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From l..@apache.org
Subject svn commit: r1178067 [1/2] - in /commons/proper/math/trunk/src: main/java/org/apache/commons/math/ main/java/org/apache/commons/math/analysis/ main/java/org/apache/commons/math/analysis/function/ main/java/org/apache/commons/math/analysis/integration/ ...
Date Sat, 01 Oct 2011 18:51:28 GMT
Author: luc
Date: Sat Oct  1 18:51:25 2011
New Revision: 1178067

URL: http://svn.apache.org/viewvc?rev=1178067&view=rev
Log:
Replaced package.html with package-info.java for package documentation.

JIRA: MATH-445

Added:
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/function/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/integration/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/interpolation/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/polynomials/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/solvers/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/complex/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/dfp/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/distribution/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/exception/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/exception/util/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/filter/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/fraction/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/genetics/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/euclidean/oned/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/euclidean/threed/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/euclidean/twod/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/partitioning/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/partitioning/utilities/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/events/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/nonstiff/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/sampling/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/direct/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/fitting/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/general/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/linear/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/univariate/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/random/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/special/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/clustering/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/correlation/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/descriptive/moment/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/descriptive/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/descriptive/rank/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/descriptive/summary/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/ranking/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/regression/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/transform/package-info.java   (with props)
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/util/package-info.java   (with props)
Removed:
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/function/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/integration/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/interpolation/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/polynomials/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/solvers/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/complex/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/dfp/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/distribution/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/exception/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/exception/util/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/filter/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/fraction/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/genetics/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/euclidean/oned/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/euclidean/threed/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/euclidean/twod/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/partitioning/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/partitioning/utilities/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/events/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/nonstiff/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/sampling/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/direct/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/fitting/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/general/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/linear/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/univariate/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/random/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/special/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/clustering/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/correlation/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/descriptive/moment/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/descriptive/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/descriptive/rank/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/descriptive/summary/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/ranking/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/regression/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/transform/package.html
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/util/package.html
Modified:
    commons/proper/math/trunk/src/site/xdoc/changes.xml

Added: commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/function/package-info.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/function/package-info.java?rev=1178067&view=auto
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/function/package-info.java (added)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/function/package-info.java Sat Oct  1 18:51:25 2011
@@ -0,0 +1,26 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *    <p>
+ *      The {@code function} package contains function objects that wrap the
+ *      methods contained in {@link java.lang.Math}, as well as common
+ *      mathematical functions such as the gaussian and sinc functions.
+ *    </p>
+ *  
+ */
+package org.apache.commons.math.analysis.function;

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Added: commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/integration/package-info.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/integration/package-info.java?rev=1178067&view=auto
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/integration/package-info.java (added)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/integration/package-info.java Sat Oct  1 18:51:25 2011
@@ -0,0 +1,22 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *     Numerical integration (quadrature) algorithms for univariate real functions.
+ *    
+ */
+package org.apache.commons.math.analysis.integration;

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Added: commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/interpolation/package-info.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/interpolation/package-info.java?rev=1178067&view=auto
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/interpolation/package-info.java (added)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/interpolation/package-info.java Sat Oct  1 18:51:25 2011
@@ -0,0 +1,22 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *     Univariate real functions interpolation algorithms.
+ *    
+ */
+package org.apache.commons.math.analysis.interpolation;

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Added: commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/package-info.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/package-info.java?rev=1178067&view=auto
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/package-info.java (added)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/package-info.java Sat Oct  1 18:51:25 2011
@@ -0,0 +1,33 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *    <p>
+ *      Parent package for common numerical analysis procedures, including root finding,
+ *      function interpolation and integration. Note that the optimization (i.e. minimization
+ *      and maximization) is a huge separate top package, despite it also operate on functions
+ *      as defined by this top-level package.
+ *    </p>
+ *    <p>
+ *      Functions interfaces are intended to be implemented by user code to represent their
+ *      domain problems. The algorithms provided by the library will then operate on these
+ *      function to find their roots, or integrate them, or ... Functions can be multivariate
+ *      or univariate, real vectorial or matrix valued, and they can be differentiable or not.
+ *    </p>
+ *  
+ */
+package org.apache.commons.math.analysis;

