efischer/BiGpairSEQ
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Change "peptide" references in code to "sequence", adding comments

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efischer
2022-02-21 00:29:34 -06:00
parent 370de79546
commit cb1f7adece
4 changed files with 39 additions and 33 deletions
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24
src/main/java/Simulator.java
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@@ -57,8 +57,8 @@ public class Simulator {
if(verbose){System.out.println("Cell maps made");}
if(verbose){System.out.println("Making well maps");}
Map<Integer, Integer> allAlphas = samplePlate.assayWellsPeptideP(alphaIndex);
Map<Integer, Integer> allBetas = samplePlate.assayWellsPeptideP(betaIndex);
Map<Integer, Integer> allAlphas = samplePlate.assayWellsSequenceS(alphaIndex);
Map<Integer, Integer> allBetas = samplePlate.assayWellsSequenceS(betaIndex);
int alphaCount = allAlphas.size();
if(verbose){System.out.println("All alphas count: " + alphaCount);}
int betaCount = allBetas.size();
@@ -296,8 +296,8 @@ public class Simulator {
System.out.println("Cell maps made");
System.out.println("Making well maps");
Map<Integer, Integer> allCDR3s = samplePlate.assayWellsPeptideP(cdr3Indices);
Map<Integer, Integer> allCDR1s = samplePlate.assayWellsPeptideP(cdr1Indices);
Map<Integer, Integer> allCDR3s = samplePlate.assayWellsSequenceS(cdr3Indices);
Map<Integer, Integer> allCDR1s = samplePlate.assayWellsSequenceS(cdr1Indices);
int CDR3Count = allCDR3s.size();
System.out.println("all CDR3s count: " + CDR3Count);
int CDR1Count = allCDR1s.size();
@@ -591,26 +591,26 @@ public class Simulator {
Map<Integer, Integer> rowSequenceCounts,
Map<Integer,Integer> columnSequenceCounts,
double[][] weights){
Map<Integer, Integer> wellNRowPeptides = null;
Map<Integer, Integer> wellNColumnPeptides = null;
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++) {
wellNRowPeptides = samplePlate.assayWellsPeptideP(n, rowSequenceIndices);
for (Integer a : wellNRowPeptides.keySet()) {
wellNRowSequences = samplePlate.assayWellsSequenceS(n, rowSequenceIndices);
for (Integer a : wellNRowSequences.keySet()) {
if(allRowSequences.containsKey(a)){
rowSequenceCounts.merge(a, 1, (oldValue, newValue) -> oldValue + newValue);
}
}
wellNColumnPeptides = samplePlate.assayWellsPeptideP(n, colSequenceIndices);
for (Integer b : wellNColumnPeptides.keySet()) {
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 : wellNRowPeptides.keySet()) {
for (Integer i : wellNRowSequences.keySet()) {
if(allRowSequences.containsKey(i)){
for (Integer j : wellNColumnPeptides.keySet()) {
for (Integer j : wellNColumnSequences.keySet()) {
if(allColumnSequences.containsKey(j)){
weights[rowSequenceToVertexMap.get(i)][columnSequenceToVertexMap.get(j) - vertexStartValue] += 1.0;
}