jung-support

[Jung-support] [Open Discussion] RE: Overlapping of Nodes?

[SourceForge.net <no...@so...>]

The following forum message was posted by e-flat at http://sourceforge.net/projects/jung/forums/forum/252062/topic/5861352:

You don't specify, but I assume that you are using the latitude and longitude
as layout coordinates.  If that is the case, then how you fix this depends on
what you want it to look like, but you obviously have complete freedom of how
to assign layout coordinates, so once you establish that you have a duplicate
(or something 'close enough', which you would need to calculate) then you could
appropriately offset the coordinates for each of the overlapping items.

Joshua

Re: [Jung-support] [Open Discussion] Limit of the zoom?

[Johannes M. <der...@gm...>]

On 21.09.2012 12:50, SourceForge.net wrote:
> The following forum message was posted by vaddelalitha at http://sourceforge.net/projects/jung/forums/forum/252062/topic/5837861:
> 
> Someone please help me to find out the minimum and maximum limit of the  zoom
> functionality in the JUNG framework?
> 
> Is there any way to add a zoom slider on the JUNG graph like zoom slider in
> google maps ?
> 
Take a look at the example:
http://jung.sourceforge.net/applet/grapheditordemo.html
You could start by implementing the  + and - Button Actions.
Also take a look at ScalingControl/VisualScalingControl and
ScalingGraphMousePlugin (mouseWheelMoved), which should be rather close
to what you need. Then you can use your own slider with a similar
implementation.

Johannes

[Jung-support] [Open Discussion] Overlapping of Nodes?

[SourceForge.net <no...@so...>]

The following forum message was posted by vaddelalitha at http://sourceforge.net/projects/jung/forums/forum/252062/topic/5861352:

What is the procedure to follow in order not to get the nodes overlapped on
the graph which are with the same Latitude and longitude values?
(Note:: Nodes on the graph will be displayed with the configured latitude and
longitude values)

Any help regarding this is highly appreciated.

[Jung-support] The Ranking Value is Null

[Bing Li <lb...@gm...>]

Dear all,

I am still a beginner to use JUNG. I noticed that sometimes some items got
ranking value, null, after ranking. What does it mean? In my program, the
value type should be double. Why is a null value assigned?

Thanks so much!

Best regards,
Bing

[Jung-support] [Open Discussion] Limit of the zoom?

[SourceForge.net <no...@so...>]

The following forum message was posted by vaddelalitha at http://sourceforge.net/projects/jung/forums/forum/252062/topic/5837861:

Someone please help me to find out the minimum and maximum limit of the  zoom
functionality in the JUNG framework?

Is there any way to add a zoom slider on the JUNG graph like zoom slider in
google maps ?

Help me with the above questions

[Jung-support] [Open Discussion] RE: Leor Zahavi- Wants to learn Java mobile

[SourceForge.net <no...@so...>]

The following forum message was posted by e-flat at http://sourceforge.net/projects/jung/forums/forum/252062/topic/5665381:

Leor:

This forum is for asking questions (and giving feedback) about the JUNG libraries.
It has nothing to do with development on Android in general.

Joshua

[Jung-support] [Open Discussion] Leor Zahavi- Wants to learn Java mobile

[SourceForge.net <no...@so...>]

The following forum message was posted by leorlahavi at http://sourceforge.net/projects/jung/forums/forum/252062/topic/5665381:

Hello everybody!

I am Leor Zahavi, really interested to learn Java mobile to develop Java application
for android phones. Please provide me tutorial and suitable JDK.

Thanks 
Leor Zahavi

[Jung-support] [Open Discussion] JUNG+Android

[SourceForge.net <no...@so...>]

The following forum message was posted by ssindhu at http://sourceforge.net/projects/jung/forums/forum/252062/topic/5665197:

Hi all...

I'm used Jung for displaying Network Topology in java.
Now i want to display the topology of the network in Android.
Is JUNG is compatible with Android?
Is any changes required,so that  jung package can be used.
Or any other packages like Jung is available for android.
Thanks in advance.

