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Merged
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Nov 17, 2022
Merged

Adopted Google Java Style #295

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0fd8f03
Spotify's fmt-maven-plugin
cicirello Nov 17, 2022
93be6d1
reformatted to Google Java style
cicirello Nov 17, 2022
4325c44
Update CHANGELOG.md
cicirello Nov 17, 2022
e040273
Update README.md
cicirello Nov 17, 2022
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Added

### Changed
* Reformatted all sourcecode to [Google Java Style](https://google.github.io/styleguide/javaguide.html)

### Deprecated

Expand All @@ -22,8 +23,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### CI/CD
* Configured the [refactor-first-maven-plugin](https://github.com/jimbethancourt/RefactorFirst) within a profile in the pom.xml.
* Configured [Spotify's fmt-maven-plugin](https://github.com/spotify/fmt-maven-plugin) to format to Google Java Style during builds.

### Other
* Adopted [Google Java Style](https://google.github.io/styleguide/javaguide.html)


## [4.3.0] - 2022-10-17
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -15,7 +15,7 @@ API documentation: https://jpt.cicirello.org/api
| __JaCoCo Test Coverage__ | [![coverage](https://raw.githubusercontent.com/cicirello/JavaPermutationTools/badges/jacoco.svg)](https://github.com/cicirello/JavaPermutationTools/actions/workflows/build.yml) [![branch coverage](https://raw.githubusercontent.com/cicirello/JavaPermutationTools/badges/branches.svg)](https://github.com/cicirello/JavaPermutationTools/actions/workflows/build.yml) |
| __Security__ | [![Snyk security score](https://snyk-widget.herokuapp.com/badge/mvn/org.cicirello/jpt/badge.svg)](https://snyk.io/vuln/maven%3Aorg.cicirello%3Ajpt) [![Snyk Known Vulnerabilities](https://snyk.io/test/github/cicirello/JavaPermutationTools/badge.svg)](https://snyk.io/test/github/cicirello/JavaPermutationTools) |
| __DOI__ | [![DOI](https://zenodo.org/badge/139182095.svg)](https://zenodo.org/badge/latestdoi/139182095) |
| __License__ | [![GitHub](https://img.shields.io/github/license/cicirello/JavaPermutationTools)](https://github.com/cicirello/JavaPermutationTools/blob/master/LICENSE) |
| __Other Information__ | [![GitHub](https://img.shields.io/github/license/cicirello/JavaPermutationTools)](https://github.com/cicirello/JavaPermutationTools/blob/master/LICENSE) [![style](https://img.shields.io/badge/style-Google%20Java%20Style-informational)](https://google.github.io/styleguide/javaguide.html) |
| __Support__ | [![GitHub Sponsors](https://img.shields.io/badge/sponsor-30363D?logo=GitHub-Sponsors&logoColor=#EA4AAA)](https://github.com/sponsors/cicirello) [![Liberapay](https://img.shields.io/badge/Liberapay-F6C915?logo=liberapay&logoColor=black)](https://liberapay.com/cicirello) [![Ko-Fi](https://img.shields.io/badge/Ko--fi-F16061?logo=ko-fi&logoColor=white)](https://ko-fi.com/cicirello) |

## How to Cite
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12 changes: 12 additions & 0 deletions pom.xml
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Expand Up @@ -314,6 +314,18 @@
</execution>
</executions>
</plugin>
<plugin>
<groupId>com.spotify.fmt</groupId>
<artifactId>fmt-maven-plugin</artifactId>
<version>2.19</version>
<executions>
<execution>
<goals>
<goal>format</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
150 changes: 79 additions & 71 deletions src/main/java/module-info.java
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Expand Up @@ -2,16 +2,16 @@
* JavaPermutationTools - A Java library for computation on permutations.
* Copyright 2005-2022 Vincent A. Cicirello, <https://www.cicirello.org/>.
*
* JavaPermutationTools is free software: you can
* redistribute it and/or modify it under the terms of the GNU
* General Public License as published by the Free Software
* Foundation, either version 3 of the License, or (at your
* JavaPermutationTools is free software: you can
* redistribute it and/or modify it under the terms of the GNU
* General Public License as published by the Free Software
* Foundation, either version 3 of the License, or (at your
* option) any later version.
*
* JavaPermutationTools is distributed in the hope
* that it will be useful, but WITHOUT ANY WARRANTY; without even
* the implied warranty of MERCHANTABILITY or FITNESS FOR A
* PARTICULAR PURPOSE. See the GNU General Public License for more
* JavaPermutationTools is distributed in the hope
* that it will be useful, but WITHOUT ANY WARRANTY; without even
* the implied warranty of MERCHANTABILITY or FITNESS FOR A
* PARTICULAR PURPOSE. See the GNU General Public License for more
* details.
*
* You should have received a copy of the GNU General Public License
Expand All @@ -20,82 +20,90 @@
*/

