Calling an alignment in a test

Hi,

I'm trying to do some testing and that involves calling an alignment. The same code works in non-test mode.

Also I have other tests in this same test class that work too and note I have the

TestGeneious.initialize();

So it's just the alignment.

Calling an alignment in a test

public List<AnnotatedPluginDocument> align(DefaultNucleotideSequence sequenceA, DefaultNucleotideSequence sequenceB) {
    List<AnnotatedPluginDocument> documentsToAlign = Stream.of(DocumentUtilities.createAnnotatedPluginDocument(sequenceA), DocumentUtilities.createAnnotatedPluginDocument(sequenceB)).collect(Collectors.toList());
    DocumentOperation alignmentOperation = PluginUtilities.getCategoryOperation(GeneiousActionOptions.Category.Alignment);
    List<AnnotatedPluginDocument> alignment = null;
    try {
        Options alignmentOptions = alignmentOperation.getOptions(documentsToAlign); // Get the options provided by the alignment operation.
        alignmentOptions.setValue("operation", "com.biomatters.plugins.translationalign.TranslationAlignmentOperation"); //Translation.
        alignmentOptions.setValue("com.biomatters.plugins.translationalign.TranslationAlignmentOperation.alignmentOptions.trans_operation", "Clustal_Alignment_PROTEIN_");
        alignment = alignmentOperation.performOperation(documentsToAlign, null, alignmentOptions);
        DefaultAlignmentDocument firstAlignedSequence = (DefaultAlignmentDocument) alignment.get(0).getDocumentOrCrash();
        List<SequenceDocument> sequencesInImmutableList = firstAlignedSequence.getSequencesInImmutableList();
        sequencesInImmutableList.forEach(System.out::println);
    } catch (DocumentOperationException e) {
        e.printStackTrace();
    }
    return alignment;

It fails with:

java.lang.RuntimeException: Something needs to have properly initialized the category options

at com.biomatters.geneious.publicapi.plugin.PluginUtilitiesImplementation.getCategoryOperation(PluginUtilitiesImplementation.java:167)
at com.biomatters.geneious.publicapi.plugin.PluginUtilities.getCategoryOperation(PluginUtilities.java:92)
at TestOpt.align(TestOpt.java:75)
at TestOpt.testAlignAndCompare(TestOpt.java:65)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:389)
at org.junit.jupiter.engine.execution.ExecutableInvoker.invoke(ExecutableInvoker.java:115)
at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.lambda$invokeTestMethod$6(TestMethodTestDescriptor.java:167)
at org.junit.jupiter.engine.execution.ThrowableCollector.execute(ThrowableCollector.java:40)
at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:163)
at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:110)
at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:57)
at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.lambda$execute$3(HierarchicalTestExecutor.java:83)
at org.junit.platform.engine.support.hierarchical.SingleTestExecutor.executeSafely(SingleTestExecutor.java:66)
at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:77)
at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.lambda$null$2(HierarchicalTestExecutor.java:92)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.lambda$execute$3(HierarchicalTestExecutor.java:92)
at org.junit.platform.engine.support.hierarchical.SingleTestExecutor.executeSafely(SingleTestExecutor.java:66)
at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:77)
at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.lambda$null$2(HierarchicalTestExecutor.java:92)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.lambda$execute$3(HierarchicalTestExecutor.java:92)
at org.junit.platform.engine.support.hierarchical.SingleTestExecutor.executeSafely(SingleTestExecutor.java:66)
at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:77)
at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:51)
at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:43)
at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:170)
at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:154)
at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:90)
at com.intellij.junit5.JUnit5IdeaTestRunner.startRunnerWithArgs(JUnit5IdeaTestRunner.java:62)
at com.intellij.rt.execution.junit.IdeaTestRunner$Repeater.startRunnerWithArgs(IdeaTestRunner.java:47)
at com.intellij.rt.execution.junit.JUnitStarter.prepareStreamsAndStart(JUnitStarter.java:242)
at com.intellij.rt.execution.junit.JUnitStarter.main(JUnitStarter.java:70)