689 lines
36 KiB
Java
689 lines
36 KiB
Java
import org.jgrapht.alg.interfaces.MatchingAlgorithm;
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import org.jgrapht.alg.matching.MaximumWeightBipartiteMatching;
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import org.jgrapht.generate.SimpleWeightedBipartiteGraphMatrixGenerator;
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import org.jgrapht.graph.DefaultWeightedEdge;
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import org.jgrapht.graph.SimpleWeightedGraph;
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import org.jheaps.tree.FibonacciHeap;
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import org.jheaps.tree.PairingHeap;
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import java.math.BigDecimal;
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import java.math.MathContext;
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import java.text.NumberFormat;
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import java.time.Instant;
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import java.time.Duration;
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import java.util.*;
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import java.util.stream.IntStream;
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import static java.lang.Float.*;
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//NOTE: "sequence" in method and variable names refers to a peptide sequence from a simulated T cell
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public class Simulator implements GraphModificationFunctions {
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private static final int cdr3AlphaIndex = 0;
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private static final int cdr3BetaIndex = 1;
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private static final int cdr1AlphaIndex = 2;
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private static final int cdr1BetaIndex = 3;
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//Make the graph needed for matching CDR3s
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public static GraphWithMapData makeGraph(CellSample cellSample, Plate samplePlate, boolean verbose) {
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Instant start = Instant.now();
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List<Integer[]> distinctCells = cellSample.getCells();
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int[] alphaIndex = {cdr3AlphaIndex};
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int[] betaIndex = {cdr3BetaIndex};
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int numWells = samplePlate.getSize();
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if(verbose){System.out.println("Making cell maps");}
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//HashMap keyed to Alphas, values Betas
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Map<Integer, Integer> distCellsMapAlphaKey = makeSequenceToSequenceMap(distinctCells, cdr3AlphaIndex, cdr3BetaIndex);
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if(verbose){System.out.println("Cell maps made");}
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if(verbose){System.out.println("Making well maps");}
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Map<Integer, Integer> allAlphas = samplePlate.assayWellsSequenceS(alphaIndex);
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Map<Integer, Integer> allBetas = samplePlate.assayWellsSequenceS(betaIndex);
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int alphaCount = allAlphas.size();
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if(verbose){System.out.println("All alphas count: " + alphaCount);}
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int betaCount = allBetas.size();
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if(verbose){System.out.println("All betas count: " + betaCount);}
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if(verbose){System.out.println("Well maps made");}
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if(verbose){System.out.println("Removing singleton sequences and sequences present in all wells.");}
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filterByOccupancyThresholds(allAlphas, 2, numWells - 1);
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filterByOccupancyThresholds(allBetas, 2, numWells - 1);
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if(verbose){System.out.println("Sequences removed");}
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int pairableAlphaCount = allAlphas.size();
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if(verbose){System.out.println("Remaining alphas count: " + pairableAlphaCount);}
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int pairableBetaCount = allBetas.size();
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if(verbose){System.out.println("Remaining betas count: " + pairableBetaCount);}
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if(verbose){System.out.println("Making vertex maps");}
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//For the SimpleWeightedBipartiteGraphMatrixGenerator, all vertices must have
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//distinct numbers associated with them. Since I'm using a 2D array, that means
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//distinct indices between the rows and columns. vertexStartValue lets me track where I switch
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//from numbering rows to columns, so I can assign unique numbers to every vertex, and then
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//subtract the vertexStartValue from betas to use their vertex labels as array indices
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Integer vertexStartValue = 0;
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//keys are sequential integer vertices, values are alphas
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Map<Integer, Integer> plateVtoAMap = makeVertexToSequenceMap(allAlphas, vertexStartValue);
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//new start value for vertex to beta map should be one more than final vertex value in alpha map
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vertexStartValue += plateVtoAMap.size();
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//keys are sequential integers vertices, values are betas
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Map<Integer, Integer> plateVtoBMap = makeVertexToSequenceMap(allBetas, vertexStartValue);
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//keys are alphas, values are sequential integer vertices from previous map
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Map<Integer, Integer> plateAtoVMap = invertVertexMap(plateVtoAMap);
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//keys are betas, values are sequential integer vertices from previous map
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Map<Integer, Integer> plateBtoVMap = invertVertexMap(plateVtoBMap);
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if(verbose){System.out.println("Vertex maps made");}
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//make adjacency matrix for bipartite graph generator
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//(technically this is only 1/4 of an adjacency matrix, but that's all you need
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//for a bipartite graph, and all the SimpleWeightedBipartiteGraphMatrixGenerator class expects.)
