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From: John V. Sichi <jsichi@gm...>  20090312 08:32:05

Thanks; this is definitely a bug (the test should be using equals instead of == in all cases). I've checked in the fix and unit test in Subversion. JVS Michaël Michaud wrote: > Hi, > > Maybe somebody can tell me if this behaviour is normal or if it's a bug. > I want to build a graph with a unique cycle (one edge, one vertex) > I use two classes MyVertex and MyEdge, a WeightedPseudograph (version > 0.7.3 of jGraphT), and here is my test case : > > v1 = new MyVertex(); > graph.addVertex(v1); > graph.addEdge(v1,v1,new MyEdge()); > ==> build a graph with 1 vertex and 1 edge, vertex has degree 2 (that is > OK!) > > v1 = new MyVertex(); > v2 = new MyVertex(); // where n2.equals(n1) > graph.addVertex(v1); > graph.addVertex(v2); > graph.addEdge(v1,v2,new MyEdge()); > ==> build a graph with 1 vertex and 1 edge, vertex has degree 4 ! > > Seems like addVertex uses equals to compare vertices and add only one > vertex if v1!=v2 but v1.equals(v2) > That's fine for me > There is still 1 vertex after addEdge, but that time, the degreeOf > method returns 4 instead of 2 > > I find this code in AbstractBaseGraph (line 1109) : > if (source != target) {getEdgeContainer(target).addEdge(e);} > //here == is used, not equals > and also this (line 1125) : > if (getEdgeSource(e).equals(getEdgeTarget(e))) { degree += 2;} > > Any help is welcome > > Michaël > > > >  > Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are > powering Web 2.0 with engaging, crossplatform capabilities. Quickly and > easily build your RIAs with Flex Builder, the Eclipse(TM)based development > software that enables intelligent coding and stepthrough debugging. > Download the free 60 day trial. http://p.sf.net/sfu/wwwadobecom > _______________________________________________ > jgraphtusers mailing list > jgraphtusers@... > https://lists.sourceforge.net/lists/listinfo/jgraphtusers > 
From: Michaël Michaud <michael.michaud@fr...>  20090312 07:52:11

Hi, Maybe somebody can tell me if this behaviour is normal or if it's a bug. I want to build a graph with a unique cycle (one edge, one vertex) I use two classes MyVertex and MyEdge, a WeightedPseudograph (version 0.7.3 of jGraphT), and here is my test case : v1 = new MyVertex(); graph.addVertex(v1); graph.addEdge(v1,v1,new MyEdge()); ==> build a graph with 1 vertex and 1 edge, vertex has degree 2 (that is OK!) v1 = new MyVertex(); v2 = new MyVertex(); // where n2.equals(n1) graph.addVertex(v1); graph.addVertex(v2); graph.addEdge(v1,v2,new MyEdge()); ==> build a graph with 1 vertex and 1 edge, vertex has degree 4 ! Seems like addVertex uses equals to compare vertices and add only one vertex if v1!=v2 but v1.equals(v2) That's fine for me There is still 1 vertex after addEdge, but that time, the degreeOf method returns 4 instead of 2 I find this code in AbstractBaseGraph (line 1109) : if (source != target) {getEdgeContainer(target).addEdge(e);} //here == is used, not equals and also this (line 1125) : if (getEdgeSource(e).equals(getEdgeTarget(e))) { degree += 2;} Any help is welcome Michaël 
From: John V. Sichi <jsichi@gm...>  20090311 20:35:11

Francesco Cioffi wrote: > Hi guys, > > I'm new to jgrapht and I would like to use as graph library in my Project. > > I must create a graph, save it in a file, and then reload it for some purpose. > > I have found some utilities for exporting but I don't found utilities > for load a graph from a file. > > > Can you suggest me, how can I do that? Right, we currently only have exporters, without importers. However, most JGraphT data structures implement Serializable, so that is one option for persistence, although I personally am not a big fan of it due to issues like incompatibilities during migration to newer versions. JVS 
From: Francesco Cioffi <fcioffi@gm...>  20090311 13:12:19

Hi guys, I'm new to jgrapht and I would like to use as graph library in my Project. I must create a graph, save it in a file, and then reload it for some purpose. I have found some utilities for exporting but I don't found utilities for load a graph from a file. Can you suggest me, how can I do that? Thank you, Francesco Cioffi 
From: John V. Sichi <jsichi@gm...>  20090309 22:44:12

