Author: ghuck
Date: 2011-08-17 09:33:42 -0700 (Wed, 17 Aug 2011)
New Revision: 26585
Modified:
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/igraphJNA.cpp
csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
Log:
Added LGL Layout
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphInterface.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphInterface.java
2011-08-17 15:28:25 UTC (rev 26584)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphInterface.java
2011-08-17 16:33:42 UTC (rev 26585)
@@ -77,6 +77,16 @@
double weights[],
double cellSize);
+ // lgl Layout
+ public static native void layoutLGL(double x[],
+ double y[],
+ int maxIt,
+ double maxDelta,
+ double area,
+ double coolExp,
+ double repulserad,
+ double cellSize);
+
// Minimum spanning tree - unweighted
public static native int minimum_spanning_tree_unweighted(int res[]);
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphPlugin.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphPlugin.java
2011-08-17 15:28:25 UTC (rev 26584)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphPlugin.java
2011-08-17 16:33:42 UTC (rev 26585)
@@ -88,7 +88,7 @@
CyLayouts.addLayout(new StarLayout(),
"Igraph");
CyLayouts.addLayout(new FruchtermanReingoldLayout(true),
"Igraph");
CyLayouts.addLayout(new FruchtermanReingoldGridLayout(true),
"Igraph");
-
+ CyLayouts.addLayout(new LGLLayout(),
"Igraph");
} catch (Exception e) {
e.printStackTrace();
Modified: csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
===================================================================
--- csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
2011-08-17 15:28:25 UTC (rev 26584)
+++ csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.cpp
2011-08-17 16:33:42 UTC (rev 26585)
@@ -245,6 +245,43 @@
destroy_graph();
}
+
+// lgl Layout
+void layoutLGL(double x[],
+ double y[],
+ int maxIt,
+ double maxDelta,
+ double area,
+ double coolExp,
+ double repulserad,
+ double cellSize) {
+
+ long int vcount = igraph_vcount(&g);
+ igraph_matrix_t locs;
+ igraph_matrix_init(&locs, vcount, 2);
+ for(int i = 0; i < vcount; i++) {
+ MATRIX(locs, i, 0) = x[i];
+ MATRIX(locs, i, 1) = y[i];
+ }
+
+ igraph_layout_lgl(&g,
+ &locs,
+ maxIt,
+ maxDelta,
+ area,
+ coolExp,
+ repulserad,
+ cellSize,
+ -1); // random root
+
+ for(int i = 0; i < vcount; i++) {
+ x[i] = MATRIX(locs, i, 0);
+ y[i] = MATRIX(locs, i, 1);
+ }
+
+}
+
+
int minimum_spanning_tree_unweighted(int res[]) {
igraph_t mst;
@@ -304,10 +341,6 @@
}
-// int igraph_minimum_spanning_tree(const igraph_t *graph, igraph_vector_t
*res,
-// const igraph_vector_t *weights);
-// int igraph_minimum_spanning_tree_prim(const igraph_t *graph, igraph_t *mst,
-// const igraph_vector_t *weights);
extern "C"{
//Simple adding of two integers
@@ -323,419 +356,10 @@
}
-//////////////////////////////
-//get nodeCount and edgeCount of the current loaded graph
-// int edgeCount(){
-// return (int)igraph_ecount(&g);
-// }
-// //Map community algorithms
-// //Note that some community algorithms work only on connected graphs
-// void fastGreedy(int membership[], double* modularity, int csize[], int*
numCluster){
-// igraph_vector_t modularity_v;
-// igraph_matrix_t merges;
-// igraph_vector_t csize_v;
-// igraph_vector_t membership_v;
-
-
-
-// igraph_vector_init(&modularity_v, 0);
-// igraph_matrix_init(&merges, 0, 0);
-// igraph_vector_init(&csize_v, 0);
-// igraph_vector_init(&membership_v, 0);
-
-// igraph_community_fastgreedy(&g, 0, &merges, &modularity_v);
-// igraph_community_to_membership(&merges, igraph_vcount(&g),
igraph_vector_which_max(&modularity_v), &membership_v, &csize_v);
-
-// //need only map modularity, membership, csize and number of clusters
-// for(int i=0; i<igraph_vector_size(&membership_v); i++){
-// membership[i] = VECTOR(membership_v)[i];
-// }
-
-// for(int i=0; i<igraph_vector_size(&csize_v); i++){
-// csize[i] = VECTOR(csize_v)[i];
-// }
-
-// *modularity = igraph_vector_max(&modularity_v);
-// *numCluster = igraph_vector_size(&csize_v);
-// }
-
-// void labelPropagation(int membership[], double* modularity){
-// igraph_vector_t membership_v;
-// igraph_vector_init(&membership_v, 0); //if i don't initialize will give
run time error
-//
//vectors and matrices will be initialized
-// igraph_real_t modularity_v;
-
-// igraph_community_label_propagation(&g, &membership_v, 0, 0, 0);
-// igraph_modularity(&g, &membership_v, &modularity_v, 0);
-
-// //Reset these parameters to avoid mistakes.