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if(verbose){System.out.println("Creating adjacency matrix");}
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//Count how many wells each alpha appears in
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Map<Integer, Integer> alphaWellCounts = new HashMap<>();
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//count how many wells each beta appears in
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Map<Integer, Integer> betaWellCounts = new HashMap<>();
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//the adjacency matrix to be used by the graph generator
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double[][] weights = new double[plateVtoAMap.size()][plateVtoBMap.size()];
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countSequencesAndFillMatrix(samplePlate, allAlphas, allBetas, plateAtoVMap,
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plateBtoVMap, alphaIndex, betaIndex, alphaWellCounts, betaWellCounts, weights);
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if(verbose){System.out.println("Matrix created");}
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//create bipartite graph
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if(verbose){System.out.println("Creating graph");}
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//the graph object
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SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph =
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new SimpleWeightedGraph<>(DefaultWeightedEdge.class);
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//the graph generator
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SimpleWeightedBipartiteGraphMatrixGenerator graphGenerator = new SimpleWeightedBipartiteGraphMatrixGenerator();
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//the list of alpha vertices
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List<Integer> alphaVertices = new ArrayList<>(plateVtoAMap.keySet()); //This will work because LinkedHashMap preserves order of entry
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graphGenerator.first(alphaVertices);
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//the list of beta vertices
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List<Integer> betaVertices = new ArrayList<>(plateVtoBMap.keySet());
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graphGenerator.second(betaVertices); //This will work because LinkedHashMap preserves order of entry
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//use adjacency matrix of weight created previously
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graphGenerator.weights(weights);
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graphGenerator.generateGraph(graph);
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if(verbose){System.out.println("Graph created");}
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Instant stop = Instant.now();
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Duration time = Duration.between(start, stop);
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//create GraphWithMapData object
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GraphWithMapData output = new GraphWithMapData(graph, numWells, samplePlate.getPopulations(), alphaCount, betaCount,
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distCellsMapAlphaKey, plateVtoAMap, plateVtoBMap, plateAtoVMap,
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plateBtoVMap, alphaWellCounts, betaWellCounts, time);
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//Set source file name in graph to name of sample plate
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output.setSourceFilename(samplePlate.getFilename());
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//return GraphWithMapData object
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return output;
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}
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//match CDR3s.
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public static MatchingResult matchCDR3s(GraphWithMapData data, String dataFilename, Integer lowThreshold,
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Integer highThreshold, Integer maxOccupancyDifference,
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Integer minOverlapPercent, boolean verbose) {
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Instant start = Instant.now();
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List<Integer[]> removedEdges = new ArrayList<>();
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boolean saveEdges = BiGpairSEQ.cacheGraph();
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int numWells = data.getNumWells();
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Integer alphaCount = data.getAlphaCount();
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Integer betaCount = data.getBetaCount();
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Map<Integer, Integer> distCellsMapAlphaKey = data.getDistCellsMapAlphaKey();
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Map<Integer, Integer> plateVtoAMap = data.getPlateVtoAMap();
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Map<Integer, Integer> plateVtoBMap = data.getPlateVtoBMap();
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Map<Integer, Integer> alphaWellCounts = data.getAlphaWellCounts();
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Map<Integer, Integer> betaWellCounts = data.getBetaWellCounts();
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SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph = data.getGraph();
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//remove edges with weights outside given overlap thresholds, add those to removed edge list
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if(verbose){System.out.println("Eliminating edges with weights outside overlap threshold values");}
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removedEdges.addAll(GraphModificationFunctions.filterByOverlapThresholds(graph, lowThreshold, highThreshold, saveEdges));
