Refactor Collection Implementations in Tests: Drop Guava for Java Native

exomiser · Apr 29, 2024 · 35240c6 · 35240c6
1 parent eab9ebe
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diff --git a/src/test/java/org/monarchinitiative/gregor/mendel/InheritanceCheckerMTSinglePersonTest.java b/src/test/java/org/monarchinitiative/gregor/mendel/InheritanceCheckerMTSinglePersonTest.java
@@ -1,29 +1,30 @@
 package org.monarchinitiative.gregor.mendel;
 
-import com.google.common.collect.ImmutableList;
-import com.google.common.collect.ImmutableMap;
 import org.monarchinitiative.gregor.pedigree.*;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
+import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 
 public class InheritanceCheckerMTSinglePersonTest extends MendelianCompatibilityCheckerTestBase {
 
  private MendelianInheritanceChecker checker;
  private List<GenotypeCalls> gcList;
- private ImmutableMap<ModeOfInheritance, ImmutableList<GenotypeCalls>> result;
+ private Map<ModeOfInheritance, List<GenotypeCalls>> result;
 
  @BeforeEach
  public void setUp() throws Exception {
- ImmutableList.Builder<PedPerson> individuals = new ImmutableList.Builder<PedPerson>();
- individuals.add(new PedPerson("ped", "I.1", "0", "0", Sex.FEMALE, Disease.AFFECTED));
- PedFileContents pedFileContents = new PedFileContents(new ImmutableList.Builder<String>().build(),
- individuals.build());
+ List<PedPerson> individuals = List.of(
+ new PedPerson("ped", "I.1", "0", "0", Sex.FEMALE, Disease.AFFECTED)
+ );
+ PedFileContents pedFileContents = new PedFileContents(List.of(),
+ individuals);
  this.pedigree = new Pedigree(pedFileContents, "ped");
 
- this.names = ImmutableList.of("I.1");
+ this.names = List.of("I.1");
 
  this.checker = new MendelianInheritanceChecker(this.pedigree);
 

diff --git a/src/test/java/org/monarchinitiative/gregor/mendel/InheritanceCheckerMTSmallTest.java b/src/test/java/org/monarchinitiative/gregor/mendel/InheritanceCheckerMTSmallTest.java
@@ -1,34 +1,34 @@
 package org.monarchinitiative.gregor.mendel;
 
-import com.google.common.collect.ImmutableList;
-import com.google.common.collect.ImmutableMap;
 import org.monarchinitiative.gregor.pedigree.*;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
+import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 
 public class InheritanceCheckerMTSmallTest extends MendelianCompatibilityCheckerTestBase {
 
  private MendelianInheritanceChecker checker;
  private List<GenotypeCalls> gcList;
- private ImmutableMap<ModeOfInheritance, ImmutableList<GenotypeCalls>> result;
+ private Map<ModeOfInheritance, List<GenotypeCalls>> result;
 
  private Pedigree inconsistentMTpedigree;
 
  @BeforeEach
  public void setUp() throws Exception {
- ImmutableList.Builder<PedPerson> individuals = new ImmutableList.Builder<PedPerson>();
+ List<PedPerson> individuals = new ArrayList<PedPerson>();
  individuals.add(new PedPerson("ped", "I.1", "0", "0", Sex.MALE, Disease.UNAFFECTED)); // father
  individuals.add(new PedPerson("ped", "I.2", "0", "0", Sex.FEMALE, Disease.AFFECTED)); // mother
  individuals.add(new PedPerson("ped", "II.1", "I.1", "I.2", Sex.MALE, Disease.AFFECTED)); // son
  individuals.add(new PedPerson("ped", "II.2", "I.1", "I.2", Sex.FEMALE, Disease.AFFECTED)); // daughter
- PedFileContents pedFileContents = new PedFileContents(new ImmutableList.Builder<String>().build(),
- individuals.build());
+ PedFileContents pedFileContents = new PedFileContents(new ArrayList<String>(),
+ individuals);
  this.pedigree = new Pedigree(pedFileContents, "ped");
 
- this.names = ImmutableList.of("I.1", "I.2", "II.1", "II.2");
+ this.names = List.of("I.1", "I.2", "II.1", "II.2");
 
  this.checker = new MendelianInheritanceChecker(this.pedigree);
 
