Package org.cybertory.MSS

Interface Summary
ExternalDataFactory The interface for classes that return external data objects given their key (name).
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.
FeaturesIntensities An interface for classes that serve up pixel intensities for zones.
FeatureTexture A means of altering the default uniform filling in of features.
IntensitiesReader An interface for reading RawIntensitiesRecord objects from a data source.
JAIParamScaler This interface implements a means of scaling a JAI operation parameter to the actual pixel size.
ListItem  
MaLayout An interface for classes to specify the size of the microarray image and the locations of the zones.
RImageLibrary An interface for classes to provide rendered image libraries.
SelfScaler Interface for JAI operation parameters to implement to indicate they can scale themselves for pixel size.
SpotterTip A SpotterTip encapsulates tip effects for a zone.
ZonesInfo An interface for classes that provide access for data about zones.
 

Class Summary
AngleBias Provides a bias in the calculation of radius in a particular direction for vertices of a randomly generated polygon.
ArgsExternalDataFactory An implementation of ExternalDataFactory that gets its data from the java command line.
BooleanArrayer Class creates a 'boolean' array from an array of type Object (that is actually filled with Boolean).
ByteArrayer Class creates a 'byte' array from an array of type Object (that is actually filled with Byte).
ChooserPanel Used in the GUI interface for the MSS.
CircleFeatureShapeFactory A flavor of FeatureShapeFactory that produces circular features, including support for the variability of location, size, and shape.
CommonScanSaveParams A class to contain parameters that are common to implementations of ScanSaveType.
Constant2OpDesc An alternate implementation of functionality in the 'constant' operation.
Constant3OpDesc An alternate implementation of functionality in the 'constant' operation.
ConvertToFloatOpDesc This class is designed to be useable in with PendingRenderedOp / PendingParameterBlockJAI.
CybertoryMark Encapsulates the image for a "CYBERTORY.ORG" marker to be placed in the upper left corner of the microarray image scan.
DataListItem  
DirtOpDesc Produce an image with random dirt specs.
DoubleArrayer Class creates a 'double' array from an array of type Object (that is actually filled with Double).
ExtensionsLoader A utility class for loading classes from a jar file.
ExternalDataFactoryImpl An implementation of ExternalDataFactory that gets its data from the java command line.
ExternalDataFilter  
ExternalDataPanel  
FeatureCharacteristics This class is a vehicle by which to override defaults for a particular feature, specifically the FeatureShapeFactory and the FeatureTexture.
FeaturesImageOpDesc An operation for creating the aspect of the image including features specific painting.
FeaturesIntensitiesImpl A standard implmentation of FeaturesIntensities that uses a constant multiple dimension array of pixel values.
FeaturesSpecs This class encapsulates general features specifications.
FeatureTextureConst An implementation of FeatureTexture that wraps a constant image.
FeatureTextureDonut This class paints a shape as an outer donut ring of one color and the inside of the ring as another color.
FeatureTextureFunction A FeatureTexture that is derived from an ImageFunction object.
FileExtensionFilter  
FImageLayout Subset of ImageLayout, but with float values instead of int values.
FirstNonzeroOpDesc An operation for Gaussian blur.
FloatArrayer Class creates a 'float' array from an array of type Object (that is actually filled with Float).
FloatSampleModel A SampleModel implementation for float pixels.
FloatTiff An image file format that stores all channels as floats in one file.
GBlurOpDesc An operation for Gaussian blur.
GradientFunction This function assumes the target image has an origin of (0,0) and a lower left corner of (1,1).
GrayscaleTiffs An image file save type that stores one channel per file, with integers for pixel values.
GridFeaturesIntensities For microarrays where all zones are the same size, located on a regular grid (evenly spaced metarows and metacols).
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.
IFunctionFromName A class for ImageFunction implementations that are instantiated using a no-parameter constructor.
ImageFunction2OpDesc An alternate implementation of functionality in the 'constant' operation.
ImagesRequest Microarray scan simulation (Image Generator class)
IntArrayer Class creates a 'int' array from an array of type Object (that is actually filled with Integer).
IntensitiesFileReader A flexible class to read feature intensities data from a flat file.
Jpeg Save type for saving an image as a JPEG file.
LongArrayer Class creates a 'long' array from an array of type Object (that is actually filled with Long).
MaDimensions A float equivalent to the Dimension class that is also a SelfScaler.
MSSApp Microarray scan simulation application
MSSCommandLine Microarray scan command line handler.
MSSGUI Microarray scan simulation GUI interface
NumberOfChannels Encapsulation of the number of channels to be in the image.
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.
PatternFileFilter  
PendingParameterBlockJAI A version of ParameterBlockJAI that handles recursive scaling to pending pixel size of parameter and source images.
PendingRenderedOp This class is analogous to RenderedOp, but in addition it handles recursive application of pixel size.
PointModifyFunction In spirit, this class is an abstract class; subclasses must override either PointModifyFunction.modifyValues(float[]) or PointModifyFunction.getModifiedValue(float) methods.
PointModifyFunctionOpDesc A JAI operation to modify pixel values, based upon a PointModifyFunction passed in.
