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Implemented storing graphs in memory for multiple pairing experiments

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efischer
2022-02-22 21:30:00 -06:00
parent fd2ec76b71
commit 68ee9e4bb6
6 changed files with 208 additions and 99 deletions
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src/main/java/GraphModificationFunctions.java Normal file
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import org.jgrapht.graph.DefaultWeightedEdge;
import org.jgrapht.graph.SimpleWeightedGraph;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
public abstract class GraphModificationFunctions {
//remove over- and under-weight edges
public static List<Integer[]> filterByOverlapThresholds(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
int low, int high) {
List<Integer[]> removedEdges = new ArrayList<>();
for(DefaultWeightedEdge e: graph.edgeSet()){
if ((graph.getEdgeWeight(e) > high) || (graph.getEdgeWeight(e) < low)){
Integer source = graph.getEdgeSource(e);
Integer target = graph.getEdgeTarget(e);
Integer weight = (int) graph.getEdgeWeight(e);
Integer[] edge = {source, target, weight};
removedEdges.add(edge);
graph.removeEdge(e);
}
}
return removedEdges;
}
//Remove edges for pairs with large occupancy discrepancy
public static List<Integer[]> filterByRelativeOccupancy(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
Map<Integer, Integer> alphaWellCounts,
Map<Integer, Integer> betaWellCounts,
Map<Integer, Integer> plateVtoAMap,
Map<Integer, Integer> plateVtoBMap,
Integer maxOccupancyDifference) {
List<Integer[]> removedEdges = new ArrayList<>();
for (DefaultWeightedEdge e : graph.edgeSet()) {
Integer alphaOcc = alphaWellCounts.get(plateVtoAMap.get(graph.getEdgeSource(e)));
Integer betaOcc = betaWellCounts.get(plateVtoBMap.get(graph.getEdgeTarget(e)));
if (Math.abs(alphaOcc - betaOcc) >= maxOccupancyDifference) {
Integer source = graph.getEdgeSource(e);
Integer target = graph.getEdgeTarget(e);
Integer weight = (int) graph.getEdgeWeight(e);
Integer[] edge = {source, target, weight};
removedEdges.add(edge);
graph.removeEdge(e);
}
}
return removedEdges;
}
//Remove edges for pairs where overlap size is significantly lower than the well occupancy
public static List<Integer[]> filterByOverlapPercent(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
Map<Integer, Integer> alphaWellCounts,
Map<Integer, Integer> betaWellCounts,
Map<Integer, Integer> plateVtoAMap,
Map<Integer, Integer> plateVtoBMap,
Integer minOverlapPercent) {
List<Integer[]> removedEdges = new ArrayList<>();
for (DefaultWeightedEdge e : graph.edgeSet()) {
Integer alphaOcc = alphaWellCounts.get(plateVtoAMap.get(graph.getEdgeSource(e)));
Integer betaOcc = betaWellCounts.get(plateVtoBMap.get(graph.getEdgeTarget(e)));
double weight = graph.getEdgeWeight(e);
double min = minOverlapPercent / 100.0;
if ((weight / alphaOcc < min) || (weight / betaOcc < min)) {
Integer source = graph.getEdgeSource(e);
Integer target = graph.getEdgeTarget(e);
Integer intWeight = (int) graph.getEdgeWeight(e);
Integer[] edge = {source, target, intWeight};
removedEdges.add(edge);
graph.removeEdge(e);
}
}
return removedEdges;
}
public static void addRemovedEdges(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
List<Integer[]> removedEdges) {
for (Integer[] edge : removedEdges) {
DefaultWeightedEdge e = graph.addEdge(edge[0], edge[1]);
graph.setEdgeWeight(e, (double) edge[2]);
}
}
}