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Added: commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/polynomials/package-info.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/polynomials/package-info.java?rev=1178067&view=auto
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/polynomials/package-info.java (added)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/polynomials/package-info.java Sat Oct  1 18:51:25 2011
@@ -0,0 +1,23 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *     Univariate real polynomials implementations, seen as differentiable
+ *     univariate real functions.
+ *    
+ */
+package org.apache.commons.math.analysis.polynomials;

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Added: commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/solvers/package-info.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/solvers/package-info.java?rev=1178067&view=auto
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/solvers/package-info.java (added)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/solvers/package-info.java Sat Oct  1 18:51:25 2011
@@ -0,0 +1,22 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *     Root finding algorithms, for univariate real functions.
+ *    
+ */
+package org.apache.commons.math.analysis.solvers;

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Added: commons/proper/math/trunk/src/main/java/org/apache/commons/math/complex/package-info.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/complex/package-info.java?rev=1178067&view=auto
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/complex/package-info.java (added)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/complex/package-info.java Sat Oct  1 18:51:25 2011
@@ -0,0 +1,23 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *     Complex number type and implementations of complex transcendental
+ *     functions.
+ *    
+ */
+package org.apache.commons.math.complex;

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Added: commons/proper/math/trunk/src/main/java/org/apache/commons/math/dfp/package-info.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/dfp/package-info.java?rev=1178067&view=auto
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/dfp/package-info.java (added)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/dfp/package-info.java Sat Oct  1 18:51:25 2011
@@ -0,0 +1,88 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *Decimal floating point library for Java
+ *
+ *<p>Another floating point class.  This one is built using radix 10000
+ *which is 10<sup>4</sup>, so its almost decimal.</p>
+ *
+ *<p>The design goals here are:
+ *<ol>
+ *  <li>Decimal math, or close to it</li>
+ *  <li>Settable precision (but no mix between numbers using different settings)</li>
+ *  <li>Portability.  Code should be keep as portable as possible.</li>
+ *  <li>Performance</li>
+ *  <li>Accuracy  - Results should always be +/- 1 ULP for basic
+ *       algebraic operation</li>
+ *  <li>Comply with IEEE 854-1987 as much as possible.
+ *       (See IEEE 854-1987 notes below)</li>
+ *</ol></p>
+ *
+ *<p>Trade offs:
+ *<ol>
+ *  <li>Memory foot print.  I'm using more memory than necessary to
+ *       represent numbers to get better performance.</li>
+ *  <li>Digits are bigger, so rounding is a greater loss.  So, if you
+ *       really need 12 decimal digits, better use 4 base 10000 digits
+ *       there can be one partially filled.</li>
+ *</ol></p>
+ *
+ *<p>Numbers are represented  in the following form:
+ *<pre>
+ *n  =  sign &times; mant &times; (radix)<sup>exp</sup>;</p>
+ *</pre>
+ *where sign is &plusmn;1, mantissa represents a fractional number between
+ *zero and one.  mant[0] is the least significant digit.
+ *exp is in the range of -32767 to 32768</p>
+ *
+ *<p>IEEE 854-1987  Notes and differences</p>
+ *
+ *<p>IEEE 854 requires the radix to be either 2 or 10.  The radix here is
+ *10000, so that requirement is not met, but  it is possible that a
+ *subclassed can be made to make it behave as a radix 10
+ *number.  It is my opinion that if it looks and behaves as a radix
+ *10 number then it is one and that requirement would be met.</p>
+ *
+ *<p>The radix of 10000 was chosen because it should be faster to operate
+ *on 4 decimal digits at once instead of one at a time.  Radix 10 behavior
+ *can be realized by add an additional rounding step to ensure that
+ *the number of decimal digits represented is constant.</p>
+ *
+ *<p>The IEEE standard specifically leaves out internal data encoding,
+ *so it is reasonable to conclude that such a subclass of this radix
+ *10000 system is merely an encoding of a radix 10 system.</p>
+ *
+ *<p>IEEE 854 also specifies the existence of "sub-normal" numbers.  This
+ *class does not contain any such entities.  The most significant radix
+ *10000 digit is always non-zero.  Instead, we support "gradual underflow"
+ *by raising the underflow flag for numbers less with exponent less than
+ *expMin, but don't flush to zero until the exponent reaches MIN_EXP-digits.
+ *Thus the smallest number we can represent would be:
+ *1E(-(MIN_EXP-digits-1)&lowast;4),  eg, for digits=5, MIN_EXP=-32767, that would
+ *be 1e-131092.</p>
+ *
+ *<p>IEEE 854 defines that the implied radix point lies just to the right
+ *of the most significant digit and to the left of the remaining digits.
+ *This implementation puts the implied radix point to the left of all
+ *digits including the most significant one.  The most significant digit
+ *here is the one just to the right of the radix point.  This is a fine
+ *detail and is really only a matter of definition.  Any side effects of
+ *this can be rendered invisible by a subclass.</p>
+ *    
+ */
+package org.apache.commons.math.dfp;

