConst.
XML wrapper for SpotterTipConst.
X_SpotterTipConst() - Constructor for class org.cybertory.MSS.X_SpotterTipConst
 
X_SpotterTipFunction - class org.cybertory.MSS.X_SpotterTipFunction.
XML wrapper for SpotterTipFunction.
X_SpotterTipFunction() - Constructor for class org.cybertory.MSS.X_SpotterTipFunction
 
X_SpotterTipLocationEffects - class org.cybertory.MSS.X_SpotterTipLocationEffects.
XML wrapper for SpotterTipLocationEffects.
X_SpotterTipLocationEffects() - Constructor for class org.cybertory.MSS.X_SpotterTipLocationEffects
 
X_SquareFeatureShapeFactory - class org.cybertory.MSS.X_SquareFeatureShapeFactory.
XML wrapper for SquareFeatureShapeFactory.
X_SquareFeatureShapeFactory() - Constructor for class org.cybertory.MSS.X_SquareFeatureShapeFactory
 
X_ZoneCharacteristics - class org.cybertory.MSS.X_ZoneCharacteristics.
XML wrapper for ZoneCharacteristics.
X_ZoneCharacteristics() - Constructor for class org.cybertory.MSS.X_ZoneCharacteristics
 
X_ZonesInfoImpl - class org.cybertory.MSS.X_ZonesInfoImpl.
XML wrapper for ZonesInfoImpl.
X_ZonesInfoImpl() - Constructor for class org.cybertory.MSS.X_ZonesInfoImpl
 
xmlFile() - Method in class org.cybertory.MSS.PropertiesListItem
 
xmlTypeName() - Method in class org.cybertory.MSS.XMLHandler
Return the label to be used in the name of schema type defs.
xmlTypeName() - Method in class org.cybertory.MSS.XMLHandlerArray
 
xmlTypeName() - Method in class org.cybertory.MSS.XMLHandlerAtomic
 
xmlTypeName() - Method in class org.cybertory.MSS.XMLHandlerStd
Return the label to be used in the name of schema type defs.
xmlTypeName() - Method in class org.cybertory.MSS.XMLHandlerSuper
Return the label to be used in the name of schema type defs.
xsd(String, Element) - Static method in class org.cybertory.MSS.XMLUtils
 
xsd(String) - Static method in class org.cybertory.MSS.XMLUtils
 
xsdAttribute(String, String) - Static method in class org.cybertory.MSS.XMLUtils
 
xsdAttribute(String, String, boolean) - Static method in class org.cybertory.MSS.XMLUtils
 
xsdComplexType(String, Element) - Static method in class org.cybertory.MSS.XMLUtils
 
xsdDocumentation(String) - Static method in class org.cybertory.MSS.XMLUtils
 
xsdElement(String) - Static method in class org.cybertory.MSS.XMLUtils
 
xsdElement(String, Element, boolean) - Static method in class org.cybertory.MSS.XMLUtils
 
xsdElement(String, Element) - Static method in class org.cybertory.MSS.XMLUtils
 
xsdElement(String, String, boolean) - Static method in class org.cybertory.MSS.XMLUtils
 
xsdElement(String, String) - Static method in class org.cybertory.MSS.XMLUtils
 
xsdEmptyElement(String) - Static method in class org.cybertory.MSS.XMLUtils
 
xsdEmptyElement(String, boolean) - Static method in class org.cybertory.MSS.XMLUtils
 
xsdGrouping(String, Element[]) - Static method in class org.cybertory.MSS.XMLUtils
 
xsdGrouping(String, Element[], boolean) - Static method in class org.cybertory.MSS.XMLUtils
 
xsdList(String) - Static method in class org.cybertory.MSS.XMLUtils
 
xsdNamespace - Static variable in class org.cybertory.MSS.XMLUtils
 
xsdRoot() - Static method in class org.cybertory.MSS.XMLUtils
 
xsdSimpleType(String, Element) - Static method in class org.cybertory.MSS.XMLUtils
 

Z

ZoneCharacteristics - class org.cybertory.MSS.ZoneCharacteristics.
Encapsulation of characteristics of a zone: spotter tip and the FeatureCharacteristics for features within this zone.
ZoneCharacteristics(SpotterTip, FeatureCharacteristics[]) - Constructor for class org.cybertory.MSS.ZoneCharacteristics
 
ZoneFeaturesImageOpDesc - class org.cybertory.MSS.ZoneFeaturesImageOpDesc.
A JAI operation for painting the features within a zone.
ZoneFeaturesImageOpDesc() - Constructor for class org.cybertory.MSS.ZoneFeaturesImageOpDesc
 
ZoneFeaturesImageOpDesc.CheckerboardFunction - class org.cybertory.MSS.ZoneFeaturesImageOpDesc.CheckerboardFunction.
Produces an image so that the number of pixels horizontally & vertically matches the number of columns and rows of features, respectively.
ZoneFeaturesImageOpDesc.CheckerboardFunction(float[][][], int) - Constructor for class org.cybertory.MSS.ZoneFeaturesImageOpDesc.CheckerboardFunction
 
ZonesInfo - interface org.cybertory.MSS.ZonesInfo.
An interface for classes that provide access for data about zones.
ZonesInfoImpl - class org.cybertory.MSS.ZonesInfoImpl.
The class holds all the information specific to a zone, including intensities data.
ZonesInfoImpl(FeaturesIntensities, MaLayout) - Constructor for class org.cybertory.MSS.ZonesInfoImpl
 
zoneCompare(RawIntensitiesRecord, RawIntensitiesRecord) - Static method in class org.cybertory.MSS.RawIntensitiesRecord
 
zoneIndex - Variable in class org.cybertory.MSS.RawIntensitiesRecord
 
zoneIndex - Variable in class org.cybertory.MSS.ZoneCharacteristics
 
zoneMetaCoordinates - Variable in class org.cybertory.MSS.GridFeaturesIntensities
 

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