Changelog

Wolfgang Hoschek Changelog

Removed com.isml.math.* package (If you need Complex numbers, download and use Jakarta Commons Math instead)
Documentation is now auto generated
Fixed Algebra.normInfinity(DoubleMatrix1D x) (T.J.Hunt@open.ac.uk)
Upgraded package util.concurrent from version 1.3.2 to 1.3.4 (package name edu.oswego... becomes EDU.oswego...)

This version breaks the 1.9 Gflop/s barrier on JDK ibm-1.4.1, RedHat 9.0, 2x IntelXeon@2.8 GHz.
Redesigned documentation and web site
Moved build system to ANT
Upgraded package util.concurrent from version 1.3.1 to 1.3.2, which is now a separate jar
Upgraded package corejava to corejava-2002-11-16, which is now licensed under LGPL.
Removed packages ViolinStrings, edu.cornell.lassp.houle.RngPack, jal.*
Colt now requires jdk 1.2.x
Fixed covariance bug in cern.jet.stat.Descriptive (scott white "scottw@eml.cc")
Fixed bug in cern.jet.random.Normal.nextDouble in combination with setState() (nick.collier@verizon.net)
Fixed bug in cern.jet.stat.quantile.EquiDepthHistogram (Brett Neumeier random@rnd.cx)
RCDoubleMatrix2D was unnecessarily restricted in shape (double)columns*rows <= Integer.MAX_VALUE). Is now only limited by nonZeroes <= Integer.MAX_VALUE

This version breaks the 1.3 Gflop barrier on JDK ibm-1.4.1, RedHat 8.0, 2x Pentium4@2.2 GHz.
Upgraded package util.concurrent from version 1.3.0 to 1.3.1
Fixed bug in cern.jet.random.Uniform.nextInt (jan.cheyns@intec.rug.ac.be)
Fixed small bug in cern.colt.Partitioning and cern.colt.matrix.doublealgo.Partitioning
Fixed Poisson.staticNextInt()
Fixed infinite loop in Logarithmic.nextDouble() for some parameter combinations
Fix for CholeskyDecomposition.solve (MG Ferreira "mgf@webmail.co.za")
cern.jet.stat.quantile.QuantileFinderFactory should ignore N if if known_N is false.
class PrintFormat is unreliable - do not use it. matrix print formatting is now reverted back to use corejava.Format instead.
MersenneTwister had a small problem, which is now fixed with Matsumotos code from 2002/1/26.
cern.jet.stat.Probability.studentT and cern.jet.random.StudentT were only defined for values >= 0
cern.colt.bitvector.BitVector.replaceFromToWith(int from, int to, boolean value) treated leading partial unit incorrectly (Olivier Janssens "oj@adhoc.be")

Added GenericSorting.mergeSort for "stable" in-place sorting of arbitrary shaped data
Upgraded the ViolinStrings package to V1.0. Michael Schmeling reports that two split methods which were contributed by Eric Jablow have been added and some minor documentation bugs have been fixed.
Upgraded package util.concurrent from version 1.2.5 to 1.3.0
Added 2d matrix versions of daxpy(), dcopy(), dscal(), dswap() to Blas, SeqBlas, SmpBlas (Martin.Schimschak@dresdner-bank.com)
MersenneTwister now also allows zero seed (Martin.Schimschak@dresdner-bank.com)
Fix for serious SparseDoubleMatrix2D and Open<type>Map performance degradation
RCDoubleMatrix2D.assign(otherMatrix) got faster
RCDoubleMatrix2D.assign(double) got faster
DenseDoubleMatrix{1,2,3}D.assign(double) got faster
DenseDoubleMatrix2D.zMult got a bit faster for very large problem sizes
Algebra.normInfinity(DoubleMatrix1D x) and Algebra.normInfinity(DoubleMatrix2D A) were incorrect (Martin.Schimschak@dresdner-bank.com)
SeqBlas.dger() and SeqBlas.dtrmv() were incorrect (Martin.Schimschak@dresdner-bank.com)
ObjectArrayList.toList() threw IndexOutOfBoundsException
RCDoubleMatrix2D was unnecessarily restricted in shape (double)columns*rows <= Integer.MAX_VALUE). Is now only limited by nonZeroes <= Integer.MAX_VALUE
cern.colt.matrix.linalg.Property.equals(..) gave wrong results when comparing exotic special cases NaN, inf, -inf.
cern.colt.matrix.doublealgo.Sorting was not NaN aware. In compliance with the JDK sorts, it now swaps NaNs to the end.
Property.isIdentity bug fix
Polynomial.p1evl javadoc was misleading

Added matrix mergesorts. Matrix quicksorts alone were not enough, because matrices are frequently sorted successively by multiple columns. In order to preserve the relative order of equal elements a so-called "stable" sort was needed. Mergesort is such a thing.

