Minimum spanning tree plugin #138
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| <?xml version="1.0" encoding="UTF-8" standalone="no"?> | ||
| <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> | ||
| <modelVersion>4.0.0</modelVersion> | ||
| <parent> | ||
| <artifactId>gephi-plugin-parent</artifactId> | ||
| <groupId>org.gephi</groupId> | ||
| <version>0.9.1</version> | ||
| </parent> | ||
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| <groupId>com.carlschroedl.gephi</groupId> | ||
| <artifactId>spanning-tree-plugin</artifactId> | ||
| <version>1.0.0</version> | ||
| <packaging>nbm</packaging> | ||
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| <name>Minimum Spanning Tree Plugin</name> | ||
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| <dependencies> | ||
| <dependency> | ||
| <groupId>org.netbeans.api</groupId> | ||
| <artifactId>org-openide-util</artifactId> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.gephi</groupId> | ||
| <artifactId>graphstore</artifactId> | ||
| <version>0.5.3</version> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.gephi</groupId> | ||
| <artifactId>statistics-api</artifactId> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.gephi</groupId> | ||
| <artifactId>utils-longtask</artifactId> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.gephi</groupId> | ||
| <artifactId>graph-api</artifactId> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.netbeans.api</groupId> | ||
| <artifactId>org-openide-util-lookup</artifactId> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.gephi</groupId> | ||
| <artifactId>io-importer-api</artifactId> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.gephi</groupId> | ||
| <artifactId>io-importer-plugin</artifactId> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.gephi</groupId> | ||
| <artifactId>io-processor-plugin</artifactId> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.netbeans.modules</groupId> | ||
| <artifactId>org-netbeans-modules-masterfs</artifactId> <!-- See http://wiki.netbeans.org/UsingFileSystemsMasterfs --> | ||
| <scope>test</scope> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>junit</groupId> | ||
| <artifactId>junit</artifactId> | ||
| <version>4.10</version> | ||
| <scope>test</scope> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.gephi</groupId> | ||
| <artifactId>filters-api</artifactId> | ||
| <scope>test</scope> | ||
| <type>jar</type> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.gephi</groupId> | ||
| <artifactId>filters-plugin</artifactId> | ||
| <scope>test</scope> | ||
| <type>jar</type> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.gephi</groupId> | ||
| <artifactId>filters-impl</artifactId> | ||
| <scope>test</scope> | ||
| <type>jar</type> | ||
| </dependency> | ||
| </dependencies> | ||
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| <build> | ||
| <plugins> | ||
| <plugin> | ||
| <groupId>org.codehaus.mojo</groupId> | ||
| <artifactId>nbm-maven-plugin</artifactId> | ||
| <configuration> | ||
| <licenseName>gpl-3.0</licenseName> | ||
| <licenseFile>gpl-3.0.txt</licenseFile> | ||
| <author>Carl Schroedl carlschroedl@gmail.com</author> | ||
| <sourceCodeUrl>https://github.com/carlschroedl/gephi-plugins</sourceCodeUrl> | ||
| <homePageUrl>https://github.com/carlschroedl/gephi-plugins/tree/minimum-spanning-tree-plugin</homePageUrl> | ||
| <publicPackages> | ||
| <publicPackage>com.carlschroedl.gephi.plugin.minimumspanningtree</publicPackage> | ||
| </publicPackages> | ||
| </configuration> | ||
| </plugin> | ||
| <plugin> | ||
| <groupId>org.apache.maven.plugins</groupId> | ||
| <artifactId>maven-surefire-plugin</artifactId> | ||
| <version>2.15</version> | ||
| </plugin> | ||
| </plugins> | ||
| </build> | ||
| <reporting> | ||
| <plugins> | ||
| <plugin> | ||
| <groupId>org.codehaus.mojo</groupId> | ||
| <artifactId>cobertura-maven-plugin</artifactId> | ||
| <version>2.6</version> | ||
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Author
There was a problem hiding this comment. Unfortunately, when triggering code coverage collection in the NetBeans UI, it disgregards the version of the coverage plugin that is specified in the pom. Instead, NetBeans uses the most recent stable release of the plugin. In this case, there are integration problems between NetBeans 8.2 and the most recent stable release of the cobertura-maven-plugin (2.7). By running the |
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| </plugin> | ||
| </plugins> | ||
| </reporting> | ||
| </project> | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,88 @@ | ||
| package com.carlschroedl.gephi.plugin.minimumspanningtree; | ||
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| import java.util.Collection; | ||
| import java.util.HashMap; | ||
| import java.util.Map; | ||
| import org.gephi.graph.api.Edge; | ||
| import org.gephi.graph.api.Graph; | ||
| import org.gephi.graph.api.Node; | ||
| import org.gephi.graph.impl.utils.MapDeepEquals; | ||
| import org.openide.util.Pair; | ||
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| /** | ||
| * This class determines whether two graphs have the same nodes and edges. Nodes | ||
| * from different graphs are considered equal if and only if their node ids are | ||
| * equal. Edges from different graphs are considered equal if and only if their | ||
| * source node ids, target node ids, and weights are equal. Two graphs are equal | ||
| * if and only if all of their nodes and edges are equal, and they have the same | ||
| * number of edges and nodes. | ||
| * All other node and edge attributes are ignored in this comparison. | ||
| */ | ||
| public class GraphTopologyEquals { | ||
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Author
There was a problem hiding this comment. I created this because I wanted my plugin's tests to assert that the result of running the algorithm was the same as a manually-verified graph loaded from file. Since I'm new to Gephi, I'm wondering if this is necessary. Are there any alternatives built in to Gephi for determining if graphs have equal topologies?
