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Expanding simulation to attempt CDR3/CDR1 matching - doubles size of cells

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efischer
2021-11-15 15:00:11 -06:00
parent c425b05d8c
commit 13b58e3204
5 changed files with 445 additions and 56 deletions
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156
src/main/java/Plate.java
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@@ -1,4 +1,3 @@
import java.sql.Array;
import java.util.*;
//Need to write function to output plate to a file that I can read in.
@@ -29,7 +28,6 @@ public class Plate {
int section = 0;
double m;
int n;
boolean drop;
while (section < numSections){
for (int i = 0; i < (size / numSections); i++) {
List<Integer[]> well = new ArrayList<>();
@@ -39,12 +37,9 @@ public class Plate {
} while (m >= cells.size() || m < 0);
n = (int) Math.floor(m);
Integer[] cellToAdd = cells.get(n).clone();
drop = Math.abs(rand.nextDouble()) < error;
if (drop) {
if (rand.nextBoolean()) {
cellToAdd[0] = -1;
} else {
cellToAdd[1] = -1;
for(int k = 0; k < cellToAdd.length; k++){
if(Math.abs(rand.nextDouble()) < error){//error applied to each peptide
cellToAdd[k] = -1;
}
}
well.add(cellToAdd);
@@ -80,24 +75,112 @@ public class Plate {
return wells;
}
public Map<Integer, Integer> assayWellsAlpha() {
return this.assayWellsAlpha(0, size);
//returns a map of counts of all the CDR3s (alphas and betas) in all wells
public Map<Integer, Integer>assayWellsCDR3(){
return this.assayWellsCDR3(0, size);
}
//returns a map of counts of all the CDR3 alphas in all wells
public Map<Integer, Integer> assayWellsCDR3Alpha() {
return this.assayWellsCDR3Alpha(0, size);
}
//returns a map of counts of all the CDR3 betas in all wells
public Map<Integer, Integer> assayWellsCDR3Beta() {
return this.assayWellsCDR3Beta(0, size);
}
//returns a map of counts of all CDR1s (alphas and betas) in all wells
public Map<Integer, Integer> assayWellsCDR1(){
return this.assayWellsCDR1(0, size);
}
//returns a map of counts of all the CDR1 alphas in all wells
public Map<Integer, Integer> assayWellsCDR1Alpha() {
return this.assayWellsCDR1Alpha(0, size);
}
//returns a map of counts of all the CDR1 betas in all wells
public Map<Integer, Integer> assayWellsCDR1Beta() {
return this.assayWellsCDR1Beta(0, size);
}
public Map<Integer, Integer> assayWellsAlpha(int n) {
return this.assayWellsAlpha(n, n+1);
//returns a map of counts of the CDR3s (alphas and betas) in a specific well
public Map<Integer, Integer>assayWellsCDR3(int n){
return this.assayWellsCDR3(n, n+1);
}
//returns a map of counts of the CDR1s (alphas and betas) in a specific well
public Map<Integer, Integer> assayWellsCDR1(int n){
return this.assayWellsCDR1(n, n+1);
}
//returns a map of counts of the CDR3 alphas in a specific well
public Map<Integer, Integer> assayWellsCDR3Alpha(int n) {
return this.assayWellsCDR3Alpha(n, n+1);
}
//returns a map of counts of the CDR3 betas in a specific well
public Map<Integer, Integer> assayWellsCDR3Beta(int n) {
return this.assayWellsCDR3Beta(n, n+1);
}
//returns a map of counts of the CDR1 alphas in a specific well
public Map<Integer, Integer> assayWellsCDR1Alpha(int n) {
return this.assayWellsCDR1Alpha(n, n+1);
}
//returns a map of counts of the CDR1 betas in a specific well
public Map<Integer, Integer> assayWellsCDR1Beta(int n) {
return this.assayWellsCDR1Beta(n, n+1);
}
public Map<Integer, Integer> assayWellsAlpha(int start, int end) {
//returns a map of the counts of the CDR3s (alphas and betas) in a range of wells
