Removed comat and protList from various scripts, changed predAllFuncs to go through row by row instead of protList to get exact same order as MF.data, made changes to clustering in mergeClusters, merge 0 clusters, use all windows in genSig to generate domSig instead of just those with base domains (2 rows).
Message switch with previous commit. Added 2 new scripts to evaluate domain-func mapping using bindingData and also to generate protein-protein similarity matrix from T_table generated from predFunc.
Changing mergeClusters to use evalclusters and not checking for function coherence after merging at this point. Use parallel pool to speed up search for kmeans.
More changes to mergeClusters and predFunc. Changed predFunc output to get similarity score rather than just return indices.