-// //*numCluster = 0;
-// //for(int i=0; i<igraph_vector_size(&membership_v); i++){
-// // csize[i] = 0;
-// //}
-
-
-// for(int i=0; i<igraph_vector_size(&membership_v); i++){
-// membership[i] = VECTOR(membership_v)[i];
-// }
-
-// *modularity = modularity_v;
-// //*modularity = 0.0;
-// }
-
-// void walkTrap(int membership[], double* modularity, int csize[], int*
numCluster){
-// igraph_vector_t modularity_v;
-// igraph_matrix_t merges;
-// igraph_vector_t csize_v;
-// igraph_vector_t membership_v;
-
-
-
-// igraph_vector_init(&modularity_v, 0);
-// igraph_matrix_init(&merges, 0, 0);
-// igraph_vector_init(&csize_v, 0);
-// igraph_vector_init(&membership_v, 0);
-
-// //igraph_community_fastgreedy(&g, 0, &merges, &modularity_v);
-// //The default step is 4 steps.
-// igraph_community_walktrap(&g, 0, 4, &merges, &modularity_v);
-
-// igraph_community_to_membership(&merges, igraph_vcount(&g),
igraph_vector_which_max(&modularity_v), &membership_v, &csize_v);
-
-// //need only map modularity, membership, csize and number of clusters
-// for(int i=0; i<igraph_vector_size(&membership_v); i++){
-// membership[i] = VECTOR(membership_v)[i];
-// }
-
-// for(int i=0; i<igraph_vector_size(&csize_v); i++){
-// csize[i] = VECTOR(csize_v)[i];
-// }
-
-// *modularity = igraph_vector_max(&modularity_v);
-// *numCluster = igraph_vector_size(&csize_v);
-// }
-
-// void edgeBetweenness(int membership[], double* modularity, int csize[],
int*numCluster){
-// //The problem of edge betweenness is that
-// //need to calculate modularity for all merges
-// igraph_vector_t modularity_v;
-// igraph_matrix_t merges;
-// igraph_vector_t csize_v;
-// igraph_vector_t membership_v;
-// igraph_vector_t result;
-// igraph_real_t modularity_max;
-
-// igraph_vector_init(&modularity_v, igraph_vcount(&g)-1); //Try to access
items beyond the limit will give array out of bounds exception
-// igraph_matrix_init(&merges, 0, 0);
-// igraph_vector_init(&csize_v, 0);
-// igraph_vector_init(&membership_v, 0);
-// igraph_vector_init(&result, 0);
-
-// igraph_community_edge_betweenness(&g, &result, 0, &merges, 0, 0);
-
-// //set step to 10
-// for(int i=0; i < igraph_vcount(&g)-1 ; i++){
-// igraph_community_to_membership(&merges, igraph_vcount(&g), i,
&membership_v, 0);
-// igraph_modularity(&g, &membership_v, &modularity_max, 0);
-
-// VECTOR(modularity_v)[i] = modularity_max; //assign modularity
vector
-// //VECTOR(modularity_v)[
-// }
-
-
-// igraph_community_to_membership(&merges, igraph_vcount(&g),
igraph_vector_which_max(&modularity_v), &membership_v, &csize_v);
-
-
