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From: Tim Jesussek <ts_ml@rc...>  20110426 11:09:53

Hi, On Mon, 25 Apr 2011 22:26:13 0700, John Sichi <jsichi@...> wrote: > Does your ProteinGraph add anything interesting? If not, you might > consider discarding it and just using the outofthebox classes > directly. Yes, it adds some functions that are specific for protein graphs, e.g. determining the Nterminus and Tterminus of the protein chain and returning different linear notations for protein graphs. I also plan to add functions that draw the graph and write them to an image file. But I think my current way of implementing the ProteinGraph class is far from perfect. I'll start a new thread for this though. > If you need it for some reason, then either do what you said at the > end to make copies of the subgraphs (using Graphs.addGraph), or else > make ProteinGraph an interface and create subclasses for extending > SimpleGraph and UndirectedSubgraph. Thanks a lot for, I didn't know about Graphs.addGraph() and it does exactly what I wanted. Here's what I do now: List<Set<SSE>> conVertSets = ci.connectedSets(); // Create graphs out of the connected sets for(Integer j = 0; j < conVertSets.size(); j++) { UndirectedSubgraph<SSE, LabeledEdge> sg = new UndirectedSubgraph<SSE, LabeledEdge>(g, conVertSets.get(j), null); ProteinGraph<SSE, LabeledEdge> psg = new ProteinGraph<SSE, LabeledEdge>(new ClassBasedEdgeFactory<SSE, LabeledEdge>(LabeledEdge.class)); Graphs.addGraph(psg, sg); } This works. :)  Tim 
From: John Sichi <jsichi@gm...>  20110426 05:26:22

Does your ProteinGraph add anything interesting? If not, you might consider discarding it and just using the outofthebox classes directly. If you need it for some reason, then either do what you said at the end to make copies of the subgraphs (using Graphs.addGraph), or else make ProteinGraph an interface and create subclasses for extending SimpleGraph and UndirectedSubgraph. JVS On Mon, Apr 25, 2011 at 4:00 AM, Tim Jesussek <ts_ml@...> wrote: > > Hi list, > > I'm new to jgrapht and I'm using it to model protein graphs. What I > need to do is split a graph G into multiple graphs, each of which should > represent a connected set of G. I have found the ConnectivityInspector > class and its connectedSets() method, but I'm not sure on how to turn > the edge set it returns into a new graph. Can anybody tell me how to do > that? > > Some more details on what I've done so far follow: I have written a > ProteinGraph class that extends SimpleGraph<V, E> and implements > UndirectedGraph<V, E>. I have also written a LabeledEdge class that > extends DefaultEdge. Both of this shouldn't make much of a difference I > guess. Here is my code so far: > > > // Creates a ProteinGraph from the connectivity matrix of all > supersecondary structures of a protein chain > ProteinGraph<SSE, LabeledEdge> g = chainCM.toJGraph(); > > // Get all connected sets > ConnectivityInspector<SSE, LabeledEdge> ci = new > ConnectivityInspector<SSE, LabeledEdge>(g); > List<Set<SSE>> conSets = ci.connectedSets(); > > // Create graphs out of the connected sets > for(Integer j = 0; j < conSets.size(); j++) { > > // I can do this... > UndirectedSubgraph<SSE, LabeledEdge> subGraph = new > UndirectedSubgraph<SSE, LabeledEdge>(g, conSets.get(j), null); > > // ... but I would like to do something like this: > ProteinGraph<SSE, LabeledEdge> psg = new UndirectedSubgraph<SSE, > LabeledEdge>(g, conSets.get(j), null); > // or > ProteinGraph<SSE, LabeledEdge> psg = subGraph.toGraph(); > } > > > Using that code, my question could also be formulated as 'How can I > turn a UndirectedSubgraph into a new Graph of a certain type (my > ProteinGraph class, in this case). Is there any way to do this? Or > should I write a new constructor for ProteinGraph that uses the SubGraph > to construct the ProteinGraph based on the vertix set and edge set in > the subgraph? > > Thanks for any hints, > > >  > Tim > >  > Fulfilling the Lean Software Promise > Lean software platforms are now widely adopted and the benefits have been > demonstrated beyond question. Learn why your peers are replacing JEE > containers with lightweight application servers  and what you can gain > from the move. http://p.sf.net/sfu/vmwaresfemails > _______________________________________________ > jgraphtusers mailing list > jgraphtusers@... > https://lists.sourceforge.net/lists/listinfo/jgraphtusers > 
From: Tim Jesussek <ts_ml@rc...>  20110425 14:47:23

