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 |
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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 |
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ExternalDataPanel |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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. |