@@ -38,13 +38,13 @@ public void setUp() throws Exception {
  * same as above but father is transmitting mitochrondrial mutation, which is
  * impossible
  */
- ImmutableList.Builder<PedPerson> individuals2 = new ImmutableList.Builder<PedPerson>();
+ List<PedPerson> individuals2 = new ArrayList<PedPerson>();
  individuals2.add(new PedPerson("ped2", "I.1", "0", "0", Sex.MALE, Disease.AFFECTED)); // father
  individuals2.add(new PedPerson("ped2", "I.2", "0", "0", Sex.FEMALE, Disease.UNAFFECTED)); // mother
  individuals2.add(new PedPerson("ped2", "II.1", "I.1", "I.2", Sex.MALE, Disease.AFFECTED)); // son
  individuals2.add(new PedPerson("ped2", "II.2", "I.1", "I.2", Sex.FEMALE, Disease.AFFECTED)); // daughter
- PedFileContents pedFileContents2 = new PedFileContents(new ImmutableList.Builder<String>().build(),
- individuals2.build());
+ PedFileContents pedFileContents2 = new PedFileContents(new ArrayList<String>(),
+ individuals2);
  this.inconsistentMTpedigree = new Pedigree(pedFileContents2, "ped2");
  }
 

diff --git a/...st/java/org/monarchinitiative/gregor/mendel/MendelianCompatibilityCheckerADLargeTest.java b/...st/java/org/monarchinitiative/gregor/mendel/MendelianCompatibilityCheckerADLargeTest.java
@@ -1,41 +1,42 @@
 package org.monarchinitiative.gregor.mendel;
 
-import com.google.common.collect.ImmutableList;
-import com.google.common.collect.ImmutableMap;
 import org.monarchinitiative.gregor.pedigree.*;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
+import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 
 public class MendelianCompatibilityCheckerADLargeTest extends MendelianCompatibilityCheckerTestBase {
 
  MendelianInheritanceChecker checker;
  List<GenotypeCalls> gcList;
- ImmutableMap<ModeOfInheritance, ImmutableList<GenotypeCalls>> result;
+ Map<ModeOfInheritance, List<GenotypeCalls>> result;
 