Hi list, I'm new to jgrapht and I'm using it to model protein graphs. What I need to do is split a graph G into multiple graphs, each of which should represent a connected set of G. I have found the ConnectivityInspector class and its connectedSets() method, but I'm not sure on how to turn the edge set it returns into a new graph. Can anybody tell me how to do that? Some more details on what I've done so far follow: I have written a ProteinGraph class that extends SimpleGraph<V, E> and implements UndirectedGraph<V, E>. I have also written a LabeledEdge class that extends DefaultEdge. Both of this shouldn't make much of a difference I guess. Here is my code so far: // Creates a ProteinGraph from the connectivity matrix of all supersecondary structures of a protein chain ProteinGraph<SSE, LabeledEdge> g = chainCM.toJGraph(); // Get all connected sets ConnectivityInspector<SSE, LabeledEdge> ci = new ConnectivityInspector<SSE, LabeledEdge>(g); List<Set<SSE>> conSets = ci.connectedSets(); // Create graphs out of the connected sets for(Integer j = 0; j < conSets.size(); j++) { // I can do this... UndirectedSubgraph<SSE, LabeledEdge> subGraph = new UndirectedSubgraph<SSE, LabeledEdge>(g, conSets.get(j), null); // ... but I would like to do something like this: ProteinGraph<SSE, LabeledEdge> psg = new UndirectedSubgraph<SSE, LabeledEdge>(g, conSets.get(j), null); // or ProteinGraph<SSE, LabeledEdge> psg = subGraph.toGraph(); } Using that code, my question could also be formulated as 'How can I turn a UndirectedSubgraph into a new Graph of a certain type (my ProteinGraph class, in this case). Is there any way to do this? Or should I write a new constructor for ProteinGraph that uses the SubGraph to construct the ProteinGraph based on the vertix set and edge set in the subgraph? Thanks for any hints,  Tim 
From: Ethan Kim <ethkim@gm...>  20110417 05:54:33

Hi, I have questions regarding the ConnectivityInspector and NeighborIndex classes. If I were to use NeighborIndex's neighborsOf(V v) method, while adding/removing edges in the graph, do I need to make a customized graph type (that extends SimpleGraph, say), and add the NeighborIndex as a listener? In other words, if I declare NeighborIndex object using a SimpleGraph object itself, a call to neighborsOf(V v) method would be inefficient? I guess similar question can be asked for ConnectivityInspector's connectedSetOf(V v), etc. On another note, how does the above neighborsOf() method differ from using Graph's method "edgesOf(V vertex)" method? Any comments would be appreciated. Thanks! Ethan Kim 
From: Diego Oliveira <diegodimap@gm...>  20110413 02:06:00

Hi Everybody, I want to change simple things like the SHAPE of the Nodes and the color of the background and font... I have this code in method *private void positionVertexAt(Object vertex, int x, int y) {* : Map attr = cell.getAttributes(); Rectangle2D b = GraphConstants.getBounds(attr); //2 = background of the NODE //5 = font of the NODE for (Object object : attr.values()) { System.out.println("MAP= " + object.toString()); } //widht //height GraphConstants.setBounds(attr, new Rectangle(x, y, WIDTH, HEIGTH));  There is a simple way right? How is it? Thank you very much!  Diego Oliveira Master's Program in Computer Science Federal University of Rio Grande do Norte  UFRN NatalRNBrazil 
From: Peter Wilkinson <proggerpete@gm...>  20110412 23:58:43

From: Joris Kinable <deus87@gm...>  20110412 22:17:59

Hey, It's easier if you post some more information about your graph. Some functions/classes that might come in handy for you: Graphs.getOppositeVertex(Graph<V,E> g, E e, V v): Gets the vertex opposite another vertex across an edge. Graph.getNeighbors() Also, check the depthFirstIterator. Besides that, you should be a bit more specific about your graph, type of graph, properties like cyclic/simple/etc. Perhaps some short code snippets. br, Joris On Sun, Apr 10, 2011 at 11:46 AM, Peter Wilkinson <proggerpete@...> wrote: > Hi, I'm working on a js dependency management project. I've been pointed at > JGraphT which seems to offer a lot of handy stuff. > > However I'm having trouble finding the specific info I want which is how I > can retrieve the vertexes in dependency order from a given starting node. > > e.g. I have a tree with 3 Vertexes A => B, B => C, A => C > > I want to iterate through the vertexes in order of A, B, C. I'm finding I > get results like A, C, B. > > Cheers, > > Pete > >  > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizonsfdev > _______________________________________________ > jgraphtusers mailing list > jgraphtusers@... > https://lists.sourceforge.net/lists/listinfo/jgraphtusers > > 
From: Joris Kinable <deus87@gm...>  20110412 22:10:04