To enable this, some minor changes were necessary. Please update your source code as follows

Old style New style

cern.colt.matrix.doublealgo.Sorting.quickSort(...)
cern.colt.matrix.doublealgo.Sorting.quickSort.sort(...) or cern.colt.matrix.doublealgo.Sorting.mergeSort.sort(...)

matrix.viewSorted(...) methods now use mergesort instead of quicksort.

New blocked algorithm improved performance of out-of-cache matrix-matrix and matrix-vector mult (Blas.dgemm and dgemv).
Added parallel implementations of assign(function) to the BLAS (Basic Linear Algebra System). See cern.colt.matrix.linalg.
Fixed a bad bug in GenericPermuting. This one caused incorrect results to LU solving.
SmpBlas.dgemm and dgemv threw exceptions when asking for transpositions.

Powerful, extendible and performant histogram abstractions, improving ways for the statistical study of experimental data.
Matrix functionality and performance improvements
Sequential and parallel implementations of the BLAS (Basic Linear Algebra System). See cern.colt.matrix.linalg.
Sparse row compressed matrix implementation - RCDoubleMatrix2D
Major performance improvements for many matrix operations, in particular optimizations detecting function objects for scaling (+,-,*,/, ...), delegating to optimized internal implementations
For performance added generalized matrix-matrix and matrix-vector mult: C = alpha*A*B + beta*C and z = alpha*A*y + beta*z with or without transpositions
Added the long awaited histogram packages hep.aida , hep.aida.ref and hep.aida.bin. The stable bins formerly found in cern.jet.histo have been moved to hep.aida.bin and cern.jet.histo has been dropped.
Added histogram and OLAP cube operators to cern.colt.matrix.doublealgo.Statistic.
Added sampling views to cern.colt.matrix.doublealgo.Statistic
Efficient matrix quicksort using precomputation; added to cern.colt.matrix.doublealgo.Sorting
Stencil methods for finite difference operations in cern.colt.matrix.doublealgo.Stencil
DoubleMatrix1D.getNonZeros(IntArrayList indexList, DoubleArrayList valueList, int maxCardinality) had a bug, hence Algebra.inverse sometimes produced wrong answers.
QRDecomposition
matrix.viewStrides() sometimes gave wrong shape
matrix.zMult(...) sometimes threw ArrayIndexOutOfBoundsExceptions
DynamicBin1D.max() sometimes gave wrong answer -infinity
Distance matrix in cern.colt.matrix.doublealgo.Statistic now works on user defined distance functions
Moved cern.colt.matrix.DoubleTransform to cern.colt.matrix.doublealgo.Transform (sorry)

Renamed to lower case: EDU.oswego.cs.dl.util.concurrent --> edu.oswego.cs.dl.util.concurrent (resolves collisions of multiple edu packages)
cern.colt.matrix.linalg.Algebra.trace() now returns a double.
Improved build process (makefile)
package cern.colt.matrix - bug fixes and performance improvements
Stronger separation of matrix interfaces and matrix implementations:
- the implementations of matrix data structures moved from package cern.colt.matrix to package cern.colt.matrix.imp
- matrix factories moved from cern.colt.matrix.algo to cern.colt.matrix
Formatter objects - Matrix formatting much extended and now also possible using java.lang.Double.toString(double)
Moved cern.jet.math.Unit and cern.jet.math.PhysicalConstants to cern.clhep
Uniform.nextDouble() now returns a value between min and max, as specified upon instance construction
package cern.colt.matrix.linalg - Linear Algebra
Additional convenience methods in matrix factories
cern.colt.matrix.DoubleTransform: Additional convenience methods for element-by-element transformations
Introduced Object matrices
A few additional methods in DynamicBin1D related to sampling, bootstrapping, correlation
Performance log of compute intensive matrix computations
Now also redistributing util.concurrent framework - Standardized, efficient utility classes commonly encountered in concurrent programming
package cern.clhep - Starting to port CLHEP (C++)

Old style	New style
`cern.colt.matrix.doublealgo.Sorting.quickSort(...)`	`cern.colt.matrix.doublealgo.Sorting.quickSort.sort(...)` or `cern.colt.matrix.doublealgo.Sorting.mergeSort.sort(...)`