All Classes Interface Summary Class Summary Enum Summary Exception Summary
| Class |
Description |
| AbstractFilter<M extends Matrix2D<R,C,V>,R,C,V> |
Base implementation of the filter interface.
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| AbstractGraph<R extends GraphNode<K,V>,K,V> |
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| AbstractGraphNode<K,V> |
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| AbstractLevelFilter<R,C> |
Abstract class representing a filter that removes things from DoubleMatrixNamed matrices based on the values
themselves.
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| AbstractMatrix<R,C,V> |
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| AbstractMatrix3D<R,C,S,V> |
TODO Document Me
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| AbstractMatrixReader<M extends Matrix2D<String,String,V>,V> |
Abstract class representing an object that can read in a Matrix2Dfrom a file. |
| AbstractOntologyMemoryBackedService |
This class has some stuff that's specific to in-memory ontologies.
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| AbstractOntologyResource |
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| AbstractOntologyService |
Base class for Jena-based ontology services.
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| AbstractRClient |
Base class for RClients
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| AffymetrixProbeNameFilter<M extends Matrix2D<R,C,V>,R,C,V> |
Remove probes that have names meeting certain rules indicating they may have low reliability.
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| AnnotationProperty |
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| AnnotationPropertyImpl |
Note that this is a concrete instance of the annotation.
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| AnnotatorClient |
Use the NCBO annotator to find ontology terms matching strings.
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| AnnotatorResponse |
This represents an Ontology terms returned by the AnnotatorClient
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| AnovaEffect |
Represents one row of an ANOVA table
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| AnovaResult |
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| BatchIterator<E> |
Example usage:
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| BFO |
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| BinaryTree<T> |
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| BinaryTreeNode<T> |
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| BitUtil |
Based on code from: Derby - Class org.apache.derbyTesting.unitTests.util.BitUtil
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| Blas |
This class contains Java versions of a number of the LINPACK
basic linear algebra subroutines (blas):
isamax_j
daxpy_j
ddot_j
dscal_j
dswap_j
dnrm2_j
dcopy_j
drotg_j
It also contains utility routines that the translator found useful
while translating the FORTRAN code to Java code.
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| BnodeFilter<T extends com.hp.hpl.jena.rdf.model.Resource> |
Detect bnodes, which are resources with null URIs.
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| BrowserLauncher |
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| ByteArrayConverter |
Class to convert byte arrays (e.g., Blobs) to and from other types of arrays.
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| CellLineOntologyService |
See http://www.obofoundry.org/cgi-bin/detail.cgi?
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| CellTypeOntologyService |
See http://www.obofoundry.org/cgi-bin/detail.cgi?
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| ChainedStatement |
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| ChainedStatementObject |
Acts as an 'anonymous' node in a statement
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| CharacteristicStatement |
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| ChebiOntologyService |
Loads the CHEBI Ontology at startup in its own thread.
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| ClassStatement |
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| ColorMap |
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| ColorMatrix<A,B> |
Creates a color matrix from a matrix of doubles
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| CompressedBitMatrix<R,C> |
Named compressed sparse bit matrix.
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| CompressedSparseDoubleMatrix<R,C> |
Supports sparse matrices (where sparse means most values are zero, not that they are missing).
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| Configuration |
Configuration of ontology services and other things.
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| ConfigUtils |
Convenience methods for loading configurations
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| Constants |
Used in some ports of statistical code.
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| CorrelationEffectMetaAnalysis |
Implementation of meta-analysis of correlations along the lines of chapter 18 of Cooper and Hedges, "Handbook of
Research Synthesis".
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| CorrelationStats |
Statistical evaluation and transformation tools for correlations.
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| CountingMap<K> |
Convenience Map that has a count as the value for each key.
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| CreateSpreadSheet |
TODO Document Me
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| DataStatement |
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| DatatypeProperty |
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| DateUtil |
Date Utility Class
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| DenseDouble3dMatrix<R,C,S> |
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| DenseDoubleMatrix<R,C> |
A dense matrix of doubles that knows about row and column names.
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| DenseDoubleMatrix1D |
Use this class when fast iteration over the matrix is of primary interest.
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| DenseObject3DMatrix<R,C,S> |
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| DensityGenerator |
An interface that describes a class that can produce values from a particular probability density.
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| DescriptiveWithMissing |
Mathematical functions for statistics that allow missing values without scotching the calculations.
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| DesignMatrix |
Represents the A matrix in regression problems posed as Ax=b.
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| DirectedGraph<K,V> |
A graph that contains DirectedGraphNodes.
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| DirectedGraphNode<K,V> |
A graph node that has the concept of parents and children.
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| Dirichlet |
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| DiseaseOntologyService |
Holds a copy of the Disease Ontology.
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| Distance |
Alternative distance and similarity metrics for vectors.
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| DoubleAddingMap<K> |
Similar to ubic.gemma.util.CountingMap.
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| DoubleMatrix<R,C> |
Abstract base class for 2D matrices of double values with named columns and rows.
