Author: ghuck
Date: 2011-06-13 19:02:32 -0700 (Mon, 13 Jun 2011)
New Revision: 25739
Added:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IsConnected.java
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/build.xml
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphInterface.java
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphPlugin.java
csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/Makefile
csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
Log:
Modified: csplugins/trunk/soc/ghuck/IgraphPlugin/build.xml
===================================================================
--- csplugins/trunk/soc/ghuck/IgraphPlugin/build.xml 2011-06-13 23:46:39 UTC
(rev 25738)
+++ csplugins/trunk/soc/ghuck/IgraphPlugin/build.xml 2011-06-14 02:02:32 UTC
(rev 25739)
@@ -43,6 +43,7 @@
<available file="${root.dir}/plugin.props" property="plugin.prop.present"/>
<available file="${root.dir}/License.txt" property="license.present"/>
<available file="${root.dir}/libigraphWrapper.dylib"
property="igraphWrapper.lib.present"/>
+ <available file="${igraph.dir}/src/.libs/libigraph.0.dylib"
property="igraph.lib.present"/>
<!-- Define the java class path -->
<path id="project.class.path">
@@ -88,7 +89,8 @@
<!-- =================================================================== -->
<!-- Creates the plugin jar file
-->
<!-- =================================================================== -->
- <target name="jar" depends="compile, copy_plugin_prop, copy_license,
copy_igraphWrapper_lib">
+ <target name="jar" depends="compile, copy_plugin_prop, copy_license,
+ copy_igraphWrapper_lib, copy_igraph_lib">
<jar destfile="${project.jar}">
<manifest> <attribute name="Cytoscape-Plugin" value="${plugin_class}"/>
</manifest>
<fileset dir="${build.dir}" includes="**"/>
@@ -118,6 +120,15 @@
</target>
<!-- =================================================================== -->
+ <!-- If igraph.lib exist, copy it to build directory -->
+ <!-- =================================================================== -->
+ <target name="copy_igraph_lib" if="igraph.lib.present">
+ <echo message="copying igraph lib to build dir"/>
+ <copy todir="${build.dir}/"
file="${igraph.dir}/src/.libs/libigraph.0.dylib"/>
+ </target>
+
+
+ <!-- =================================================================== -->
<!-- Copy jar file to Cytoscape plugin folder -->
<!-- =================================================================== -->
<target name="copy_jar" depends="jar">
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphInterface.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphInterface.java
2011-06-13 23:46:39 UTC (rev 25738)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphInterface.java
2011-06-14 02:02:32 UTC (rev 25739)
@@ -12,214 +12,19 @@
*/
public class IgraphInterface {
- public IgraphInterface() {
- igraph INSTANCE = (igraph) Native.loadLibrary((Platform.isWindows() ?
"msvcrt" : "c"),
- igraph.class);
+ static{
+ //load the dynamic library
+ Native.register("igraphWrapper");
}
-
- public interface igraph extends Library {
-
- public class Igraph_vector_t extends Structure {
- DoubleByReference stor_begin;
- DoubleByReference stor_end;
- DoubleByReference end;
- }
-
- public class Igraph_t extends Structure {
- int n;
- int directed;
- Igraph_vector_t from;
- Igraph_vector_t to;
- Igraph_vector_t oi;
- Igraph_vector_t ii;
- Igraph_vector_t os;
- Igraph_vector_t is;
- // void *attr;
- }
-
-
- /* -------------------------------------------------- */
- /* Data types */
- /* -------------------------------------------------- */
-
- /*
- typedef int igraph_integer_t;
- typedef double igraph_real_t;
- typedef int igraph_bool_t;
-
-
- typedef struct igraph_s {
- igraph_integer_t n;
- igraph_bool_t directed;
- igraph_vector_t from;
- igraph_vector_t to;
- igraph_vector_t oi;
- igraph_vector_t ii;
- igraph_vector_t os;
- igraph_vector_t is;
- void *attr;
