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Refactor cdr3 matching to use new Vertex class

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efischer
2022-02-26 09:49:16 -06:00
parent 75b2aa9553
commit 1ea68045ce
4 changed files with 81 additions and 75 deletions
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70
src/main/java/GraphModificationFunctions.java
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@@ -2,23 +2,25 @@ 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
static List<Integer[]> filterByOverlapThresholds(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
static Map<Vertex[], Integer> filterByOverlapThresholds(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
int low, int high, boolean saveEdges) {
List<Integer[]> removedEdges = new ArrayList<>();
Map<Vertex[], Integer> removedEdges = new HashMap<>();
//List<Integer[]> removedEdges = new ArrayList<>();
for (DefaultWeightedEdge e : graph.edgeSet()) {
if ((graph.getEdgeWeight(e) > high) || (graph.getEdgeWeight(e) < low)) {
if(saveEdges) {
Integer source = graph.getEdgeSource(e);
Integer target = graph.getEdgeTarget(e);
Vertex source = graph.getEdgeSource(e);
Vertex target = graph.getEdgeTarget(e);
Integer weight = (int) graph.getEdgeWeight(e);
Integer[] edge = {source, target, weight};
removedEdges.add(edge);
Vertex[] edge = {source, target};
removedEdges.put(edge, weight);
}
else {
graph.setEdgeWeight(e, 0.0);
@@ -26,7 +28,7 @@ public interface GraphModificationFunctions {
}
}
if(saveEdges) {
for (Integer[] edge : removedEdges) {
for (Vertex[] edge : removedEdges.keySet()) {
graph.removeEdge(edge[0], edge[1]);
}
}
@@ -34,23 +36,19 @@ public interface GraphModificationFunctions {
}
//Remove edges for pairs with large occupancy discrepancy
static List<Integer[]> filterByRelativeOccupancy(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
Map<Integer, Integer> alphaWellCounts,
Map<Integer, Integer> betaWellCounts,
Map<Integer, Integer> plateVtoAMap,
Map<Integer, Integer> plateVtoBMap,
static Map<Vertex[], Integer> filterByRelativeOccupancy(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
Integer maxOccupancyDifference, boolean saveEdges) {
List<Integer[]> removedEdges = new ArrayList<>();
Map<Vertex[], Integer> removedEdges = new HashMap<>();
for (DefaultWeightedEdge e : graph.edgeSet()) {
Integer alphaOcc = alphaWellCounts.get(plateVtoAMap.get(graph.getEdgeSource(e)));
Integer betaOcc = betaWellCounts.get(plateVtoBMap.get(graph.getEdgeTarget(e)));
Integer alphaOcc = graph.getEdgeSource(e).getOccupancy();
Integer betaOcc = graph.getEdgeTarget(e).getOccupancy();
if (Math.abs(alphaOcc - betaOcc) >= maxOccupancyDifference) {
if (saveEdges) {
Integer source = graph.getEdgeSource(e);
Integer target = graph.getEdgeTarget(e);
Vertex source = graph.getEdgeSource(e);
Vertex target = graph.getEdgeTarget(e);
Integer weight = (int) graph.getEdgeWeight(e);
Integer[] edge = {source, target, weight};
removedEdges.add(edge);
Vertex[] edge = {source, target};
removedEdges.put(edge, weight);
}
else {
graph.setEdgeWeight(e, 0.0);
@@ -58,7 +56,7 @@ public interface GraphModificationFunctions {
}
}
if(saveEdges) {
for (Integer[] edge : removedEdges) {
for (Vertex[] edge : removedEdges.keySet()) {
graph.removeEdge(edge[0], edge[1]);
}
}
@@ -66,26 +64,22 @@ public interface GraphModificationFunctions {
}
//Remove edges for pairs where overlap size is significantly lower than the well occupancy
static List<Integer[]> filterByOverlapPercent(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
Map<Integer, Integer> alphaWellCounts,
Map<Integer, Integer> betaWellCounts,
Map<Integer, Integer> plateVtoAMap,
Map<Integer, Integer> plateVtoBMap,
static Map<Vertex[], Integer> filterByOverlapPercent(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
Integer minOverlapPercent,
boolean saveEdges) {
List<Integer[]> removedEdges = new ArrayList<>();
Map<Vertex[], Integer> removedEdges = new HashMap<>();
for (DefaultWeightedEdge e : graph.edgeSet()) {
Integer alphaOcc = alphaWellCounts.get(plateVtoAMap.get(graph.getEdgeSource(e)));
Integer betaOcc = betaWellCounts.get(plateVtoBMap.get(graph.getEdgeTarget(e)));
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) {
Integer source = graph.getEdgeSource(e);
Integer target = graph.getEdgeTarget(e);
if (saveEdges) {
Vertex source = graph.getEdgeSource(e);
Vertex target = graph.getEdgeTarget(e);
Integer intWeight = (int) graph.getEdgeWeight(e);
Integer[] edge = {source, target, intWeight};
removedEdges.add(edge);
Vertex[] edge = {source, target};
removedEdges.put(edge, intWeight);
}
else {
graph.setEdgeWeight(e, 0.0);
@@ -93,18 +87,18 @@ public interface GraphModificationFunctions {
}
}
if(saveEdges) {
for (Integer[] edge : removedEdges) {
for (Vertex[] edge : removedEdges.keySet()) {
graph.removeEdge(edge[0], edge[1]);
}
}
return removedEdges;
}
static void addRemovedEdges(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
List<Integer[]> removedEdges) {
for (Integer[] edge : removedEdges) {
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, (double) edge[2]);
graph.setEdgeWeight(e, removedEdges.get(edge));
}
}