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| DoubleMatrix3D<R,C,S> |
TODO Document Me
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| DoubleMatrixFactory |
Use this factory to create matrices of type selected at runtime (String parameterization only)
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| DoubleMatrixReader |
Reader for basecode.dataStructure.matrix.DoubleMatrix.
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| DoublePoint |
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| Dqrsl |
This class contains the LINPACK DQRDC (QR decomposition)
and DQRSL (QR solve) routines.
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| ExcelUtil |
Utilities for dealign with Microsoft Excel spreadsheets as implemented in commons-poi.
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| ExperimentalFactorOntologyService |
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| FastRowAccessDoubleMatrix<R,C> |
Dense 2D matrix implementation designed for very fast access of entire rows.
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| FileTools |
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| Filter<M extends Matrix2D<R,C,V>,R,C,V> |
An interface representing the functionality of a class that can filter 2-d matrix-based data by row-oriented
criteria.
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| FMAOntologyService |
Holds a copy of the FMA Ontology on disk.
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| GenericAnovaResult |
A generic representation of an R-style ANOVA table, including interactions.
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| GenericOntologyService |
A way to create ad hoc ontology services (in memory) for testing
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| GenericStreamConsumer |
See http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html
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| Graph<R extends GraphNode<K,V>,K,V> |
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| GraphNode<K,V> |
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| Histogram |
A simple histogram.
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| HistogramReader |
Reads histograms stored in flat files
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| HistogramSampler |
Implements a simple (not very efficient) sampling algorithm for empirical distributions.
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| HistogramWriter |
Print an hep.aidia.IHistogram1Dobject to a text file.
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| HTest |
Representation of the R htest class.
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| HumanDevelopmentOntologyService |
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| HumanPhenotypeOntologyService |
See http://bioportal.bioontology.org/ontologies/45774?
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| IndexerSelector |
Used to limit which parts of ontologies get indexed for searching.
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| InstanceStatement |
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| IntegerMatrix<R,C> |
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| ItemLevelFilter<R,C> |
Filter that removes individual values that are outside of a range.
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| JenaUtils |
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| JGradientBar |
A GUI legend component that displays a color map as a color gradient from min to max, traversing all the colors in
the color map.
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| JRIClient |
R connection implementation that uses the dynamic library interface JRI.
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| KruskalWallis |
Perform a Kruskal-Wallis test.
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| KSTest |
Class to perform the Kolmogorov-Smirnov test.
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| LeastSquaresFit |
For performing "bulk" linear model fits, but also offers simple methods for simple univariate and multivariate
regression for a single vector of dependent variables (data).
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| LinearModelSummary |
Represents the results of a linear model analysis from R.
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| Link |
Implements comparable, which sorts by the 'x' coordinate and then secondarily by the 'y' coordinate.
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| MammalianPhenotypeOntologyService |
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| MapReader |
Reads a tab-delimited file with keys in first column, values in second.
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| MathUtil |
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| Matrix2D<R,C,V> |
Represents a matrix with index columns and rows.
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| Matrix3D<R,C,S,V> |
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| MatrixDisplay<R,C> |
A visual component for displaying a color matrix
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| MatrixNormalizer<R,C> |
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| MatrixRowStats |
Convenience functions for getting row statistics from matrices.
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| MatrixStats |
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| MatrixUtil |
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| MatrixWriter<R,C> |
Class for writing matrices to disk
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| MeanDifferenceMetaAnalysis |
Meta-analysis methods from chapter 18 of Cooper and Hedges, sections 2.1 and 3.1
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| MeanVarianceEstimator |
Estimate mean-variance relationship and use this to compute weights for least squares fitting.
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| MedicOntologyService |
MEDIC ONTOLOGY USED BY PHENOCARTA, its represents MESH terms as a tree so with can use the parent structure that a
normal mesh term doesnt have
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| MetaAnalysis |
Statistics for meta-analysis.
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| ModeratedTstat |
Implements methods described in
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| MouseDevelopmentOntologyService |
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| MultipleTestCorrection |
Methods for p-value correction of sets of hypothesis tests.
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| NetUtils |
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| NIFSTDOntologyService |
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| NormalProbabilityComputer |
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| ObiService |
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| ObjectMatrix<R,C,V> |
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| ObjectMatrixImpl<R,C,V> |
Matrix that can hold any type of object
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| ObjectProperty |
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| ObjectPropertyImpl |
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| OBO |
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| OmimAnnotatorClient |
to use the OMIM api
TODO Document Me
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| OneWayAnovaResult |
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| OntologyCardinalityRestriction |
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| OntologyCardinalityRestriction.CardinalityType |
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| OntologyCardinalityRestrictionImpl |
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| OntologyClassRestriction |
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| OntologyClassRestrictionImpl |
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| OntologyDatatypeRestriction |
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| OntologyDatatypeRestrictionImpl |
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| OntologyIndexer |
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| OntologyIndividual |
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| OntologyIndividualImpl |
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| OntologyLoader |
Reads ontologies from OWL resources
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| OntologyProperty |
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| OntologyPropertyImpl |
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| OntologyResource |
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| OntologyRestriction |
Note: this only handle 'someof' and 'allof' restrictions, not cardinality.
