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Relocate overlap threshold filters

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efischer
2022-02-20 03:05:56 -06:00
parent cb2c5a6024
commit d1c37b5ccd
4 changed files with 42 additions and 57 deletions
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27
src/main/java/Simulator.java
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@@ -45,8 +45,7 @@ public class Simulator {
}
//Make the graph needed for matching CDR3s
public static GraphWithMapData makeGraph(List<Integer[]> distinctCells, Plate samplePlate, Integer lowThreshold,
Integer highThreshold, boolean verbose) {
public static GraphWithMapData makeGraph(List<Integer[]> distinctCells, Plate samplePlate, boolean verbose) {
Instant start = Instant.now();
int[] alphaIndex = {cdr3AlphaIndex};
int[] betaIndex = {cdr3BetaIndex};
@@ -70,9 +69,9 @@ public class Simulator {
//Remove saturating-occupancy sequences because they have no signal value.
//Remove sequences with total occupancy below minimum pair overlap threshold
if(verbose){System.out.println("Removing sequences present in all wells.");}
if(verbose){System.out.println("Removing sequences with occupancy below the minimum overlap threshold");}
filterByOccupancyThreshold(allAlphas, lowThreshold, numWells - 1);
filterByOccupancyThreshold(allBetas, lowThreshold, numWells - 1);
//if(verbose){System.out.println("Removing sequences with occupancy below the minimum overlap threshold");}
filterByOccupancyThreshold(allAlphas, 1, numWells - 1);
filterByOccupancyThreshold(allBetas, 1, numWells - 1);
if(verbose){System.out.println("Sequences removed");}
int pairableAlphaCount = allAlphas.size();
if(verbose){System.out.println("Remaining alphas count: " + pairableAlphaCount);}
@@ -130,25 +129,20 @@ public class Simulator {
graphGenerator.generateGraph(graph);
if(verbose){System.out.println("Graph created");}
//remove weights outside given overlap thresholds
if(verbose){System.out.println("Eliminating edges with weights outside overlap threshold values");}
filterByOccupancyThreshold(graph, lowThreshold, highThreshold);
if(verbose){System.out.println("Over- and under-weight edges set to 0.0");}
Instant stop = Instant.now();
Duration time = Duration.between(start, stop);
//return GraphWithMapData object
return new GraphWithMapData(graph, numWells, samplePlate.getConcentrations(), alphaCount, betaCount, lowThreshold, highThreshold,
return new GraphWithMapData(graph, numWells, samplePlate.getConcentrations(), alphaCount, betaCount,
distCellsMapAlphaKey, plateVtoAMap, plateVtoBMap, plateAtoVMap,
plateBtoVMap, alphaWellCounts, betaWellCounts, time);
}
//match CDR3s.
public static MatchingResult matchCDR3s(GraphWithMapData data, Integer maxOccupancyDifference,
Integer minOverlapPercent, boolean verbose) {
public static MatchingResult matchCDR3s(GraphWithMapData data, Integer lowThreshold, Integer highThreshold,
Integer maxOccupancyDifference, Integer minOverlapPercent,
boolean verbose) {
Instant start = Instant.now();
int numWells = data.getNumWells();
Integer highThreshold = data.getHighThreshold();
Integer lowThreshold = data.getLowThreshold();
Integer alphaCount = data.getAlphaCount();
Integer betaCount = data.getBetaCount();
Map<Integer, Integer> distCellsMapAlphaKey = data.getDistCellsMapAlphaKey();
@@ -158,6 +152,11 @@ public class Simulator {
Map<Integer, Integer> betaWellCounts = data.getBetaWellCounts();
SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph = data.getGraph();
//remove weights outside given overlap thresholds
if(verbose){System.out.println("Eliminating edges with weights outside overlap threshold values");}
filterByOccupancyThreshold(graph, lowThreshold, highThreshold);
if(verbose){System.out.println("Over- and under-weight edges set to 0.0");}
//Filter by overlap size
if(verbose){System.out.println("Eliminating edges with weights less than " + minOverlapPercent.toString() +
" percent of vertex occupancy value.");}