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@@ -0,0 +1,20 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *Implementations of common discrete and continuous distributions.
+ */
+package org.apache.commons.math.distribution;

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+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/exception/package-info.java Sat Oct  1 18:51:25 2011
@@ -0,0 +1,23 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *     Specialized exceptions for algorithms errors. The exceptions can be localized
+ *     using simple java properties.
+ *    
+ */
+package org.apache.commons.math.exception;

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+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/exception/util/package-info.java Sat Oct  1 18:51:25 2011
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+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *    Classes supporting exception localization.
+ *  
+ */
+package org.apache.commons.math.exception.util;

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+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/filter/package-info.java Sat Oct  1 18:51:25 2011
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+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *Implementations of common discrete-time linear filters.
+ */
+package org.apache.commons.math.filter;

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+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/fraction/package-info.java Sat Oct  1 18:51:25 2011
@@ -0,0 +1,22 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *    Fraction number type and fraction number formatting.
+ *  
+ */
+package org.apache.commons.math.fraction;

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--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/genetics/package-info.java (added)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/genetics/package-info.java Sat Oct  1 18:51:25 2011
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+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *<p>
+ *This package provides Genetic Algorithms components and implementations.
+ *</p>
+ *
+ */
+package org.apache.commons.math.genetics;

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+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/euclidean/oned/package-info.java Sat Oct  1 18:51:25 2011
@@ -0,0 +1,24 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *<p>
+ *This package provides basic 1D geometry components.
+ *</p>
+ *
+ */
+package org.apache.commons.math.geometry.euclidean.oned;

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+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/euclidean/threed/package-info.java Sat Oct  1 18:51:25 2011
@@ -0,0 +1,24 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *<p>
+ *This package provides basic 3D geometry components.
+ *</p>
+ *
+ */
+package org.apache.commons.math.geometry.euclidean.threed;

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@@ -0,0 +1,24 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *<p>
+ *This package provides basic 2D geometry components.
+ *</p>
+ *
+ */
+package org.apache.commons.math.geometry.euclidean.twod;

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+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/package-info.java Sat Oct  1 18:51:25 2011
@@ -0,0 +1,25 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *<p>
+ *This package is the top level package for geometry. It provides only a few interfaces
+ *related to vectorial/affine spaces that are implemented in sub-packages.
+ *</p>
+ *
+ */
+package org.apache.commons.math.geometry;

