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New class NodesAndEdges (simple graph class), some added javadocs
Better handling of graph averaging for different thresholds Refactored predict to doAveraging, not returning anymore a Grap but rather modifying the reference
Added GraphAverager class and PredEval class. GraphAverager copied from HomologyPredictor (in CMPredict): doing the averaging correctly now Added method evaluatePrediction to Graph Some refactoring in Alignment and better javadocs
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