Thanks,
Sindhu

Re: [Jung-support] Overlapping Vertices

[Johannes M. <der...@gm...>]

On 07.09.2012 12:20, Johannes Müller wrote:
> Hi,
> 
> I have a component consisting of several overlapping vertices.
> Sometimes, the smaller vertices are hidden beneath the larger Vertex.
> How can you influence whether a vertex a is above or below vertex b?
> 
> Thanks a lot,
> Johannes
> 

Sorry for troubling you; I should have searched the archives in advance.
I found the following answer to be useful:
http://sourceforge.net/mailarchive/message.php?msg_id=11547420

Since I use an instance of SparseMultigraph, I subclassed it and simply
changed the unsorted HashMap of vertices to a LinkedHashMap.

Thanks,
Johannes

--------------------------------------------------------------------------

/**
 * A SparseMultigraph which keeps vertices sorted by insertion order,
 * so that in the visual representation recently added vertices
 * overlap previously added vertices.
 */
@SuppressWarnings("serial")
public class SortedSparseMultiGraph<V,E> extends SparseMultigraph<V,E> {
	

    /**
     * Creates a new instance.
     */
    public SortedSparseMultiGraph()
    {
        vertices = new LinkedHashMap<V, Pair<Set<E>>>();
    }
}

[Jung-support] Overlapping Vertices

[Johannes M. <der...@gm...>]

Hi,

I have a component consisting of several overlapping vertices.
Sometimes, the smaller vertices are hidden beneath the larger Vertex.
How can you influence whether a vertex a is above or below vertex b?

Thanks a lot,
Johannes

[Jung-support] [Open Discussion] RE: EppsteinPowerLawGenerator problem

[SourceForge.net <no...@so...>]

The following forum message was posted by e-flat at http://sourceforge.net/projects/jung/forums/forum/252062/topic/5587556:

Salvador:

You need to read the documentation before posting.  Take a look at what the
graph generator class actually does.

I also strongly recommend that you take a look at one of the many available
Java tutorials, e.g.: http://docs.oracle.com/javase/tutorial/
That will help you get more familiar with Java.  As with any other Java library,
JUNG is going to be difficult to use properly if you're not very familiar with
Java itself.

Joshua

[Jung-support] [Open Discussion] RE: EppsteinPowerLawGenerator problem

[SourceForge.net <no...@so...>]

The following forum message was posted by  at http://sourceforge.net/projects/jung/forums/forum/252062/topic/5587556:

ok i solve this problem. Thanks a lot!

Another issue is that i want to visualize the graph with Gephi. I am trying
to write the graph to a .paj file with PajekNetWriter class, but the first argument
must be Graph<V,E>.
I think my generated graph is stored as an factory interface and i can't use
it with the aforementioned class. How can i solve this problem?

[Jung-support] [Open Discussion] RE: EppsteinPowerLawGenerator problem

[SourceForge.net <no...@so...>]

The following forum message was posted by e-flat at http://sourceforge.net/projects/jung/forums/forum/252062/topic/5587556:

Salvador, this is a common Java problem.  Do a search on "java equals hashcode"
and you'll find many, many articles about it.

That said, the problem here is actually even more fundamental: you didn't initialize
graphFactory, so calling create() on it (which is what a brief perusal of the
code would have shown you was happening) resulted in an NPE.

After you fix that, you may need to revisit the equals/hashCode issue.

Joshua

[Jung-support] [Open Discussion] RE: EppsteinPowerLawGenerator problem

[SourceForge.net <no...@so...>]

The following forum message was posted by  at http://sourceforge.net/projects/jung/forums/forum/252062/topic/5587556:

i don't think i understand, can you gine me an example?

