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Merge branch 'master' of github.com:mastodon-sc/mastodon-pasteur
2 parents b648ba1 + 39ddfee commit 84dbd40

30 files changed

+386
-22
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Diff for: ‎LICENSE.txt

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Copyright (c) 2019 - 2022, Tobias Pietzsch, Jean-Yves Tinevez
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Copyright (c) 2019 - 2023, Tobias Pietzsch, Jean-Yves Tinevez
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All rights reserved.
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Redistribution and use in source and binary forms, with or without modification,

Diff for: ‎pom.xml

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<groupId>org.mastodon</groupId>
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<artifactId>mastodon-pasteur</artifactId>
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<version>1.0.0-beta-7-SNAPSHOT</version>
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<version>1.0.0-beta-8-SNAPSHOT</version>
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<name>Mastodon Pasteur Plugins</name>
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<description>Mastodon plugins developed in the context of Pasteur users projects.</description>
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<mailingLists>
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<mailingList>
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<name>ImageJ Forum</name>
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<archive>http://forum.imagej.net/</archive>
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<archive>https://forum.image.sc/</archive>
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</mailingList>
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</mailingLists>
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<license.organizationName>Mastodon authors</license.organizationName>
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<license.copyrightOwners>Tobias Pietzsch, Jean-Yves Tinevez</license.copyrightOwners>
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<mastodon.version>1.0.0-beta-27-SNAPSHOT</mastodon.version>
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<mastodon-tracking.version>1.0.0-beta-14-SNAPSHOT</mastodon-tracking.version>
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<mastodon.version>1.0.0-beta-27</mastodon.version>
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<mastodon-tracking.version>1.0.0-beta-14</mastodon-tracking.version>
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<!-- NB: Deploy releases to the SciJava Maven repository. -->
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<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>

Diff for: ‎src/main/java/org/mastodon/mamut/io/csv/AutoDetectCSVSeparator.java

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* #%L
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* mastodon-pasteur
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* %%
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* Copyright (C) 2019 - 2022 Tobias Pietzsch, Jean-Yves Tinevez
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* Copyright (C) 2019 - 2023 Tobias Pietzsch, Jean-Yves Tinevez
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:

Diff for: ‎src/main/java/org/mastodon/mamut/io/csv/CSVImporter.java

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* #%L
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* mastodon-pasteur
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* %%
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* Copyright (C) 2019 - 2022 Tobias Pietzsch, Jean-Yves Tinevez
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* Copyright (C) 2019 - 2023 Tobias Pietzsch, Jean-Yves Tinevez
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:

Diff for: ‎src/main/java/org/mastodon/mamut/io/csv/plugin/CSVImporterPlugin.java

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* #%L
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* mastodon-pasteur
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* %%
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* Copyright (C) 2019 - 2022 Tobias Pietzsch, Jean-Yves Tinevez
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* Copyright (C) 2019 - 2023 Tobias Pietzsch, Jean-Yves Tinevez
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:

Diff for: ‎src/main/java/org/mastodon/mamut/io/csv/plugin/ui/CSVImporterPanel.java

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* #%L
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* mastodon-pasteur
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* %%
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* Copyright (C) 2019 - 2022 Tobias Pietzsch, Jean-Yves Tinevez
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* Copyright (C) 2019 - 2023 Tobias Pietzsch, Jean-Yves Tinevez
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:

Diff for: ‎src/main/java/org/mastodon/mamut/io/csv/plugin/ui/CSVImporterUIController.java

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* #%L
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* mastodon-pasteur
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* %%
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* Copyright (C) 2019 - 2022 Tobias Pietzsch, Jean-Yves Tinevez
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* Copyright (C) 2019 - 2023 Tobias Pietzsch, Jean-Yves Tinevez
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:

Diff for: ‎src/main/java/org/mastodon/mamut/nearest/Builder.java

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/*-
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* #%L
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* mastodon-pasteur
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* %%
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* Copyright (C) 2019 - 2023 Tobias Pietzsch, Jean-Yves Tinevez
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
17+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.mastodon.mamut.nearest;
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import org.mastodon.mamut.feature.SpotIntensityFeature;

Diff for: ‎src/main/java/org/mastodon/mamut/nearest/NearestObjectStatComputation.java

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/*-
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* #%L
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* mastodon-pasteur
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* %%
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* Copyright (C) 2019 - 2023 Tobias Pietzsch, Jean-Yves Tinevez
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
9+
*
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* 1. Redistributions of source code must retain the above copyright notice,
11+
* this list of conditions and the following disclaimer.
12+
* 2. Redistributions in binary form must reproduce the above copyright notice,
13+
* this list of conditions and the following disclaimer in the documentation
14+
* and/or other materials provided with the distribution.
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*
16+
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
17+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
18+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
19+
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
24+
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.mastodon.mamut.nearest;
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import java.util.ArrayList;

