From 5ecaa74afff8e25fa451bea72799bb1b2f656d9d Mon Sep 17 00:00:00 2001
From: Mark Woon <markwoon@gmail.com>
Date: Sat, 27 Apr 2024 22:51:52 -0700
Subject: [PATCH] fix(datamanager): remove populationFrequency from named
 allele (never used)

---
 .../definition/model/NamedAllele.java         | 21 ++-----------------
 .../pharmcat/haplotype/MatchData.java         |  2 --
 .../pharmcat/haplotype/model/BaseMatch.java   |  2 --
 3 files changed, 2 insertions(+), 23 deletions(-)

diff --git a/src/main/java/org/pharmgkb/pharmcat/definition/model/NamedAllele.java b/src/main/java/org/pharmgkb/pharmcat/definition/model/NamedAllele.java
index f9b997e14..ed38b4aff 100644
--- a/src/main/java/org/pharmgkb/pharmcat/definition/model/NamedAllele.java
+++ b/src/main/java/org/pharmgkb/pharmcat/definition/model/NamedAllele.java
@@ -6,7 +6,6 @@
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 import java.util.SortedSet;
 import java.util.regex.Pattern;
 import com.google.common.base.Objects;
@@ -39,9 +38,6 @@ public class NamedAllele implements Comparable<NamedAllele> {
   @SerializedName("cpicAlleles")
   private final String[] m_cpicAlleles;
   @Expose
-  @SerializedName("populationFrequency")
-  private Map<String, String> m_popFreqMap;
-  @Expose
   @SerializedName(value = "reference", alternate = {"matchesreferencesequence"})
   private final boolean m_isReference;
   //-- variables after this point are used by NamedAlleleMatcher --//
@@ -296,18 +292,6 @@ public SortedSet<VariantLocus> getMissingPositions() {
   }
 
 
-  /**
-   * A mapping of population name to allele frequency
-   */
-  public Map<String, String> getPopFreqMap() {
-    return m_popFreqMap;
-  }
-
-  public void setPopFreqMap(Map<String, String> popFreqMap) {
-    m_popFreqMap = popFreqMap;
-  }
-
-
   @Override
   public String toString() {
     return m_name + " [" + m_id + "]";
@@ -338,13 +322,12 @@ public boolean equals(Object o) {
     }
     return Objects.equal(m_name, that.getName()) &&
         Objects.equal(m_id, that.getId()) &&
-        Arrays.equals(m_alleles, that.getAlleles()) &&
-        Objects.equal(m_popFreqMap, that.getPopFreqMap());
+        Arrays.equals(m_alleles, that.getAlleles());
   }
 
   @Override
   public int hashCode() {
-    return Objects.hashCode(m_name, m_id, m_alleles, m_popFreqMap);
+    return Objects.hashCode(m_name, m_id, m_alleles);
   }
 
 
diff --git a/src/main/java/org/pharmgkb/pharmcat/haplotype/MatchData.java b/src/main/java/org/pharmgkb/pharmcat/haplotype/MatchData.java
index 4c8bb2803..8d335c67c 100644
--- a/src/main/java/org/pharmgkb/pharmcat/haplotype/MatchData.java
+++ b/src/main/java/org/pharmgkb/pharmcat/haplotype/MatchData.java
@@ -153,7 +153,6 @@ void marshallHaplotypes(String gene, SortedSet<NamedAllele> allHaplotypes, boole
 
         NamedAllele newHap = new NamedAllele(hap.getId(), hap.getName(), availableAlleles, cpicAlleles,
             missingPositions, hap.isReference());
-        newHap.setPopFreqMap(hap.getPopFreqMap());
         newHap.initialize(m_positions);
         if (newHap.getScore() > 0) {
           m_haplotypes.add(newHap);
@@ -211,7 +210,6 @@ void defaultMissingAllelesToReference() {
 
       NamedAllele fixedHap = new NamedAllele(hap.getId(), hap.getName(), newAlleles, cpicAlleles,
           hap.getMissingPositions(), hap.isReference());
-      fixedHap.setPopFreqMap(hap.getPopFreqMap());
       fixedHap.initialize(m_positions, hap.getScore());
       updatedHaplotypes.add(fixedHap);
     }
diff --git a/src/main/java/org/pharmgkb/pharmcat/haplotype/model/BaseMatch.java b/src/main/java/org/pharmgkb/pharmcat/haplotype/model/BaseMatch.java
index 151e1e439..da2d4432d 100644
--- a/src/main/java/org/pharmgkb/pharmcat/haplotype/model/BaseMatch.java
+++ b/src/main/java/org/pharmgkb/pharmcat/haplotype/model/BaseMatch.java
@@ -114,14 +114,12 @@ public void finalizeCombinationHaplotype(MatchData matchData, boolean findPartia
 
       NamedAllele partialHap = new NamedAllele(hap.getId(), builder.toString(), hap.getAlleles(),
           hap.getCpicAlleles(), hap.getMissingPositions(), false, hap.getNumCombinations(), partials.size());
-      partialHap.setPopFreqMap(hap.getPopFreqMap());
       partialHap.initialize(refVariants);
       m_haplotype = partialHap;
 
     } else {
       NamedAllele newHap = new NamedAllele(hap.getId(), hap.getName(), hap.getAlleles(),
           hap.getCpicAlleles(), hap.getMissingPositions(), hap.isReference(), hap.getNumCombinations(), 0);
-      newHap.setPopFreqMap(hap.getPopFreqMap());
       newHap.initialize(refVariants);
       m_haplotype = newHap;
     }