[Jung-support] [Open Discussion] RE: EppsteinPowerLawGenerator problem

[SourceForge.net <no...@so...>]

The following forum message was posted by tomnelson at http://sourceforge.net/projects/jung/forums/forum/252062/topic/5587556:

jung graphs are java collections. For any java object to work properly in a
collection, it must implement equals and hashCode. You must properly implement
equals and hashCode in your node and edge classes.

[Jung-support] [Open Discussion] EppsteinPowerLawGenerator problem

[SourceForge.net <no...@so...>]

The following forum message was posted by  at http://sourceforge.net/projects/jung/forums/forum/252062/topic/5587556:

Hello!
I am trying to learn the jung library but i am facing some difficulties. I want
to generate a graph with EppsteinPowerLawGenerator.
Here s my code:
[code]public class Generator {
	int edgecount = 0;
	int numV, numE, iter;
	Factory<Graph<node,edge>> graphFactory;
	Factory<node> nodeFactory = new Factory<node>() {
		public node create() {
			return new node(1);
		}
	};
	Factory<edge> edgeFactory = new Factory<edge>() {
		public edge create() {
			return new edge(3);
		}
	};
	
	public void GraphCreation(int numV, int numE, int iter) {
		EppsteinPowerLawGenerator<node,edge> gg = 
				new EppsteinPowerLawGenerator<node,edge>(graphFactory, nodeFactory, edgeFactory,
numV, numE, iter);
		gg.create();
	}
	
	public static void main(String args[]) {
		Generator g = new Generator();
		g.GraphCreation(10,10,500);
		System.out.println("All good");
	}
	
	
	class node {
		int id;
		public node(int id) {
			this.id = id;
		}
		public String toString() {
			return "V"+id;
		}
	}
	class edge {
		int id;
		int weight;
		public edge(int weight) {
			this.id = edgecount++;
			this.weight = weight;
		}
		public String toString(){
			return "E"+id;
		}
	}
	
}
[/code]

And here is my error message:
[quote]Exception in thread "main" java.lang.NullPointerException
	at edu.uci.ics.jung.algorithms.generators.random.EppsteinPowerLawGenerator.init
ializeGraph(EppsteinPowerLawGenerator.java:60)
	at edu.uci.ics.jung.algorithms.generators.random.EppsteinPowerLawGenerator.crea
te(EppsteinPowerLawGenerator.java:87)
	at Generator.GraphCreation(Generator.java:25)
	at Generator.main(Generator.java:30)
[/quote]

Probably i have some rookiw mistake in my java code (because i am a rookie)
but i can't figure out the solution.
Please help!

[Jung-support] [Open Discussion] RE: NPE with KleinbergSmallWorldGenerator

[SourceForge.net <no...@so...>]

The following forum message was posted by e-flat at http://sourceforge.net/projects/jung/forums/forum/252062/topic/3458819:

Salvador, please post your complete stack trace and specify which version of
JUNG you're using.  The original problem report doesn't appear to make any sense
based on the current code (line 165 doesn't look like a likely place for an
NPE).

Joshua

[Jung-support] [Open Discussion] RE: NPE with KleinbergSmallWorldGenerator

[SourceForge.net <no...@so...>]

The following forum message was posted by  at http://sourceforge.net/projects/jung/forums/forum/252062/topic/3458819:

disgoseek 

Did you figure out what's the problem, becuase i am facing the same problem

Re: [Jung-support] Announcing the availability of a subgraph matching tool

[Joshua O'M. <jos...@gm...>]

Haibin:

Thanks to you and your collaborators for making this tool publicly
available.  We're always happy to see extensions to, and tools/libraries
that use, JUNG.

