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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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13
src/main/java/Equations.java
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@@ -8,6 +8,9 @@ public abstract class Equations {
return (int) ((Math.random() * (max - min)) + min); return (int) ((Math.random() * (max - min)) + min);
} }
//pValue calculation as described in original pairSEQ paper.
//Included for comparison with original results.
//Not used by BiGpairSEQ for matching.
public static double pValue(Integer w, Integer w_a, Integer w_b, double w_ab_d) { public static double pValue(Integer w, Integer w_a, Integer w_b, double w_ab_d) {
int w_ab = (int) w_ab_d; int w_ab = (int) w_ab_d;
double pv = 0.0; double pv = 0.0;
@@ -18,6 +21,9 @@ public abstract class Equations {
return pv; return pv;
} }
//Implementation of the (corrected) probability equation from pairSEQ paper.
//Included for comparison with original results.
//Not used by BiGpairSEQ for matching.
private static double probPairedByChance(Integer w, Integer w_a, Integer w_b, Integer w_ab){ private static double probPairedByChance(Integer w, Integer w_a, Integer w_b, Integer w_ab){
BigInteger numer1 = choose(w, w_ab); BigInteger numer1 = choose(w, w_ab);
BigInteger numer2 = choose(w - w_ab, w_a - w_ab); BigInteger numer2 = choose(w - w_ab, w_a - w_ab);
@@ -30,10 +36,9 @@ public abstract class Equations {
return prob.doubleValue(); return prob.doubleValue();
} }
/*
* This works because nC(k+1) = nCk * (n-k)/(k+1) //This works because nC(k+1) = nCk * (n-k)/(k+1)
* Since nC0 = 1, can start there and generate all the rest. //Since nC0 = 1, can start there and generate all the rest.
*/
public static BigInteger choose(final int N, final int K) { public static BigInteger choose(final int N, final int K) {
BigInteger nCk = BigInteger.ONE; BigInteger nCk = BigInteger.ONE;
for (int k = 0; k < K; k++) { for (int k = 0; k < K; k++) {

32
src/main/java/Plate.java
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@@ -68,7 +68,7 @@ public class Plate {
} }
Integer[] cellToAdd = cells.get(n).clone(); Integer[] cellToAdd = cells.get(n).clone();
for(int k = 0; k < cellToAdd.length; k++){ for(int k = 0; k < cellToAdd.length; k++){
if(Math.abs(rand.nextDouble()) < error){//error applied to each peptide if(Math.abs(rand.nextDouble()) < error){//error applied to each seqeunce
cellToAdd[k] = -1; cellToAdd[k] = -1;
} }
} }
@@ -98,7 +98,7 @@ public class Plate {
n = (int) Math.floor(m); n = (int) Math.floor(m);
Integer[] cellToAdd = cells.get(n).clone(); Integer[] cellToAdd = cells.get(n).clone();
for(int k = 0; k < cellToAdd.length; k++){ for(int k = 0; k < cellToAdd.length; k++){
if(Math.abs(rand.nextDouble()) < error){//error applied to each peptide if(Math.abs(rand.nextDouble()) < error){//error applied to each sequence
cellToAdd[k] = -1; cellToAdd[k] = -1;
} }
} }
@@ -134,30 +134,30 @@ public class Plate {
return wells; return wells;
} }
//returns a map of the counts of the peptide at cell index pIndex, in all wells //returns a map of the counts of the sequence at cell index sIndex, in all wells
public Map<Integer, Integer> assayWellsPeptideP(int... pIndices){ public Map<Integer, Integer> assayWellsSequenceS(int... sIndices){
return this.assayWellsPeptideP(0, size, pIndices); return this.assayWellsSequenceS(0, size, sIndices);
} }
//returns a map of the counts of the peptide at cell index pIndex, in a specific well //returns a map of the counts of the sequence at cell index sIndex, in a specific well
public Map<Integer, Integer> assayWellsPeptideP(int n, int... pIndices) { return this.assayWellsPeptideP(n, n+1, pIndices);} public Map<Integer, Integer> assayWellsSequenceS(int n, int... sIndices) { return this.assayWellsSequenceS(n, n+1, sIndices);}
//returns a map of the counts of the peptide at cell index pIndex, 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<Integer, Integer> assayWellsPeptideP(int start, int end, int... pIndices) { public Map<Integer, Integer> assayWellsSequenceS(int start, int end, int... sIndices) {
Map<Integer,Integer> assay = new HashMap<>(); Map<Integer,Integer> assay = new HashMap<>();
for(int pIndex: pIndices){ for(int pIndex: sIndices){
for(int i = start; i < end; i++){ for(int i = start; i < end; i++){
countPeptides(assay, wells.get(i), pIndex); countSequences(assay, wells.get(i), pIndex);
} }
} }
return assay; return assay;
} }
//For the peptides at cell indices pIndices, counts number of unique peptides 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 countPeptides(Map<Integer, Integer> wellMap, List<Integer[]> well, int... pIndices) { private void countSequences(Map<Integer, Integer> wellMap, List<Integer[]> well, int... sIndices) {
for(Integer[] cell : well) { for(Integer[] cell : well) {
for(int pIndex: pIndices){ for(int sIndex: sIndices){
if(cell[pIndex] != -1){ if(cell[sIndex] != -1){
wellMap.merge(cell[pIndex], 1, (oldValue, newValue) -> oldValue + newValue); wellMap.merge(cell[sIndex], 1, (oldValue, newValue) -> oldValue + newValue);
} }
} }
} }

