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);
}
public static void ClusterProteins(ref string[][] proteinIds, ref string[][] pepSeqs)
{
int n = proteinIds.Length;
for (int i = 0; i < n; i++)
{
Array.Sort(pepSeqs[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(pepSeqs[i], pepSeqs[j]));
}
}
int count;
do
{
count = 0;
int start = 0;
while (true)
{
int container = -1;
int contained = -1;
for (int i = start; i < proteinIds.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);
}
pepSeqs[contained] = new string[0];
proteinIds[container] = ArrayUtil.Concat(proteinIds[container], proteinIds[contained]);
proteinIds[contained] = new string[0];
start = contained + 1;
count++;
}
} while (count > 0);
List <int> valids = new List <int>();
for (int i = 0; i < n; i++)
{
if (pepSeqs[i].Length > 0)
{
valids.Add(i);
}
}
int[] a = valids.ToArray();
proteinIds = ArrayUtil.SubArray(proteinIds, a);
pepSeqs = ArrayUtil.SubArray(pepSeqs, a);
}