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+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/partitioning/package-info.java Sat Oct  1 18:51:25 2011
@@ -0,0 +1,108 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *This package provides classes to implement Binary Space Partition trees.
+ *
+ *<p>
+ *{@link org.apache.commons.math.geometry.partitioning.BSPTree BSP trees}
+ *are an efficient way to represent parts of space and in particular
+ *polytopes (line segments in 1D, polygons in 2D and polyhedrons in 3D)
+ *and to operate on them. The main principle is to recursively subdivide
+ *the space using simple hyperplanes (points in 1D, lines in 2D, planes
+ *in 3D).
+ *</p>
+ *
+ *<p>
+ *We start with a tree composed of a single node without any cut
+ *hyperplane: it represents the complete space, which is a convex
+ *part. If we add a cut hyperplane to this node, this represents a
+ *partition with the hyperplane at the node level and two half spaces at
+ *each side of the cut hyperplane. These half-spaces are represented by
+ *two child nodes without any cut hyperplanes associated, the plus child
+ *which represents the half space on the plus side of the cut hyperplane
+ *and the minus child on the other side. Continuing the subdivisions, we
+ *end up with a tree having internal nodes that are associated with a
+ *cut hyperplane and leaf nodes without any hyperplane which correspond
+ *to convex parts.
+ *</p>
+ *
+ *<p>
+ *When BSP trees are used to represent polytopes, the convex parts are
+ *known to be completely inside or outside the polytope as long as there
+ *is no facet in the part (which is obviously the case if the cut
+ *hyperplanes have been chosen as the underlying hyperplanes of the
+ *facets (this is called an autopartition) and if the subdivision
+ *process has been continued until all facets have been processed. It is
+ *important to note that the polytope is <em>not</em> defined by a
+ *single part, but by several convex ones. This is the property that
+ *allows BSP-trees to represent non-convex polytopes despites all parts
+ *are convex. The {@link
+ *org.apache.commons.math.geometry.partitioning.Region Region} class is
+ *devoted to this representation, it is build on top of the {@link
+ *org.apache.commons.math.geometry.partitioning.BSPTree BSPTree} class using
+ *boolean objects as the leaf nodes attributes to represent the
+ *inside/outside property of each leaf part, and also adds various
+ *methods dealing with boundaries (i.e. the separation between the
+ *inside and the outside parts).
+ *</p>
+ *
+ *<p>
+ *Rather than simply associating the internal nodes with an hyperplane,
+ *we consider <em>sub-hyperplanes</em> which correspond to the part of
+ *the hyperplane that is inside the convex part defined by all the
+ *parent nodes (this implies that the sub-hyperplane at root node is in
+ *fact a complete hyperplane, because there is no parent to bound
+ *it). Since the parts are convex, the sub-hyperplanes are convex, in
+ *3D the convex parts are convex polyhedrons, and the sub-hyperplanes
+ *are convex polygons that cut these polyhedrons in two
+ *sub-polyhedrons. Using this definition, a BSP tree completely
+ *partitions the space. Each point either belongs to one of the
+ *sub-hyperplanes in an internal node or belongs to one of the leaf
+ *convex parts.
+ *</p>
+ *
+ *<p>
+ *In order to determine where a point is, it is sufficient to check its
+ *position with respect to the root cut hyperplane, to select the
+ *corresponding child tree and to repeat the procedure recursively,
+ *until either the point appears to be exactly on one of the hyperplanes
+ *in the middle of the tree or to be in one of the leaf parts. For
+ *this operation, it is sufficient to consider the complete hyperplanes,
+ *there is no need to check the points with the boundary of the
+ *sub-hyperplanes, because this check has in fact already been realized
+ *by the recursive descent in the tree. This is very easy to do and very
+ *efficient, especially if the tree is well balanced (the cost is
+ *<code>O(log(n))</code> where <code>n</code> is the number of facets)
+ *or if the first tree levels close to the root discriminate large parts
+ *of the total space.
+ *</p>
+ *
+ *<p>
+ *One of the main sources for the development of this package was Bruce
+ *Naylor, John Amanatides and William Thibault paper <a
+ *href="http://www.cs.yorku.ca/~amana/research/bsptSetOp.pdf">Merging
+ *BSP Trees Yields Polyhedral Set Operations</a> Proc. Siggraph '90,
+ *Computer Graphics 24(4), August 1990, pp 115-124, published by the
+ *Association for Computing Machinery (ACM). The same paper can also be
+ *found <a
+ *href="http://www.cs.utexas.edu/users/fussell/courses/cs384g/bsp_treemerge.pdf">here</a>.
+ *</p>
+ *
+ *
+ */
+package org.apache.commons.math.geometry.partitioning;