/**
*
*
* <h2>JavaPermutationTools - A Java library for computation on permutations</h2>
*
* <p>Copyright &copy; 2005-2022 <a href="https://www.cicirello.org/" target=_top>Vincent A. Cicirello</a>.</p>
*
* <p><a href="https://doi.org/10.21105/joss.00950"><img
* src="http://joss.theoj.org/papers/10.21105/joss.00950/status.svg"
* alt="DOI:10.21105/joss.00950" height="20" width="168"></a>
* <a href="https://search.maven.org/artifact/org.cicirello/jpt"><img
* src="https://img.shields.io/maven-central/v/org.cicirello/jpt.svg?logo=apachemaven"
* alt="Maven Central" height="20" width="153"></a>
* <a href="https://github.com/cicirello/JavaPermutationTools/releases"><img
* src="https://img.shields.io/github/v/release/cicirello/JavaPermutationTools?logo=GitHub"
* alt="GitHub release (latest by date)" height="20" width="111"></a>
* <a href="https://github.com/cicirello/JavaPermutationTools"><img
* src="https://jpt.cicirello.org/images/GitHub.svg"
* alt="GitHub Repository" width="68" height="20"></a>
* <a href="https://github.com/cicirello/JavaPermutationTools/blob/master/LICENSE"><img
* src="https://img.shields.io/github/license/cicirello/JavaPermutationTools"
* alt="GNU General Public License Version 3 (GPLv3)" height="20" width="102"></a>
* </p>
* <p>Copyright &copy; 2005-2022 <a href="https://www.cicirello.org/" target=_top>Vincent A.
* Cicirello</a>.
*
* <p><a href="https://doi.org/10.21105/joss.00950"><img
* src="http://joss.theoj.org/papers/10.21105/joss.00950/status.svg" alt="DOI:10.21105/joss.00950"
* height="20" width="168"></a> <a href="https://search.maven.org/artifact/org.cicirello/jpt"><img
* src="https://img.shields.io/maven-central/v/org.cicirello/jpt.svg?logo=apachemaven" alt="Maven
* Central" height="20" width="153"></a> <a
* href="https://github.com/cicirello/JavaPermutationTools/releases"><img
* src="https://img.shields.io/github/v/release/cicirello/JavaPermutationTools?logo=GitHub"
* alt="GitHub release (latest by date)" height="20" width="111"></a> <a
* href="https://github.com/cicirello/JavaPermutationTools"><img
* src="https://jpt.cicirello.org/images/GitHub.svg" alt="GitHub Repository" width="68"
* height="20"></a> <a
* href="https://github.com/cicirello/JavaPermutationTools/blob/master/LICENSE"><img
* src="https://img.shields.io/github/license/cicirello/JavaPermutationTools" alt="GNU General
* Public License Version 3 (GPLv3)" height="20" width="102"></a>
*
* <h3>About the JavaPermutationTools Library</h3>
*
* <p>JavaPermutationTools (JPT) is a Java library for representing and generating permutations
* and sequences, as well as performing computation on permutations and sequences. This includes
* implementations of a variety of permutation distance metrics as well as distance metrics on
* sequences (i.e., Strings, arrays, and other ordered data types).</p>
*
* <p>The <a href="https://github.com/cicirello/JavaPermutationTools" target=_top>source code</a>
* is hosted on GitHub; and is licensed under the
* <a href="https://www.gnu.org/licenses/gpl-3.0.html" target=_top>GNU General Public License
* Version 3 (GPLv3)</a>. The library's jar files are regularly published
* to <a href="https://search.maven.org/artifact/org.cicirello/jpt" target=_top>Maven Central</a>,
* from which it is easily imported into software projects using Maven and other
* commonly used build tools. Additionally, there is a
* GitHub <a href="https://github.com/cicirello/jpt-examples" target=_top>repository of
* example programs</a> that show basic usage of the JPT library, as well as replication programs that
* reproduce results found in published papers.</p>
*
* <p>For more information see the <a href="https://jpt.cicirello.org/" target=_top>JavaPermutationTools
* website</a>. Potential contributors, please see the source repository, and/or
* contact <a href="https://www.cicirello.org/" target=_top>Vincent A. Cicirello</a>.</p>
*
* <p>JavaPermutationTools (JPT) is a Java library for representing and generating permutations and
* sequences, as well as performing computation on permutations and sequences. This includes
* implementations of a variety of permutation distance metrics as well as distance metrics on
* sequences (i.e., Strings, arrays, and other ordered data types).
*
* <p>The <a href="https://github.com/cicirello/JavaPermutationTools" target=_top>source code</a> is
* hosted on GitHub; and is licensed under the <a href="https://www.gnu.org/licenses/gpl-3.0.html"
* target=_top>GNU General Public License Version 3 (GPLv3)</a>. The library's jar files are
* regularly published to <a href="https://search.maven.org/artifact/org.cicirello/jpt"
* target=_top>Maven Central</a>, from which it is easily imported into software projects using
* Maven and other commonly used build tools. Additionally, there is a GitHub <a
* href="https://github.com/cicirello/jpt-examples" target=_top>repository of example programs</a>
* that show basic usage of the JPT library, as well as replication programs that reproduce results
* found in published papers.
*
* <p>For more information see the <a href="https://jpt.cicirello.org/"
* target=_top>JavaPermutationTools website</a>. Potential contributors, please see the source
* repository, and/or contact <a href="https://www.cicirello.org/" target=_top>Vincent A.
* Cicirello</a>.
*
* <h3>How to Cite</h3>
*
* <p>If you use the JPT library in your research, please cite the following
* article which describes the library:</p>
* <p>If you use the JPT library in your research, please cite the following article which describes
* the library:
*
* <ul>
* <li>Vincent A. Cicirello.
* <a href="https://www.cicirello.org/publications/cicirello2018joss.html">JavaPermutationTools: A Java Library of Permutation Distance Metrics</a>.
* <i>Journal of Open Source Software</i>, 3(31), 950, November 2018.
* <a href="https://www.cicirello.org/publications/cicirello2018joss.pdf">[PDF]</a> <a href="https://www.cicirello.org/publications/cicirello2018joss.bib">[BIB]</a> <a href="https://doi.org/10.21105/joss.00950">[DOI]</a></li>
* <li>Vincent A. Cicirello. <a
* href="https://www.cicirello.org/publications/cicirello2018joss.html">JavaPermutationTools:
* A Java Library of Permutation Distance Metrics</a>. <i>Journal of Open Source Software</i>,
* 3(31), 950, November 2018. <a
* href="https://www.cicirello.org/publications/cicirello2018joss.pdf">[PDF]</a> <a
* href="https://www.cicirello.org/publications/cicirello2018joss.bib">[BIB]</a> <a
* href="https://doi.org/10.21105/joss.00950">[DOI]</a>
* </ul>
*
* <h3>Support JavaPermutationTools</h3>
*
* <p><a href="https://github.com/sponsors/cicirello"><img src="https://jpt.cicirello.org/images/github-sponsors.svg" alt="GitHub Sponsors" width="107" height="28"></a>
* <a href="https://liberapay.com/cicirello"><img src="https://jpt.cicirello.org/images/Liberapay.svg" alt="Liberapay" width="119" height="28"></a>
* <a href="https://ko-fi.com/cicirello"><img src="https://jpt.cicirello.org/images/ko-fi.svg" alt="Ko-Fi" width="82" height="28"></a></p>
* <p><a href="https://github.com/sponsors/cicirello"><img
* src="https://jpt.cicirello.org/images/github-sponsors.svg" alt="GitHub Sponsors" width="107"
* height="28"></a> <a href="https://liberapay.com/cicirello"><img
* src="https://jpt.cicirello.org/images/Liberapay.svg" alt="Liberapay" width="119" height="28"></a>
* <a href="https://ko-fi.com/cicirello"><img src="https://jpt.cicirello.org/images/ko-fi.svg"
* alt="Ko-Fi" width="82" height="28"></a>
*
* @author <a href=https://www.cicirello.org/ target=_top>Vincent A. Cicirello</a>,
* <a href=https://www.cicirello.org/ target=_top>https://www.cicirello.org/</a>
* @author <a href=https://www.cicirello.org/ target=_top>Vincent A. Cicirello</a>, <a
* href=https://www.cicirello.org/ target=_top>https://www.cicirello.org/</a>
*/
module org.cicirello.jpt {
exports org.cicirello.permutations;
exports org.cicirello.permutations.distance;
exports org.cicirello.sequences;
exports org.cicirello.sequences.distance;
// Specified transitive on these to minimize the impact
// of the introduction of modules on users' existing code
// that might assume access to the classes/interfaces from these
// modules. Strictly speaking, these do not need to be transitive
// for jpt because jpt's public interface does not depend on anything
// in these (e.g., no objects of any classes from these modules are
// returned or expected as parameters).
requires transitive org.cicirello.rho_mu;
requires transitive org.cicirello.core;
exports org.cicirello.permutations;
exports org.cicirello.permutations.distance;
exports org.cicirello.sequences;
exports org.cicirello.sequences.distance;

