SAMI/MissingNodes_SrcCode2014/CalcPHsAffinityByAA_samiA.m

function [ affinity ] = CalcPHsAffinityByAA( data, actual_graph_size, num_missing_nodes, connectPlaceholdersToNeighbors)
    % sigal 29.10.13 
    % based on CalculateAffinityByAdamicAdar_Sparse

    % adamic/adar(i,j) = sum( 1 / log(num_neighbors(k) | k is a
    % neighbor of both i and j

    fprintf('CalcPHsAffinityByAA: NNZ(data) = %d\n', nnz(data));

    firstPH = actual_graph_size-num_missing_nodes+1;
    numPHs = size(data,1) - firstPH +1;

    %n = size(data,1);
    %diag_indices = 1:n+1:n*n;
    %data(diag_indices) = 1; %we consider each node as a neighbor of itself to obtain higher connectivity in the affinity matrix - i.e. each node will have a positive affinity to all its neighbors
    if connectPlaceholdersToNeighbors > 0
          data = ConnectMissingNodesToNeighborsNeighbors( data, actual_graph_size, num_missing_nodes);
    end
    affinity = zeros(numPHs,numPHs);

    s_cols = sum(data(:,firstPH:end),2);         % give the #PH neighbors per node (nx1)?
    fprintf('CalcPHsAffinityByAA: NNZ(s_cols) = %d\n', nnz(s_cols));
    for k = 1 : size(data,1)
        if s_cols(k) > 0
            %find all the neighbors of k
            neighbors_k_vec = data(k,:);
            neighbors_k_vec(k) = 1;%we consider each node as a neighbor of itself to obtain higher connectivity in the affinity matrix - i.e. each node will have a positive affinity to all its neighbors
            neighbors_k = find(neighbors_k_vec);
            num_neighbors_k = size(neighbors_k, 2);
            %sigal - only need to calcluate for PHs (thus indexes are updated accordingly)
            phs_neighbors_k_idc = neighbors_k>=firstPH; 
            phs_neighbors_k = neighbors_k(1,phs_neighbors_k_idc)-firstPH+1; 

            if num_neighbors_k > 1 && size(phs_neighbors_k,2) > 0
                w = 1;
                inv_log_num_neighbors_k = w / log(num_neighbors_k);
                for i  = phs_neighbors_k
                    for j = phs_neighbors_k
                        affinity(i,j) = affinity(i,j) + inv_log_num_neighbors_k;
                        affinity(j,i) = affinity(i,j);
                    end
                end
            end
        end
    end

    %sigal 29.10.13 - normolize by diagonal min
    v = diag(affinity);
    max_val = min(v);
    %max_val = max(max(affinity));

    affinity = affinity ./ max_val;

    for i = 1 : size(affinity,1)
        affinity(i,i) = 1;
    end
    %sigal 29.10.13 - end 


    affinity = sparse(affinity);

end