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+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *<p>
+ *This package provides multidimensional ordering features for partitioning.
+ *</p>
+ *
+ */
+package org.apache.commons.math.geometry.partitioning.utilities;

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+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *Linear algebra support.
+ */
+package org.apache.commons.math.linear;

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+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/events/package-info.java Sat Oct  1 18:51:25 2011
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+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *<p>
+ *This package provides classes to handle discrete events occurring during
+ *Ordinary Differential Equations integration.
+ *</p>
+ *
+ *<p>
+ *Discrete events detection is based on switching functions. The user provides
+ *a simple {@link org.apache.commons.math.ode.events.EventHandler#g g(t, y)}
+ *function depending on the current time and state. The integrator will monitor
+ *the value of the function throughout integration range and will trigger the
+ *event when its sign changes. The magnitude of the value is almost irrelevant,
+ *it should however be continuous (but not necessarily smooth) for the sake of
+ *root finding. The steps are shortened as needed to ensure the events occur
+ *at step boundaries (even if the integrator is a fixed-step integrator).
+ *</p>
+ *
+ *<p>
+ *When an event is triggered, several different options are available:
+ *</p>
+ *<ul>
+ *  <li>integration can be stopped (this is called a G-stop facility),</li>
+ *  <li>the state vector or the derivatives can be changed,</li>
+ *  <li>or integration can simply go on.</li>
+ *</ul>
+ *
+ *<p>
+ *The first case, G-stop, is the most common one. A typical use case is when an
+ *ODE must be solved up to some target state is reached, with a known value of
+ *the state but an unknown occurrence time. As an example, if we want to monitor
+ *a chemical reaction up to some predefined concentration for the first substance,
+ *we can use the following switching function setting:
+ *<pre>
+ *  public double g(double t, double[] y) {
+ *    return y[0] - targetConcentration;
+ *  }
+ *
+ *  public int eventOccurred(double t, double[] y) {
+ *    return STOP;
+ *  }
+ *</pre>
+ *</p>
+ *
+ *<p>
+ *The second case, change state vector or derivatives is encountered when dealing
+ *with discontinuous dynamical models. A typical case would be the motion of a
+ *spacecraft when thrusters are fired for orbital maneuvers. The acceleration is
+ *smooth as long as no maneuver are performed, depending only on gravity, drag,
+ *third body attraction, radiation pressure. Firing a thruster introduces a
+ *discontinuity that must be handled appropriately by the integrator. In such a case,
+ *we would use a switching function setting similar to this:
+ *<pre>
+ *  public double g(double t, double[] y) {
+ *    return (t - tManeuverStart) &lowast; (t - tManeuverStop);
+ *  }
+ *
+ *  public int eventOccurred(double t, double[] y) {
+ *    return RESET_DERIVATIVES;
+ *  }
+ *</pre>
+ *</p>
+ *
+ *<p>
+ *The third case is useful mainly for monitoring purposes, a simple example is:
+ *<pre>
+ *  public double g(double t, double[] y) {
+ *    return y[0] - y[1];
+ *  }
+ *
+ *  public int eventOccurred(double t, double[] y) {
+ *    logger.log("y0(t) and y1(t) curves cross at t = " + t);
+ *    return CONTINUE;
+ *  }
+ *</pre>
+ *</p>
+ *
+ *
+ */
+package org.apache.commons.math.ode.events;

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+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *<p>
+ *This package provides classes to solve non-stiff Ordinary Differential Equations problems.
+ *</p>
+ *
+ *
+ */
+package org.apache.commons.math.ode.nonstiff;