// Specified transitive on these to minimize the impact
// of the introduction of modules on users' existing code
// that might assume access to the classes/interfaces from these
// modules. Strictly speaking, these do not need to be transitive
// for jpt because jpt's public interface does not depend on anything
// in these (e.g., no objects of any classes from these modules are
// returned or expected as parameters).
requires transitive org.cicirello.rho_mu;
requires transitive org.cicirello.core;
}
62 changes: 31 additions & 31 deletions src/main/java/org/cicirello/permutations/IllegalPermutationStateException.java
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*
* This file is part of JavaPermutationTools (https://jpt.cicirello.org/).
*
* JavaPermutationTools is free software: you can
* redistribute it and/or modify it under the terms of the GNU
* General Public License as published by the Free Software
* Foundation, either version 3 of the License, or (at your
* JavaPermutationTools is free software: you can
* redistribute it and/or modify it under the terms of the GNU
* General Public License as published by the Free Software
* Foundation, either version 3 of the License, or (at your
* option) any later version.
*
* JavaPermutationTools is distributed in the hope
* that it will be useful, but WITHOUT ANY WARRANTY; without even
* the implied warranty of MERCHANTABILITY or FITNESS FOR A
* PARTICULAR PURPOSE. See the GNU General Public License for more
* JavaPermutationTools is distributed in the hope
* that it will be useful, but WITHOUT ANY WARRANTY; without even
* the implied warranty of MERCHANTABILITY or FITNESS FOR A
* PARTICULAR PURPOSE. See the GNU General Public License for more
* details.
*
* You should have received a copy of the GNU General Public License
Expand All @@ -23,30 +23,30 @@

