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Merge pull request #21 from rcsb/v0.2.2
Version 0.2.2 of mmtf-java
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169 changes: 169 additions & 0 deletions
169
mmtf-codec/src/test/java/org/rcsb/mmtf/encoder/TestEncoderUtils.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,169 @@ | ||
| package org.rcsb.mmtf.encoder; | ||
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| import org.junit.Test; | ||
| import static org.junit.Assert.*; | ||
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| import java.io.IOException; | ||
| import java.nio.file.Path; | ||
| import java.nio.file.Paths; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
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| import org.rcsb.mmtf.api.StructureAdapterInterface; | ||
| import org.rcsb.mmtf.api.StructureDataInterface; | ||
| import org.rcsb.mmtf.codec.CharCodecs; | ||
| import org.rcsb.mmtf.codec.FloatCodecs; | ||
| import org.rcsb.mmtf.codec.IntCodecs; | ||
| import org.rcsb.mmtf.codec.OptionParser; | ||
| import org.rcsb.mmtf.codec.StringCodecs; | ||
| import org.rcsb.mmtf.dataholders.BioAssemblyData; | ||
| import org.rcsb.mmtf.dataholders.BioAssemblyTransformation; | ||
| import org.rcsb.mmtf.dataholders.Entity; | ||
| import org.rcsb.mmtf.dataholders.Group; | ||
| import org.rcsb.mmtf.decoder.GenericDecoder; | ||
| import org.rcsb.mmtf.decoder.ReaderUtils; | ||
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| /** | ||
| * Tests for the {@link EncoderUtils} class of static methods. | ||
| * @author Anthony Bradley | ||
| * | ||
| */ | ||
| public class TestEncoderUtils { | ||
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| /** | ||
| * Test that all of the codecs can handle and empty input array. | ||
| */ | ||
| @Test | ||
| public void testEmptyArrs() { | ||
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| for (FloatCodecs inputCodec : FloatCodecs.values()) { | ||
| testOutput(EncoderUtils.encodeByteArr(inputCodec, new float[] {}, 0), | ||
| inputCodec.getCodecId()); | ||
| } | ||
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| for (CharCodecs inputCodec : CharCodecs.values()) { | ||
| testOutput(EncoderUtils.encodeByteArr(inputCodec, new char[] {}, 0), | ||
| inputCodec.getCodecId()); | ||
| } | ||
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| for (IntCodecs inputCodec : IntCodecs.values()) { | ||
| testOutput(EncoderUtils.encodeByteArr(inputCodec, new int[] {}, 0), | ||
| inputCodec.getCodecId()); | ||
| } | ||
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| for (StringCodecs inputCodec : StringCodecs.values()) { | ||
| testOutput(EncoderUtils.encodeByteArr(inputCodec, new String[] {}, 0), | ||
| inputCodec.getCodecId()); | ||
| } | ||
| } | ||
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| /** | ||
| * Test that Bioassemblies can be generated correctly form a {@link StructureDataInterface} | ||
| * to a {@link StructureAdapterInterface} | ||
| */ | ||
| @Test | ||
| public void testGenerateBioassemblies() { | ||
| List<BioAssemblyData> bioAssemblyData = new ArrayList<>(); | ||
| BioAssemblyData bioAssemblyOne = new BioAssemblyData("1"); | ||
| bioAssemblyData.add(bioAssemblyOne); | ||
| List<BioAssemblyTransformation> bioAssemblyOneTransforms = new ArrayList<>(); | ||
| BioAssemblyTransformation bioassOneTransOne = new BioAssemblyTransformation(); | ||
| bioassOneTransOne.setChainIndexList(new int[]{1,2,3,4}); | ||
| bioassOneTransOne.setMatrix(new double[]{1.0,2.0,3.0,4.0}); | ||
| bioAssemblyOneTransforms.add(bioassOneTransOne); | ||
| BioAssemblyTransformation bioassOneTransTwo = new BioAssemblyTransformation(); | ||
| bioassOneTransTwo.setChainIndexList(new int[]{5,7,11}); | ||
| bioassOneTransTwo.setMatrix(new double[]{5.0,2.0,8.0,4.0}); | ||
| bioAssemblyOneTransforms.add(bioassOneTransTwo); | ||
| bioAssemblyOne.setTransformList(bioAssemblyOneTransforms); | ||
| AdapterToStructureData adapterToStructureData = new AdapterToStructureData(); | ||
| adapterToStructureData.initStructure(0,0,0,0,0,"DUMMY"); | ||
| for (int i=0; i< bioAssemblyData.size(); i++){ | ||
| for (int j=0; j< bioAssemblyData.get(i).getTransformList().size();j++) | ||
| adapterToStructureData.setBioAssemblyTrans(i, | ||
| bioAssemblyData.get(i).getTransformList().get(j).getChainIndexList(), | ||
| bioAssemblyData.get(i).getTransformList().get(j).getMatrix(), | ||