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if(verbose){System.out.println("Over- and under-weight edges removed");}
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//remove edges between vertices with too small an overlap size, add those to removed edge list
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if(verbose){System.out.println("Eliminating edges with weights less than " + minOverlapPercent.toString() +
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" percent of vertex occupancy value.");}
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removedEdges.addAll(GraphModificationFunctions.filterByOverlapPercent(graph, alphaWellCounts, betaWellCounts,
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plateVtoAMap, plateVtoBMap, minOverlapPercent, saveEdges));
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if(verbose){System.out.println("Edges with weights too far below a vertex occupancy value removed");}
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//Filter by relative occupancy
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if(verbose){System.out.println("Eliminating edges between vertices with occupancy difference > "
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+ maxOccupancyDifference);}
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removedEdges.addAll(GraphModificationFunctions.filterByRelativeOccupancy(graph, alphaWellCounts, betaWellCounts,
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plateVtoAMap, plateVtoBMap, maxOccupancyDifference, saveEdges));
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if(verbose){System.out.println("Edges between vertices of with excessively different occupancy values " +
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"removed");}
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//Find Maximum Weighted Matching
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if(verbose){System.out.println("Finding maximum weighted matching");}
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MaximumWeightBipartiteMatching maxWeightMatching;
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//Use correct heap type for priority queue
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String heapType = BiGpairSEQ.getPriorityQueueHeapType();
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switch (heapType) {
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case "PAIRING" -> {
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maxWeightMatching = new MaximumWeightBipartiteMatching(graph,
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plateVtoAMap.keySet(),
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plateVtoBMap.keySet(),
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i -> new PairingHeap(Comparator.naturalOrder()));
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}
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case "FIBONACCI" -> {
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maxWeightMatching = new MaximumWeightBipartiteMatching(graph,
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plateVtoAMap.keySet(),
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plateVtoBMap.keySet(),
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i -> new FibonacciHeap(Comparator.naturalOrder()));
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}
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default -> {
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maxWeightMatching = new MaximumWeightBipartiteMatching(graph,
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plateVtoAMap.keySet(),
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plateVtoBMap.keySet());
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}
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}
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//get the matching
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MatchingAlgorithm.Matching<String, DefaultWeightedEdge> graphMatching = maxWeightMatching.getMatching();
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if(verbose){System.out.println("Matching completed");}
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Instant stop = Instant.now();
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//Header for CSV file
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List<String> header = new ArrayList<>();
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header.add("Alpha");
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header.add("Alpha well count");
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header.add("Beta");
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header.add("Beta well count");
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header.add("Overlap well count");
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header.add("Matched correctly?");
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header.add("P-value");
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//Results for csv file
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List<List<String>> allResults = new ArrayList<>();
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NumberFormat nf = NumberFormat.getInstance(Locale.US);
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MathContext mc = new MathContext(3);
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Iterator<DefaultWeightedEdge> weightIter = graphMatching.iterator();
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DefaultWeightedEdge e;
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int trueCount = 0;
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int falseCount = 0;
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boolean check;
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Map<Integer, Integer> matchMap = new HashMap<>();
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while(weightIter.hasNext()) {
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e = weightIter.next();
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Integer source = graph.getEdgeSource(e);
