BiGpairSEQ/src/main/java/GraphModificationFunctions.java

import org.jgrapht.graph.DefaultWeightedEdge;
import org.jgrapht.graph.SimpleWeightedGraph;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

public interface GraphModificationFunctions {

    //remove over- and under-weight edges, return removed edges
    static Map<Vertex[], Integer> filterByOverlapThresholds(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
                                                            int low, int high, boolean saveEdges) {
        Map<Vertex[], Integer> removedEdges = new HashMap<>();
        for (DefaultWeightedEdge e : graph.edgeSet()) {
            if ((graph.getEdgeWeight(e) > high) || (graph.getEdgeWeight(e) < low)) {
                if(saveEdges) {
                    Vertex source = graph.getEdgeSource(e);
                    Vertex target = graph.getEdgeTarget(e);
                    Integer weight = (int) graph.getEdgeWeight(e);
                    Vertex[] edge = {source, target};
                    removedEdges.put(edge, weight);
                }
                else {
                    graph.setEdgeWeight(e, 0.0);
                }
            }
        }
        if(saveEdges) {
            for (Vertex[] edge : removedEdges.keySet()) {
                graph.removeEdge(edge[0], edge[1]);
            }
        }
        return removedEdges;
    }

    //Remove edges for pairs with large occupancy discrepancy, return removed edges
    static Map<Vertex[], Integer> filterByRelativeOccupancy(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
                                                  Integer maxOccupancyDifference, boolean saveEdges) {
        Map<Vertex[], Integer> removedEdges = new HashMap<>();
        for (DefaultWeightedEdge e : graph.edgeSet()) {
            Integer alphaOcc = graph.getEdgeSource(e).getOccupancy();
            Integer betaOcc = graph.getEdgeTarget(e).getOccupancy();
            if (Math.abs(alphaOcc - betaOcc) >= maxOccupancyDifference) {
                if (saveEdges) {
                    Vertex source = graph.getEdgeSource(e);
                    Vertex target = graph.getEdgeTarget(e);
                    Integer weight = (int) graph.getEdgeWeight(e);
                    Vertex[] edge = {source, target};
                    removedEdges.put(edge, weight);
                }
                else {
                    graph.setEdgeWeight(e, 0.0);
                }
            }
        }
        if(saveEdges) {
            for (Vertex[] edge : removedEdges.keySet()) {
                graph.removeEdge(edge[0], edge[1]);
            }
        }
        return removedEdges;
    }

    //Remove edges for pairs where overlap size is significantly lower than the well occupancy, return removed edges
    static Map<Vertex[], Integer> filterByOverlapPercent(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
                                                         Integer minOverlapPercent,
                                                         boolean saveEdges) {
        Map<Vertex[], Integer> removedEdges = new HashMap<>();
        for (DefaultWeightedEdge e : graph.edgeSet()) {
            Integer alphaOcc = graph.getEdgeSource(e).getOccupancy();
            Integer betaOcc = graph.getEdgeTarget(e).getOccupancy();
            double weight = graph.getEdgeWeight(e);
            double min = minOverlapPercent / 100.0;
            if ((weight / alphaOcc < min) || (weight / betaOcc < min)) {
                if (saveEdges) {
                    Vertex source = graph.getEdgeSource(e);
                    Vertex target = graph.getEdgeTarget(e);
                    Integer intWeight = (int) graph.getEdgeWeight(e);
                    Vertex[] edge = {source, target};
                    removedEdges.put(edge, intWeight);
                }
                else {
                    graph.setEdgeWeight(e, 0.0);
                }
            }
        }
        if(saveEdges) {
            for (Vertex[] edge : removedEdges.keySet()) {
                graph.removeEdge(edge[0], edge[1]);
            }
        }
        return removedEdges;
    }

    static Map<Vertex[], Integer> filterByRelativeReadCount (SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph, Integer threshold, boolean saveEdges) {
        Map<Vertex[], Integer> removedEdges = new HashMap<>();
        Boolean passes;
        for (DefaultWeightedEdge e : graph.edgeSet()) {
            Integer alphaReadCount = graph.getEdgeSource(e).getReadCount();
            Integer betaReadCount = graph.getEdgeTarget(e).getReadCount();
            passes = RelativeReadCountFilterFunction(threshold, alphaReadCount, betaReadCount);
            if (!passes) {
                if (saveEdges) {
                    Vertex source = graph.getEdgeSource(e);
                    Vertex target = graph.getEdgeTarget(e);
                    Integer intWeight = (int) graph.getEdgeWeight(e);
                    Vertex[] edge = {source, target};
                    removedEdges.put(edge, intWeight);
                }
                else {
                    graph.setEdgeWeight(e, 0.0);
                }
            }
        }
        if(saveEdges) {
            for (Vertex[] edge : removedEdges.keySet()) {
                graph.removeEdge(edge[0], edge[1]);
            }
        }
        return removedEdges;
    }

    static Boolean RelativeReadCountFilterFunction(Integer threshold, Integer alphaReadCount, Integer betaReadCount) {
        return Math.abs(alphaReadCount - betaReadCount) < threshold;
    }

    static void addRemovedEdges(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
                                Map<Vertex[], Integer> removedEdges) {
        for (Vertex[] edge : removedEdges.keySet()) {
            DefaultWeightedEdge e = graph.addEdge(edge[0], edge[1]);
            graph.setEdgeWeight(e, removedEdges.get(edge));
        }
    }



}