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Refactor plate assay methods to use maps passed as parameters rather than returning maps

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eugenefischer
2022-09-26 17:00:25 -05:00
parent 36c628cde5
commit 19a2a35f07
2 changed files with 16 additions and 14 deletions
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14
src/main/java/Plate.java
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@@ -149,24 +149,22 @@ public class Plate {
} }
//returns a map of the counts of the sequence at cell index sIndex, in all wells //returns a map of the counts of the sequence at cell index sIndex, in all wells
public Map<String, Integer> assayWellsSequenceS(int... sIndices){ public void assayWellsSequenceS(Map<String, Integer> sequences, int... sIndices){
return this.assayWellsSequenceS(0, size, sIndices); this.assayWellsSequenceS(sequences, 0, size, sIndices);
} }
//returns a map of the counts of the sequence at cell index sIndex, in a specific well //returns a map of the counts of the sequence at cell index sIndex, in a specific well
public Map<String, Integer> assayWellsSequenceS(int n, int... sIndices) { public void assayWellsSequenceS(Map<String, Integer> sequences, int n, int... sIndices) {
return this.assayWellsSequenceS(n, n+1, sIndices); this.assayWellsSequenceS(sequences, n, n+1, sIndices);
} }
//returns a map of the counts of the sequence at cell index sIndex, in a range of wells //returns a map of the counts of the sequence at cell index sIndex, in a range of wells
public Map<String, Integer> assayWellsSequenceS(int start, int end, int... sIndices) { public void assayWellsSequenceS(Map<String, Integer> sequences, int start, int end, int... sIndices) {
Map<String, Integer> assay = new HashMap<>();
for(int sIndex: sIndices){ for(int sIndex: sIndices){
for(int i = start; i < end; i++){ for(int i = start; i < end; i++){
countSequences(assay, wells.get(i), sIndex); countSequences(sequences, wells.get(i), sIndex);
} }
} }
return assay;
} }
//For the sequences at cell indices sIndices, counts number of unique sequences in the given well into the given map //For the sequences at cell indices sIndices, counts number of unique sequences in the given well into the given map
private void countSequences(Map<String, Integer> wellMap, List<String[]> well, int... sIndices) { private void countSequences(Map<String, Integer> wellMap, List<String[]> well, int... sIndices) {

16
src/main/java/Simulator.java
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@@ -36,8 +36,10 @@ public class Simulator implements GraphModificationFunctions {
if(verbose){System.out.println("Making well maps");} if(verbose){System.out.println("Making well maps");}
Map<String, Integer> allAlphas = samplePlate.assayWellsSequenceS(alphaIndices); Map<String, Integer> allAlphas = new HashMap<>();
Map<String, Integer> allBetas = samplePlate.assayWellsSequenceS(betaIndices); samplePlate.assayWellsSequenceS(allAlphas, alphaIndices);
Map<String, Integer> allBetas = new HashMap<>();
samplePlate.assayWellsSequenceS(allBetas, betaIndices);
int alphaCount = allAlphas.size(); int alphaCount = allAlphas.size();
if(verbose){System.out.println("All alphas count: " + alphaCount);} if(verbose){System.out.println("All alphas count: " + alphaCount);}
int betaCount = allBetas.size(); int betaCount = allBetas.size();
@@ -658,18 +660,20 @@ public class Simulator implements GraphModificationFunctions {
Map<String, Integer> rowSequenceCounts, Map<String, Integer> rowSequenceCounts,
Map<String, Integer> columnSequenceCounts, Map<String, Integer> columnSequenceCounts,
double[][] weights){ double[][] weights){
Map<String, Integer> wellNRowSequences = null; Map<String, Integer> wellNRowSequences;
Map<String, Integer> wellNColumnSequences = null; Map<String, Integer> wellNColumnSequences;
int vertexStartValue = rowSequenceToVertexMap.size(); int vertexStartValue = rowSequenceToVertexMap.size();
int numWells = samplePlate.getSize(); int numWells = samplePlate.getSize();
for (int n = 0; n < numWells; n++) { for (int n = 0; n < numWells; n++) {
wellNRowSequences = samplePlate.assayWellsSequenceS(n, rowSequenceIndices); wellNRowSequences = new HashMap<>();
samplePlate.assayWellsSequenceS(wellNRowSequences, n, rowSequenceIndices);
for (String a : wellNRowSequences.keySet()) { for (String a : wellNRowSequences.keySet()) {
if(allRowSequences.containsKey(a)){ if(allRowSequences.containsKey(a)){
rowSequenceCounts.merge(a, 1, (oldValue, newValue) -> oldValue + newValue); rowSequenceCounts.merge(a, 1, (oldValue, newValue) -> oldValue + newValue);
} }
} }
wellNColumnSequences = samplePlate.assayWellsSequenceS(n, colSequenceIndices); wellNColumnSequences = new HashMap<>();
samplePlate.assayWellsSequenceS(wellNColumnSequences, n, colSequenceIndices);
for (String b : wellNColumnSequences.keySet()) { for (String b : wellNColumnSequences.keySet()) {
if(allColumnSequences.containsKey(b)){ if(allColumnSequences.containsKey(b)){
columnSequenceCounts.merge(b, 1, (oldValue, newValue) -> oldValue + newValue); columnSequenceCounts.merge(b, 1, (oldValue, newValue) -> oldValue + newValue);