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+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *<p>
+ *This package provides classes to solve Ordinary Differential Equations problems.
+ *</p>
+ *
+ *<p>
+ *This package solves Initial Value Problems of the form
+ *<code>y'=f(t,y)</code> with <code>t<sub>0</sub></code> and
+ *<code>y(t<sub>0</sub>)=y<sub>0</sub></code> known. The provided
+ *integrators compute an estimate of <code>y(t)</code> from
+ *<code>t=t<sub>0</sub></code> to <code>t=t<sub>1</sub></code>.
+ *It is also possible to get thederivatives with respect to the initial state
+ *<code>dy(t)/dy(t<sub>0</sub>)</code> or the derivatives with
+ *respect to some ODE parameters <code>dy(t)/dp</code>.
+ *</p>
+ *
+ *<p>
+ *All integrators provide dense output. This means that besides
+ *computing the state vector at discrete times, they also provide a
+ *cheap mean to get the state between the time steps. They do so through
+ *classes extending the {@link
+ *org.apache.commons.math.ode.sampling.StepInterpolator StepInterpolator}
+ *abstract class, which are made available to the user at the end of
+ *each step.
+ *</p>
+ *
+ *<p>
+ *All integrators handle multiple discrete events detection based on switching
+ *functions. This means that the integrator can be driven by user specified
+ *discrete events. The steps are shortened as needed to ensure the events occur
+ *at step boundaries (even if the integrator is a fixed-step
+ *integrator). When the events are triggered, integration can be stopped
+ *(this is called a G-stop facility), the state vector can be changed,
+ *or integration can simply go on. The latter case is useful to handle
+ *discontinuities in the differential equations gracefully and get
+ *accurate dense output even close to the discontinuity.
+ *</p>
+ *
+ *<p>
+ *The user should describe his problem in his own classes
+ *(<code>UserProblem</code> in the diagram below) which should implement
+ *the {@link org.apache.commons.math.ode.FirstOrderDifferentialEquations
+ *FirstOrderDifferentialEquations} interface. Then he should pass it to
+ *the integrator he prefers among all the classes that implement the
+ *{@link org.apache.commons.math.ode.FirstOrderIntegrator
+ *FirstOrderIntegrator} interface.
+ *</p>
+ *
+ *<p>
+ *The solution of the integration problem is provided by two means. The
+ *first one is aimed towards simple use: the state vector at the end of
+ *the integration process is copied in the <code>y</code> array of the
+ *{@link org.apache.commons.math.ode.FirstOrderIntegrator#integrate
+ *FirstOrderIntegrator.integrate} method. The second one should be used
+ *when more in-depth information is needed throughout the integration
+ *process. The user can register an object implementing the {@link
+ *org.apache.commons.math.ode.sampling.StepHandler StepHandler} interface or a
+ *{@link org.apache.commons.math.ode.sampling.StepNormalizer StepNormalizer}
+ *object wrapping a user-specified object implementing the {@link
+ *org.apache.commons.math.ode.sampling.FixedStepHandler FixedStepHandler}
+ *interface into the integrator before calling the {@link
+ *org.apache.commons.math.ode.FirstOrderIntegrator#integrate
+ *FirstOrderIntegrator.integrate} method. The user object will be called
+ *appropriately during the integration process, allowing the user to
+ *process intermediate results. The default step handler does nothing.
+ *</p>
+ *
+ *<p>
+ *{@link org.apache.commons.math.ode.ContinuousOutputModel
+ *ContinuousOutputModel} is a special-purpose step handler that is able
+ *to store all steps and to provide transparent access to any
+ *intermediate result once the integration is over. An important feature
+ *of this class is that it implements the <code>Serializable</code>
+ *interface. This means that a complete continuous model of the
+ *integrated function throughout the integration range can be serialized
+ *and reused later (if stored into a persistent medium like a filesystem
+ *or a database) or elsewhere (if sent to another application). Only the
+ *result of the integration is stored, there is no reference to the
+ *integrated problem by itself.
+ *</p>
+ *
+ *<p>
+ *Other default implementations of the {@link
+ *org.apache.commons.math.ode.sampling.StepHandler StepHandler} interface are
+ *available for general needs ({@link
+ *org.apache.commons.math.ode.sampling.DummyStepHandler DummyStepHandler}, {@link
+ *org.apache.commons.math.ode.sampling.StepNormalizer StepNormalizer}) and custom
+ *implementations can be developed for specific needs. As an example,
+ *if an application is to be completely driven by the integration
+ *process, then most of the application code will be run inside a step
+ *handler specific to this application.
+ *</p>
+ *
+ *<p>
+ *Some integrators (the simple ones) use fixed steps that are set at
+ *creation time. The more efficient integrators use variable steps that
+ *are handled internally in order to control the integration error with
+ *respect to a specified accuracy (these integrators extend the {@link
+ *org.apache.commons.math.ode.nonstiff.AdaptiveStepsizeIntegrator
+ *AdaptiveStepsizeIntegrator} abstract class). In this case, the step
+ *handler which is called after each successful step shows up the
+ *variable stepsize. The {@link
+ *org.apache.commons.math.ode.sampling.StepNormalizer StepNormalizer} class can
+ *be used to convert the variable stepsize into a fixed stepsize that
+ *can be handled by classes implementing the {@link
+ *org.apache.commons.math.ode.sampling.FixedStepHandler FixedStepHandler}
+ *interface. Adaptive stepsize integrators can automatically compute the
+ *initial stepsize by themselves, however the user can specify it if he
+ *prefers to retain full control over the integration or if the
+ *automatic guess is wrong.
+ *</p>
+ *
+ *<p>
+ *<table border="1" align="center">
+ *<tr BGCOLOR="#CCCCFF"><td colspan=2><font size="+2">Fixed Step Integrators</font></td></tr>
+ *<tr BGCOLOR="#EEEEFF"><font size="+1"><td>Name</td><td>Order</td></font></tr>
+ *<tr><td>{@link org.apache.commons.math.ode.nonstiff.EulerIntegrator Euler}</td><td>1</td></tr>
+ *<tr><td>{@link org.apache.commons.math.ode.nonstiff.MidpointIntegrator Midpoint}</td><td>2</td></tr>
+ *<tr><td>{@link org.apache.commons.math.ode.nonstiff.ClassicalRungeKuttaIntegrator Classical Runge-Kutta}</td><td>4</td></tr>
+ *<tr><td>{@link org.apache.commons.math.ode.nonstiff.GillIntegrator Gill}</td><td>4</td></tr>
+ *<tr><td>{@link org.apache.commons.math.ode.nonstiff.ThreeEighthesIntegrator 3/8}</td><td>4</td></tr>
+ *</table>
+ *</p>
+ *
+ *<table border="1" align="center">
+ *<tr BGCOLOR="#CCCCFF"><td colspan=3><font size="+2">Adaptive Stepsize Integrators</font></td></tr>
+ *<tr BGCOLOR="#EEEEFF"><font size="+1"><td>Name</td><td>Integration Order</td><td>Error Estimation Order</td></font></tr>
+ *<tr><td>{@link org.apache.commons.math.ode.nonstiff.HighamHall54Integrator Higham and Hall}</td><td>5</td><td>4</td></tr>
+ *<tr><td>{@link org.apache.commons.math.ode.nonstiff.DormandPrince54Integrator Dormand-Prince 5(4)}</td><td>5</td><td>4</td></tr>
+ *<tr><td>{@link org.apache.commons.math.ode.nonstiff.DormandPrince853Integrator Dormand-Prince 8(5,3)}</td><td>8</td><td>5 and 3</td></tr>
+ *<tr><td>{@link org.apache.commons.math.ode.nonstiff.GraggBulirschStoerIntegrator Gragg-Bulirsch-Stoer}</td><td>variable (up to 18 by default)</td><td>variable</td></tr>
+ *<tr><td>{@link org.apache.commons.math.ode.nonstiff.AdamsBashforthIntegrator Adams-Bashforth}</td><td>variable</td><td>variable</td></tr>
+ *<tr><td>{@link org.apache.commons.math.ode.nonstiff.AdamsMoultonIntegrator Adams-Moulton}</td><td>variable</td><td>variable</td></tr>
+ *</table>
+ *</p>
+ *
+ *<p>
+ *In the table above, the {@link org.apache.commons.math.ode.nonstiff.AdamsBashforthIntegrator
+ *Adams-Bashforth} and {@link org.apache.commons.math.ode.nonstiff.AdamsMoultonIntegrator
+ *Adams-Moulton} integrators appear as variable-step ones. This is an experimental extension
+ *to the classical algorithms using the Nordsieck vector representation.
+ *</p>
+ *
+ *
+ */
+package org.apache.commons.math.ode;