-// for(int i=0; i<igraph_vector_size(&membership_v); i++){
-// membership[i] = VECTOR(membership_v)[i];
-// }
-
-// for(int i=0; i<igraph_vector_size(&csize_v); i++){
-// csize[i] = VECTOR(csize_v)[i];
-// }
-
-// *modularity = igraph_vector_max(&modularity_v);
-// *numCluster = igraph_vector_size(&csize_v);
-
-
-// //*modularity = 0;
-// }
-
-// void spinGlass(int membership[], double* modularity, int csize[],
int*numCluster){
-// igraph_real_t modularity_v;
-// igraph_matrix_t merges;
-// igraph_vector_t csize_v;
-// igraph_vector_t membership_v;
-// //igraph_vector_t result;
-// //igraph_real_t modularity_max;
-
-// //igraph_vector_init(&modularity_v, 0); //Try to access items beyond
the limit will give array out of bounds exception
-// igraph_matrix_init(&merges, 0, 0);
-// igraph_vector_init(&csize_v, 0);
-// igraph_vector_init(&membership_v, 0);
-// //igraph_vector_init(&result, 0);
-
-// //Possible to change to parameter to make it converge faster
-// igraph_community_spinglass(&g, 0, &modularity_v, 0, &membership_v,
&csize_v, 25, 0, 1.0, 0.1, 0.99, IGRAPH_SPINCOMM_UPDATE_SIMPLE, 1.0);
-
-// //Here
-
-// for(int i=0; i<igraph_vector_size(&membership_v); i++){
-// membership[i] = VECTOR(membership_v)[i];
-// }
-
-// for(int i=0; i<igraph_vector_size(&csize_v); i++){
-// csize[i] = VECTOR(csize_v)[i];
-// }
-
-// *modularity = modularity_v;
-// *numCluster = igraph_vector_size(&csize_v);
-// }
-
-// void spinGlassSingle(int targetNode, int community[], int* community_size){
-// //igraph_real_t modularity_v;
-// //igraph_matrix_t merges;
-// //igraph_vector_t csize_v;
-// //igraph_vector_t membership_v;
-// //igraph_vector_t result;
-// //igraph_real_t modularity_max;
-
-// //igraph_vector_init(&modularity_v, 0); //Try to access items beyond
the limit will give array out of bounds exception
-// //igraph_matrix_init(&merges, 0, 0);
-// //igraph_vector_init(&csize_v, 0);
-// //igraph_vector_init(&membership_v, 0);
-// //igraph_vector_init(&result, 0);
-
-// igraph_vector_t community_v;
-// igraph_vector_init(&community_v, 0);
-
-// igraph_community_spinglass_single(&g, 0, targetNode, &community_v, 0,
0, 0, 0, 25, IGRAPH_SPINCOMM_UPDATE_SIMPLE, 1.0);
-// *community_size = igraph_vector_size(&community_v);
-// for(int i=0; i<igraph_vector_size(&community_v); i++){
-// community[i] = VECTOR(community_v)[i];
-// }
-
-// //return the community surrounding the given vertex
-
-// }
-
-// void leadingEigenvector(int membership[], double* modularity){
-// igraph_matrix_t merges;
-// igraph_vector_t membership_v;
-// igraph_arpack_options_t options;
-
-// //Dosen't really change the outcome.
