The java code of algorithm of structure entroy minimisation example java -jar deDoc.jar xxx/xxx/xxx/hicGraph
We treat Hic matrix as the adjacent matrix of the hicGraph which is the input of this algorithm. The format is 3 1 2 1.0 1 3 2.0 2 3 3.0 The first line is the number of bins in the graph The second line is the edge: first_bin second_bin reads .splitted by space. The node_id start from 1. Resultfile (hicGraph.deDoc(E) or hicGraph.deDoc(M)) is the result of communities found by algorithm deDoc(E) or deDoc(M). Each line is a tad. And it will print the 2D-nSE of the hicGraph.
To compute 1D-nSE, use command java -jar onednSE.jar xxx/xxx/xxx/hicGraph The result is the 1D-nSE of this hicGraph.
To get the java source code, you just need to decompress deDoc.jar and onednSE.jar using software such as WinRAR.
P.S. The input Hi-C matrix should be symmetric matrix