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Integer target = graph.getEdgeTarget(e);
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//The match map is all matches found, not just true matches!
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matchMap.put(plateVtoAMap.get(source), plateVtoBMap.get(target));
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check = plateVtoBMap.get(target).equals(distCellsMapAlphaKey.get(plateVtoAMap.get(source)));
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if(check) {
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trueCount++;
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}
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else {
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falseCount++;
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}
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List<String> result = new ArrayList<>();
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result.add(plateVtoAMap.get(source).toString());
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//alpha well count
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result.add(alphaWellCounts.get(plateVtoAMap.get(source)).toString());
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result.add(plateVtoBMap.get(target).toString());
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//beta well count
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result.add(betaWellCounts.get(plateVtoBMap.get(target)).toString());
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//overlap count
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result.add(Double.toString(graph.getEdgeWeight(e)));
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result.add(Boolean.toString(check));
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double pValue = Equations.pValue(numWells, alphaWellCounts.get(plateVtoAMap.get(source)),
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betaWellCounts.get(plateVtoBMap.get(target)), graph.getEdgeWeight(e));
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BigDecimal pValueTrunc = new BigDecimal(pValue, mc);
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result.add(pValueTrunc.toString());
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allResults.add(result);
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}
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//Metadata comments for CSV file
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String algoType = "LEDA book with heap: " + heapType;
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int min = Math.min(alphaCount, betaCount);
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//rate of attempted matching
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double attemptRate = (double) (trueCount + falseCount) / min;
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BigDecimal attemptRateTrunc = new BigDecimal(attemptRate, mc);
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//rate of pairing error
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double pairingErrorRate = (double) falseCount / (trueCount + falseCount);
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BigDecimal pairingErrorRateTrunc;
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if(Double.isFinite(pairingErrorRate)) {
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pairingErrorRateTrunc = new BigDecimal(pairingErrorRate, mc);
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}
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else{
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pairingErrorRateTrunc = new BigDecimal(-1, mc);
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}
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//get list of well populations
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Integer[] wellPopulations = data.getWellPopulations();
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//make string out of populations list
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StringBuilder populationsStringBuilder = new StringBuilder();
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populationsStringBuilder.append(wellPopulations[0].toString());
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for(int i = 1; i < wellPopulations.length; i++){
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populationsStringBuilder.append(", ");
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populationsStringBuilder.append(wellPopulations[i].toString());
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}
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String wellPopulationsString = populationsStringBuilder.toString();
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//total simulation time
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Duration time = Duration.between(start, stop);
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time = time.plus(data.getTime());
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Map<String, String> metadata = new LinkedHashMap<>();
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metadata.put("sample plate filename", data.getSourceFilename());
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metadata.put("graph filename", dataFilename);
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metadata.put("algorithm type", algoType);
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metadata.put("well populations", wellPopulationsString);
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metadata.put("total alphas found", alphaCount.toString());
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metadata.put("total betas found", betaCount.toString());
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metadata.put("high overlap threshold", highThreshold.toString());
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metadata.put("low overlap threshold", lowThreshold.toString());
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metadata.put("minimum overlap percent", minOverlapPercent.toString());
