fix: fix haplotype name sorting

build.gradle

@@ -64,7 +64,7 @@ dependencies {
       [group: 'org.apache.logging.log4j', name: 'log4j-to-slf4j', version: '2.23.1'],
       [group: 'org.apache.poi', name: 'poi-ooxml', version: '5.2.5'],
       [group: 'org.checkerframework', name: 'checker-qual', version: '3.39.0'],
-      [group: 'org.pharmgkb', name: 'pgkb-common', version: '0.7.2'],
+      [group: 'org.pharmgkb', name: 'pgkb-common', version: '0.7.3'],
       [group: 'org.pharmgkb', name: 'vcf-parser', version: '0.3.1'],
       [group: 'org.slf4j', name: 'slf4j-api', version: '2.0.13'],
   )

src/main/java/org/pharmgkb/pharmcat/util/HaplotypeNameComparator.java

@@ -2,29 +2,19 @@
 
 import java.util.Comparator;
 import java.util.List;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 import org.pharmgkb.pharmcat.haplotype.model.CombinationMatch;
 
 import static org.pharmgkb.pharmcat.haplotype.model.CombinationMatch.COMBINATION_NAME_SPLITTER;
 import static org.pharmgkb.pharmcat.haplotype.model.CombinationMatch.extractCombinationName;
 
 
 /**
- * Comparator for haplotype names that take combination names and HGVS names into account.
- * <p>
- * <b>WARNING!  DANGER!</b> This comparator does NOT comply with the comparator contract.
- * It DOES NOT GUARANTEE TRANSITIVITY (i.e. if A > B and B > C, then A > C) if all haplotype names being compared are
- * not of like kind (i.e. all HGVS, all strict star pattern, all loose star pattern, or all non-star pattern).
- * See {@link org.pharmgkb.common.comparator.HaplotypeNameComparator} for details.
- * <p>
- * Support for HGVS names is just a band-aid on this problem to support DPYD.
+ * Comparator for haplotype names that take combination names into account.
  *
  * @author Mark Woon
  */
 public class HaplotypeNameComparator implements Comparator<String> {
   private static final Comparator<String> sf_comparator = new HaplotypeNameComparator();
-  private static final Pattern sf_hgvsPattern = Pattern.compile("(?:.*:)?[cgnmopr]\\.(\\d+).*");
 
   /**
    * Gets an instance of this comparator.
@@ -44,9 +34,13 @@ public int compare(String name1, String name2) {
     }
     if (name1 == null) {
       return -1;
-    } else if (name2 == null) {
+    }
+    if (name2 == null) {
       return 1;
     }
+    if (name1.equals(name2)) {
+      return 0;
+    }
 
     boolean c1 = CombinationMatch.isCombinationName(name1);
     boolean c2 = CombinationMatch.isCombinationName(name2);
@@ -66,20 +60,15 @@ public int compare(String name1, String name2) {
         return rez;
       }
 
-      name1 = h1.get(0);
-      name2 = h2.get(0);
-    }
-
-    // sort HGVS based names nicely
-    Matcher h1 = sf_hgvsPattern.matcher(name1);
-    Matcher h2 = sf_hgvsPattern.matcher(name2);
-    if (h1.matches() && h2.matches()) {
-      int p1 = Integer.parseInt(h1.group(1));
-      int p2 = Integer.parseInt(h2.group(1));
-      if (p1 == p2) {
-        return name1.compareTo(name2);
+      for (int x = 0; x < h1.size(); x += 1) {
+        String n1 = h1.get(x);
+        String n2 = h2.get(x);
+        rez = org.pharmgkb.common.comparator.HaplotypeNameComparator.getComparator().compare(n1, n2);
+        if (rez != 0) {
+          return rez;
+        }
       }
-      return Integer.compare(p1, p2);
+      return 0;
     }
 
     return org.pharmgkb.common.comparator.HaplotypeNameComparator.getComparator().compare(name1, name2);

src/test/java/org/pharmgkb/pharmcat/util/HaplotypeNameComparatorTest.java

@@ -38,6 +38,12 @@ void testComboSortName() {
     names.add("[*3 + *4]");
     names.add("[*2 + *3]");
     assertEquals("[*2 + *3]", names.first());
+
+
+    names = new TreeSet<>(new HaplotypeNameComparator());
+    names.add("[*2 + *4]");
+    names.add("[*2 + *3]");
+    assertEquals("[*2 + *3]", names.first());
   }
 
   @Test