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+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *<p>
+ *This package provides classes to handle sampling steps during
+ *Ordinary Differential Equations integration.
+ *</p>
+ *
+ *<p>
+ *In addition to computing the evolution of the state vector at some grid points, all
+ *ODE integrators also build up interpolation models of this evolution <em>inside</em> the
+ *last computed step. If users are interested in these interpolators, they can register a
+ *{@link org.apache.commons.math.ode.sampling.StepHandler StepHandler} instance using the
+ *{@link org.apache.commons.math.ode.FirstOrderIntegrator#addStepHandler addStepHandler}
+ *method which is supported by all integrators. The integrator will call this instance
+ *at the end of each accepted step and provide it the interpolator. The user can do
+ *whatever he wants with this interpolator, which computes both the state and its
+ *time-derivative. A typical use of step handler is to provide some output to monitor
+ *the integration process.
+ *</p>
+ *
+ *<p>
+ *In a sense, this is a kind of Inversion Of Control: rather than having the master
+ *application driving the slave integrator by providing the target end value for
+ *the free variable, we get a master integrator scheduling the free variable
+ *evolution and calling the slave application callbacks that were registered at
+ *configuration time.
+ *</p>
+ *
+ *<p>
+ *Since some integrators may use variable step size, the generic {@link
+ *org.apache.commons.math.ode.sampling.StepHandler StepHandler} interface can be called
+ *either at regular or irregular rate. This interface allows to navigate to any location
+ *within the last computed step, thanks to the provided {@link
+ *org.apache.commons.math.ode.sampling.StepInterpolator StepInterpolator} object.
+ *If regular output is desired (for example in order to write an ephemeris file), then
+ *the simpler {@link org.apache.commons.math.ode.sampling.FixedStepHandler FixedStepHandler}
+ *interface can be used. Objects implementing this interface should be wrapped within a
+ *{@link org.apache.commons.math.ode.sampling.StepNormalizer StepNormalizer} instance
+ *in order to be registered to the integrator.
+ *</p>
+ *
+ *
+ */
+package org.apache.commons.math.ode.sampling;