Diff for: ‎src/main/java/org/mastodon/mamut/nearest/NearestObjectStatFeature.java

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/*-
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* #%L
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* mastodon-pasteur
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* %%
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* Copyright (C) 2019 - 2023 Tobias Pietzsch, Jean-Yves Tinevez
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
13+
* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
17+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.mastodon.mamut.nearest;
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import java.util.HashMap;

Diff for: ‎src/main/java/org/mastodon/mamut/nearest/NearestObjectStatModel.java

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/*-
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* #%L
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* mastodon-pasteur
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* %%
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* Copyright (C) 2019 - 2023 Tobias Pietzsch, Jean-Yves Tinevez
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
9+
*
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* 1. Redistributions of source code must retain the above copyright notice,
11+
* this list of conditions and the following disclaimer.
12+
* 2. Redistributions in binary form must reproduce the above copyright notice,
13+
* this list of conditions and the following disclaimer in the documentation
14+
* and/or other materials provided with the distribution.
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*
16+
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
17+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
18+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
19+
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
21+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.mastodon.mamut.nearest;
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import java.util.ArrayList;

Diff for: ‎src/main/java/org/mastodon/mamut/nearest/NearestObjectStatPlugin.java

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/*-
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* #%L
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* mastodon-pasteur
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* %%
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* Copyright (C) 2019 - 2023 Tobias Pietzsch, Jean-Yves Tinevez
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
9+
*
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* 1. Redistributions of source code must retain the above copyright notice,
11+
* this list of conditions and the following disclaimer.
12+
* 2. Redistributions in binary form must reproduce the above copyright notice,
13+
* this list of conditions and the following disclaimer in the documentation
14+
* and/or other materials provided with the distribution.
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*
16+
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
17+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
18+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
19+
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
21+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.mastodon.mamut.nearest;
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import java.awt.event.ActionEvent;
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public class NearestObjectStatPlugin implements MamutPlugin
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{
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public static final String[] MENU_PATH = new String[] { "Plugins" };
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public static final String[] MENU_PATH = new String[] { "Plugins", "Compute Feature" };
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public static final String SHOW_NEAREST_NEIGHBORS_STATS_DIALOG_ACTION = "generate statistics on nearest neighbors";
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static
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{
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menuTexts.put( SHOW_NEAREST_NEIGHBORS_STATS_DIALOG_ACTION, "Generate statistics on nearest neighbors" );
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menuTexts.put( SHOW_NEAREST_NEIGHBORS_STATS_DIALOG_ACTION, "Statistics on nearest neighbors" );
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}
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private final ShowDialogAction toggleDialog = new ShowDialogAction();

Diff for: ‎src/main/java/org/mastodon/mamut/nearest/ui/NearestObjectStatController.java

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/*-
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* #%L
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* mastodon-pasteur
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* %%
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* Copyright (C) 2019 - 2023 Tobias Pietzsch, Jean-Yves Tinevez
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
13+
* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
17+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.mastodon.mamut.nearest.ui;
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import java.util.Timer;

Diff for: ‎src/main/java/org/mastodon/mamut/nearest/ui/NearestObjectStatListPanel.java

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/*-
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* #%L
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* mastodon-pasteur
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* %%
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* Copyright (C) 2019 - 2023 Tobias Pietzsch, Jean-Yves Tinevez
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* %%
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* Redistribution and use in source and binary forms, with or without
8+
* modification, are permitted provided that the following conditions are met:
9+
*
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* 1. Redistributions of source code must retain the above copyright notice,
11+
* this list of conditions and the following disclaimer.
12+
* 2. Redistributions in binary form must reproduce the above copyright notice,
13+
* this list of conditions and the following disclaimer in the documentation
14+
* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
17+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
23+
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.mastodon.mamut.nearest.ui;
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import java.awt.BorderLayout;

Diff for: ‎src/main/java/org/mastodon/mamut/nearest/ui/NearestObjectStatMainPanel.java

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/*-
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* #%L
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* mastodon-pasteur
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* %%
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* Copyright (C) 2019 - 2023 Tobias Pietzsch, Jean-Yves Tinevez
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* %%
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* Redistribution and use in source and binary forms, with or without
8+
* modification, are permitted provided that the following conditions are met:
9+
*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
13+
* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.mastodon.mamut.nearest.ui;
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import java.awt.BorderLayout;

Diff for: ‎src/main/java/org/mastodon/mamut/nearest/ui/NearestObjectStatModelIO.java

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/*-
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* #%L
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* mastodon-pasteur
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* %%
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* Copyright (C) 2019 - 2023 Tobias Pietzsch, Jean-Yves Tinevez
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
11+
* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
13+
* this list of conditions and the following disclaimer in the documentation
14+
* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
21+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
22+
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
23+
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.mastodon.mamut.nearest.ui;
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import static org.yaml.snakeyaml.DumperOptions.FlowStyle.FLOW;

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