Cache everything

src/main/java/CellFileReader.java

@@ -13,6 +13,7 @@ public class CellFileReader {
 
     private String filename;
     private List<Integer[]> distinctCells = new ArrayList<>();
+    private Integer cdr1Freq;
 
     public CellFileReader(String filename) {
         if(!filename.matches(".*\\.csv")){
@@ -38,19 +39,37 @@ public class CellFileReader {
                 cell[3] = Integer.valueOf(record.get("Beta CDR1"));
                 distinctCells.add(cell);
             }
+
+
         } catch(IOException ex){
             System.out.println("cell file " + filename + " not found.");
             System.err.println(ex);
         }
+
+        //get CDR1 frequency
+        ArrayList<Integer> cdr1Alphas = new ArrayList<>();
+        for (Integer[] cell : distinctCells) {
+            cdr1Alphas.add(cell[3]);
+        }
+        double count = cdr1Alphas.stream().distinct().count();
+        count = Math.ceil(distinctCells.size() / count);
+        cdr1Freq = (int) count;
+
+    }
+
+    public CellSample getCellSample() {
+        return new CellSample(distinctCells, cdr1Freq);
     }
 
     public String getFilename() { return filename;}
 
-    public List<Integer[]> getCells(){
+    //Refactor everything that uses this to have access to a Cell Sample and get the cells there instead.
+    public List<Integer[]> getListOfDistinctCellsDEPRECATED(){
         return distinctCells;
     }
 
-    public Integer getCellCount() {
+    public Integer getCellCountDEPRECATED() {
+        //Refactor everything that uses this to have access to a Cell Sample and get the count there instead.
         return distinctCells.size();
     }
 }