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Added method using matrix builder

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efischer
2021-11-09 21:26:10 -06:00
parent 82d5500ae8
commit 8280382ca7
1 changed files with 68 additions and 18 deletions
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86
src/main/java/Simulation.java
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@@ -1,6 +1,7 @@
import org.jgrapht.Graph; import org.jgrapht.Graph;
import org.jgrapht.alg.interfaces.MatchingAlgorithm; import org.jgrapht.alg.interfaces.MatchingAlgorithm;
import org.jgrapht.alg.matching.MaximumWeightBipartiteMatching; import org.jgrapht.alg.matching.MaximumWeightBipartiteMatching;
import org.jgrapht.generate.SimpleWeightedBipartiteGraphMatrixGenerator;
import org.jgrapht.graph.DefaultWeightedEdge; import org.jgrapht.graph.DefaultWeightedEdge;
import org.jgrapht.graph.SimpleWeightedGraph; import org.jgrapht.graph.SimpleWeightedGraph;
@@ -74,28 +75,36 @@ public class Simulation {
int alphaCount = allAlphas.size(); int alphaCount = allAlphas.size();
int betaCount = allBetas.size(); int betaCount = allBetas.size();
//Using Integers instead of Strings to label vertices so I can do clever stuff with indices if I need to
// when I refactor to use a 2d array to make the graph
Integer vertexStartValue = 0;
//keys are sequential integer vertices, values are alphas //keys are sequential integer vertices, values are alphas
Map<String, Integer> plateVtoAMap = getVertexToPeptideMap(allAlphas, "A"); Map<Integer, Integer> plateVtoAMap = getVertexToPeptideMap(allAlphas, vertexStartValue);
//New start value for vertex to beta map should be one more than final vertex value in alpha map
vertexStartValue += plateVtoAMap.size();
//keys are sequential integers vertices, values are betas //keys are sequential integers vertices, values are betas
Map<String, Integer> plateVtoBMap = getVertexToPeptideMap(allBetas, "B"); Map<Integer, Integer> plateVtoBMap = getVertexToPeptideMap(allBetas, vertexStartValue);
//keys are alphas, values are sequential integer vertices from previous map //keys are alphas, values are sequential integer vertices from previous map
Map<Integer, String> plateAtoVMap = invertVertexMap(plateVtoAMap); Map<Integer, Integer> plateAtoVMap = invertVertexMap(plateVtoAMap);
//keys are betas, values are sequential integer vertices from previous map //keys are betas, values are sequential integer vertices from previous map
Map<Integer, String> plateBtoVMap = invertVertexMap(plateVtoBMap); Map<Integer, Integer> plateBtoVMap = invertVertexMap(plateVtoBMap);
//OUTPUT //OUTPUT
System.out.println("Maps made"); System.out.println("Maps made");
System.out.println("Creating Graph"); System.out.println("Creating Graph");
//construct graph //construct graph
SimpleWeightedGraph<String, DefaultWeightedEdge> graph = new SimpleWeightedGraph<String, DefaultWeightedEdge>(DefaultWeightedEdge.class); SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph = new SimpleWeightedGraph<Integer, DefaultWeightedEdge>(DefaultWeightedEdge.class);
//add vertices //add vertices
for(String v: plateVtoAMap.keySet()) { for(Integer v: plateVtoAMap.keySet()) {
graph.addVertex(v); graph.addVertex(v);
} }
for(String v: plateVtoBMap.keySet()) { for(Integer v: plateVtoBMap.keySet()) {
graph.addVertex(v); graph.addVertex(v);
} }
//add edges, where weights are number of wells the peptides share in common. //add edges, where weights are number of wells the peptides share in common.
//If this is too slow, can make a 2d array and use the SimpleWeightedGraphMatrixGenerator class //If this is too slow, can make a 2d array and use the SimpleWeightedGraphMatrixGenerator class
Map<Integer, Integer> wellNAlphas = null; Map<Integer, Integer> wellNAlphas = null;
@@ -113,6 +122,7 @@ public class Simulation {
for(Integer b: wellNBetas.keySet()){ for(Integer b: wellNBetas.keySet()){
betaWellCounts.merge(b, 1, (oldValue, newValue) -> oldValue + newValue); betaWellCounts.merge(b, 1, (oldValue, newValue) -> oldValue + newValue);
} }
for(Integer i: wellNAlphas.keySet()) { for(Integer i: wellNAlphas.keySet()) {
for(Integer j: wellNBetas.keySet()){ for(Integer j: wellNBetas.keySet()){
addEdgeOrWeight(graph, plateAtoVMap.get(i), plateBtoVMap.get(j)); addEdgeOrWeight(graph, plateAtoVMap.get(i), plateBtoVMap.get(j));
@@ -120,6 +130,46 @@ public class Simulation {
} }
} }
/*
//The above code works, but is too memory intensive. Going to try with a 2D array of doubles.