  @BeforeEach
  public void setUp() throws Exception {
- ImmutableList.Builder<PedPerson> individuals = new ImmutableList.Builder<PedPerson>();
- individuals.add(new PedPerson("ped", "I.1", "0", "0", Sex.MALE, Disease.UNAFFECTED)); // grandfather
- individuals.add(new PedPerson("ped", "I.2", "0", "0", Sex.FEMALE, Disease.UNAFFECTED)); // grandmother
- individuals.add(new PedPerson("ped", "II.1", "I.1", "I.2", Sex.MALE, Disease.UNAFFECTED)); // p1
- individuals.add(new PedPerson("ped", "II.2", "I.1", "I.2", Sex.MALE, Disease.AFFECTED)); // p2
- individuals.add(new PedPerson("ped", "II.3", "I.1", "I.2", Sex.FEMALE, Disease.UNAFFECTED)); // p3
- individuals.add(new PedPerson("ped", "II.4", "I.1", "I.2", Sex.FEMALE, Disease.AFFECTED)); // p4
- individuals.add(new PedPerson("ped", "II.5", "I.1", "I.2", Sex.UNKNOWN, Disease.UNKNOWN)); // p5
- individuals.add(new PedPerson("ped", "III.1", "II.1", "0", Sex.FEMALE, Disease.UNAFFECTED)); // c1
- individuals.add(new PedPerson("ped", "III.2", "II.1", "0", Sex.MALE, Disease.UNAFFECTED)); // c2
- individuals.add(new PedPerson("ped", "III.3", "II.2", "0", Sex.MALE, Disease.AFFECTED)); // c3
- individuals.add(new PedPerson("ped", "III.4", "II.2", "0", Sex.FEMALE, Disease.UNAFFECTED)); // c4
- individuals.add(new PedPerson("ped", "III.5", "0", "II.3", Sex.FEMALE, Disease.UNAFFECTED)); // c5
- individuals.add(new PedPerson("ped", "III.6", "0", "II.4", Sex.MALE, Disease.AFFECTED)); // c6
- PedFileContents pedFileContents = new PedFileContents(new ImmutableList.Builder<String>().build(),
- individuals.build());
+ List<PedPerson> individuals = List.of(
+ new PedPerson("ped", "I.1", "0", "0", Sex.MALE, Disease.UNAFFECTED), // grandfather
+ new PedPerson("ped", "I.2", "0", "0", Sex.FEMALE, Disease.UNAFFECTED), // grandmother
+ new PedPerson("ped", "II.1", "I.1", "I.2", Sex.MALE, Disease.UNAFFECTED), // p1
+ new PedPerson("ped", "II.2", "I.1", "I.2", Sex.MALE, Disease.AFFECTED), // p2
+ new PedPerson("ped", "II.3", "I.1", "I.2", Sex.FEMALE, Disease.UNAFFECTED), // p3
+ new PedPerson("ped", "II.4", "I.1", "I.2", Sex.FEMALE, Disease.AFFECTED), // p4
+ new PedPerson("ped", "II.5", "I.1", "I.2", Sex.UNKNOWN, Disease.UNKNOWN), // p5
+ new PedPerson("ped", "III.1", "II.1", "0", Sex.FEMALE, Disease.UNAFFECTED), // c1
+ new PedPerson("ped", "III.2", "II.1", "0", Sex.MALE, Disease.UNAFFECTED), // c2
+ new PedPerson("ped", "III.3", "II.2", "0", Sex.MALE, Disease.AFFECTED), // c3
+ new PedPerson("ped", "III.4", "II.2", "0", Sex.FEMALE, Disease.UNAFFECTED), // c4
+ new PedPerson("ped", "III.5", "0", "II.3", Sex.FEMALE, Disease.UNAFFECTED), // c5
+ new PedPerson("ped", "III.6", "0", "II.4", Sex.MALE, Disease.AFFECTED) // c6
+ );
+ PedFileContents pedFileContents = new PedFileContents(List.of(),
+ individuals);
  this.pedigree = new Pedigree(pedFileContents, "ped");
 
- this.names = ImmutableList.of("I.1", "I.2", "II.1", "II.2", "II.3", "II.4", "II.5", "III.1", "III.2", "III.3",
+ this.names = List.of("I.1", "I.2", "II.1", "II.2", "II.3", "II.4", "II.5", "III.1", "III.2", "III.3",
  "III.4", "III.5", "III.6");
 
  this.checker = new MendelianInheritanceChecker(this.pedigree);

diff --git a/...t/java/org/monarchinitiative/gregor/mendel/MendelianCompatibilityCheckerADMediumTest.java b/...t/java/org/monarchinitiative/gregor/mendel/MendelianCompatibilityCheckerADMediumTest.java
@@ -1,42 +1,42 @@
 package org.monarchinitiative.gregor.mendel;
 
-import com.google.common.collect.ImmutableList;
-import com.google.common.collect.ImmutableMap;
 import org.monarchinitiative.gregor.pedigree.*;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
+import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 
 public class MendelianCompatibilityCheckerADMediumTest extends MendelianCompatibilityCheckerTestBase {
 
  MendelianInheritanceChecker checker;
  List<GenotypeCalls> gcList;
- ImmutableMap<ModeOfInheritance, ImmutableList<GenotypeCalls>> result;
+ Map<ModeOfInheritance, List<GenotypeCalls>> result;
 