- } igraph_t;
-
-
- typedef struct TYPE(igraph_vector) {
- BASE* stor_begin;
- BASE* stor_end;
- BASE* end;
- } TYPE(igraph_vector);
-
- */
-
- /* -------------------------------------------------- */
- /* Interface */
- /* -------------------------------------------------- */
-
- /*
- int igraph_empty(igraph_t *graph, igraph_integer_t n, igraph_bool_t
directed);
- int igraph_empty_attrs(igraph_t *graph, igraph_integer_t n,
igraph_bool_t directed, void *attr);
- int igraph_destroy(igraph_t *graph);
- int igraph_copy(igraph_t *to, const igraph_t *from);
- int igraph_add_edges(igraph_t *graph, const igraph_vector_t *edges,
- void *attr);
- int igraph_add_vertices(igraph_t *graph, igraph_integer_t nv,
- void *attr);
- int igraph_delete_edges(igraph_t *graph, igraph_es_t edges);
- int igraph_delete_vertices(igraph_t *graph, const igraph_vs_t
vertices);
- int igraph_delete_vertices_idx(igraph_t *graph, const igraph_vs_t
vertices,
- igraph_vector_t *idx,
- igraph_vector_t *invidx);
- igraph_integer_t igraph_vcount(const igraph_t *graph);
- igraph_integer_t igraph_ecount(const igraph_t *graph);
- int igraph_neighbors(const igraph_t *graph, igraph_vector_t *neis,
igraph_integer_t vid,
- igraph_neimode_t mode);
- igraph_bool_t igraph_is_directed(const igraph_t *graph);
- int igraph_degree(const igraph_t *graph, igraph_vector_t *res,
- const igraph_vs_t vids, igraph_neimode_t mode,
- igraph_bool_t loops);
- int igraph_edge(const igraph_t *graph, igraph_integer_t eid,
- igraph_integer_t *from, igraph_integer_t *to);
- int igraph_edges(const igraph_t *graph, igraph_es_t eids,
- igraph_vector_t *edges);
- int igraph_get_eid(const igraph_t *graph, igraph_integer_t *eid,
- igraph_integer_t from, igraph_integer_t to,
- igraph_bool_t directed, igraph_bool_t error);
- int igraph_get_eids(const igraph_t *graph, igraph_vector_t *eids,
- const igraph_vector_t *pairs,
- const igraph_vector_t *path,
- igraph_bool_t directed, igraph_bool_t error);
- int igraph_get_eids_multi(const igraph_t *graph, igraph_vector_t *eids,
- const igraph_vector_t *pairs,
- const igraph_vector_t *path,
- igraph_bool_t directed, igraph_bool_t error);
- int igraph_incident(const igraph_t *graph, igraph_vector_t *eids,
igraph_integer_t vid,
- igraph_neimode_t mode);
-
- #define IGRAPH_FROM(g,e) (VECTOR((g)->from)[(long int)(e)])
- #define IGRAPH_TO(g,e) (VECTOR((g)->to) [(long int)(e)])
- #define IGRAPH_OTHER(g,e,v) (IGRAPH_TO(g,(e))==(v) ?
IGRAPH_FROM((g),(e)) : IGRAPH_TO((g),(e)))
- */
-
-
- /* -------------------------------------------------- */
- /* Constants */
- /* -------------------------------------------------- */
-
- /*
- typedef enum { IGRAPH_UNDIRECTED=0, IGRAPH_DIRECTED=1 }
igraph_i_directed_t;
-
- typedef enum { IGRAPH_NO_LOOPS=0, IGRAPH_LOOPS=1 } igraph_i_loops_t;
-
- typedef enum { IGRAPH_ASCENDING=0, IGRAPH_DESCENDING=1 }
igraph_order_t;
-
- typedef enum { IGRAPH_OUT=1, IGRAPH_IN=2, IGRAPH_ALL=3,
- IGRAPH_TOTAL=3 } igraph_neimode_t;
-
- typedef enum { IGRAPH_WEAK=1, IGRAPH_STRONG=2 } igraph_connectedness_t;
-
- typedef enum { IGRAPH_ADJ_DIRECTED=0,
- IGRAPH_ADJ_UNDIRECTED=1, IGRAPH_ADJ_MAX=1,
- IGRAPH_ADJ_UPPER, IGRAPH_ADJ_LOWER, IGRAPH_ADJ_MIN,
- IGRAPH_ADJ_PLUS } igraph_adjacency_t;
-
- typedef enum { IGRAPH_STAR_OUT=0, IGRAPH_STAR_IN,
- IGRAPH_STAR_UNDIRECTED,
- IGRAPH_STAR_MUTUAL } igraph_star_mode_t;
-
- typedef enum { IGRAPH_TREE_OUT=0, IGRAPH_TREE_IN,
- IGRAPH_TREE_UNDIRECTED } igraph_tree_mode_t;
-
- typedef enum { IGRAPH_ERDOS_RENYI_GNP=0,
- IGRAPH_ERDOS_RENYI_GNM } igraph_erdos_renyi_t;
-
- typedef enum { IGRAPH_GET_ADJACENCY_UPPER=0,
- IGRAPH_GET_ADJACENCY_LOWER,
- IGRAPH_GET_ADJACENCY_BOTH } igraph_get_adjacency_t;
-
- typedef enum { IGRAPH_DEGSEQ_SIMPLE=0,
- IGRAPH_DEGSEQ_VL } igraph_degseq_t;
-
- typedef enum { IGRAPH_FILEFORMAT_EDGELIST=0,
- IGRAPH_FILEFORMAT_NCOL,
- IGRAPH_FILEFORMAT_PAJEK,
- IGRAPH_FILEFORMAT_LGL,
- IGRAPH_FILEFORMAT_GRAPHML } igraph_fileformat_type_t;
