All Classes and Interfaces
Class
Description
Base class for all ontologies built-in to the baseCode project.
Base implementation of the filter interface.
Abstract class representing a filter that removes things from DoubleMatrixNamed matrices based on the values
themselves.
TODO Document Me
Abstract class representing an object that can read in a
Matrix2Dfrom a file.Base class for RClients
Remove probes that have names meeting certain rules indicating they may have low reliability.
Use the NCBO annotator to find ontology terms matching strings.
This represents an Ontology terms returned by the AnnotatorClient
Represents one row of an ANOVA table
Deprecated.
Example usage:
Based on code from: Derby - Class org.apache.derbyTesting.unitTests.util.BitUtil
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.
Deprecated.
use
BLAS insteadClass to convert byte arrays (e.g., Blobs) to and from other types of arrays.
An ontology service that loads an ontology from a classpath resource.
Creates a color matrix from a matrix of doubles
Named compressed sparse bit matrix.
Supports sparse matrices (where sparse means most values are zero, not that they are missing).
Configuration of ontology services and other things.
Convenience methods for loading configurations
Used in some ports of statistical code.
Implementation of meta-analysis of correlations along the lines of chapter 18 of Cooper and Hedges, "Handbook of
Research Synthesis".
Statistical evaluation and transformation tools for correlations.
Convenience Map that has a count as the value for each key.
TODO Document Me
Date Utility Class
A dense matrix of doubles that knows about row and column names.
Use this class when fast iteration over the matrix is of primary interest.
An interface that describes a class that can produce values from a particular probability density.
Mathematical functions for statistics that allow missing values without scotching the calculations.
Represents the A matrix in regression problems posed as Ax=b.
A graph that contains DirectedGraphNodes.
A graph node that has the concept of parents and children.
Deprecated.
use MONDO instead
Alternative distance and similarity metrics for vectors.
Similar to ubic.gemma.util.CountingMap.
Abstract base class for 2D matrices of double values with named columns and rows.
TODO Document Me
Use this factory to create matrices of type selected at runtime (String parameterization only)
Reader for
.
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basecode.dataStructure.matrix.DoubleMatrixThis class contains the LINPACK DQRDC (QR decomposition)
and DQRSL (QR solve) routines.
Utilities for dealign with Microsoft Excel spreadsheets as implemented in commons-poi.
Dense 2D matrix implementation designed for very fast access of entire rows.
An interface representing the functionality of a class that can filter 2-d matrix-based data by row-oriented
criteria.
Deprecated.
this ontology is inactive, use UBERON instead
A way to create ad-hoc in-memory ontology services.
See http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html
A simple histogram.
Reads histograms stored in flat files
Implements a simple (not very efficient) sampling algorithm for empirical distributions.
Print an
object to a text file.
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hep.aidia.IHistogram1DRepresentation of the R htest class.
Deprecated.
this ontology was last updated in unmaintained since 2013
Filter that removes individual values that are outside of a range.
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.
R connection implementation that uses the dynamic library interface JRI.
Perform a Kruskal-Wallis test.
Class to perform the Kolmogorov-Smirnov test.
Deprecated.
use
LAPACK insteadFor performing "bulk" linear model fits, but also offers simple methods for simple univariate and multivariate
regression for a single vector of dependent variables (data).
Implements comparable, which sorts by the 'x' coordinate and then secondarily by the 'y' coordinate.
Reads a tab-delimited file with keys in first column, values in second.
Represents a matrix with index columns and rows.
A visual component for displaying a color matrix
Convenience functions for getting row statistics from matrices.
Class for writing matrices to disk
Meta-analysis methods from chapter 18 of Cooper and Hedges, sections 2.1 and 3.1
Estimate mean-variance relationship and use this to compute weights for least squares fitting.
Deprecated.
Statistics for meta-analysis.
Implements methods described in
Methods for p-value correction of sets of hypothesis tests.
Deprecated.
Matrix that can hold any type of object
to use the OMIM api
TODO Document Me
Simple in-memory implementation of
OntologyProperty.Note: this only handle 'someof' and 'allof' restrictions, not cardinality.
Base class for exceptions raised by
and others.
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OntologyService#findTerm(String)Represents a search result from an ontology.
Represents a statement triplet in an ontology.
A light-weight version of OntologyTerms.
Generates a parameter map from a class using reflection, usefull for storing experimental parameters
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
A class to convert parametergrabber information/instances into excel speadsheet lines
Compute area under precision recall
Very simple class to produce String versions of beans and other objects.
Matrix that holds primitives, with an available object representation of the values.
An interface that describes objects that can produce probabilities according to some distribution.
QR with pivoting.
Fill arrays with random values
Calculate rank statistics for arrays.
A row-compressed 1D matrix.
Abstraction of a connection to R
Get a connection to R, somehow (if possible).
Tools to help make regression testing easier, but also useful for other purposes.
Functions for calculating Receiver operator characteristics.
Filter a data matrix according to flags given in a separate matrix.
Remove rows from a matrix based on some row-based statistic.
Remove rows from a matrix that are missing too many points.
Remove or retain rows that are on a list.
SVD for DoubleMatrix.
Methods for moving averages, loess
A sparse matrix that knows about row and column names.
A sparse matrix class where the rows are ragged and compressed.
Best data structure for reading really big, really sparse matrices when a matrix represetation is needed.
Assorted special functions, primarily concerning probability distributions.
Processing spreadsheet values.
This class is to determine what information is put in the spreadsheet and its column position
Miscellaneous functions used for statistical analysis.
Prints status info to stderr
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).
A NamedMatrix containing String objects.
Reader for
invalid reference
basecode.dataStructure.matrix.StringMatrixImplemented to store string based many to many relationships.
An implementation based on Jena TDB.
Generate probabilities from the uniform distribution.
An ontology service that loads an ontology from a URL.
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
Wishart distribution, used to simulate covariance matrices.
ARPACKinstead