  @BeforeEach
  public void setUp() throws Exception {
- ImmutableList.Builder<PedPerson> individuals = new ImmutableList.Builder<PedPerson>();
- individuals.add(new PedPerson("ped", "I.1", "0", "0", Sex.MALE, Disease.UNAFFECTED)); // grandfather
- individuals.add(new PedPerson("ped", "I.2", "0", "0", Sex.FEMALE, Disease.UNAFFECTED)); // grandmother
- individuals.add(new PedPerson("ped", "II.1", "I.1", "I.2", Sex.MALE, Disease.UNAFFECTED)); // uncle
- individuals.add(new PedPerson("ped", "II.2", "I.1", "I.2", Sex.MALE, Disease.AFFECTED)); // father
- individuals.add(new PedPerson("ped", "II.3", "0", "0", Sex.FEMALE, Disease.UNAFFECTED)); // mother
- individuals.add(new PedPerson("ped", "III.1", "II.2", "II.3", Sex.FEMALE, Disease.AFFECTED)); // daughter
- individuals.add(new PedPerson("ped", "III.2", "II.2", "II.3", Sex.MALE, Disease.UNAFFECTED)); // son
- PedFileContents pedFileContents = new PedFileContents(new ImmutableList.Builder<String>().build(),
-  individuals.build());
+ List<PedPerson> individuals = List.of(
+  new PedPerson("ped", "I.1", "0", "0", Sex.MALE, Disease.UNAFFECTED), // grandfather
+  new PedPerson("ped", "I.2", "0", "0", Sex.FEMALE, Disease.UNAFFECTED), // grandmother
+  new PedPerson("ped", "II.1", "I.1", "I.2", Sex.MALE, Disease.UNAFFECTED), // uncle
+  new PedPerson("ped", "II.2", "I.1", "I.2", Sex.MALE, Disease.AFFECTED), // father
+  new PedPerson("ped", "II.3", "0", "0", Sex.FEMALE, Disease.UNAFFECTED), // mother
+  new PedPerson("ped", "III.1", "II.2", "II.3", Sex.FEMALE, Disease.AFFECTED), // daughter
+  new PedPerson("ped", "III.2", "II.2", "II.3", Sex.MALE, Disease.UNAFFECTED) // son
+ );
+ PedFileContents pedFileContents = new PedFileContents(List.of(), individuals);
  this.pedigree = new Pedigree(pedFileContents, "ped");
 
- this.names = ImmutableList.of("I.1", "I.2", "II.1", "II.2", "II.3", "III.1", "III.2");
-
+ this.names = List.of("I.1", "I.2", "II.1", "II.2", "II.3", "III.1", "III.2");
  this.checker = new MendelianInheritanceChecker(this.pedigree);
 
  this.result = null;
  this.gcList = null;
  }
 
+
  @Test
  public void testSizeOfPedigree() {
  Assertions.assertEquals(7, pedigree.getMembers().size());

diff --git a/...ava/org/monarchinitiative/gregor/mendel/MendelianCompatibilityCheckerADSingletonTest.java b/...ava/org/monarchinitiative/gregor/mendel/MendelianCompatibilityCheckerADSingletonTest.java
@@ -1,28 +1,29 @@
 package org.monarchinitiative.gregor.mendel;
 
-import com.google.common.collect.ImmutableList;
-import com.google.common.collect.ImmutableMap;
 import org.monarchinitiative.gregor.pedigree.*;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
+import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 
 public class MendelianCompatibilityCheckerADSingletonTest extends MendelianCompatibilityCheckerTestBase {
 
  MendelianInheritanceChecker checker;
  List<GenotypeCalls> gcList;
- ImmutableMap<ModeOfInheritance, ImmutableList<GenotypeCalls>> result;
+ Map<ModeOfInheritance, List<GenotypeCalls>> result;
 
  @BeforeEach
  public void setUp() throws Exception {
- ImmutableList.Builder<PedPerson> individuals = new ImmutableList.Builder<PedPerson>();
- individuals.add(new PedPerson("ped", "I.1", "0", "0", Sex.MALE, Disease.AFFECTED));
- PedFileContents pedFileContents = new PedFileContents(new ImmutableList.Builder<String>().build(),
- individuals.build());
+ List<PedPerson> individuals = List.of(
+ new PedPerson("ped", "I.1", "0", "0", Sex.MALE, Disease.AFFECTED)
+ );
+ PedFileContents pedFileContents = new PedFileContents(List.of(),
+ individuals);
  this.pedigree = new Pedigree(pedFileContents, "ped");
- this.names = ImmutableList.of("I.1");
+ this.names = List.of("I.1");
 
  this.checker = new MendelianInheritanceChecker(this.pedigree);
 

diff --git a/...st/java/org/monarchinitiative/gregor/mendel/MendelianCompatibilityCheckerADSmallTest.java b/...st/java/org/monarchinitiative/gregor/mendel/MendelianCompatibilityCheckerADSmallTest.java
@@ -1,32 +1,32 @@
 package org.monarchinitiative.gregor.mendel;
 