-
- typedef enum { IGRAPH_REWIRING_SIMPLE=0 } igraph_rewiring_t;
-
- typedef enum { IGRAPH_EDGEORDER_ID=0,
- IGRAPH_EDGEORDER_FROM,
- IGRAPH_EDGEORDER_TO } igraph_edgeorder_type_t;
-
- typedef enum { IGRAPH_TO_DIRECTED_ARBITRARY=0,
- IGRAPH_TO_DIRECTED_MUTUAL } igraph_to_directed_t;
-
- typedef enum { IGRAPH_TO_UNDIRECTED_EACH=0,
- IGRAPH_TO_UNDIRECTED_COLLAPSE,
- IGRAPH_TO_UNDIRECTED_MUTUAL} igraph_to_undirected_t;
-
- typedef enum { IGRAPH_VCONN_NEI_ERROR=0,
- IGRAPH_VCONN_NEI_NUMBER_OF_NODES,
- IGRAPH_VCONN_NEI_IGNORE,
- IGRAPH_VCONN_NEI_NEGATIVE } igraph_vconn_nei_t;
-
- typedef enum { IGRAPH_SPINCOMM_UPDATE_SIMPLE=0,
- IGRAPH_SPINCOMM_UPDATE_CONFIG } igraph_spincomm_update_t;
-
- typedef enum { IGRAPH_DONT_SIMPLIFY=0,
- IGRAPH_SIMPLIFY } igraph_lazy_adlist_simplify_t;
-
- typedef enum { IGRAPH_TRANSITIVITY_NAN=0,
- IGRAPH_TRANSITIVITY_ZERO } igraph_transitivity_mode_t;
-
- typedef enum { IGRAPH_SPINCOMM_IMP_ORIG=0,
- IGRAPH_SPINCOMM_IMP_NEG } igraph_spinglass_implementation_t;
-
- typedef enum { IGRAPH_COMMCMP_VI = 0,
- IGRAPH_COMMCMP_NMI,
- IGRAPH_COMMCMP_SPLIT_JOIN,
- IGRAPH_COMMCMP_RAND,
- IGRAPH_COMMCMP_ADJUSTED_RAND } igraph_community_comparison_t;
-
- typedef enum { IGRAPH_ADD_WEIGHTS_NO = 0,
- IGRAPH_ADD_WEIGHTS_YES,
- IGRAPH_ADD_WEIGHTS_IF_PRESENT } igraph_add_weights_t;
-
- typedef enum { IGRAPH_BARABASI_BAG = 0,
- IGRAPH_BARABASI_PSUMTREE,
- IGRAPH_BARABASI_PSUMTREE_MULTIPLE} igraph_barabasi_algorithm_t;
-
- typedef enum { IGRAPH_SUBGRAPH_AUTO = 0,
- IGRAPH_SUBGRAPH_COPY_AND_DELETE,
- IGRAPH_SUBGRAPH_CREATE_FROM_SCRATCH
- } igraph_subgraph_implementation_t;
-
- typedef igraph_real_t igraph_scalar_function_t(const igraph_vector_t
*var,
- const igraph_vector_t
*par,
- void* extra);
- typedef void igraph_vector_function_t(const igraph_vector_t *var,
- const igraph_vector_t *par,
- igraph_vector_t* res, void*
extra);
- */
-
-
- }
+
+ public static native int nativeAdd(int a, int b);
+
+ public static native void createGraph(int edgeArray[], int length);
+
+ //Test whether the graph is connected
+ public static native boolean isConnected();
+
+ //Simplify the graph for community ananlysis
+ public static native void simplify();
+
}
\ No newline at end of file
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphPlugin.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphPlugin.java
2011-06-13 23:46:39 UTC (rev 25738)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphPlugin.java
2011-06-14 02:02:32 UTC (rev 25739)
@@ -33,6 +33,8 @@
import javax.swing.JOptionPane;
import javax.swing.JPanel;
+import com.sun.jna.*;
+
/** ---------------------------IgraphPlugin-----------------------------
* This plugin allows to call some of igraph functions from Cytoscape
* @author Gerardo Huck
@@ -45,27 +47,37 @@
*/
public IgraphPlugin() {
- // Make sure Igraph library is extracted in the plugins folder
- checkLib();
+ // Make sure libraries are extracted in the plugins folder
+ checkLib("igraphWrapper");
+ checkLib("igraph.0");
// Load igraph
- loadIgraph();
+ //loadIgraph();
// Use JNA to print a simple message
- HelloWorld.hello();
+ //HelloWorld.hello();
- // Add an element in menu toolbar
+ String userDir = System.getProperty("user.dir");
+// JOptionPane.showMessageDialog( Cytoscape.getDesktop(), "user dir:"+
userDir);
+ NativeLibrary.addSearchPath("igraphWrapper", userDir + "/plugins");
+
+// JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
IgraphInterface.nativeAdd(10, 20));
+
+ // Add elements in menu toolbar
NodeCount nodeCountAction = new NodeCount(this);
Cytoscape.getDesktop().getCyMenus().addCytoscapeAction((CytoscapeAction)
nodeCountAction);
+
+ IsConnected isConnectedAction = new IsConnected(this);
+
Cytoscape.getDesktop().getCyMenus().addCytoscapeAction((CytoscapeAction)
isConnectedAction);
}
private boolean isOldVersion(){
return false;
}
- private void checkLib() {
+ private void checkLib(String lib) {
