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First attempt at command line arguments

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efischer
2021-11-19 17:31:18 -06:00
parent 3d0a843cea
commit 981e24011d
3 changed files with 157 additions and 51 deletions
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54
src/main/java/Simulator.java
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@@ -48,43 +48,44 @@ public class Simulator {
}
public static MatchingResult matchCDR3s(List<Integer[]> distinctCells,
Plate samplePlate, Integer lowThreshold, Integer highThreshold){
System.out.println("Cells: " + distinctCells.size());
Plate samplePlate, Integer lowThreshold,
Integer highThreshold, boolean verbose){
if(verbose){System.out.println("Cells: " + distinctCells.size());}
Instant start = Instant.now();
int numWells = samplePlate.getSize();
int[] alphaIndex = {cdr3AlphaIndex};
int[] betaIndex = {cdr3BetaIndex};
System.out.println("Making cell maps");
if(verbose){System.out.println("Making cell maps");}
//HashMap keyed to Alphas, values Betas
Map<Integer, Integer> distCellsMapAlphaKey = makePeptideToPeptideMap(distinctCells, 0, 1);
System.out.println("Cell maps made");
if(verbose){System.out.println("Cell maps made");}
System.out.println("Making well maps");
if(verbose){System.out.println("Making well maps");}
Map<Integer, Integer> allAlphas = samplePlate.assayWellsPeptideP(alphaIndex);
Map<Integer, Integer> allBetas = samplePlate.assayWellsPeptideP(betaIndex);
int alphaCount = allAlphas.size();
System.out.println("all alphas count: " + alphaCount);
if(verbose){System.out.println("all alphas count: " + alphaCount);}
int betaCount = allBetas.size();
System.out.println("all betas count: " + betaCount);
if(verbose){System.out.println("all betas count: " + betaCount);}
System.out.println("Well maps made");
if(verbose){System.out.println("Well maps made");}
//Remove saturating-occupancy peptides because they have no signal value.
//Remove below-minimum-overlap-threshold peptides because they can't possibly have an overlap with another
//peptide that's above the threshold.
System.out.println("Removing peptides present in all wells.");
System.out.println("Removing peptides with occupancy below the minimum overlap threshold");
if(verbose){System.out.println("Removing peptides present in all wells.");}
if(verbose){System.out.println("Removing peptides with occupancy below the minimum overlap threshold");}
filterByOccupancyThreshold(allAlphas, lowThreshold, numWells - 1);
filterByOccupancyThreshold(allBetas, lowThreshold, numWells - 1);
System.out.println("Peptides removed");
if(verbose){System.out.println("Peptides removed");}
int pairableAlphaCount = allAlphas.size();
System.out.println("Remaining alpha count: " + pairableAlphaCount);
if(verbose){System.out.println("Remaining alpha count: " + pairableAlphaCount);}
int pairableBetaCount = allBetas.size();
System.out.println("Remaining beta count: " + pairableBetaCount);
if(verbose){System.out.println("Remaining beta count: " + pairableBetaCount);}
System.out.println("Making vertex maps");
if(verbose){System.out.println("Making vertex maps");}
//For the SimpleWeightedBipartiteGraphMatrixGenerator, all vertices must have
// distinct numbers associated with them. Since I'm using a 2D array, that means
// distinct indices between the rows and columns. vertexStartValue lets me track where I switch
@@ -101,9 +102,9 @@ public class Simulator {
Map<Integer, Integer> plateAtoVMap = invertVertexMap(plateVtoAMap);
//keys are betas, values are sequential integer vertices from previous map
Map<Integer, Integer> plateBtoVMap = invertVertexMap(plateVtoBMap);
System.out.println("Vertex maps made");
if(verbose){System.out.println("Vertex maps made");}
System.out.println("Creating adjacency matrix");
if(verbose){System.out.println("Creating adjacency matrix");}
//Count how many wells each alpha appears in
Map<Integer, Integer> alphaWellCounts = new HashMap<>();
//count how many wells each beta appears in
@@ -112,9 +113,9 @@ public class Simulator {
countPeptidesAndFillMatrix(samplePlate, allAlphas, allBetas, plateAtoVMap,
plateBtoVMap, alphaIndex, betaIndex, alphaWellCounts, betaWellCounts, weights);
System.out.println("matrix created");
if(verbose){System.out.println("matrix created");}
System.out.println("creating graph");
if(verbose){System.out.println("creating graph");}
SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph =
new SimpleWeightedGraph<>(DefaultWeightedEdge.class);
SimpleWeightedBipartiteGraphMatrixGenerator graphGenerator = new SimpleWeightedBipartiteGraphMatrixGenerator();
@@ -126,18 +127,18 @@ public class Simulator {
graphGenerator.second(betaVertices); //This will work because LinkedHashMap preserves order of entry
graphGenerator.weights(weights);
graphGenerator.generateGraph(graph);
System.out.println("Graph created");
if(verbose){System.out.println("Graph created");}
System.out.println("Eliminating edges with weights outside threshold values");
if(verbose){System.out.println("Eliminating edges with weights outside threshold values");}
filterByOccupancyThreshold(graph, lowThreshold, highThreshold);
System.out.println("Over- and under-weight edges set to 0.0");
if(verbose){System.out.println("Over- and under-weight edges set to 0.0");}
System.out.println("Finding maximum weighted matching");
if(verbose){System.out.println("Finding maximum weighted matching");}
MaximumWeightBipartiteMatching maxWeightMatching =
new MaximumWeightBipartiteMatching(graph, plateVtoAMap.keySet(), plateVtoBMap.keySet());
MatchingAlgorithm.Matching<String, DefaultWeightedEdge> graphMatching = maxWeightMatching.getMatching();
System.out.println("Matching completed");
if(verbose){System.out.println("Matching completed");}
Instant stop = Instant.now();
//Header for CSV file
@@ -209,10 +210,13 @@ public class Simulator {
comments.add("Pairing error rate: " + pairingErrorRateTrunc);
Duration time = Duration.between(start, stop);
comments.add("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
for(String s: comments){
System.out.println(s);
if(verbose){
for(String s: comments){
System.out.println(s);
}
}
return new MatchingResult(samplePlate.getSourceFileName(), comments, header, allResults, matchMap, time);
}