-import com.google.common.collect.ImmutableList;
-import com.google.common.collect.ImmutableMap;
 import org.monarchinitiative.gregor.pedigree.*;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
 import java.util.List;
+import java.util.Map;
 
 public class MendelianCompatibilityCheckerADSmallTest extends MendelianCompatibilityCheckerTestBase {
 
  MendelianInheritanceChecker checker;
  List<GenotypeCalls> gcList;
- ImmutableMap<ModeOfInheritance, ImmutableList<GenotypeCalls>> result;
+ Map<ModeOfInheritance, List<GenotypeCalls>> result;
 
  @BeforeEach
  public void setUp() throws Exception {
- ImmutableList.Builder<PedPerson> individuals = new ImmutableList.Builder<PedPerson>();
- individuals.add(new PedPerson("ped", "I.1", "0", "0", Sex.MALE, Disease.AFFECTED)); // father
- individuals.add(new PedPerson("ped", "I.2", "0", "0", Sex.FEMALE, Disease.UNAFFECTED)); // mother
- individuals.add(new PedPerson("ped", "II.1", "I.1", "I.2", Sex.MALE, Disease.AFFECTED)); // son
- individuals.add(new PedPerson("ped", "II.2", "I.1", "I.2", Sex.FEMALE, Disease.UNAFFECTED)); // daughter
- PedFileContents pedFileContents = new PedFileContents(new ImmutableList.Builder<String>().build(),
- individuals.build());
+ List<PedPerson> individuals = List.of(
+ new PedPerson("ped", "I.1", "0", "0", Sex.MALE, Disease.AFFECTED), // father
+ new PedPerson("ped", "I.2", "0", "0", Sex.FEMALE, Disease.UNAFFECTED), // mother
+ new PedPerson("ped", "II.1", "I.1", "I.2", Sex.MALE, Disease.AFFECTED), // son
+ new PedPerson("ped", "II.2", "I.1", "I.2", Sex.FEMALE, Disease.UNAFFECTED) // daughter
+ );
+ PedFileContents pedFileContents = new PedFileContents(List.of(),
+ individuals);
  this.pedigree = new Pedigree(pedFileContents, "ped");
 
- this.names = ImmutableList.of("I.1", "I.2", "II.1", "II.2");
+ this.names = List.of("I.1", "I.2", "II.1", "II.2");
 
  this.checker = new MendelianInheritanceChecker(this.pedigree);
 

diff --git a/...ava/org/monarchinitiative/gregor/mendel/MendelianCompatibilityCheckerADVerySmallTest.java b/...ava/org/monarchinitiative/gregor/mendel/MendelianCompatibilityCheckerADVerySmallTest.java
@@ -1,30 +1,29 @@
 package org.monarchinitiative.gregor.mendel;
 
-import com.google.common.collect.ImmutableList;
-import com.google.common.collect.ImmutableMap;
 import org.monarchinitiative.gregor.pedigree.*;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
 import java.util.List;
+import java.util.Map;
 
 public class MendelianCompatibilityCheckerADVerySmallTest extends MendelianCompatibilityCheckerTestBase {
 
  MendelianInheritanceChecker checker;
  List<GenotypeCalls> gcList;
- ImmutableMap<ModeOfInheritance, ImmutableList<GenotypeCalls>> result;
+ Map<ModeOfInheritance, List<GenotypeCalls>> result;
 
  @BeforeEach
  public void setUp() throws Exception {
- ImmutableList.Builder<PedPerson> individuals = new ImmutableList.Builder<PedPerson>();
- individuals.add(new PedPerson("ped", "I.1", "0", "0", Sex.MALE, Disease.UNAFFECTED)); // father
- individuals.add(new PedPerson("ped", "II.1", "I.1", "0", Sex.MALE, Disease.AFFECTED)); // son
- PedFileContents pedFileContents = new PedFileContents(new ImmutableList.Builder<String>().build(),
- individuals.build());
+ List<PedPerson> individuals = List.of(
+  new PedPerson("ped", "I.1", "0", "0", Sex.MALE, Disease.UNAFFECTED), // father
+  new PedPerson("ped", "II.1", "I.1", "0", Sex.MALE, Disease.AFFECTED)); // son
+ PedFileContents pedFileContents = new PedFileContents(List.of(),
+ individuals);
  this.pedigree = new Pedigree(pedFileContents, "ped");
 