// TODO: Make this cross-platform
- File dynamicLib = new File ("./plugins/libigraph.dylib");
+ File dynamicLib = new File ("./plugins/lib" + lib + ".dylib");
if (!dynamicLib.exists() || isOldVersion()){
String message;
try {
@@ -73,7 +85,7 @@
getCodeSource().getLocation().toString().
substring(6);
JarFile jar = new JarFile("./plugins/igraphPlugin.jar");
- ZipEntry entry = jar.getEntry("libigraph.dylib");
+ ZipEntry entry = jar.getEntry("lib" + lib + ".dylib");
File efile = new File("./plugins/", entry.getName());
InputStream in =
@@ -90,7 +102,7 @@
out.close();
in.close();
- message = "Igraph library extracted!";
+ message = lib + " library extracted!";
}
catch (Exception e) {
e.printStackTrace();
@@ -126,11 +138,12 @@
try {
// Change the value and load the library.
System.setProperty("java.library.path", "./plugins" + ":" +
orig_path);
- System.loadLibrary("igraph");
+ // System.loadLibrary("igraph.0");
+ System.loadLibrary("igraphWrapper");
}
- catch (UnsatisfiedLinkError error){
- String message = "Problem detected while loading igraph
Library.\n"
+ catch (UnsatisfiedLinkError error) {
+ String message = "Problem detected while loading library.\n"
+ error.getMessage()
+ "\nPlease check your plugins folder.";
JOptionPane.showMessageDialog(Cytoscape.getDesktop(), message);
@@ -144,11 +157,11 @@
field.setAccessible(accessible);
}
}
- catch (Exception exception){
+ catch (Exception exception) {
res = false;
}
- finally{
+ finally {
return res;
}
}
Added:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IsConnected.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IsConnected.java
(rev 0)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IsConnected.java
2011-06-14 02:02:32 UTC (rev 25739)
@@ -0,0 +1,123 @@
+package cytoscape.plugins.igraph;
+
+import java.awt.event.ActionEvent;
+import javax.swing.JOptionPane;
+import java.util.*;
+
+import cytoscape.Cytoscape;
+import cytoscape.*;
+import cytoscape.data.*;
+import cytoscape.plugin.CytoscapePlugin;
+import cytoscape.util.CytoscapeAction;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+
+import giny.model.*;
+
+import com.sun.jna.Library;
+import com.sun.jna.Native;
+import com.sun.jna.Platform;
+
+public class IsConnected extends CytoscapeAction {
+
+
+ private IgraphTaskThread t; //This thread is actually where the action is
+ private Thread currentThread;
+
+
+ public IsConnected(IgraphPlugin myPlugin) {
+ super("IsConnected");
+ setPreferredMenu("Plugins.Igraph");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Is Connected?: "
+ isConnected());
+ }
+
+ public boolean isConnected() {
+
+ loadGraph_optimized();
+ return IgraphInterface.isConnected(); //Only call this function if the
graph has been loaded
+
+
+// boolean res = false;
+// try {
+// ArrayList<Integer> nodes = loadGraph_optimized();
+// JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Graph
loaded...Number of nodes: " + nodes.size());
+// res = IgraphInterface.isConnected();
+// }
+// catch (Exception e) {
+// e.printStackTrace();
+// JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Igraph
Plugin error:\n" + e.getMessage());
+// res = false;
+// }
+// finally{
+// return res;
+// }
+
+
+// t = new IgraphTaskThread();
+// t.setAlgorithm(1);
+
+// //This marks the current thread
+// currentThread = Thread.currentThread();
+
+// t.start();
+// try{
+// t.join(); //Join the background thread running the algorithm
with the current thread showing the progressbar
+// }
+// catch(InterruptedException e){
+// //System.out.println("Algorithm terminated");
+// //The failed C algorithm may cause issues here
+// e.printStackTrace();
+// JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Igraph
Plugin error:\n" + e.getMessage());
+// }
+
+// return t.getResult();
+ }
+
+ //This will load the graph into c
+ public static ArrayList<Integer> loadGraph_optimized(){
+
+ // Nodes are ordered according to node array.