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("Cell maps made");}
if(verbose){System.out.println("Making well maps");} if(verbose){System.out.println("Making well maps");}
Map<Integer, Integer> allAlphas = samplePlate.assayWellsPeptideP(alphaIndex); Map<Integer, Integer> allAlphas = samplePlate.assayWellsSequenceS(alphaIndex);
Map<Integer, Integer> allBetas = samplePlate.assayWellsPeptideP(betaIndex); Map<Integer, Integer> allBetas = samplePlate.assayWellsSequenceS(betaIndex);
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();
@@ -296,8 +296,8 @@ public class Simulator {
System.out.println("Cell maps made"); System.out.println("Cell maps made");
System.out.println("Making well maps"); System.out.println("Making well maps");
Map<Integer, Integer> allCDR3s = samplePlate.assayWellsPeptideP(cdr3Indices); Map<Integer, Integer> allCDR3s = samplePlate.assayWellsSequenceS(cdr3Indices);
Map<Integer, Integer> allCDR1s = samplePlate.assayWellsPeptideP(cdr1Indices); Map<Integer, Integer> allCDR1s = samplePlate.assayWellsSequenceS(cdr1Indices);
int CDR3Count = allCDR3s.size(); int CDR3Count = allCDR3s.size();
System.out.println("all CDR3s count: " + CDR3Count); System.out.println("all CDR3s count: " + CDR3Count);
int CDR1Count = allCDR1s.size(); int CDR1Count = allCDR1s.size();
@@ -591,26 +591,26 @@ public class Simulator {
Map<Integer, Integer> rowSequenceCounts, Map<Integer, Integer> rowSequenceCounts,
Map<Integer,Integer> columnSequenceCounts, Map<Integer,Integer> columnSequenceCounts,
double[][] weights){ double[][] weights){
Map<Integer, Integer> wellNRowPeptides = null; Map<Integer, Integer> wellNRowSequences = null;
Map<Integer, Integer> wellNColumnPeptides = null; Map<Integer, Integer> wellNColumnSequences = null;
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++) {
wellNRowPeptides = samplePlate.assayWellsPeptideP(n, rowSequenceIndices); wellNRowSequences = samplePlate.assayWellsSequenceS(n, rowSequenceIndices);
for (Integer a : wellNRowPeptides.keySet()) { for (Integer 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);
} }
} }
wellNColumnPeptides = samplePlate.assayWellsPeptideP(n, colSequenceIndices); wellNColumnSequences = samplePlate.assayWellsSequenceS(n, colSequenceIndices);
for (Integer b : wellNColumnPeptides.keySet()) { for (Integer 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);
} }
} }
for (Integer i : wellNRowPeptides.keySet()) { for (Integer i : wellNRowSequences.keySet()) {
if(allRowSequences.containsKey(i)){ if(allRowSequences.containsKey(i)){
for (Integer j : wellNColumnPeptides.keySet()) { for (Integer j : wellNColumnSequences.keySet()) {
if(allColumnSequences.containsKey(j)){ if(allColumnSequences.containsKey(j)){
weights[rowSequenceToVertexMap.get(i)][columnSequenceToVertexMap.get(j) - vertexStartValue] += 1.0; weights[rowSequenceToVertexMap.get(i)][columnSequenceToVertexMap.get(j) - vertexStartValue] += 1.0;
} }

3
src/main/java/UserInterface.java
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@@ -681,7 +681,8 @@ public class UserInterface {
System.out.println("This program simulates BiGpairSEQ, a graph theory based adaptation"); System.out.println("This program simulates BiGpairSEQ, a graph theory based adaptation");
System.out.println("of the pairSEQ algorithm for pairing T cell receptor sequences."); System.out.println("of the pairSEQ algorithm for pairing T cell receptor sequences.");
System.out.println(); System.out.println();
System.out.println("For full documentation, see: https://gitea.ejsf.synology.me/efischer/BiGpairSEQ"); System.out.println("For full documentation, view readme.md file distributed with this code");
System.out.println("or visit https://gitea.ejsf.synology.me/efischer/BiGpairSEQ.");
System.out.println(); System.out.println();
System.out.println("pairSEQ citation:"); System.out.println("pairSEQ citation:");
System.out.println("Howie, B., Sherwood, A. M., et. al."); System.out.println("Howie, B., Sherwood, A. M., et. al.");