- this.names = ImmutableList.of("I.1", "II.1");
+ this.names = List.of("I.1", "II.1");
 
  this.checker = new MendelianInheritanceChecker(this.pedigree);
 

diff --git a/...t/java/org/monarchinitiative/gregor/mendel/MendelianCompatibilityCheckerARLarge2Test.java b/...t/java/org/monarchinitiative/gregor/mendel/MendelianCompatibilityCheckerARLarge2Test.java
@@ -1,35 +1,36 @@
 package org.monarchinitiative.gregor.mendel;
 
-import com.google.common.collect.ImmutableList;
-import com.google.common.collect.ImmutableMap;
 import org.monarchinitiative.gregor.pedigree.*;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
+import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 
 public class MendelianCompatibilityCheckerARLarge2Test extends MendelianCompatibilityCheckerTestBase {
 
  MendelianInheritanceChecker checker;
  List<GenotypeCalls> gcList;
- ImmutableMap<ModeOfInheritance, ImmutableList<GenotypeCalls>> result;
+ Map<ModeOfInheritance, List<GenotypeCalls>> result;
 
  @BeforeEach
  public void setUp() throws Exception {
- ImmutableList.Builder<PedPerson> individuals = new ImmutableList.Builder<PedPerson>();
- individuals.add(new PedPerson("ped", "I.1", "0", "0", Sex.MALE, Disease.UNAFFECTED)); // grandgrandfather
- individuals.add(new PedPerson("ped", "I.2", "0", "0", Sex.FEMALE, Disease.UNAFFECTED)); // grandgrandmother
- individuals.add(new PedPerson("ped", "II.1", "I.1", "I.2", Sex.FEMALE, Disease.AFFECTED)); // parent1
- individuals.add(new PedPerson("ped", "II.2", "I.1", "I.2", Sex.MALE, Disease.UNAFFECTED)); // parent2
- individuals.add(new PedPerson("ped", "II.3", "0", "0", Sex.FEMALE, Disease.UNAFFECTED)); // parent3
- individuals.add(new PedPerson("ped", "III.1", "II.2", "II.3", Sex.MALE, Disease.AFFECTED)); // child1
- individuals.add(new PedPerson("ped", "III.2", "II.2", "II.3", Sex.FEMALE, Disease.UNAFFECTED)); // child2
- PedFileContents pedFileContents = new PedFileContents(new ImmutableList.Builder<String>().build(),
- individuals.build());
+ List<PedPerson> individuals = List.of(
+ new PedPerson("ped", "I.1", "0", "0", Sex.MALE, Disease.UNAFFECTED), // grandgrandfather
+ new PedPerson("ped", "I.2", "0", "0", Sex.FEMALE, Disease.UNAFFECTED), // grandgrandmother
+ new PedPerson("ped", "II.1", "I.1", "I.2", Sex.FEMALE, Disease.AFFECTED), // parent1
+ new PedPerson("ped", "II.2", "I.1", "I.2", Sex.MALE, Disease.UNAFFECTED), // parent2
+ new PedPerson("ped", "II.3", "0", "0", Sex.FEMALE, Disease.UNAFFECTED), // parent3
+ new PedPerson("ped", "III.1", "II.2", "II.3", Sex.MALE, Disease.AFFECTED), // child1
+ new PedPerson("ped", "III.2", "II.2", "II.3", Sex.FEMALE, Disease.UNAFFECTED) // child2
+ );
+ PedFileContents pedFileContents = new PedFileContents(List.of(),
+ individuals);
  this.pedigree = new Pedigree(pedFileContents, "ped");
 
- this.names = ImmutableList.of("I.1", "I.2", "II.1", "II.2", "II.3", "III.1", "III.2");
+ this.names = List.of("I.1", "I.2", "II.1", "II.2", "II.3", "III.1", "III.2");
 
  this.checker = new MendelianInheritanceChecker(this.pedigree);