-// //options.mxiter = 5000000;
-
-// igraph_real_t modularity_v;
-
-// igraph_matrix_init(&merges, 0, 0);
-// igraph_vector_init(&membership_v, 0);
-// igraph_arpack_options_init(&options);
-
-// igraph_community_leading_eigenvector(&g, &merges, &membership_v, -1,
&options);
-// igraph_modularity(&g, &membership_v, &modularity_v, 0);
-
-// *modularity = modularity_v;
-// for(int i=0; i<igraph_vector_size(&membership_v); i++){
-// membership[i] = VECTOR(membership_v)[i];
-// }
-// }
-
-
-
-
-
-// int igraph_layout_fruchterman_reingold(const igraph_t *graph,
igraph_matrix_t *res,
-// igraph_integer_t niter, igraph_real_t
maxdelta,
-// igraph_real_t area, igraph_real_t
coolexp,
-// igraph_real_t repulserad, igraph_bool_t
use_seed,
-// const igraph_vector_t *weight);
-
-
-
-// void layoutRandom(double x[], double y[]){
-// igraph_matrix_t locs;
-// igraph_matrix_init(&locs, 0, 0);
-// igraph_layout_random(&g, &locs);
-
-// long int nRow = igraph_matrix_nrow(&locs);
-// long int nCol = igraph_matrix_ncol(&locs);
-// for(int i=0; i<nRow; i++){
-// x[i] = MATRIX(locs, i, 0);
-// y[i] = MATRIX(locs, i, 1);
-// }
-// }
-
-// //This one also needs scaling
-// //Let's actually do scaling in java then, it's liner time anyway
-// void layoutGraphOpt(double x[], double y[], int iter, double nodeCharge,
double nodeMass, int springLength, double springConstant, double maxSaMovement,
bool useSeed){
-
-// //This algorithm can work on a current seting, so will intialize res
with x and y first
-// long int vcount = igraph_vcount(&g);
-// igraph_matrix_t locs;
-// igraph_matrix_init(&locs, vcount, 2); //2 col, with x and y
-
-// //Res need to be initalized
-// for(int i=0; i<vcount; i++){
-// MATRIX(locs, i, 0) = x[i];
-// MATRIX(locs, i, 1) = y[i];
-// }
-
-// //It will be quite painful to make dialogs to set values for these crap
-// igraph_layout_graphopt(&g, &locs, iter, nodeCharge, nodeMass,
springLength, springConstant, maxSaMovement, useSeed);
-// for(int i=0; i<vcount; i++){
-// x[i] = MATRIX(locs, i, 0);
-// y[i] = MATRIX(locs, i, 1);
-// }
-
-// }
-
-// //still not working
-// void layoutDRL(double x[], double y[], bool useSeed, int mode){
-
-
-// long int vcount = igraph_vcount(&g);
-// igraph_matrix_t locs;
-// igraph_matrix_init(&locs, vcount, 2);
-// for(int i=0; i<vcount; i++){
-// MATRIX(locs, i, 0) = x[i];
-// MATRIX(locs, i, 1) = y[i];
-// }
-
-// /*
-// igraph_layout_drl_options_t options;
-// if(mode == 1){
-// igraph_layout_drl_options_init(&options,
IGRAPH_LAYOUT_DRL_COARSEN);
-// }
-// else if(mode == 2){
-// igraph_layout_drl_options_init(&options,
IGRAPH_LAYOUT_DRL_COARSEST);
-// }
-// else if(mode == 3){
-// igraph_layout_drl_options_init(&options,
IGRAPH_LAYOUT_DRL_REFINE);
-// }
-// else if(mode == 4){
-// igraph_layout_drl_options_init(&options,
IGRAPH_LAYOUT_DRL_FINAL);
-// }
-// else {
-// igraph_layout_drl_options_init(&options,
IGRAPH_LAYOUT_DRL_DEFAULT);
-// }
-// */
-
-// igraph_layout_drl_options_t options;
-// igraph_layout_drl_options_init(&options, IGRAPH_LAYOUT_DRL_COARSEN);
-
-// //Force directed DRL
-// igraph_layout_drl(&g, &locs, 0, &options, 0, 0);
-
-// //Return
-// for(int i=0; i<vcount; i++){
-// x[i] = MATRIX(locs, i, 0);