Sure. Best thing you could do is just download the jgraphx package and follow their tutorial on how to build a graph using jgrahpx. Next you take your jgrapht graph and you replicate your graph in jgraphx. Jgraphx has quite some fancy coloring support. Just change the property of a vertex/edge. For example, set the property: "fillColor=blue". br, Joris On Wed, Apr 6, 2011 at 7:43 PM, <jlosman@...> wrote: > Is there a way to make each vertex a different color? > > > >  > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizonsfdev > _______________________________________________ > jgraphtusers mailing list > jgraphtusers@... > https://lists.sourceforge.net/lists/listinfo/jgraphtusers > 
From: Peter Wilkinson <proggerpete@gm...>  20110410 09:46:06

Hi, I'm working on a js dependency management project. I've been pointed at JGraphT which seems to offer a lot of handy stuff. However I'm having trouble finding the specific info I want which is how I can retrieve the vertexes in dependency order from a given starting node. e.g. I have a tree with 3 Vertexes A => B, B => C, A => C I want to iterate through the vertexes in order of A, B, C. I'm finding I get results like A, C, B. Cheers, Pete 
From: <jlosman@ol...>  20110406 17:43:22

Is there a way to make each vertex a different color? 
From: Daniel Bell <DBell@it...>  20110406 08:48:05

Hi Alejandro, I had a similar situation a couple of years ago. John suggested using org.jgrapht.traverse.ClosestFirstIterator, a delegate of DijkstraShortestPath, which solved my problem. I ended up implementing something very similar to DijkstraShortestPath to calculate all shortest paths, but unfortunately couldn't contribute it at the time. Hope that helps. http://jgraphtusers.107614.n3.nabble.com/Allshortestpathsproblemtd107976.html Cheers, Daniel Original Message From: Alexander Herz [mailto:alexander.herz@...] Sent: Wednesday, April 06, 2011 4:19 PM To: jgraphtusers@... Subject: Re: [jgraphtusers] Dijkstra Algorithm Hi, I realized this as well. What John probably means is that Dijkstra is supposed to give you single soure shortest pairs, so the shortest paths from a singlde node to all other nodes in the graph. Currently, jgrapht only returns the shortest path in between two nodes (and it is unclear if it caches any information or if each call to Dijkstra has to recompute everything). Also it wold be nice to get some more shortest path algos for specific graphs (like DAG). Alex Am 06.04.2011 06:39, schrieb John Sichi: > If you want all pairs, use FloydWarshallShortestPaths instead. > > JVS > > On Tue, Apr 5, 2011 at 1:53 PM, Alejandro Riveros Cruz > <lalejandrocruz@...> wrote: >> Hi, >> >> First of all thanks for your great work in the design and support of >> JGraphT. >> Currently i'm working in my master final work, in this work i need to >> calculate some similarity measures, based on path distances between vertex >> over directed graphs, for this purpose a develop a java program that >> performs the calculus using jgrapht. >> Currently i have some problems, first the graphs are big, each graph has in >> average 50000 vertex and more than 50000 edges. >> I read about the Dijkstra algorithm and i know that if using the appropiate >> structure i.e. a priority queue, this algorithm can perform the search of >> all shortest path between a selected vertex and all other vertex, in a >> computational reasonable time. >> >> Searching on jGraphT library i found a Dijkstra implementaion for searching >> the shortest path between two nodes, but no the implementation for searching >> the shortest path between all nodes, for this reason i need to know if my >> assumption about the implementation of Dijkstra is true? in such case, you >> have planned the release of that algorithm soon? >> >> >> Thanks in advance, >> >> Alejandro Riveros >> >>  >> Alejandro Riveros Cruz >> Ingeniero de Sistemas >> Universidad Nacional de Colombia >> >>  >> Xperia(TM) PLAY >> It's a major breakthrough. An authentic gaming >> smartphone on the nation's most reliable network. >> And it wants your games. >> http://p.sf.net/sfu/verizonsfdev >> _______________________________________________ >> jgraphtusers mailing list >> jgraphtusers@... >> https://lists.sourceforge.net/lists/listinfo/jgraphtusers >> >> >  > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizonsfdev > _______________________________________________ > jgraphtusers mailing list > jgraphtusers@... > https://lists.sourceforge.net/lists/listinfo/jgraphtusers   Lehrstuhl I2 Seidl Sprachen und Beschreibungsstrukturen der Informatik Institut fuer Informatik Technische Universitaet Muenchen Boltzmannstrasse 3 85748 Garching http://www2.in.tum.de Telefon: +89 289 181806 Fax: +89 289 18161   Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizonsfdev _______________________________________________ jgraphtusers mailing list jgraphtusers@... https://lists.sourceforge.net/lists/listinfo/jgraphtusers 
From: Alexander Herz <alexander.herz@my...>  20110406 06:51:24

