Two problems

I carried on with my own matrix comparison method, in which sliding window is used. Two problems have been identified:
1. I have only computed the distance between A and B where A is before B by name. The distance between B and A should also be computed.
2. In clustering, the ordering of the matrices' appearance is important. For instance, A, B and C are three matrices. Assume A is a single-member cluster. The distance between A and C is bigger than threshold (they are not in the same cluster). And that d(B, C) < d(A,B)< threshold. d(B,C) and d(A,B) are the smallest two distances between matrix B and others. If B appears before C, then B is clustered with A (d(A,B) satisfies the two conditions). If C appears before B, a new cluster is built with a single member C, and when B is examined, B will be clustered with C, since their distance is the smallest.