Uses of Package
org.strbio.math

Packages that use org.strbio.math

org.strbio.math	These classes perform functions related to mathematics and statistics.
org.strbio.mol	These classes represent objects or concepts useful to structural biologists.
org.strbio.mol.lib	These classes represent conceptual objects used in structural biology algorithms.
org.strbio.mol.lib.pred2ary	These classes represent conceptual objects used in the Pred2ary program, which are probably not very useful for other purposes.
org.strbio.util	These classes perform general purpose utility functions.
org.strbio.util.graph	These classes perform utility functions related to 2D and 3D graphics.

Classes in org.strbio.math used by org.strbio.math

Bin
a class which does 1-D histogram-bins.

DHalfMatrix
like an upper triangular DMatrix.

DMatrix
a class to encapsulate a 2-D matrix of doubles.

DVector
a class to encapsulate a 1-D array of doubles.

DVectorSet
A class to encapsulate a set of points, where each point is represented as a DVector.

FHalfMatrix
like an upper triangular DMatrix.

FMatrix
a class to encapsulate a 2-D matrix of floats.

FVector
a class to encapsulate a 1-D array of floats.

IMatrix
a class to encapsulate a 2-D matrix of integers Can do a bunch of math functions, and save/load from a file.

IVector
a class to encapsulate a 1-D matrix of integers.

Sampler
This is a special case of Bin that samples data and can later return statistics like average, standard deviation.

StatsMatrix
This class describes a special kind of integer matrix which is used for keeping stats on how well a predictive procedure is performing.

Classes in org.strbio.math used by org.strbio.mol

DHalfMatrix
like an upper triangular DMatrix.

DMatrix
a class to encapsulate a 2-D matrix of doubles.

DVector
a class to encapsulate a 1-D array of doubles.

IVector
a class to encapsulate a 1-D matrix of integers.

Classes in org.strbio.math used by org.strbio.mol.lib

DMatrix
a class to encapsulate a 2-D matrix of doubles.

DVector
a class to encapsulate a 1-D array of doubles.

IMatrix
a class to encapsulate a 2-D matrix of integers Can do a bunch of math functions, and save/load from a file.

IVector
a class to encapsulate a 1-D matrix of integers.

Classes in org.strbio.math used by org.strbio.mol.lib.pred2ary

CorrectMatrix
If your prediction is yes/no, or if you are only interested in stats on correctness and incorrectness, you can create a matrix which is 2xN, where N is the number of possible categories in reality, and data[0][i] indicates the number of wrong predictions of things belonging to catogory i (you predicted them as something other than i), while data[1][i] indicates the number of correct predictions of things belonging to category i.

IMatrix
a class to encapsulate a 2-D matrix of integers Can do a bunch of math functions, and save/load from a file.

SimMatrix
This is a NxN matrix, where data[i][j] indicates the number of times something was actually i, but predicted to be j.

Classes in org.strbio.math used by org.strbio.util

DMatrix
a class to encapsulate a 2-D matrix of doubles.

Classes in org.strbio.math used by org.strbio.util.graph

DVector
a class to encapsulate a 1-D array of doubles.

DVectorSet
A class to encapsulate a set of points, where each point is represented as a DVector.