Initial Commit - works well, but too memory intensive

2021-11-09 20:24:22 -06:00
commit 82d5500ae8
3 changed files with 339 additions and 0 deletions
--- a/src/main/java/Plate.java
+++ b/src/main/java/Plate.java
@@ -0,0 +1,102 @@
+import java.sql.Array;
+import java.util.*;
+
+public class Plate {
+    private List<List<Integer[]>> wells;
+    private Random rand = new Random();
+    private int size;
+    private double error;
+
+    public Plate (int size, double error) {
+        this.size = size;
+        this.error = error;
+        wells = new ArrayList<>();
+    }
+
+    public void fillWells(List<Integer[]> cells, int[] concentrations, double stdDev) {
+        int numSections = concentrations.length;
+        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<>();
+                for (int j = 0; j < concentrations[section]; j++) {
+                    do {
+                        m = Math.abs(rand.nextGaussian()) * stdDev;
+                    } while (m >= cells.size());
+                    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;
+                        }
+                    }
+                    well.add(cellToAdd);
+                }
+                wells.add(well);
+            }
+            section++;
+        }
+    }
+
+    public Map<Integer, Integer> assayWellsAlpha() {
+        return this.assayWellsAlpha(0, size);
+    }
+
+    public Map<Integer, Integer> assayWellsAlpha(int n) {
+        return this.assayWellsAlpha(n, n+1);
+    }
+
+    public Map<Integer, Integer> assayWellsAlpha(int start, int end) {
+        Map<Integer, Integer> assay = new HashMap<>();
+        for(int i = start; i < end; i++){
+            countAlphas(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){
+        for(Integer[] cell : well) {
+            if(cell[0] != -1){
+                //keys are alphas, value is how many of them have been assayed
+                wellMap.merge(cell[0], 1, (oldValue, newValue) -> oldValue + newValue);
+            }
+        }
+    }
+
+    //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){
+        for(Integer[] cell : well) {
+            if(cell[1] != -1){
+                wellMap.merge(cell[1], 1, (oldValue, newValue) -> oldValue + newValue);
+            }
+        }
+    }
+
+
+}