Thanks Guillaume. I'll poke around a bit and update the Javadoc with what I find. Olivier, if you are interested in implementing one of the newer algorithms, we can incorporate that into the library too. JVS gu boulmi wrote: > Hi, > > I have not implemented this algorithm based on a reference paper. So, > it's not Jimenez and Marzal! > Though I'm sure that what I've written is not new and must have > been explained previously in many papers. > > The algorithm is a *variant of the BellmanFord algorithm* but instead > of only storing the best path I store the "*k*" best paths at each pass > (se differences between methods KShortestPathsIterator#next and > BellmanFordIterator#next). > > Complexity "*/m*n/*" is because it's a variant of BellmanFord (whose > complexity is /*O(m*n)*/) and the "*/k/*" factor is because the method > RankingPathElementList#addPathElements is /*O(k)*/ where *k* is the > number of expected paths to be computed (by the way I notice that this > "O(k)" piece of information is not in the javadoc documentation). > > If you find a paper pointing to this kind of algorithm, feel free to > update the javadoc documentation. > > Regards, > > Guillaume > >  En date de : *Mer 4.3.09, John V. Sichi /<jsichi@...>/* a écrit : > > De: John V. Sichi <jsichi@...> > Objet: Re: Question on JGraphT > À: lefevrol@... > Cc: jgraphtusers@..., boulmigu@... > Date: Mercredi 4 Mars 2009, 1h09 > > Olivier Lefevre wrote: > > Hi, > > > > What is the algorithm used for Kshortest paths in JGraphT: the REA > algorithm of Jimenez and Marzal? > > > > Regards, > > > > Olivier Lefevre > > Freelance bioinformatics developer > > Berlin, Germany > > Greetings Olivier, > > I don't know the answer, so I'm cc'ing your question to the users > mailing list, as well as Guillaume Boulmier, who developed this code. > > Jimenez and Marzal is O(m+Knlog(m/n)), whereas Guillaume's comments have > O(K*m*n) for the running time. > > JVS > > 
From: John V. Sichi <jsichi@gm...>  20090309 22:10:18

maria esther sanchez wrote: > I was wondering if there is a method in JGraphT to get the aislated > subgraphs inside a graph? (Like the graphs inside a graph) To find them, you can use org.jgrapht.alg.ConnectivityInspector or StrongConnectivityInspector. To manipulate them individually once you find them, you can use org.jgrapht.graph.Subgraph (or one of its variants such as DirectedSubgraph). JVS 
From: gu boulmi <boulmigu@ya...>  20090309 13:30:06

Hi, I have not implemented this algorithm based on a reference paper. So, it's not Jimenez and Marzal! Though I'm sure that what I've written is not new and must have been explained previously in many papers. The algorithm is a variant of the BellmanFord algorithm but instead of only storing the best path I store the "k" best paths at each pass (se differences between methods KShortestPathsIterator#next and BellmanFordIterator#next). Complexity "m*n" is because it's a variant of BellmanFord (whose complexity is O(m*n)) and the "k" factor is because the method RankingPathElementList#addPathElements is O(k) where k is the number of expected paths to be computed (by the way I notice that this "O(k)" piece of information is not in the javadoc documentation). If you find a paper pointing to this kind of algorithm, feel free to update the javadoc documentation. Regards, Guillaume  En date de : Mer 4.3.09, John V. Sichi <jsichi@...> a écrit : De: John V. Sichi <jsichi@...> Objet: Re: Question on JGraphT À: lefevrol@... Cc: jgraphtusers@..., boulmigu@... Date: Mercredi 4 Mars 2009, 1h09 Olivier Lefevre wrote: > Hi, > > What is the algorithm used for Kshortest paths in JGraphT: the REA algorithm of Jimenez and Marzal? > > Regards, > > Olivier Lefevre > Freelance bioinformatics developer > Berlin, Germany Greetings Olivier, I don't know the answer, so I'm cc'ing your question to the users mailing list, as well as Guillaume Boulmier, who developed this code. Jimenez and Marzal is O(m+Knlog(m/n)), whereas Guillaume's comments have O(K*m*n) for the running time. JVS 
From: gu boulmi <boulmigu@ya...>  20090309 13:22:49

Hi, I have not implemented this algorithm based on a reference paper, though I'm sure that what I've written is not new and must have been explained previously in many papers. The algorithm is a variant of the BellmanFord algorithm but instead of only storing the best path I store the "k" best paths at each pass (se differences between KShortestPathsIterator#next and BellmanFordIterator#next). Complexity "m*n" is because it's a variant of BellmanFord and the "k" factor is because the method RankingPathElementList#addPathElements is O(k). If you find  En date de : Mer 4.3.09, John V. Sichi <jsichi@...> a écrit : De: John V. Sichi <jsichi@...> Objet: Re: Question on JGraphT À: lefevrol@... Cc: jgraphtusers@..., boulmigu@... Date: Mercredi 4 Mars 2009, 1h09 Olivier Lefevre wrote: > Hi, > > What is the algorithm used for Kshortest paths in JGraphT: the REA algorithm of Jimenez and Marzal? > > Regards, > > Olivier Lefevre > Freelance bioinformatics developer > Berlin, Germany Greetings Olivier, I don't know the answer, so I'm cc'ing your question to the users mailing list, as well as Guillaume Boulmier, who developed this code. Jimenez and Marzal is O(m+Knlog(m/n)), whereas Guillaume's comments have O(K*m*n) for the running time. JVS 
From: gu boulmi <boulmigu@ya...>  20090309 12:59:50