-// y[i] = MATRIX(locs, i, 1);
-// }
-
-// }
-
-
-// //
-// void layoutKamadaKawai(double x[], double y[], int iter, double sigma,
double initTemp, double coolExp, double kkConsts, bool useSeed){
-// long int vcount = igraph_vcount(&g);
-// igraph_matrix_t locs;
-// igraph_matrix_init(&locs, vcount, 2);
-// for(int i=0; i<vcount; i++){
-// MATRIX(locs, i, 0) = x[i];
-// MATRIX(locs, i, 1) = y[i];
-// }
-
-// igraph_layout_kamada_kawai(&g, &locs, iter, sigma, initTemp, coolExp,
kkConsts, useSeed);
-// for(int i=0; i<vcount; i++){
-// x[i] = MATRIX(locs, i, 0);
-// y[i] = MATRIX(locs, i, 1);
-// }
-// }
-
-// //Tree like structure
-// void layoutReingoldTilford(double x[], double y[], int root){
-// long int vcount = igraph_vcount(&g);
-// igraph_matrix_t locs;
-// igraph_matrix_init(&locs, vcount, 2);
-// for(int i=0; i<vcount; i++){
-// MATRIX(locs, i, 0) = x[i];
-// MATRIX(locs, i, 1) = y[i];
-// }
-
-// igraph_layout_reingold_tilford(&g, &locs, root);
-
-// //This is nice, can specify a root
-// for(int i=0; i<vcount; i++){
-// x[i] = MATRIX(locs, i, 0);
-// y[i] = MATRIX(locs, i, 1);
-// }
-
-// }
-
-// //circular
-// void layoutReingoldTilfordCircular(double x[], double y[], int root){
-// long int vcount = igraph_vcount(&g);
-// igraph_matrix_t locs;
-// igraph_matrix_init(&locs, vcount, 2);
-// for(int i=0; i<vcount; i++){
-// MATRIX(locs, i, 0) = x[i];
-// MATRIX(locs, i, 1) = y[i];
-// }
-
-// igraph_layout_reingold_tilford_circular(&g, &locs, root);
-
-// //
-// for(int i=0; i<vcount; i++){
-// x[i] = MATRIX(locs, i, 0);
-// y[i] = MATRIX(locs, i, 1);
-// }
-
-// }
-
-// //grid
-// void layoutGridFruchtermanReingold(double x[], double y[], int iter, double
maxDelta, double area, double coolExp, double repulserad, double cellSize, bool
useSeed){
-// long int vcount = igraph_vcount(&g);
-// igraph_matrix_t locs;
-// igraph_matrix_init(&locs, vcount, 2);
-// for(int i=0; i<vcount; i++){
-// MATRIX(locs, i, 0) = x[i];
-// MATRIX(locs, i, 1) = y[i];
-// }
-
-// igraph_layout_grid_fruchterman_reingold(&g, &locs, iter, maxDelta,
area, coolExp, repulserad, cellSize, useSeed);
-
-// for(int i=0; i<vcount; i++){
-// x[i] = MATRIX(locs, i, 0);
-// y[i] = MATRIX(locs, i, 1);
-// }
-
-// }
-
-// //lgl
-// void layoutLGL(double x[], double y[], int maxIt, double maxDelta, double
area, double coolExp, double repulserad, double cellSize, int root){
-// long int vcount = igraph_vcount(&g);
-// igraph_matrix_t locs;
-// igraph_matrix_init(&locs, vcount, 2);
-// for(int i=0; i<vcount; i++){
-// MATRIX(locs, i, 0) = x[i];
-// MATRIX(locs, i, 1) = y[i];
-// }
-
-// igraph_layout_lgl(&g, &locs, maxIt, maxDelta, area, coolExp,
repulserad, cellSize, root);
-
-// for(int i=0; i<vcount; i++){
-// x[i] = MATRIX(locs, i, 0);
-// y[i] = MATRIX(locs, i, 1);
-// }
-
-// }
-
//
///////////////////////////////////////////////////////////////////////////////
// //Shortest path function
@@ -763,108 +387,3 @@
// }
-
-
-
-
-
-
-
-//
///////////////////////////////////////////////////////////////////////////////
-// //These are testing functions
-// void nativeArrayTest(int data[]){
-// //try to pass unitialized array
-// //Allocated to a different memory address, the passed array is not
affected.
