private static int GetContainer(int contained, IndexedBitMatrix contains)
{
int n = contains.RowCount;
for (int i = 0; i < n; i++){
if (contains.Get(i, contained)){
return i;
}
}
return -1;
}
private static void ClusterRows(ref int[][] rowInds, ref string[][] geneIds)
{
int n = rowInds.Length;
for (int i = 0; i < n; i++){
Array.Sort(geneIds[i]);
}
IndexedBitMatrix contains = new IndexedBitMatrix(n, n);
for (int i = 0; i < n; i++){
for (int j = 0; j < n; j++){
if (i == j){
continue;
}
contains.Set(i, j, Contains(geneIds[i], geneIds[j]));
}
}
int count;
do{
count = 0;
int start = 0;
while (true){
int container = -1;
int contained = -1;
for (int i = start; i < rowInds.Length; i++){
container = GetContainer(i, contains);
if (container != -1){
contained = i;
break;
}
}
if (container == -1){
break;
}
for (int i = 0; i < n; i++){
contains.Set(i, contained, false);
contains.Set(contained, i, false);
}
geneIds[contained] = new string[0];
rowInds[container] = ArrayUtils.Concat(rowInds[container], rowInds[contained]);
rowInds[contained] = new int[0];
start = contained + 1;
count++;
}
} while (count > 0);
List<int> valids = new List<int>();
for (int i = 0; i < n; i++){
if (geneIds[i].Length > 0){
valids.Add(i);
}
}
int[] a = valids.ToArray();
rowInds = ArrayUtils.SubArray(rowInds, a);
geneIds = ArrayUtils.SubArray(geneIds, a);
}