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Refactor for better encapsulation with CellSamples

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efischer
2022-02-27 14:51:53 -06:00
parent 8ebfc1469f
commit a5f7c0641d
2 changed files with 3 additions and 3 deletions
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3
src/main/java/InteractiveInterface.java
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@@ -304,8 +304,7 @@ public class InteractiveInterface {
System.out.println("Returning to main menu."); System.out.println("Returning to main menu.");
} }
else{ else{
List<Integer[]> cells = cellSample.getCells(); GraphWithMapData data = Simulator.makeGraph(cellSample, plate, true);
GraphWithMapData data = Simulator.makeGraph(cells, plate, true);
assert filename != null; assert filename != null;
if(BiGpairSEQ.outputBinary()) { if(BiGpairSEQ.outputBinary()) {
GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data); GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);

3
src/main/java/Simulator.java
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@@ -24,8 +24,9 @@ public class Simulator implements GraphModificationFunctions {
private static final int cdr1BetaIndex = 3; private static final int cdr1BetaIndex = 3;
//Make the graph needed for matching CDR3s //Make the graph needed for matching CDR3s
public static GraphWithMapData makeGraph(List<Integer[]> distinctCells, Plate samplePlate, boolean verbose) { public static GraphWithMapData makeGraph(CellSample cellSample, Plate samplePlate, boolean verbose) {
Instant start = Instant.now(); Instant start = Instant.now();
List<Integer[]> distinctCells = cellSample.getCells();
int[] alphaIndex = {cdr3AlphaIndex}; int[] alphaIndex = {cdr3AlphaIndex};
int[] betaIndex = {cdr3BetaIndex}; int[] betaIndex = {cdr3BetaIndex};