#SetP is still bugged!
print(`SetP has bugs!`):
#read `W:\\CLIQUE.txt`:

Help:=proc(): print(`CompG(V), Score(G,P), SetP(S,k)`):end:


#CompG(V): Given a set V of vertices outputs
#the complete graph on V
CompG:=proc(V) local i,j:
[V, {seq(seq({V[i],V[j]},j=1..i-1),i=2..nops(V))}]:
end:


#Score(G,P): Inputs a simple graph G=[V,E]
#and a set partition P of V outputs its score

Score:=proc(G,P) local i,G1,E,E1:
G1:=[ {seq( op(P[i]),i=1..nops(P))},

{seq( op(CompG(P[i])[2]),i=1..nops(P))} ]:

if G[1]<>G1[1] then
 ERROR(`Bad input`):
fi:

E:=G[2]: E1:=G1[2]:

nops(E minus E1) + nops(E1 minus E) :


end:

#SetP(S,k): the set of set-partitions of a set S
#into k non-empty subsets
SetP:=proc(S,k) local i,S1,RandG,SP1,SP2:
#needs more work
if k=0 then
 RETURN({}):
fi:

if nops(S)<k then
 RETURN({}):
fi:
if nops(S)=k then
  RETURN({ seq( {S[i]},i=1..nops(S))}):
fi:

RandG:=S[1]:
S1:=S minus {RandG}:

SP1:=SetP(S1,k):
SP2:=SetP(S1,k-1):

 {seq( SP2[i] union {{RandG}},i=1..nops(SP2)),

seq(seq( 
{ op(1..j-1,SP1[i]), SP1[i][j] union {RandG}, op(j+1..k,SP1[i]) },
j=1..nops(SP1[i])),
i=1..nops(SP1))
}:



end:



#PCC(G,k,LogLogN,LogN): applies the PCC algorithm
#of Jones-Pevzner's masterpiece Bioinformatics Algorithms
#p. 352 with #S' replaced by the integer LogLogN
#and #S'' replaced by the integer LogN

PCC:=proc(G,k,LogLogN,LogN) local S,n,Sp,Spp,bestScore:

S:=G[1]:
n:=nops(S):

bestScore:=min(binomial(nops(G[1]),2)-nops(G[2]),nops(G[2])):

Sp:=randcomb(S,LogLogN):

Spp:=randcomp(S minus Sp, LogN):





end: