From 9184274066170eebfea0585461c1f3107a633d9b Mon Sep 17 00:00:00 2001
From: Jules Jacobsen <j.jacobsen@qmul.ac.uk>
Date: Wed, 13 Mar 2019 11:42:14 +0000
Subject: [PATCH] Refactor FrequencyData to use array-based implementation

---
 .../core/model/frequency/FrequencyData.java   | 51 ++++++++++++++-----
 1 file changed, 37 insertions(+), 14 deletions(-)

diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyData.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyData.java
index 4054fb07c..dd6a20bd6 100644
--- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyData.java
+++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyData.java
@@ -36,6 +36,8 @@ public class FrequencyData {
 
     private static final FrequencyData EMPTY_DATA = new FrequencyData(RsId.empty(), Collections.emptyList());
 
+    private static final int NUM_FREQ_SOURCES = FrequencySource.values().length;
+
     private static final float VERY_RARE_SCORE = 1f;
     private static final float NOT_RARE_SCORE = 0f;
 
@@ -46,7 +48,7 @@ public class FrequencyData {
     private final float[] values;
 
     public static FrequencyData of(RsId rsId, Collection<Frequency> frequencies) {
-        return validate(rsId, new ArrayList<>(frequencies));
+        return validate(rsId, frequencies);
     }
 
     public static FrequencyData of(RsId rsId, Frequency frequency) {
@@ -69,10 +71,7 @@ public static FrequencyData empty() {
         return EMPTY_DATA;
     }
 
-    /**
-     * IMPORTANT ensure that a copy of the input data has been provided to this method as the contents will be sorted
-     */
-    private static FrequencyData validate(RsId rsId, List<Frequency> frequencies) {
+    private static FrequencyData validate(RsId rsId, Collection<Frequency> frequencies) {
         Objects.requireNonNull(rsId, "RsId cannot be null");
         Objects.requireNonNull(frequencies, "frequency data cannot be null");
 
@@ -86,21 +85,45 @@ private static FrequencyData validate(RsId rsId, List<Frequency> frequencies) {
         return new FrequencyData(rsId, frequencies);
     }
 
-    private FrequencyData(RsId rsId, List<Frequency> knownFrequencies) {
+    private FrequencyData(RsId rsId, Collection<Frequency> frequencies) {
         this.rsId = rsId.getId();
 
-        this.size = knownFrequencies.size();
+        // use natural ordering by FrequencySource - this class is a kind of EnumMap, but we're using primitives to store
+        // the values. This means that duplicated FrequencySource will be overwritten. In practice this shouldn't happen
+        // as they are extracted from a map instance.
+        Frequency[] sorted = orderByFrequencySource(frequencies);
+
+        this.size = countNotNullFrequencies(sorted);
         this.sources = new FrequencySource[size];
         this.values = new float[size];
 
-        // use natural ordering by FrequencySource - this class is a kind of EnumMap
-        knownFrequencies.sort(Comparator.comparing(Frequency::getSource));
-        for (int i = 0; i < knownFrequencies.size(); i++) {
-            Frequency entry = knownFrequencies.get(i);
-            // consider replacing this with FrequencySource.ordinal().
-            sources[i] = entry.getSource();
-            values[i] = entry.getFrequency();
+        int pos = 0;
+        for (Frequency entry : sorted) {
+            if (entry != null) {
+                sources[pos] = entry.getSource();
+                values[pos] = entry.getFrequency();
+                pos++;
+            }
+        }
+    }
+
+    private Frequency[] orderByFrequencySource(Collection<Frequency> frequencies) {
+        Frequency[] sorted = new Frequency[NUM_FREQ_SOURCES];
+        for (Frequency frequency : frequencies) {
+            FrequencySource frequencySource = frequency.getSource();
+            sorted[frequencySource.ordinal()] = frequency;
+        }
+        return sorted;
+    }
+
+    private int countNotNullFrequencies(Frequency[] sorted) {
+        int notNull = 0;
+        for (Frequency frequency : sorted) {
+            if (frequency != null) {
+                notNull++;
+            }
         }
+        return notNull;
     }
 
     //RSID ought to belong to the Variant, not the frequencyData, but its here for convenience