| bioAssemblyData.get(i).getName()); | ||
| } | ||
| List<BioAssemblyData> generateBioass = EncoderUtils.generateBioassemblies(adapterToStructureData); | ||
| assertEquals(bioAssemblyData.get(0).getName(), generateBioass.get(0).getName()); | ||
| assertArrayEquals(bioAssemblyData.get(0).getTransformList().get(0).getChainIndexList(), | ||
| generateBioass.get(0).getTransformList().get(0).getChainIndexList()); | ||
| assertArrayEquals(bioAssemblyData.get(0).getTransformList().get(0).getMatrix(), | ||
| generateBioass.get(0).getTransformList().get(0).getMatrix(),0.0); | ||
| } | ||
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| /** | ||
| * Test that the entity type can be retrieved from a chain index | ||
| */ | ||
| @Test | ||
| public void testGetEntityType() { | ||
| StructureDataInterface structureDataInterface = getDefaultFullData(); | ||
| assertEquals(EncoderUtils.getTypeFromChainId(structureDataInterface, 0),"polymer"); | ||
| assertEquals(EncoderUtils.getTypeFromChainId(structureDataInterface, 1),"non-polymer"); | ||
| assertEquals(EncoderUtils.getTypeFromChainId(structureDataInterface, 2),"non-polymer"); | ||
| assertEquals(EncoderUtils.getTypeFromChainId(structureDataInterface, 3),"non-polymer"); | ||
| assertEquals(EncoderUtils.getTypeFromChainId(structureDataInterface, 4),"non-polymer"); | ||
| assertEquals(EncoderUtils.getTypeFromChainId(structureDataInterface, 5),"water"); | ||
| } | ||
|
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| /** | ||
| * Test that the entityList can be generated correctly. | ||
| */ | ||
| @Test | ||
| public void testGenerateEntityList() { | ||
| StructureDataInterface structureDataInterface = getDefaultFullData(); | ||
| Entity[] entities = EncoderUtils.generateEntityList(structureDataInterface); | ||
| assertEquals(entities.length, 4); | ||
| assertArrayEquals(entities[0].getChainIndexList(), new int[] {0}); | ||
| assertArrayEquals(entities[1].getChainIndexList(), new int[] {1}); | ||
| assertArrayEquals(entities[2].getChainIndexList(), new int[] {2,3,4}); | ||
| assertArrayEquals(entities[3].getChainIndexList(), new int[] {5}); | ||
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| assertEquals(entities[0].getDescription(),"BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2B"); | ||
| assertEquals(entities[1].getDescription(),"4-FLUOROBENZAMIDOXIME"); | ||
| assertEquals(entities[2].getDescription(),"METHANOL"); | ||
| assertEquals(entities[3].getDescription(),"water"); | ||
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| assertEquals(entities[0].getSequence(),"SMSVKKPKRDDSKDLALCSMILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEKKWTDTFKVS"); | ||
| assertEquals(entities[1].getSequence(),""); | ||
| assertEquals(entities[2].getSequence(),""); | ||
| assertEquals(entities[3].getSequence(),""); | ||
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| assertEquals(entities[0].getType(),"polymer"); | ||
| assertEquals(entities[1].getType(),"non-polymer"); | ||
| assertEquals(entities[2].getType(),"non-polymer"); | ||
| assertEquals(entities[3].getType(),"water"); | ||
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| } | ||
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| /** | ||
| * Test that the groupList can be generated correctly | ||
| */ | ||
| @Test | ||
| public void testGenerateGroupMap() { | ||
| StructureDataInterface structureDataInterface = getDefaultFullData(); | ||
| Group[] groupList = EncoderUtils.generateGroupList(structureDataInterface); | ||
| assertEquals(groupList.length, 29); | ||
| } | ||
|
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| /** | ||
| * Get the default data for the full format. | ||
| * @return a {@link StructureDataInterface} for the full data. | ||
| */ | ||
| private StructureDataInterface getDefaultFullData() { | ||
| ClassLoader classLoader = getClass().getClassLoader(); | ||
| Path inFile = Paths.get(classLoader.getResource("mmtf/4cup.mmtf").getFile()); | ||
| try { | ||
| return new GenericDecoder(ReaderUtils.getDataFromFile(inFile)); | ||
| } catch (IOException e) { | ||
| e.printStackTrace(); | ||
| throw new RuntimeException(); | ||
| } | ||
| } | ||
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| private void testOutput(byte[] encodeByteArr, int codecId) { | ||
| assertArrayEquals(encodeByteArr, new OptionParser(codecId, 0, 0).getHeader()); | ||
| } | ||
| } |
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