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metadata.put("maximum occupancy difference", maxOccupancyDifference.toString());
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metadata.put("pairing attempt rate", attemptRateTrunc.toString());
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metadata.put("correct pairing count", Integer.toString(trueCount));
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metadata.put("incorrect pairing count", Integer.toString(falseCount));
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metadata.put("pairing error rate", pairingErrorRateTrunc.toString());
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metadata.put("simulation time (seconds)", nf.format(time.toSeconds()));
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//create MatchingResult object
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MatchingResult output = new MatchingResult(metadata, header, allResults, matchMap, time);
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if(verbose){
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for(String s: output.getComments()){
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System.out.println(s);
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}
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}
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if(saveEdges) {
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//put the removed edges back on the graph
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System.out.println("Restoring removed edges to graph.");
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GraphModificationFunctions.addRemovedEdges(graph, removedEdges);
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}
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//return MatchingResult object
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return output;
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}
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//Commented out CDR1 matching until it's time to re-implement it
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// //Simulated matching of CDR1s to CDR3s. Requires MatchingResult from prior run of matchCDR3s.
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// public static MatchingResult[] matchCDR1s(List<Integer[]> distinctCells,
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// Plate samplePlate, Integer lowThreshold,
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// Integer highThreshold, MatchingResult priorResult){
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// Instant start = Instant.now();
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// Duration previousTime = priorResult.getTime();
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// Map<Integer, Integer> previousMatches = priorResult.getMatchMap();
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// int numWells = samplePlate.getSize();
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// int[] cdr3Indices = {cdr3AlphaIndex, cdr3BetaIndex};
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// int[] cdr1Indices = {cdr1AlphaIndex, cdr1BetaIndex};
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//
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// System.out.println("Making previous match maps");
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// Map<Integer, Integer> cdr3AtoBMap = previousMatches;
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// Map<Integer, Integer> cdr3BtoAMap = invertVertexMap(cdr3AtoBMap);
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// System.out.println("Previous match maps made");
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//
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// System.out.println("Making cell maps");
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// Map<Integer, Integer> alphaCDR3toCDR1Map = makeSequenceToSequenceMap(distinctCells, cdr3AlphaIndex, cdr1AlphaIndex);
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// Map<Integer, Integer> betaCDR3toCDR1Map = makeSequenceToSequenceMap(distinctCells, cdr3BetaIndex, cdr1BetaIndex);
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// System.out.println("Cell maps made");
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//
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// System.out.println("Making well maps");
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// Map<Integer, Integer> allCDR3s = samplePlate.assayWellsSequenceS(cdr3Indices);
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// Map<Integer, Integer> allCDR1s = samplePlate.assayWellsSequenceS(cdr1Indices);
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// int CDR3Count = allCDR3s.size();
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// System.out.println("all CDR3s count: " + CDR3Count);
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// int CDR1Count = allCDR1s.size();
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// System.out.println("all CDR1s count: " + CDR1Count);
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// System.out.println("Well maps made");
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//
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// System.out.println("Removing unpaired CDR3s from well maps");
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// List<Integer> unpairedCDR3s = new ArrayList<>();
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// for(Integer i: allCDR3s.keySet()){
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// if(!(cdr3AtoBMap.containsKey(i) || cdr3BtoAMap.containsKey(i))){
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// unpairedCDR3s.add(i);
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// }
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// }
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// for(Integer i: unpairedCDR3s){
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// allCDR3s.remove(i);
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// }
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// System.out.println("Unpaired CDR3s removed.");