Member
There was a problem hiding this comment. I don't think there are builtin methods for this, but this is a small class. Great that you have tests!
Author
There was a problem hiding this comment. Ok. Cool. Thanks for confirming that I'm not duplicating existing Gephi functionality. |
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| private static Pair getSourceTargetPair(Edge e) { | ||
| Object aSourceId = e.getSource().getId(); | ||
| Object aTargetId = e.getTarget().getId(); | ||
| Pair<Object, Object> pair = Pair.of(aSourceId, aTargetId); | ||
| return pair; | ||
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| } | ||
| /** | ||
| * Compares edge collections based on source node id , target node id, and edge weight. | ||
| * @param aEdgeCollection | ||
| * @param bEdgeCollection | ||
| * @return true if all edges in both collections match, otherwise false. | ||
| */ | ||
| public static boolean edgeCollectionsAreEqual(Collection<Edge> aEdgeCollection, Collection<Edge> bEdgeCollection) { | ||
| boolean equal = true; | ||
| if (aEdgeCollection.size() == bEdgeCollection.size()) { | ||
| Map<Pair<Object, Object>, Double> aEdgeMap = new HashMap<Pair<Object, Object>, Double>(); | ||
| for (Edge aEdge : aEdgeCollection) { | ||
| double weight = aEdge.getWeight(); | ||
| aEdgeMap.put(getSourceTargetPair(aEdge), weight); | ||
| } | ||
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| Map<Pair<Object, Object>, Double> bEdgeMap = new HashMap<Pair<Object, Object>, Double>(); | ||
| for (Edge bEdge : bEdgeCollection) { | ||
| double weight = bEdge.getWeight(); | ||
| bEdgeMap.put(getSourceTargetPair(bEdge), weight); | ||
| } | ||
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| equal = MapDeepEquals.mapDeepEquals(aEdgeMap, bEdgeMap); | ||
| } else { | ||
| equal = false; | ||
| } | ||
| return equal; | ||
| } | ||
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| public static boolean graphsHaveSameTopology(Graph a, Graph b) { | ||
| boolean equal = true; | ||
| a.writeLock(); | ||
| b.writeLock(); | ||
| try { | ||
| if (a.getNodeCount() == b.getNodeCount() && a.getEdgeCount() == b.getEdgeCount()) { | ||
| for (Node aNode : a.getNodes()) { | ||
| Node bNode = b.getNode(aNode.getId()); | ||
| if (null == bNode) { | ||
| equal = false; | ||
| break; | ||
| } else { | ||
| Collection<Edge> aEdges = a.getEdges(aNode).toCollection(); | ||
| Collection<Edge> bEdges = b.getEdges(bNode).toCollection(); | ||
| if (!edgeCollectionsAreEqual(aEdges, bEdges)) { | ||
| equal = false; | ||
| break; | ||
| } | ||
| } | ||
| } | ||
| } else { | ||
| equal = false; | ||
| } | ||
| } finally { | ||
| a.writeUnlock(); | ||
| b.writeUnlock(); | ||
| } | ||
| return equal; | ||
| } | ||
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| } | ||
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Is it ok that this is a release version instead of a SNAPSHOT?
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No problem, your plugin can declare any version number you want. Just future updates will need to increase it.
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Sounds good!