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| OntologyRestrictionImpl |
Represents a restriction on instances that are subclasses of this.
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| OntologySearch |
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| OntologySearch |
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| OntologySearch.SearchResult<T extends com.hp.hpl.jena.rdf.model.RDFNode> |
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| OntologySearchException |
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| OntologySearchJenaException |
Base class for Jena-related ontology search exceptions.
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| OntologyService |
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| OntologyTerm |
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| OntologyTermImpl |
Represents a class in an ontology
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| OntologyTermSimple |
A light-weight version of OntologyTerms.
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| ParameterGrabber |
Generates a parameter map from a class using reflection, usefull for storing experimental parameters
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| ParamKeeper |
Keeps track of results in the form of several key/value maps (each one can represent an experiment run), can output
to spreadsheet or csv file
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| ParamSpreadSheet |
A class to convert parametergrabber information/instances into excel speadsheet lines
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| Point |
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| PrecisionRecall |
Compute area under precision recall
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| PredicateFilter<T> |
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| PrettyPrinter |
Very simple class to produce String versions of beans and other objects.
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| PrimitiveMatrix<R,C,V> |
Matrix that holds primitives, with an available object representation of the values.
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| ProbabilityComputer |
An interface that describes objects that can produce probabilities according to some distribution.
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| PropertyFactory |
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| QRDecomposition |
QR with pivoting.
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| RandomChooser |
Fill arrays with random values
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| Rank |
Calculate rank statistics for arrays.
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| RCDoubleMatrix1D |
A row-compressed 1D matrix.
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| RClient |
Abstraction of a connection to R
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| RConnectionFactory |
Get a connection to R, somehow (if possible).
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| RegressionTesting |
Tools to help make regression testing easier, but also useful for other purposes.
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| RestrictionFactory |
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| RestrictionWithOnPropertyFilter |
Filter that retain only the restrictions on any of the given properties.
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| RestrictionWithValuesFromFilter |
Match Restriction with values from any of the given resources.
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| RetryWithoutWildcardFailedException |
Exception raised when retrying a search without a wildcard still fails.
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| RO |
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| ROC |
Functions for calculating Receiver operator characteristics.
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| RowAbsentFilter<M extends Matrix2D<R,C,V>,R,C,V> |
Filter a data matrix according to flags given in a separate matrix.
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| RowLevelFilter<R,C> |
Remove rows from a matrix based on some row-based statistic.
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| RowMissingFilter<M extends Matrix2D<R,C,V>,R,C,V> |
Remove rows from a matrix that are missing too many points.
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| RowNameFilter<M extends Matrix2D<R,C,V>,R,C,V> |
Remove or retain rows that are on a list.
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| RServeClient |
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| SearchIndex |
Customization to deal with MultiReader and 'open' while indexing is going on ...?
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| SequenceOntologyService |
Support for the Sequence Ontology
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| SingularValueDecomposition<R,C> |
SVD for DoubleMatrix.
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| Smooth |
Methods for moving averages, loess
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| SparseDoubleMatrix<R,C> |
A sparse matrix that knows about row and column names.
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| SparseDoubleMatrixReader |
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| SparseRaggedDoubleMatrix<R,C> |
A sparse matrix class where the rows are ragged and compressed.
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| SparseRaggedMatrixReader |
Best data structure for reading really big, really sparse matrices when a matrix represetation is needed.
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| SpecFunc |
Assorted special functions, primarily concerning probability distributions.
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| SpreadSheetFilter |
Processing spreadsheet values.
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| SpreadSheetSchema |
This class is to determine what information is put in the spreadsheet and its column position
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| SQLUtils |
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| Stats |
Miscellaneous functions used for statistical analysis.
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| StatusDebugLogger |
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| StatusStderr |
Prints status info to stderr
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| StatusViewer |
Intended use is to display 'status' information or other messages to users in a non-disruptive fashion (though the
actual use is up to the implementer).
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| StringConverter |
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| StringDistance |
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| StringMatrix<R,C> |
A NamedMatrix containing String objects.
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| StringMatrixReader |
Reader for basecode.dataStructure.matrix.StringMatrix
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| StringToStringSetMap |
Implemented to store string based many to many relationships.
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| StringUtil |
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| TwoWayAnovaResult |
Represents a two-way ANOVA table
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| UberonOntologyService |
Uberon
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| UndirectedGraphNode<K,V> |
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| UniformDensityComputer |
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| UniformProbabilityComputer |
Generate probabilities from the uniform distribution.
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| UnitsOntologyService |
Support for the units ontology
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| Util |
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| Visitable |
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| Wilcoxon |
Implements methods from supplementary file I of "Comparing functional annotation analyses with Catmap", Thomas
Breslin, Patrik Ed�n and Morten Krogh, BMC Bioinformatics 2004, 5:193 doi:10.1186/1471-2105-5-193
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| Wishart |
Wishart distribution, used to simulate covariance matrices.
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