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// System.out.println("Remaining CDR3 count: " + allCDR3s.size());
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//
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// System.out.println("Removing below-minimum-overlap-threshold and saturating-occupancy CDR1s");
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// filterByOccupancyThreshold(allCDR1s, lowThreshold, numWells - 1);
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// System.out.println("CDR1s removed.");
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// System.out.println("Remaining CDR1 count: " + allCDR1s.size());
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//
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// System.out.println("Making vertex maps");
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//
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// //For the SimpleWeightedBipartiteGraphMatrixGenerator, all vertices must have
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// // distinct numbers associated with them. Since I'm using a 2D array, that means
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// // distinct indices between the rows and columns. vertexStartValue lets me track where I switch
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// // from numbering rows to columns, so I can assign unique numbers to every vertex, and then
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// // subtract the vertexStartValue from CDR1s to use their vertex labels as array indices
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// Integer vertexStartValue = 0;
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// //keys are sequential integer vertices, values are CDR3s
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// Map<Integer, Integer> plateVtoCDR3Map = makeVertexToSequenceMap(allCDR3s, vertexStartValue);
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// //New start value for vertex to CDR1 map should be one more than final vertex value in CDR3 map
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// vertexStartValue += plateVtoCDR3Map.size();
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// //keys are sequential integers vertices, values are CDR1s
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// Map<Integer, Integer> plateVtoCDR1Map = makeVertexToSequenceMap(allCDR1s, vertexStartValue);
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// //keys are CDR3s, values are sequential integer vertices from previous map
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// Map<Integer, Integer> plateCDR3toVMap = invertVertexMap(plateVtoCDR3Map);
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// //keys are CDR1s, values are sequential integer vertices from previous map
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// Map<Integer, Integer> plateCDR1toVMap = invertVertexMap(plateVtoCDR1Map);
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// System.out.println("Vertex maps made");
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//
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// System.out.println("Creating adjacency matrix");
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// //Count how many wells each CDR3 appears in
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// Map<Integer, Integer> cdr3WellCounts = new HashMap<>();
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// //count how many wells each CDR1 appears in
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// Map<Integer, Integer> cdr1WellCounts = new HashMap<>();
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// //add edges, where weights are number of wells the peptides share in common.
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// //If this is too slow, can make a 2d array and use the SimpleWeightedGraphMatrixGenerator class
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// Map<Integer, Integer> wellNCDR3s = null;
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// Map<Integer, Integer> wellNCDR1s = null;
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// double[][] weights = new double[plateVtoCDR3Map.size()][plateVtoCDR1Map.size()];
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// countSequencesAndFillMatrix(samplePlate, allCDR3s, allCDR1s, plateCDR3toVMap, plateCDR1toVMap,
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// cdr3Indices, cdr1Indices, cdr3WellCounts, cdr1WellCounts, weights);
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// System.out.println("Matrix created");
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//
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// System.out.println("Creating graph");
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// SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph =
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// new SimpleWeightedGraph<>(DefaultWeightedEdge.class);
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//
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// SimpleWeightedBipartiteGraphMatrixGenerator graphGenerator = new SimpleWeightedBipartiteGraphMatrixGenerator();
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// List<Integer> cdr3Vertices = new ArrayList<>(plateVtoCDR3Map.keySet()); //This will work because LinkedHashMap preserves order of entry
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// graphGenerator.first(cdr3Vertices);
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// List<Integer> cdr1Vertices = new ArrayList<>(plateVtoCDR1Map.keySet());
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// graphGenerator.second(cdr1Vertices); //This will work because LinkedHashMap preserves order of entry
|
|
// graphGenerator.weights(weights);
|
|
// graphGenerator.generateGraph(graph);
|
|
// System.out.println("Graph created");
|
|
//
|
|
// System.out.println("Removing edges outside of weight thresholds");
|
|
// filterByOccupancyThreshold(graph, lowThreshold, highThreshold);
|
|
// System.out.println("Over- and under-weight edges set to 0.0");
|
|
//
|
|
// System.out.println("Finding first maximum weighted matching");
