I am using a great git SourceTree app

For some reason even though I have two branches; they were shown a single branch (even when merging).

Even though before it showed as two separate branches:

Solution

The solution was to perform a merge; and to check the option for “create a commit even if merge resolved via fast-forward”

Some of the properties don’t seem to get read; so you may consider manipulating some values programmatically, e.g. log.setLevel(Level.ALL);

For more information on the NetBeans logging see this post.

Keywords/Refs:

When trying to bind events to a java bean; context menu shows no bindings.

Solution

Use context menu of the object and select Properties/Binding as show bellow:

This particular behavior was explained in this post:

A few things to remember, though: the done() method is NOT abstract, so you aren’t required to override it. You should, though. If your doInBackground() implementation throws an exception, that exception will be swallowed unless done() has been overridden. Also, don’t make changes to your GUI from inside the doInBackground(), unless you useSwingUtilities.invokeLater(Runnable), as doInBackground() is executed from a different thread than the EDT and making GUI changes from a background thread is asking for strange and inexplicable bugs.

Note that you need to call the get() method; I have solved this problem by adding the following to the class extending SwingWorker:

    @Override
    protected void done(){
        try {
            get();
        } catch (InterruptedException ex) {
            Exceptions.printStackTrace(ex);
        } catch (ExecutionException ex) {
            Exceptions.printStackTrace(ex);
        }
    }

Keywords & References

Netbeans has a shortcoming/bug of adding space to the jar names of dist.  Including jars with spaces may prevent them from loading and result in the java.lang.ClassNotFoundException thrown by the java.net.URLClassLoader.

Solution

To change the filename of the jar files that will be build for distribution.  Change the variable dist.jar=${dist.dir}/good-jar-name.jar in file nbproject/project.properties

Keywords & Potential References:

file name whitespace

Getting exceptions:

java.lang.ClassNotFoundException starting from ModuleCL

java.lang.ClassNotFoundException: org.activeintel.network.optimization.algorithms.GeneticOptimizer
	at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	at org.netbeans.ProxyClassLoader.loadClass(ProxyClassLoader.java:262)

Solution

It seemed to be caused by the name of the jar file; in my case it had some dashes and spaces; renaming the jar (removing all dashes and spaces) has solved the problem

To see how to rename dist jar in Netbeans see this post.

Keywords:

Netbeans, Gephi, module, library, jar

When I created a JUnit unit test for a Gephi’s module (NetBeans) there seemed to be no way to execute it; since the “Test”, “Test File”, “Run File” were all greyed out (disabled).

Solution

Right click on the module and select “Create NBM”; then restart gephi so that the module is re-initialized; this seems to fix it (may need to also execute Clean and Build and then Run).

- OLD

This is an old and somewhat more detailed description of the problem

Problem

I tried to get unit tests set up for my gephi’s module (module’s zip).  It does not seem to work well; there are quite a few NullpointerExcpetions caused by Lookup and ImportController etc. It does look like that it is a problem caused by NetBeans rather than Gephi itself.

Even the most basic task does not seem to work:

        //Init a project - and therefore a workspace
        ProjectController pc = Lookup.getDefault().lookup(ProjectController.class);
        pc.newProject();
        Workspace workspace = pc.getCurrentWorkspace();

        //Get controllers and models
        ImportController importController = Lookup.getDefault().lookup(ImportController.class);
        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getModel();

        File file = new File(getClass().getResource("/org/activeintel/gephi/les-miserables.gexf").toURI());

        //Import file
        Container container = importController.importFile(file);

        //Append imported data to GraphAPI
        importController.process(container, new DefaultProcessor(), workspace);

The following error is thrown:

GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getModel();

Testcase: testDoTheDew(org.activeintel.gephi.DriverTest):	Caused an ERROR
null
java.lang.NullPointerException
	at org.activeintel.gephi.DriverTest.testDoTheDew

Solution

The work around was to create a regular netbeans project and then to included the toolkit.jar (which could be built by using ant).

Suggested approach is: http://wiki.gephi.org/index.php/NetBeans_Tips#How_to_use_other_modules_in_Unit_Test (thanks Mathieu for pointing it out)

I have not tried it yet; will update the post as soon as I do.

Comments

For more information see comments at the very end of the post.

Keywords & References

Yesterday (cont.)

null

Yesterday (cont.)

Yesterday (cont.)

Update: I have created a jgrapht-gephi library that works well for algorithm-centric tasks.

Keywords:

Gephi graph model graphmodel implementation source java class implements class provides an implementation of GraphModel in Gephi

Gephi is currently by far the best library for visualizing and interacting with graphs, it also has a large number of algorithms (many of them through plugins).

However since Gephi is oriented towards UI aspects, it’s graph implementation has quite a heavy overhead.  In addition manipulation of graphs is geared towards UI as well; e.g. only one graphModel per workspace, etc.

To solve the above problem I have combined JGraphT with Gephi.

For more details see the rest of the post and
https://github.com/gephi/gephi/issues/526
https://forum.gephi.org/viewtopic.php?f=27&t=1639

It seems that the main libraries (not including Gephi) focused on algorithms are JGraphT and JUNG.

SubGraphs

JGraphT has a nice Subgraph class.

JUNG does not have an explicit subgraph; the indirect usage of subgraphs seems to be only for the task of filtering.

Algorithms

 Graph Interface

Seem quite similar for both; see examples bellow.

JGraphT

// @see http://sourceforge.net/apps/mediawiki/jgrapht/index.php?title=jgrapht:HelloWorld

        UndirectedGraph<String, DefaultEdge> g =
            new SimpleGraph<String, DefaultEdge>(DefaultEdge.class);

        String v1 = "v1";
        String v2 = "v2";
        String v3 = "v3";
        String v4 = "v4";

        // add the vertices
        g.addVertex(v1);
        g.addVertex(v2);
        g.addVertex(v3);
        g.addVertex(v4);

        // add edges to create a circuit
        g.addEdge(v1, v2);
        g.addEdge(v2, v3);
        g.addEdge(v3, v4);
        g.addEdge(v4, v1);

        return g;

 JUNG

// @see http://www.grotto-networking.com/JUNG/JUNG2-Tutorial.pdf
// Graph<V, E> where V is the type of the vertices
        // and E is the type of the edges
        Graph<Integer, String> g = new SparseMultigraph<Integer, String>();
        // Add some vertices. From above we defined these to be type Integer.
        g.addVertex((Integer)1);
        g.addVertex((Integer)2);
        g.addVertex((Integer)3);
        // Add some edges. From above we defined these to be of type String
        // Note that the default is for undirected edges.
        g.addEdge("Edge-A", 1, 2); // Note that Java 1.5 auto-boxes primitives
        g.addEdge("Edge-B", 2, 3);

Keywords

graph clustering modularity network optimization