double[][] weights = new double[plateVtoAMap.size()][plateVtoBMap.size()];
Map<Integer, Integer> wellNAlphas = null;
Map<Integer, Integer> wellNBetas = null;
//Count how many wells each alpha appears in
Map<Integer, Integer> alphaWellCounts = new HashMap<>();
//count how many wells each beta appears in
Map<Integer, Integer> betaWellCounts = new HashMap<>();
for (int n = 0; n < numWells; n++) {
wellNAlphas = samplePlate.assayWellsAlpha(n);
for(Integer a: wellNAlphas.keySet()){
alphaWellCounts.merge(a, 1, (oldValue, newValue) -> oldValue + newValue);
}
wellNBetas = samplePlate.assayWellsBeta(n);
for(Integer b: wellNBetas.keySet()){
betaWellCounts.merge(b, 1, (oldValue, newValue) -> oldValue + newValue);
}
for(Integer i: wellNAlphas.keySet()) {
for(Integer j: wellNBetas.keySet()){
weights[plateAtoVMap.get(i)][plateBtoVMap.get(j) - vertexStartValue] += 1.0;
}
}
}
SimpleWeightedBipartiteGraphMatrixGenerator graphGenerator = new SimpleWeightedBipartiteGraphMatrixGenerator();
SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph = new SimpleWeightedGraph<Integer, DefaultWeightedEdge>(DefaultWeightedEdge.class);
List<Integer> alphaVertices = new ArrayList<>();
alphaVertices.addAll(plateVtoAMap.keySet()); //This will work because LinkedHashMap preserves order of entry
graphGenerator.first(alphaVertices);
List<Integer> betaVertices = new ArrayList<>();
betaVertices.addAll(plateVtoBMap.keySet());
graphGenerator.second(betaVertices); //This will work because LinkedHashMap preserves order of entry
graphGenerator.weights(weights);
graphGenerator.generateGraph(graph);
*/
//OUTPUT //OUTPUT
System.out.println("Graph created"); System.out.println("Graph created");
System.out.println("Finding maximum weighted matching"); System.out.println("Finding maximum weighted matching");
@@ -143,8 +193,8 @@ public class Simulation {
if(graph.getEdgeWeight(e) <= 2.0) { if(graph.getEdgeWeight(e) <= 2.0) {
continue; continue;
} }
String source = graph.getEdgeSource(e); Integer source = graph.getEdgeSource(e);
String target = graph.getEdgeTarget(e); Integer target = graph.getEdgeTarget(e);
//Need map of each peptide and number of wells it appears in. //Need map of each peptide and number of wells it appears in.
check =printData(graph.getEdgeWeight(e), source, alphaWellCounts.get(plateVtoAMap.get(source)), target, betaWellCounts.get(plateVtoBMap.get(target)), distCellsMapAlphaKey, plateVtoAMap, plateVtoBMap); check =printData(graph.getEdgeWeight(e), source, alphaWellCounts.get(plateVtoAMap.get(source)), target, betaWellCounts.get(plateVtoBMap.get(target)), distCellsMapAlphaKey, plateVtoAMap, plateVtoBMap);
if(check) { if(check) {
@@ -183,25 +233,25 @@ public class Simulation {
} }
private static Map<String, Integer> getVertexToPeptideMap(Map<Integer, Integer> peptides, String prefix) { private static Map<Integer, Integer> getVertexToPeptideMap(Map<Integer, Integer> peptides, Integer startValue) {
Map<String, Integer> map = new LinkedHashMap<>(); Map<Integer, Integer> map = new LinkedHashMap<>(); //LinkedHashMap to preserve order of entry
Integer index = 0; Integer index = startValue;
for (Integer k: peptides.keySet()) { for (Integer k: peptides.keySet()) {
map.put(prefix + index, k); map.put(index, k);
index++; index++;
} }
return map; return map;
} }
private static Map<Integer, String> invertVertexMap(Map<String, Integer> map) { private static Map<Integer, Integer> invertVertexMap(Map<Integer, Integer> map) {
Map<Integer, String> inverse = new HashMap<>(); Map<Integer, Integer> inverse = new HashMap<>();
for(String k: map.keySet()) { for(Integer k: map.keySet()) {
inverse.put(map.get(k), k); inverse.put(map.get(k), k);
} }
return inverse; return inverse;
} }
private static void addEdgeOrWeight(Graph g, String v1, String v2) { private static void addEdgeOrWeight(Graph g, Integer v1, Integer v2) {
if (g.containsEdge(v1, v2)) { if (g.containsEdge(v1, v2)) {
g.setEdgeWeight(v1, v2, g.getEdgeWeight(g.getEdge(v1, v2)) + 1.0); g.setEdgeWeight(v1, v2, g.getEdgeWeight(g.getEdge(v1, v2)) + 1.0);
} }
@@ -211,7 +261,7 @@ public class Simulation {
//System.out.println("added!"); //System.out.println("added!");
} }
private static boolean printData (Double edgeWeight, String source, Integer sourceCount, String target, Integer targetCount, Map<Integer,Integer> AtoBMap, Map<String,Integer> VtoAMap, Map<String, Integer> VtoBMap) { private static boolean printData (Double edgeWeight, Integer source, Integer sourceCount, Integer target, Integer targetCount, Map<Integer,Integer> AtoBMap, Map<Integer,Integer> VtoAMap, Map<Integer, Integer> VtoBMap) {
//placeholder for real calculations //placeholder for real calculations
int trueCount = 0; int trueCount = 0;
int falseCount = 0; int falseCount = 0;