public Map<Integer, Integer>assayWellsCDR3(int start, int end){
Map<Integer,Integer> assay = new HashMap<>();
for(int i = start; i < end; i++){
countCDR3Alphas(assay, wells.get(i));
countCDR3Betas(assay,wells.get(i));
}
return assay;
}
//returns a map of the counts of the CDR1s (alphas and betas) in a range of wells
public Map<Integer, Integer>assayWellsCDR1(int start, int end){
Map<Integer,Integer> assay = new HashMap<>();
for(int i = start; i < end; i++){
countCDR1Alphas(assay, wells.get(i));
countCDR1Betas(assay,wells.get(i));
}
return assay;
}
//returns a map of the counts of the CDR3 alphas in a range of wells
public Map<Integer, Integer> assayWellsCDR3Alpha(int start, int end) {
Map<Integer, Integer> assay = new HashMap<>();
for(int i = start; i < end; i++){
countAlphas(assay, wells.get(i));
countCDR3Alphas(assay, wells.get(i));
}
return assay;
}
//returns a map of the counts of the CDR3 betas in a range of wells
public Map<Integer, Integer> assayWellsCDR3Beta(int start, int end) {
Map<Integer, Integer> assay = new HashMap<>();
for(int i = start; i < end; i++){
countCDR3Betas(assay, wells.get(i));
}
return assay;
}
//returns a map of the counts of the CDR1 alphas in a range of wells
public Map<Integer, Integer> assayWellsCDR1Alpha(int start, int end) {
Map<Integer, Integer> assay = new HashMap<>();
for(int i = start; i < end; i++){
countCDR1Alphas(assay, wells.get(i));
}
return assay;
}
//returns a map of the counts of the CDR1 betas in a range of wells
public Map<Integer, Integer> assayWellsCDR1Beta(int start, int end) {
Map<Integer, Integer> assay = new HashMap<>();
for(int i = start; i < end; i++){
countCDR1Betas(assay, wells.get(i));
}
return assay;
}
//given a map, counts distinct alphas in a well
private void countAlphas(Map<Integer, Integer> wellMap, List<Integer[]> well){
//given a map, counts distinct CDR3 alphas in a well
private void countCDR3Alphas(Map<Integer, Integer> wellMap, List<Integer[]> well){
for(Integer[] cell : well) {
if(cell[0] != -1){
//keys are alphas, value is how many of them have been assayed
@@ -105,34 +188,29 @@ public class Plate {
}
}
}
//assays all wells
public Map<Integer, Integer> assayWellsBeta() {
return this.assayWellsBeta(0, size);
}
//assays a specific well
public Map<Integer, Integer> assayWellsBeta(int n) {
return this.assayWellsBeta(n, n+1);
}
//assays a range of wells
public Map<Integer, Integer> assayWellsBeta(int start, int end) {
Map<Integer, Integer> assay = new HashMap<>();
for(int i = start; i < end; i++){
countBetas(assay, wells.get(i));
}
return assay;
}
//given a map, counts distinct betas in a well
private void countBetas(Map<Integer, Integer> wellMap, List<Integer[]> well){
//given a map, counts distinct CDR3 betas in a well
private void countCDR3Betas(Map<Integer, Integer> wellMap, List<Integer[]> well){
for(Integer[] cell : well) {
if(cell[1] != -1){
wellMap.merge(cell[1], 1, (oldValue, newValue) -> oldValue + newValue);
}
}
}
//given a map, counts distinct CDR1 alphas in a well
private void countCDR1Alphas(Map<Integer, Integer> wellMap, List<Integer[]> well){
for(Integer[] cell: well){
if(cell[2] != -1){
wellMap.merge(cell[2], 1, (oldValue, newValue) -> oldValue + newValue);
}
}
}
//given a map, counts distinct CDR1 betas in a well
private void countCDR1Betas(Map<Integer, Integer> wellMap, List<Integer[]> well){
for(Integer[] cell: well){
if(cell[3] != -1){
wellMap.merge(cell[3], 1, (oldValue, newValue) -> oldValue + newValue);
}
}
}
}