|
|
// MaximumWeightBipartiteMatching firstMaxWeightMatching =
|
|
// new MaximumWeightBipartiteMatching(graph, plateVtoCDR3Map.keySet(), plateVtoCDR1Map.keySet());
|
|
// MatchingAlgorithm.Matching<String, DefaultWeightedEdge> graphMatching = firstMaxWeightMatching.getMatching();
|
|
// System.out.println("First maximum weighted matching found");
|
|
//
|
|
//
|
|
// //first processing run
|
|
// Map<Integer, Integer> firstMatchCDR3toCDR1Map = new HashMap<>();
|
|
// Iterator<DefaultWeightedEdge> weightIter = graphMatching.iterator();
|
|
// DefaultWeightedEdge e;
|
|
// while(weightIter.hasNext()){
|
|
// e = weightIter.next();
|
|
//// if(graph.getEdgeWeight(e) < lowThreshold || graph.getEdgeWeight(e) > highThreshold) {
|
|
//// continue;
|
|
//// }
|
|
// Integer source = graph.getEdgeSource(e);
|
|
// Integer target = graph.getEdgeTarget(e);
|
|
// firstMatchCDR3toCDR1Map.put(plateVtoCDR3Map.get(source), plateVtoCDR1Map.get(target));
|
|
// }
|
|
// System.out.println("First pass matches: " + firstMatchCDR3toCDR1Map.size());
|
|
//
|
|
// System.out.println("Removing edges from first maximum weighted matching");
|
|
// //zero out the edge weights in the matching
|
|
// weightIter = graphMatching.iterator();
|
|
// while(weightIter.hasNext()){
|
|
// graph.removeEdge(weightIter.next());
|
|
// }
|
|
// System.out.println("Edges removed");
|
|
//
|
|
// //Generate a new matching
|
|
// System.out.println("Finding second maximum weighted matching");
|
|
// MaximumWeightBipartiteMatching secondMaxWeightMatching =
|
|
// new MaximumWeightBipartiteMatching(graph, plateVtoCDR3Map.keySet(), plateVtoCDR1Map.keySet());
|
|
// graphMatching = secondMaxWeightMatching.getMatching();
|
|
// System.out.println("Second maximum weighted matching found");
|
|
//
|
|
//
|
|
// //second processing run
|
|
// Map<Integer, Integer> secondMatchCDR3toCDR1Map = new HashMap<>();
|
|
// weightIter = graphMatching.iterator();
|
|
// while(weightIter.hasNext()){
|
|
// e = weightIter.next();
|
|
//// if(graph.getEdgeWeight(e) < lowThreshold || graph.getEdgeWeight(e) > highThreshold) {
|
|
//// continue;
|
|
//// }
|
|
// Integer source = graph.getEdgeSource(e);
|
|
//// if(!(CDR3AtoBMap.containsKey(source) || CDR3BtoAMap.containsKey(source))){
|
|
//// continue;
|
|
//// }
|
|
// Integer target = graph.getEdgeTarget(e);
|
|
// secondMatchCDR3toCDR1Map.put(plateVtoCDR3Map.get(source), plateVtoCDR1Map.get(target));
|
|
// }
|
|
// System.out.println("Second pass matches: " + secondMatchCDR3toCDR1Map.size());
|
|
//
|
|
// System.out.println("Mapping first pass CDR3 alpha/beta pairs");
|
|
// //get linked map for first matching attempt
|
|
// Map<Integer, Integer> firstMatchesMap = new LinkedHashMap<>();
|
|
// for(Integer alphaCDR3: cdr3AtoBMap.keySet()) {
|
|
// if (!(firstMatchCDR3toCDR1Map.containsKey(alphaCDR3))) {
|
|
// continue;
|
|
// }
|
|
// Integer betaCDR3 = cdr3AtoBMap.get(alphaCDR3);
|
|
// if (!(firstMatchCDR3toCDR1Map.containsKey(betaCDR3))) {
|
|
// continue;
|
|
// }
|
|
// firstMatchesMap.put(alphaCDR3, firstMatchCDR3toCDR1Map.get(alphaCDR3));
|
|
// firstMatchesMap.put(betaCDR3, firstMatchCDR3toCDR1Map.get(betaCDR3));
|
|
// }
|
|
// System.out.println("First pass CDR3 alpha/beta pairs mapped");
|
|
//
|
|
// System.out.println("Mapping second pass CDR3 alpha/beta pairs.");
|
|
// System.out.println("Finding CDR3 pairs that swapped CDR1 matches between first pass and second pass.");
|
|
// //Look for matches that simply swapped already-matched alpha and beta CDR3s
|
|
// Map<Integer, Integer> dualMatchesMap = new LinkedHashMap<>();
|
|
// for(Integer alphaCDR3: cdr3AtoBMap.keySet()) {
|
|
// if (!(firstMatchCDR3toCDR1Map.containsKey(alphaCDR3) && secondMatchCDR3toCDR1Map.containsKey(alphaCDR3))) {
|
|
// continue;
|
|
// }
|
|
// Integer betaCDR3 = cdr3AtoBMap.get(alphaCDR3);
|
|
// if (!(firstMatchCDR3toCDR1Map.containsKey(betaCDR3) && secondMatchCDR3toCDR1Map.containsKey(betaCDR3))) {
|
|
// continue;
|
|
// }
|
|
// if(firstMatchCDR3toCDR1Map.get(alphaCDR3).equals(secondMatchCDR3toCDR1Map.get(betaCDR3))){
|
|
// if(firstMatchCDR3toCDR1Map.get(betaCDR3).equals(secondMatchCDR3toCDR1Map.get(alphaCDR3))){
|
|
// dualMatchesMap.put(alphaCDR3, firstMatchCDR3toCDR1Map.get(alphaCDR3));
|
|
// dualMatchesMap.put(betaCDR3, firstMatchCDR3toCDR1Map.get(betaCDR3));
|
|
// }
|
|
// }
|
|
// }
|
|
// System.out.println("Second pass mapping made. Dual CDR3/CDR1 pairings found.");
|
|
//
|
|
// Instant stop = Instant.now();
|
|
// //results for first map
|
|
// System.out.println("RESULTS FOR FIRST PASS MATCHING");
|
|
// List<List<String>> allResults = new ArrayList<>();
|
|
// Integer trueCount = 0;
|
|
// Iterator iter = firstMatchesMap.keySet().iterator();
|
|
//
|
|
// while(iter.hasNext()){
|
|
// Boolean proven = false;
|
|
// List<String> tmp = new ArrayList<>();
|
|
// tmp.add(iter.next().toString());
|
|
// tmp.add(iter.next().toString());
|
|
// tmp.add(firstMatchesMap.get(Integer.valueOf(tmp.get(0))).toString());
|
|
// tmp.add(firstMatchesMap.get(Integer.valueOf(tmp.get(1))).toString());
|
|
// if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(2)))){
|
|
// if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(3)))){
|
|
// proven = true;
|
|
// }
|
|
// }
|
|
// else if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(3)))){
|
|
// if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(2)))){
|
|
// proven = true;
|
|
// }
|
|
// }
|
|
// tmp.add(proven.toString());
|
|
// allResults.add(tmp);
|
|
// if(proven){
|
|
// trueCount++;
|
|
// }
|
|
// }
|
|
//
|
|
// List<String> comments = new ArrayList<>();
|
|
// comments.add("Plate size: " + samplePlate.getSize() + " wells");
|
|
// comments.add("Previous pairs found: " + previousMatches.size());
|
|
// comments.add("CDR1 matches attempted: " + allResults.size());
|
|
// double attemptRate = (double) allResults.size() / previousMatches.size();
|
|
// comments.add("Matching attempt rate: " + attemptRate);
|
|
// comments.add("Number of correct matches: " + trueCount);
|
|
// double correctRate = (double) trueCount / allResults.size();
|
|
// comments.add("Correct matching rate: " + correctRate);