Joshua
for the JUNG Development Team

On Wed, Aug 22, 2012 at 1:49 PM, Liu, Haibin <HAI...@uc...>wrote:

> Dear JUNG library users,
>
> We are pleased to announce the availability of the ESM, an exact subgraph
> matching
> tool for dependency graphs.
>
> It is the Java implementation of the exact subgraph matching algorithm we
> designed for matching
> dependency graphs. It uses the graph definition of the JUNG library.The
> subgraph matching problem
> (subgraph isomorphism) is NP-complete. We designed a simple exact subgraph
> matching (ESM) algorithm
> for dependency graphs using a backtracking approach. The total worst-case
> algorithm complexity is
> O(n^2 * k^n) where n is the number of vertices and k is the vertex degree.
>
> We have demonstrated the successful usage of this tool in three biomedical
> information extraction (relation and event) applications: BioNLP 2011
> shared tasks on event
> extraction, Protein-Residue association detection and Protein-Protein
> interaction identification.
>
> The ESM takes two graphs as input, one is considered as subgraph (smaller)
> and the other
> is considered as a graph (bigger). It provides three main public methods
> for different subgraph matching needs:
>
> (1) isSubgraphIsomorphism()
>
> Determine if the input subgraph is subsumed by the input graph
>
> (2) isGraphIsomorphism()
>
> Determine if two input graphs are isomorphic to each other, based on the
> fact that
> if two graphs are subgraph isomorphic to each other, then they are
> isomorphic to
> each other
>
> (3) getSubgraphMatchingMatches()
>
> Retrieve specific matching results of all possible matchings between the
> input subgraph
> and the input graph because a subgraph can sometimes match different
> places of a graph.
>
>
> For more details about our ESM algorithm, the analysis on time complexity,
> and the
> different applications of the algorithm, see the section "Related
> Publications"  in the ReadMe
> file for the complete list of our ESM-related publications.
>
> The tool itself is available on SourceForge as a Maven project at
> http://esmalgorithm.sourceforge.net/ and can be accessed via a Maven
> repository, as indicated there.
>
> We hope you will be able to make good use of this tool in your work.
>
> Haibin Liu, Vlado Keselj, Christian Blouin and Karin Verspoor
>
> --
> Haibin Liu, PhD
> Postdoctoral Researcher, Hunter Lab, University of Colorado School of
> Medicine
> Aurora, CO, 80045 USA
> Email: hai...@uc...<mailto:hai...@uc...>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Jung-support mailing list
> Jun...@li...
> https://lists.sourceforge.net/lists/listinfo/jung-support
>



-- 
jos...@gm.........sites.google.com/site/joshuaomadadhain/
   Joshua O'Madadhain: Information Scientist, Musician, Philosopher-At-Tall
It's that moment of dawning comprehension that I live for.  -- Bill
Watterson
 My opinions are too rational and insightful to be those of any
organization.

[Jung-support] Announcing the availability of a subgraph matching tool

[Liu, H. <HAIBIN.LIU@UCDENVER.EDU>]

Dear JUNG library users,

We are pleased to announce the availability of the ESM, an exact subgraph matching 
tool for dependency graphs. 

It is the Java implementation of the exact subgraph matching algorithm we designed for matching 
dependency graphs. It uses the graph definition of the JUNG library.The subgraph matching problem 
(subgraph isomorphism) is NP-complete. We designed a simple exact subgraph matching (ESM) algorithm 
for dependency graphs using a backtracking approach. The total worst-case algorithm complexity is 
O(n^2 * k^n) where n is the number of vertices and k is the vertex degree. 

We have demonstrated the successful usage of this tool in three biomedical 
information extraction (relation and event) applications: BioNLP 2011 shared tasks on event 
extraction, Protein-Residue association detection and Protein-Protein interaction identification.

The ESM takes two graphs as input, one is considered as subgraph (smaller) and the other 
is considered as a graph (bigger). It provides three main public methods for different subgraph matching needs: 

(1) isSubgraphIsomorphism()

Determine if the input subgraph is subsumed by the input graph

(2) isGraphIsomorphism()

Determine if two input graphs are isomorphic to each other, based on the fact that 
if two graphs are subgraph isomorphic to each other, then they are isomorphic to 
each other

(3) getSubgraphMatchingMatches()

Retrieve specific matching results of all possible matchings between the input subgraph 
and the input graph because a subgraph can sometimes match different places of a graph.