Hi, I realized this as well. What John probably means is that Dijkstra is supposed to give you single soure shortest pairs, so the shortest paths from a singlde node to all other nodes in the graph. Currently, jgrapht only returns the shortest path in between two nodes (and it is unclear if it caches any information or if each call to Dijkstra has to recompute everything). Also it wold be nice to get some more shortest path algos for specific graphs (like DAG). Alex Am 06.04.2011 06:39, schrieb John Sichi: > If you want all pairs, use FloydWarshallShortestPaths instead. > > JVS > > On Tue, Apr 5, 2011 at 1:53 PM, Alejandro Riveros Cruz > <lalejandrocruz@...> wrote: >> Hi, >> >> First of all thanks for your great work in the design and support of >> JGraphT. >> Currently i'm working in my master final work, in this work i need to >> calculate some similarity measures, based on path distances between vertex >> over directed graphs, for this purpose a develop a java program that >> performs the calculus using jgrapht. >> Currently i have some problems, first the graphs are big, each graph has in >> average 50000 vertex and more than 50000 edges. >> I read about the Dijkstra algorithm and i know that if using the appropiate >> structure i.e. a priority queue, this algorithm can perform the search of >> all shortest path between a selected vertex and all other vertex, in a >> computational reasonable time. >> >> Searching on jGraphT library i found a Dijkstra implementaion for searching >> the shortest path between two nodes, but no the implementation for searching >> the shortest path between all nodes, for this reason i need to know if my >> assumption about the implementation of Dijkstra is true? in such case, you >> have planned the release of that algorithm soon? >> >> >> Thanks in advance, >> >> Alejandro Riveros >> >>  >> Alejandro Riveros Cruz >> Ingeniero de Sistemas >> Universidad Nacional de Colombia >> >>  >> Xperia(TM) PLAY >> It's a major breakthrough. An authentic gaming >> smartphone on the nation's most reliable network. >> And it wants your games. >> http://p.sf.net/sfu/verizonsfdev >> _______________________________________________ >> jgraphtusers mailing list >> jgraphtusers@... >> https://lists.sourceforge.net/lists/listinfo/jgraphtusers >> >> >  > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizonsfdev > _______________________________________________ > jgraphtusers mailing list > jgraphtusers@... > https://lists.sourceforge.net/lists/listinfo/jgraphtusers   Lehrstuhl I2 Seidl Sprachen und Beschreibungsstrukturen der Informatik Institut fuer Informatik Technische Universitaet Muenchen Boltzmannstrasse 3 85748 Garching http://www2.in.tum.de Telefon: +89 289 181806 Fax: +89 289 18161  
From: John Sichi <jsichi@gm...>  20110406 04:39:45

If you want all pairs, use FloydWarshallShortestPaths instead. JVS On Tue, Apr 5, 2011 at 1:53 PM, Alejandro Riveros Cruz <lalejandrocruz@...> wrote: > Hi, > > First of all thanks for your great work in the design and support of > JGraphT. > Currently i'm working in my master final work, in this work i need to > calculate some similarity measures, based on path distances between vertex > over directed graphs, for this purpose a develop a java program that > performs the calculus using jgrapht. > Currently i have some problems, first the graphs are big, each graph has in > average 50000 vertex and more than 50000 edges. > I read about the Dijkstra algorithm and i know that if using the appropiate > structure i.e. a priority queue, this algorithm can perform the search of > all shortest path between a selected vertex and all other vertex, in a > computational reasonable time. > > Searching on jGraphT library i found a Dijkstra implementaion for searching > the shortest path between two nodes, but no the implementation for searching > the shortest path between all nodes, for this reason i need to know if my > assumption about the implementation of Dijkstra is true? in such case, you > have planned the release of that algorithm soon? > > > Thanks in advance, > > Alejandro Riveros > >  > Alejandro Riveros Cruz > Ingeniero de Sistemas > Universidad Nacional de Colombia > >  > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizonsfdev > _______________________________________________ > jgraphtusers mailing list > jgraphtusers@... > https://lists.sourceforge.net/lists/listinfo/jgraphtusers > > 
From: Alejandro Riveros Cruz <lalejandrocruz@gm...>  20110405 20:53:59

Hi, First of all thanks for your great work in the design and support of JGraphT. Currently i'm working in my master final work, in this work i need to calculate some similarity measures, based on path distances between vertex over directed graphs, for this purpose a develop a java program that performs the calculus using jgrapht. Currently i have some problems, first the graphs are big, each graph has in average 50000 vertex and more than 50000 edges. I read about the Dijkstra algorithm and i know that if using the appropiate structure i.e. a priority queue, this algorithm can perform the search of all shortest path between a selected vertex and all other vertex, in a computational reasonable time. Searching on jGraphT library i found a Dijkstra implementaion for searching the shortest path between two nodes, but no the implementation for searching the shortest path between all nodes, for this reason i need to know if my assumption about the implementation of Dijkstra is true? in such case, you have planned the release of that algorithm soon? Thanks in advance, Alejandro Riveros  Alejandro Riveros Cruz Ingeniero de Sistemas Universidad Nacional de Colombia 