Hi, I'm Implmentation  En date de : Mer 4.3.09, John V. Sichi <jsichi@...> a écrit : De: John V. Sichi <jsichi@...> Objet: Re: Question on JGraphT À: lefevrol@... Cc: jgraphtusers@..., boulmigu@... Date: Mercredi 4 Mars 2009, 1h09 Olivier Lefevre wrote: > Hi, > > What is the algorithm used for Kshortest paths in JGraphT: the REA algorithm of Jimenez and Marzal? > > Regards, > > Olivier Lefevre > Freelance bioinformatics developer > Berlin, Germany Greetings Olivier, I don't know the answer, so I'm cc'ing your question to the users mailing list, as well as Guillaume Boulmier, who developed this code. Jimenez and Marzal is O(m+Knlog(m/n)), whereas Guillaume's comments have O(K*m*n) for the running time. JVS 
From: John V. Sichi <jsichi@gm...>  20090304 08:19:30

maria esther sanchez wrote: > Hello! I am having trouble with the references. I would like to know how > to duplicate, clone or copy a graph in with there are no references amog > them. I tryed this method: Graphs.addGraph(simpleGraph,graph)... but i > still have the same problem. If a modify a vertex from simplegrap, the > node that corresponds to graph is modified also. > How can i make a copy that does afect from the graph that i am copying, > and the other way arround. > Thank u for you help! Hi Maria, You can code this as follows: 1) create a Map<V,V> m 2) write a new cloneAllVertices like addAllVertices which does vPrime = v.clone(), adds an entry (v,vPrime) to m, and puts vPrime in the destination graph 3) write a new addAllEdgesForClones like addAllEdges which uses m to map each s and t to sPrime and tPrime before calling addEdge I forget how the interactions between generics and clone work out, but if you get a generic version of this working along with a unit test, please send it to me and I'll check it in as a new utility method on class org.jgrapht.Graphs. JVS 
From: John V. Sichi <jsichi@gm...>  20090304 08:03:02

Bhavesh Sanghvi wrote: > I am interested in a digraph which may also contain bidirectional edges > (preferably with weight). Later, I wish to detect cycles this graph > (specifically for this reason, I cannot use two directional edges as > they would be identified in the cycle). > > > > Please let me know if it is possible to create such a graph using > JGraphT. I searched for bidirectional edges, however, was not able to > find it. Hi Bhavesh, Following the Mathworld definition, http://mathworld.wolfram.com/DirectedGraph.html a bidirectional edge is equivalent to a pair of oppositelydirected edges. The ability to mix directed with undirected edges in the same graph isn't something we're planning to add since it is an uncommon requirement and would complicate the internals considerably. Perhaps you could you can write a modified version of the cycle detector which ignores cycles of length 2? JVS 
From: maria esther sanchez <tete_quiero@ho...>  20090304 06:49:05

Hello! I am having trouble with the references. I would like to know how to duplicate, clone or copy a graph in with there are no references amog them. I tryed this method: Graphs.addGraph(simpleGraph,graph)... but i still have the same problem. If a modify a vertex from simplegrap, the node that corresponds to graph is modified also. How can i make a copy that does afect from the graph that i am copying, and the other way arround. Thank u for you help! Atte tete _________________________________________________________________ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009 
From: Bhavesh Sanghvi <bsanghvi@cs...>  20090304 00:10:55

Hello, I am interested in a digraph which may also contain bidirectional edges (preferably with weight). Later, I wish to detect cycles this graph (specifically for this reason, I cannot use two directional edges as they would be identified in the cycle). Please let me know if it is possible to create such a graph using JGraphT. I searched for bidirectional edges, however, was not able to find it. Thanks for your help!  Thanks & regards, Bhavesh Sanghvi P.S. Please excuse me for crossposting on both forum and mailing list. I was not sure if they are synched or not. 
From: John V. Sichi <jsichi@gm...>  20090304 00:09:47

Olivier Lefevre wrote: > Hi, > > What is the algorithm used for Kshortest paths in JGraphT: > the REA algorithm of Jimenez and Marzal? > > Regards, > > Olivier Lefevre > Freelance bioinformatics developer > Berlin, Germany Greetings Olivier, I don't know the answer, so I'm cc'ing your question to the users mailing list, as well as Guillaume Boulmier, who developed this code. Jimenez and Marzal is O(m+Knlog(m/n)), whereas Guillaume's comments have O(K*m*n) for the running time. JVS 