+ CyNetwork network = Cytoscape.getCurrentNetwork();
+
+ ArrayList<Integer> selectedNodeIndices = new ArrayList<Integer>();
+
+ int[] edgeIndicesArray = network.getEdgeIndicesArray();
+ int[] nodeArray = network.getNodeIndicesArray();
+
+ // Create a reverse mapping
+ HashMap<Integer, Integer> nodeIdMapping = new HashMap<Integer,
Integer>(nodeArray.length);
+ for(int i=0; i<nodeArray.length; i++){
+ nodeIdMapping.put(nodeArray[i], i);
+ }
+
+ // Get the selectedNodes
+ // Return the selected node array list
+ Iterator<Node> nodeIt = network.getSelectedNodes().iterator();
+ while(nodeIt.hasNext()){
+
+ Node node = nodeIt.next();
+ ////System.out.println("This is gd:" +
nodeIdMapping.get(node.getRootGraphIndex()));
+
selectedNodeIndices.add(nodeIdMapping.get(node.getRootGraphIndex()));
+ }
+
+ //If this works then it will be a lot faster
+ int[] edgeArray = new int[edgeIndicesArray.length * 2];
+
+ //Get all edges, then simplify in igraph
+ for(int i = 0; i < edgeIndicesArray.length; i++){
+
+ edgeArray[i*2] =
nodeIdMapping.get(network.getEdgeSourceIndex(edgeIndicesArray[i]));
+ edgeArray[i*2 + 1] =
nodeIdMapping.get(network.getEdgeTargetIndex(edgeIndicesArray[i]));
+ }
+
+ IgraphInterface.createGraph(edgeArray, edgeArray.length);
+ IgraphInterface.simplify();
+
+ return selectedNodeIndices;
+ }
+
+}
\ No newline at end of file
Modified: csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/Makefile
===================================================================
--- csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/Makefile
2011-06-13 23:46:39 UTC (rev 25738)
+++ csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/Makefile
2011-06-14 02:02:32 UTC (rev 25739)
@@ -1,16 +1,20 @@
all: libigraphWrapper.dylib
-libigraphWrapper.dylib: igraphJNA.cpp igraphJNA.h
- g++ -fPIC -shared -soname,libigraphWrapper.dylib ${CFLAGS} ${LIB_FLAGS}
-o libigraphWrapper.dylib igraphJNA.cpp
+igraphJNA.o : igraphJNA.cpp igraphJNA.h
+ g++ -c -fPIC ${CFLAGS} ${STATIC_LIBS} -o igraphJNA.o igraphJNA.cpp
+libigraphWrapper.dylib : igraphJNA.o
+ g++ -shared -soname,libigraphWrapper.dylib ${LIB_FLAGS}-o
libigraphWrapper.dylib igraphJNA.o
+
clean :
+ rm igraphJNA.o
rm libIgraphWrapper.dylib
CFLAGS=-I${IGRAPH_PATH}/include
LIB_FLAGS=-L${IGRAPH_PATH}/src/.libs -ligraph
+STATIC_LIBS=-L${IGRAPH_PATH}/src/libs/
+IGRAPH_PATH=/Users/gerardohuck/igraph
-IGRAPH_PATH := /Users/gerardohuck/igraph/
-
Modified: csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
===================================================================
--- csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
2011-06-13 23:46:39 UTC (rev 25738)
+++ csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
2011-06-14 02:02:32 UTC (rev 25739)
@@ -1,15 +1,7 @@
//Author Gang Su
//[email protected]
-//functions to be exported
-//The purpose of this program, is to port some of the igraph funcions/focus on
community structure detection
-//To cytoscape.