For more details about our ESM algorithm, the analysis on time complexity, and the 
different applications of the algorithm, see the section "Related Publications"  in the ReadMe
file for the complete list of our ESM-related publications.

The tool itself is available on SourceForge as a Maven project at 
http://esmalgorithm.sourceforge.net/ and can be accessed via a Maven 
repository, as indicated there.

We hope you will be able to make good use of this tool in your work.

Haibin Liu, Vlado Keselj, Christian Blouin and Karin Verspoor

--
Haibin Liu, PhD
Postdoctoral Researcher, Hunter Lab, University of Colorado School of Medicine
Aurora, CO, 80045 USA
Email: hai...@uc...<mailto:hai...@uc...>

[Jung-support] [Open Discussion] RE: PageRank values

[SourceForge.net <no...@so...>]

The following forum message was posted by e-flat at http://sourceforge.net/projects/jung/forums/forum/252062/topic/5563813:

(1) This is a known property of PageRank-like algorithms where alpha = 0.  What
value did you assign to alpha?  (Think about how PageRank works; there's a link
to the original paper in the documentation.)
(2) If you remove vertices with no outgoing edges, you may create vertices with
no outgoing edges.  Bear this in mind.  :)

Joshua

[Jung-support] [Open Discussion] PageRank values

[SourceForge.net <no...@so...>]

The following forum message was posted by picassoavex at http://sourceforge.net/projects/jung/forums/forum/252062/topic/5563813:

Hello again guys,

I´ve been working on a connected network, and I´ve learned that vertex without
any out edges seems to create a "black hole" on the PageRank algorithm and so
the score for every one would be zero.

I´ve removed them. I still get only zero values and values very close to zero
( like 0.23423E-6 and results like that).

Can you give me a hint about this?

Thanks in advance.

[Jung-support] [Open Discussion] BFSDistanceLabeler

[SourceForge.net <no...@so...>]

The following forum message was posted by adamjava at http://sourceforge.net/projects/jung/forums/forum/252062/topic/5521187:

Hi all,
I want to use [b] getVerticesInOrderVisited()[/b] method of  [b]BFSDistanceLabeler
[/b] class. Although it is not said explicitly in javadoc, it seems to me that
[b] initialize() [/b]should be called prior to invoking
[b] getVerticesInOrderVisited()[/b]. Am I right?
If [b]no[/b], what is the source vertex for underlying BFS search?
Regards,
Adam

[Jung-support] [Open Discussion] Closeness Centrality on Directed Graph

[SourceForge.net <no...@so...>]

The following forum message was posted by picassoavex at http://sourceforge.net/projects/jung/forums/forum/252062/topic/5510764:

Hello Everyone,

Is there a way to properly normalize a vertex score on directed graphs?

Let me explain with an example: A simple hierarchy

Vertices: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9

Edges:
(0, 1)
(0, 2)
(0, 3)
(1, 4)
(1, 5)
(2, 6)
(2, 7)
(3, 8)
(3, 9)

Let´s suppose their weight is 1.0. Look at vertex 0 and vertex 1:

Without averaging: closeness(0) = 1 / 15 = 0.0666  and  closeness(1) = 1 / 2
= 0.5

With averaging: closeness(0) = 9 / 15 = 0.6  and  closeness(1) = 2 / 2 = 1.0

In both cases vertex 1 gets a better score. 
That doesn´t make much sense because vertex 1 can only get to vertex 4 and 5.
On the other hand we have vertex 0 with a lower closeness, but from it we can
get to every other vertex ( 1 - 9 ).

If it was an undirected graph, this problem wouldn´t come up.

Can someone give me some hints on how to deal with this?

Thank You.
Cheers          

[Jung-support] [Open Discussion] RE: Highlighting Shortest Path?

[SourceForge.net <no...@so...>]

The following forum message was posted by sean-p-w at http://sourceforge.net/projects/jung/forums/forum/252062/topic/5495863:

Fair enough, I'll try to figure it out some more.