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Merge pull request #240 from ebi-uniprot/2024_05
2024 05
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11 changes: 11 additions & 0 deletions
11
core-domain/src/main/java/org/uniprot/core/uniparc/SequenceFeatureLocation.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| package org.uniprot.core.uniparc; | ||
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| import java.io.Serializable; | ||
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| public interface SequenceFeatureLocation extends Serializable { | ||
| int getStart(); | ||
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| int getEnd(); | ||
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| String getAlignment(); | ||
| } |
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47 changes: 47 additions & 0 deletions
47
core-domain/src/main/java/org/uniprot/core/uniparc/impl/SequenceFeatureLocationBuilder.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| package org.uniprot.core.uniparc.impl; | ||
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| import org.uniprot.core.Builder; | ||
| import org.uniprot.core.uniparc.SequenceFeatureLocation; | ||
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| import javax.annotation.Nonnull; | ||
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| public class SequenceFeatureLocationBuilder implements Builder<SequenceFeatureLocation> { | ||
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| private int start; | ||
| private int end; | ||
| private String alignment; | ||
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| @Nonnull | ||
| @Override | ||
| public SequenceFeatureLocation build() { | ||
| return new SequenceFeatureLocationImpl(start,end,alignment); | ||
| } | ||
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| public @Nonnull SequenceFeatureLocationBuilder range(int start, int end) { | ||
| this.start = start; | ||
| this.end = end; | ||
| return this; | ||
| } | ||
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| public @Nonnull SequenceFeatureLocationBuilder start(int start) { | ||
| this.start = start; | ||
| return this; | ||
| } | ||
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| public @Nonnull SequenceFeatureLocationBuilder end(int end) { | ||
| this.end = end; | ||
| return this; | ||
| } | ||
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| public @Nonnull SequenceFeatureLocationBuilder alignment(String alignment) { | ||
| this.alignment = alignment; | ||
| return this; | ||
| } | ||
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| public static @Nonnull SequenceFeatureLocationBuilder from(@Nonnull SequenceFeatureLocation instance) { | ||
| return new SequenceFeatureLocationBuilder() | ||
| .start(instance.getStart()) | ||
| .end(instance.getEnd()) | ||
| .alignment(instance.getAlignment()); | ||
| } | ||
| } |
41 changes: 41 additions & 0 deletions
41
core-domain/src/main/java/org/uniprot/core/uniparc/impl/SequenceFeatureLocationImpl.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| package org.uniprot.core.uniparc.impl; | ||
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| import org.uniprot.core.Location; | ||
| import org.uniprot.core.uniparc.SequenceFeatureLocation; | ||
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| import java.util.Objects; | ||
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| public class SequenceFeatureLocationImpl extends Location implements SequenceFeatureLocation{ | ||
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| private static final long serialVersionUID = -4804406936471873484L; | ||
| private String alignment; | ||
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| SequenceFeatureLocationImpl(){ | ||
| super(0, 0); | ||
| } | ||
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| SequenceFeatureLocationImpl(int start, int end, String alignment) { | ||
| super(start, end); | ||
| this.alignment = alignment; | ||
| } | ||
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| @Override | ||
| public String getAlignment() { | ||
| return alignment; | ||
| } | ||
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| @Override | ||
| public boolean equals(Object o) { | ||
| if (this == o) return true; | ||
| if (o == null || getClass() != o.getClass()) return false; | ||
| if (!super.equals(o)) return false; | ||
| SequenceFeatureLocationImpl that = (SequenceFeatureLocationImpl) o; | ||
| return Objects.equals(alignment, that.alignment); | ||
| } | ||
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| @Override | ||
| public int hashCode() { | ||
| return Objects.hash(super.hashCode(), alignment); | ||
| } | ||
| } |
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55 changes: 55 additions & 0 deletions
55
...omain/src/test/java/org/uniprot/core/uniparc/impl/SequenceFeatureLocationBuilderTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| package org.uniprot.core.uniparc.impl; | ||
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| import org.junit.jupiter.api.Test; | ||
| import org.uniprot.core.Property; | ||
| import org.uniprot.core.uniparc.SequenceFeatureLocation; | ||
| import org.uniprot.core.uniparc.UniParcCrossReference; | ||
| import org.uniprot.core.uniparc.UniParcDatabase; | ||
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| import java.time.LocalDate; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
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| import static org.junit.jupiter.api.Assertions.*; | ||
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| class SequenceFeatureLocationBuilderTest { | ||
| @Test | ||
| void testStart() { | ||
| int start = 10; | ||
| SequenceFeatureLocation location = | ||
| new SequenceFeatureLocationBuilder().start(start).build(); | ||
| assertEquals(start, location.getStart()); | ||
| } | ||
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| @Test | ||
| void testEnd() { | ||
| int end = 20; | ||
| SequenceFeatureLocation location = | ||
| new SequenceFeatureLocationBuilder().end(end).build(); | ||
| assertEquals(end, location.getEnd()); | ||
| } | ||
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| @Test | ||
| void testRange() { | ||
| int start = 10; | ||
| int end = 20; | ||
| SequenceFeatureLocation location = | ||
| new SequenceFeatureLocationBuilder().range(start, end).build(); | ||
| assertEquals(start, location.getStart()); | ||
| assertEquals(end, location.getEnd()); | ||
| } | ||
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| @Test | ||
| void testAlignment() { | ||
| String alignment = "M55"; | ||
| SequenceFeatureLocation location = | ||
| new SequenceFeatureLocationBuilder().alignment(alignment).build(); | ||
| assertEquals(alignment, location.getAlignment()); | ||
| } | ||
| @Test | ||
| void testFromSequenceFeatureLocation() { | ||
| SequenceFeatureLocation location = new SequenceFeatureLocationImpl(10, 20, "VALUE"); | ||
| SequenceFeatureLocation fromLocation = SequenceFeatureLocationBuilder.from(location).build(); | ||
| assertEquals(location, fromLocation); | ||
| } | ||
| } |
30 changes: 30 additions & 0 deletions
30
core-domain/src/test/java/org/uniprot/core/uniparc/impl/SequenceFeatureLocationImplTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| package org.uniprot.core.uniparc.impl; | ||
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| import org.junit.jupiter.api.Test; | ||
| import org.uniprot.core.uniparc.SequenceFeatureLocation; | ||
| import org.uniprot.core.uniparc.UniParcCrossReference; | ||
| import org.uniprot.core.uniparc.UniParcDatabase; | ||
| import org.uniprot.core.uniprotkb.taxonomy.impl.OrganismBuilder; | ||
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| import java.time.LocalDate; | ||
| import java.util.Collections; | ||
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| import static org.junit.jupiter.api.Assertions.*; | ||
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| class SequenceFeatureLocationImplTest { | ||
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| @Test | ||
| void needDefaultConstructorForJsonDeserialization() { | ||
| SequenceFeatureLocation obj = new SequenceFeatureLocationImpl(); | ||
| assertNotNull(obj); | ||
| } | ||
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| @Test | ||
| void builderFrom_constructorImp_shouldCreate_equalObject() { | ||
| SequenceFeatureLocationImpl impl = | ||
| new SequenceFeatureLocationImpl(10,20, "component"); | ||
| SequenceFeatureLocation obj = SequenceFeatureLocationBuilder.from(impl).build(); | ||
| assertTrue(impl.equals(obj) && obj.equals(impl)); | ||
| assertEquals(impl.hashCode(), obj.hashCode()); | ||
| } | ||
| } |
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