-
-
-
-
-
/*include this igraph.h first*/
#include "igraph.h"
#include "igraphJNA.h"
@@ -27,24 +19,28 @@
//use a global graph object
//Make sure there's only one active graph @ a time to reduce confusions
igraph_t g;
+int existsGraph = 0;
void createGraph(int edgeArray[], int length){
- igraph_vector_t v;
- igraph_vector_init(&v, length);
- for(int i=0; i<length; i++){
- VECTOR(v)[i] = edgeArray[i];
- }
+ // Destroy old graph if it exists
+ if (existsGraph) {
+ igraph_destroy(&g);
+ existsGraph = 0;
+ }
- //Create undirected graphs here.
- //Can be extended to create directed graph.
- //But the problem is the original graph may contain both
- //Directed an undirected edges.
- igraph_create(&g, &v, 0, 0);
- //cout << "Graph Created";
- //igraph_bool_t simple;
- //igraph_is_simple(&g, &simple);
- //return (bool)simple;
+ igraph_vector_t v;
+ igraph_vector_init(&v, length);
+ for(int i=0; i<length; i++){
+ VECTOR(v)[i] = edgeArray[i];
+ }
+
+ igraph_create(&g, &v, 0, 0);
+ existsGraph = 1;
+ printf("Graph created! Number of nodes: %d\n", nodeCount());
+
+ // Free resources no longer needed
+ igraph_vector_destroy(&v);
}
//Boolean, test whether the current graph is simple
@@ -56,16 +52,16 @@
// //return 1;
// }
-// bool isConnected(){
-// igraph_bool_t connected;
-// igraph_is_connected(&g, &connected, IGRAPH_STRONG);
-// return (bool)connected;
-// }
+bool isConnected(){
+ igraph_bool_t connected;
+ igraph_is_connected(&g, &connected, IGRAPH_STRONG);
+ return (bool)connected;
+}
-// void simplify(){
-// igraph_simplify(&g, 1, 1);
-// }
-// //////////////////////////////
+void simplify(){
+ igraph_simplify(&g, 1, 1, 0);
+}
+//////////////////////////////
// void clusters(int membership[], int csize[], int* numCluster){
// igraph_vector_t membership_v;
// igraph_vector_t csize_v;
@@ -91,10 +87,10 @@
// }
-// //get nodeCount and edgeCount of the current loaded graph
-// int nodeCount(){
-// return (int)igraph_vcount(&g);
-// }
+//get nodeCount and edgeCount of the current loaded graph
+int nodeCount(){
+ return (int)igraph_vcount(&g);
+}
// int edgeCount(){
// return (int)igraph_ecount(&g);
@@ -578,13 +574,13 @@
// }
-// //extern "C"{
-// //Simple adding of two integers
-// int nativeAdd( int a, int b )
-// {
-// return( a + b );
-// }
-
+extern "C"{
+//Simple adding of two integers
+ int nativeAdd( int a, int b )
+ {
+ return( a + b );
+ }
+}
// //Add one to the passed integer via pointer
// void nativeIncrement(int* iptr){
// *iptr += 1;
Modified: csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
===================================================================
--- csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
2011-06-13 23:46:39 UTC (rev 25738)
+++ csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
2011-06-14 02:02:32 UTC (rev 25739)
@@ -5,7 +5,7 @@
extern "C"
{
//test functions
-/* int nativeAdd( int a, int b ); */
+ int nativeAdd( int a, int b );
/* void nativeIncrement(int* iptr); */
/* int nativeArrayReset(int data[], int length); */
/* int nativeCountAdd(int value); */
@@ -18,10 +18,10 @@
//igraph functions
void createGraph(int edgeArray[], int length);
/* bool isSimple(); */
-/* bool isConnected(); */
-/* void simplify(); */
+ bool isConnected();
+ void simplify();
/* void clusters(int membership[], int csize[], int* numCluster); */
-/* int nodeCount(); */
+ int nodeCount();
/* int edgeCount(); */
/* void fastGreedy(int membership[], double* modularity, int csize[], int *
numCluster); */
--
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