PolygonFactory An object instance of PolygonFactory is a factory to create polygons of a specified degree of variability.
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.
PolynomialNoiseTerm Describes a term in a noise polynomial, used in PolynomialNoiseFunction.
PrimitiveArrayer Base class for a series of classes to change arrays from objects to primitive types.
PropertiesListItem  
RawIntensitiesData A wrapper for access to intensities data.
RawIntensitiesRecord Encapsulates the raw intensities data for one feature as well as its location (indices) in the microarray grid.
RImageFileLibrary A library of image files, either in a directory or as specified in a hash containing a map to the image file locations.
Scan The top class in the hierarchy of data describing a simulated microarray scan.
Scanner Image scanner class, used by Scan class (which calls this class' Scanner.saveImages(org.cybertory.MSS.PendingRenderedOp, java.lang.String, float) method).
ScanSaveType Base class for image file save type.
ShortArrayer Class creates a 'short' array from an array of type Object (that is actually filled with Short).
SimpleFunction  
SpotterTipConst An implementation of SpotterTip that uses a constant image.
SpotterTipContact A struct-like class that encapsulates data about the contact point of a spotter tip.
SpotterTipFunction An implementation of SpotterTip that uses an ImageFunction.
SpotterTipLocationEffects The encapsulation of parameters that effect the location of the spotter tip center.
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.
Tiffer  
TiltOpDesc Tilt : a JAI operation to rotate the entire image, gracefully dealing with edge effects.
X_AngleBias XML wrapper for AngleBias.
X_BorderExtender XML wrapper for BorderExtender.
X_Builtins Class to initialize various data types and JAI operations.
X_CircleFeatureShapeFactory XML wrapper for CircleFeatureShapeFactory.
X_CommonScanSaveParams XML wrapper for CommonScanSaveParams.
X_FeatureCharacteristics XML wrapper for FeatureCharacteristics.
X_FeaturesIntensitiesImpl XML wrapper for FeaturesIntensitiesImpl.
X_FeaturesSpecs XML wrapper for FeaturesSpecs.
X_FeatureTextureConst XML wrapper for FeatureTextureConst.
X_FeatureTextureDonut  
X_FeatureTextureFunction XML wrapper for FeatureTextureFunction.
X_File XML wrapper for File.
X_FImageLayout XML wrapper for FImageLayout.
X_FloatTiff XML wrapper for FloatTiff.
X_GradientFunction  
X_GrayscaleTiffs XML wrapper for GrayscaleTiffs.
X_GridFeaturesIntensities XML wrapper for GridFeaturesIntensities.
X_GridMaLayout XML wrapper for GridMaLayout.
X_IFunctionFromName XML wrapper for ImageFunction instantiated from a class name.
X_IntensitiesFileReader XML wrapper for IntensitiesFileReader.
X_Jpeg XML wrapper for Jpeg.
X_MaDimensions XML wrapper for MaDimensions.
X_NumberOfChannels XML wrapper for NumberOfChannels.
X_OperationJAI  
X_Packed2ZonesMaLayout XML wrapper for Packed2ZonesMaLayout.
X_PendingRenderedOp XML wrapper for PendingRenderedOp.
X_PolynomialNoiseFunction XML wrapper for PolynomialNoiseFunction.
X_PolynomialNoiseTerm XML wrapper for PolynomialTerm.
X_Properties XML wrapper for Properties.
X_Random XML wrapper for Random.
X_RawIntensitiesData XML wrapper for RawIntensitiesData.
X_RawIntensitiesRecord XML wrapper for RawIntensitiesRecord.
X_RenderedImage XML wrapper for RenderedImage.
X_RImageFileLibrary XML wrapper for RImageFileLibrary.
X_Scan XML wrapper for Scan.
X_Scanner XML wrapper for Scanner.
X_SpotterTipConst XML wrapper for SpotterTipConst.
X_SpotterTipFunction XML wrapper for SpotterTipFunction.
X_SpotterTipLocationEffects XML wrapper for SpotterTipLocationEffects.
X_SquareFeatureShapeFactory XML wrapper for SquareFeatureShapeFactory.
X_ZoneCharacteristics XML wrapper for ZoneCharacteristics.
X_ZonesInfoImpl XML wrapper for ZonesInfoImpl.
XMLAltData Encapsulation of the handling of external and forward cached objects for access while parsing the XML.
XMLChildFilter Encapsulate the selection of appropriate child elements in XML parsing.
XMLChooser  
XMLHandler The base class for code associated with handled data types, including functionality for generating XML Schema and parsing the corresponding XML data.
XMLHandlerArray This class is to handle arrays of non-atomic types.
XMLHandlerAtomic One class that can serve for XMLHandler instances for all of: primitive types (int, float, boolean, etc.) and their object equivalents (Integer, Float, ...
XMLHandlerStd The base class for most custom handler extensions.
XMLHandlerSuper Class for automatic generation of XML handlers for super classes of the custom handlers.
XMLInspector  
XMLUtils General utilities for formatting and parsing XML.
ZoneCharacteristics Encapsulation of characteristics of a zone: spotter tip and the FeatureCharacteristics for features within this zone.
ZoneFeaturesImageOpDesc A JAI operation for painting the features within a zone.
ZonesInfoImpl The class holds all the information specific to a zone, including intensities data.
 

Exception Summary
DatException Exception for use in parsing flat file data.
DatMissingColumn An exception for when flat file data is missing a required column.
ExtDataFormatException An exception for when external data is of the wrong format -- occurs while trying to parse a string.
ExtensionLoadException An exception for errors in loading extension classes.
ExternalDataException An exception for any error related to fetching external data.
XMLFormatException Exception for errors in XML format.
XMLMissingAltData Exception for when alternate data (external or backward cached) is missing.
XMLMissingElementException Exception for a missing element while parsing XML.
XMLParseException Exception for errors in parsing XML.
XMLUnhandledTypeException Exception for when an unhandled data type occurs in the parameters for JAI operation.