-// data = new int[10];
-// for(int i=0; i<10; i++){
-// data[i] = i;
-// }
-// }
-
-
-// int nativeCountAdd(int value){
-// count += value;
-// return count;
-// }
-
-
-// //Add one to the passed integer via pointer
-// void nativeIncrement(int* iptr){
-// *iptr += 1;
-// //return a;
-// }
-
-// //Reset all the elements in integer array to 0
-// //return the number of operations
-// int nativeArrayReset(int data[], int length){
-// int i;
-// for(i=0; i<length; i++){
-// data[i] = 10;
-// }
-// return i;
-// }
-
-
-// //Try to allocate some memory by malloc
-// //This is the test for,
-// void nativeMemoryAllocate(int **data, int *length){
-// //try that the memory allocation is done in c
-// *length = 10;
-// *data = (int*) malloc (*length * sizeof(int)); //allocate the space for
array of length 10, this is equivalent to initialized the first item in data ...
-
-// for(int i=0; i < *length; i++){
-// //**data = i;
-// //*data++; //move the pointer
-// (*data)[i] = i;
-// }
-
-// //This won't waste array space
-// //For vectors, just need to do a int **data
-// }
-
-// //This is not working very well...need int**data instead of int* data
-// void nativePointerMemoryAllocate(int *data, int *length){
-// *length = 10;
-// data = (int*) malloc ( *length * sizeof(int)); //however, the memory is
not freed. Wonder how long it will persist in memory.
-
-// for(int i=0; i< *length; i++){
-// data[i] = i+10;
-// }
-// }
-
-// void nativeListAllocate(int*** data, int** list_lengths, int* data_length){
-// //data containing pointers
-// *data_length = 2;
-// *list_lengths = (int*) malloc (*data_length * sizeof(int)); //The first
element this pointer is pointing to, and the only one
-
-// //int** data;
-
-
-// //The problem is that data must be pointer to pointers
-// *data = (int**) malloc(*data_length * sizeof(int*));
-
-// //didn't allocate space for the arrays in data
-
-
-// //initialize some list_lengths
-// (*list_lengths)[0] = 3;
-// (*list_lengths)[1] = 4; //Onluy two elements
-
-// //allocate memory for data
-// //When getting a vector it's a lot different than this
-// for(int i=0; i< *data_length; i++){
-// (*data)[i] = (int*) malloc ( (*list_lengths)[i] * sizeof(int));
-// }
-
-
-
-
-// //This way to assign value is funky
-// for(int i=0; i< *data_length; i++){
-// for(int j=0; j < (*list_lengths)[i]; j++ ){
-// ((*data)[i])[j] = i+j*10;
-// }
-// }
-
-// //*data_ref = data;
-// }
Modified: csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
===================================================================
--- csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
2011-08-17 15:28:25 UTC (rev 26584)
+++ csplugins/trunk/soc/ghuck/IgraphPlugin/src/igraphWrapper/igraphJNA.h
2011-08-17 16:33:42 UTC (rev 26585)
@@ -60,7 +60,16 @@
double weights[],
double cellSize);
-
+ // lgl Layout
+ void layoutLGL(double x[],
+ double y[],
+ int maxIt,
+ double maxDelta,
+ double area,
+ double coolExp,
+ double repulserad,
+ double cellSize);
+
// Minimum spanning tree - unweighted
int minimum_spanning_tree_unweighted(int res[]);
--
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