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Implement read count for vertices

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eugenefischer
2022-09-26 19:42:19 -05:00
parent 19a2a35f07
commit 199c81f983
6 changed files with 93 additions and 15 deletions
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34
src/main/java/GraphModificationFunctions.java
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@@ -12,7 +12,6 @@ public interface GraphModificationFunctions {
static Map<Vertex[], Integer> filterByOverlapThresholds(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
int low, int high, boolean saveEdges) {
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) {
@@ -94,6 +93,37 @@ public interface GraphModificationFunctions {
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()) {
@@ -102,4 +132,6 @@ public interface GraphModificationFunctions {
}
}
}