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--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/direct/package-info.java (added)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/direct/package-info.java Sat Oct  1 18:51:25 2011
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+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *<p>
+ *This package provides optimization algorithms that don't require derivatives.
+ *</p>
+ *
+ */
+package org.apache.commons.math.optimization.direct;

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+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/fitting/package-info.java Sat Oct  1 18:51:25 2011
@@ -0,0 +1,30 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *This package provides classes to perform curve fitting.
+ *
+ *<p>Curve fitting is a special case of a least squares problem
+ *were the parameters are the coefficients of a function <code>f</code>
+ *whose graph <code>y=f(x)</code> should pass through sample points, and
+ *were the objective function is the squared sum of residuals
+ *<code>f(x<sub>i</sub>)-y<sub>i</sub></code> for observed points
+ *(x<sub>i</sub>, y<sub>i</sub>).</p>
+ *
+ *
+ */
+package org.apache.commons.math.optimization.fitting;

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--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/general/package-info.java (added)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/general/package-info.java Sat Oct  1 18:51:25 2011
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+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *This package provides optimization algorithms that require derivatives.
+ *
+ */
+package org.apache.commons.math.optimization.general;

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--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/linear/package-info.java (added)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/linear/package-info.java Sat Oct  1 18:51:25 2011
@@ -0,0 +1,22 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+/**
+ *
+ *This package provides optimization algorithms for linear constrained problems.
+ *
+ */
+package org.apache.commons.math.optimization.linear;



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