|
|
// NumberFormat nf = NumberFormat.getInstance(Locale.US);
|
|
// Duration time = Duration.between(start, stop);
|
|
// time = time.plus(previousTime);
|
|
// comments.add("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
|
|
// for(String s: comments){
|
|
// System.out.println(s);
|
|
// }
|
|
//
|
|
//
|
|
//
|
|
// List<String> headers = new ArrayList<>();
|
|
// headers.add("CDR3 alpha");
|
|
// headers.add("CDR3 beta");
|
|
// headers.add("first matched CDR1");
|
|
// headers.add("second matched CDR1");
|
|
// headers.add("Correct match?");
|
|
//
|
|
// MatchingResult firstTest = new MatchingResult(samplePlate.getSourceFileName(),
|
|
// comments, headers, allResults, dualMatchesMap, time);
|
|
//
|
|
// //results for dual map
|
|
// System.out.println("RESULTS FOR SECOND PASS MATCHING");
|
|
// allResults = new ArrayList<>();
|
|
// trueCount = 0;
|
|
// iter = dualMatchesMap.keySet().iterator();
|
|
// while(iter.hasNext()){
|
|
// Boolean proven = false;
|
|
// List<String> tmp = new ArrayList<>();
|
|
// tmp.add(iter.next().toString());
|
|
// tmp.add(iter.next().toString());
|
|
// tmp.add(dualMatchesMap.get(Integer.valueOf(tmp.get(0))).toString());
|
|
// tmp.add(dualMatchesMap.get(Integer.valueOf(tmp.get(1))).toString());
|
|
// if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(2)))){
|
|
// if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(3)))){
|
|
// proven = true;
|
|
// }
|
|
// }
|
|
// else if(alphaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(0))).equals(Integer.valueOf(tmp.get(3)))){
|
|
// if(betaCDR3toCDR1Map.get(Integer.valueOf(tmp.get(1))).equals(Integer.valueOf(tmp.get(2)))){
|
|
// proven = true;
|
|
// }
|
|
// }
|
|
// tmp.add(proven.toString());
|
|
// allResults.add(tmp);
|
|
// if(proven){
|
|
// trueCount++;
|
|
// }
|
|
// }
|
|
//
|
|
// comments = new ArrayList<>();
|
|
// comments.add("Plate size: " + samplePlate.getSize() + " wells");
|
|
// comments.add("Previous pairs found: " + previousMatches.size());
|
|
// comments.add("High overlap threshold: " + highThreshold);
|
|
// comments.add("Low overlap threshold: " + lowThreshold);
|
|
// comments.add("CDR1 matches attempted: " + allResults.size());
|
|
// attemptRate = (double) allResults.size() / previousMatches.size();
|
|
// comments.add("Matching attempt rate: " + attemptRate);
|
|
// comments.add("Number of correct matches: " + trueCount);
|
|
// correctRate = (double) trueCount / allResults.size();
|
|
// comments.add("Correct matching rate: " + correctRate);
|
|
// comments.add("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
|
|
//
|
|
// for(String s: comments){
|
|
// System.out.println(s);
|
|
// }
|
|
//
|
|
// System.out.println("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
|
|
// MatchingResult dualTest = new MatchingResult(samplePlate.getSourceFileName(), comments, headers,
|
|
// allResults, dualMatchesMap, time);
|
|
// MatchingResult[] output = {firstTest, dualTest};
|
|
// return output;
|
|
// }
|
|
|
|
//Remove sequences based on occupancy
|
|
public static void filterByOccupancyThresholds(Map<Integer, Integer> wellMap, int low, int high){
|
|
List<Integer> noise = new ArrayList<>();
|
|
for(Integer k: wellMap.keySet()){
|
|
if((wellMap.get(k) > high) || (wellMap.get(k) < low)){
|
|
noise.add(k);
|
|
}
|
|
}
|
|
for(Integer k: noise) {
|
|
wellMap.remove(k);
|
|
}
|
|
}
|
|
|
|
//Counts the well occupancy of the row peptides and column peptides into given maps, and
|
|
//fills weights in the given 2D array
|
|
private static void countSequencesAndFillMatrix(Plate samplePlate,
|
|
Map<Integer,Integer> allRowSequences,
|
|
Map<Integer,Integer> allColumnSequences,
|
|
Map<Integer,Integer> rowSequenceToVertexMap,
|
|
Map<Integer,Integer> columnSequenceToVertexMap,
|
|
int[] rowSequenceIndices,
|
|
int[] colSequenceIndices,
|
|
Map<Integer, Integer> rowSequenceCounts,
|
|
Map<Integer,Integer> columnSequenceCounts,
|
|
double[][] weights){
|
|
Map<Integer, Integer> wellNRowSequences = null;
|
|
Map<Integer, Integer> wellNColumnSequences = null;
|
|
int vertexStartValue = rowSequenceToVertexMap.size();
|
|
int numWells = samplePlate.getSize();
|
|
for (int n = 0; n < numWells; n++) {
|
|
wellNRowSequences = samplePlate.assayWellsSequenceS(n, rowSequenceIndices);
|
|
for (Integer a : wellNRowSequences.keySet()) {
|
|
if(allRowSequences.containsKey(a)){
|
|
rowSequenceCounts.merge(a, 1, (oldValue, newValue) -> oldValue + newValue);
|
|
}
|
|
}
|
|
wellNColumnSequences = samplePlate.assayWellsSequenceS(n, colSequenceIndices);
|
|
for (Integer b : wellNColumnSequences.keySet()) {
|
|
if(allColumnSequences.containsKey(b)){
|
|
columnSequenceCounts.merge(b, 1, (oldValue, newValue) -> oldValue + newValue);
|
|
}
|
|
}
|
|
for (Integer i : wellNRowSequences.keySet()) {
|
|
if(allRowSequences.containsKey(i)){
|
|
for (Integer j : wellNColumnSequences.keySet()) {
|
|
if(allColumnSequences.containsKey(j)){
|
|
weights[rowSequenceToVertexMap.get(i)][columnSequenceToVertexMap.get(j) - vertexStartValue] += 1.0;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
}
|
|
}
|
|
|
|
private static Map<Integer, Integer> makeSequenceToSequenceMap(List<Integer[]> cells, int keySequenceIndex,
|
|
int valueSequenceIndex){
|
|
Map<Integer, Integer> keySequenceToValueSequenceMap = new HashMap<>();
|
|
for (Integer[] cell : cells) {
|
|
keySequenceToValueSequenceMap.put(cell[keySequenceIndex], cell[valueSequenceIndex]);
|
|
}
|
|
return keySequenceToValueSequenceMap;
|
|
}
|
|
|
|
private static Map<Integer, Integer> makeVertexToSequenceMap(Map<Integer, Integer> sequences, Integer startValue) {
|
|
Map<Integer, Integer> map = new LinkedHashMap<>(); //LinkedHashMap to preserve order of entry
|
|
Integer index = startValue; //is this necessary? I don't think I use this.
|
|
for (Integer k: sequences.keySet()) {
|
|
map.put(index, k);
|
|
index++;
|
|
}
|
|
return map;
|
|
}
|
|
|
|
private static Map<Integer, Integer> invertVertexMap(Map<Integer, Integer> map) {
|
|
Map<Integer, Integer> inverse = new HashMap<>();
|
|
for (Integer k : map.keySet()) {
|
|
inverse.put(map.get(k), k);
|
|
}
|
|
return inverse;
|
|
}
|
|
|
|
}
|