/**
* This is a {@link RuntimeException} that is thrown by certain methods of the {@link Permutation}
* class to indicate that the Permutation object's state is invalid, and any subsequent calls
* to methods on that object may be unpredictable.
* class to indicate that the Permutation object's state is invalid, and any subsequent calls to
* methods on that object may be unpredictable.
*
* @author <a href=https://www.cicirello.org/ target=_top>Vincent A. Cicirello</a>,
* <a href=https://www.cicirello.org/ target=_top>https://www.cicirello.org/</a>
* @author <a href=https://www.cicirello.org/ target=_top>Vincent A. Cicirello</a>, <a
* href=https://www.cicirello.org/ target=_top>https://www.cicirello.org/</a>
*/
public class IllegalPermutationStateException extends RuntimeException {
/**
* Construct an IllegalPermutationStateException without specifying a cause.
*
* @param message A descriptive message about the exception that is thrown.
*/
public IllegalPermutationStateException(String message) {
super(message);
}
/**
* Construct an IllegalPermutationStateException.
*
* @param message A descriptive message about the exception that is thrown.
* @param cause The cause of the exception.
*/
public IllegalPermutationStateException(String message, Throwable cause) {
super(message, cause);
}

/**
* Construct an IllegalPermutationStateException without specifying a cause.
*
* @param message A descriptive message about the exception that is thrown.
*/
public IllegalPermutationStateException(String message) {
super(message);
}

/**
* Construct an IllegalPermutationStateException.
*
* @param message A descriptive message about the exception that is thrown.
* @param cause The cause of the exception.
*/
public IllegalPermutationStateException(String message, Throwable cause) {
super(message, cause);
}
}
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