Refactoring of class names as per discussions.

mmtf-common/src/main/java/org/rcsb/mmtf/dataholders/MmtfBean.java → mmtf-common/src/main/java/org/rcsb/mmtf/dataholders/MmtfEncodedStructure.java

@@ -11,7 +11,7 @@
  * @author Anthony Bradley
  */
 @JsonIgnoreProperties(ignoreUnknown = true)
-public class MmtfBean implements Serializable {
+public class MmtfEncodedStructure implements Serializable {
 
 
 	/** The number to divide coordinate int values by. */
@@ -147,7 +147,7 @@ public class MmtfBean implements Serializable {
 	private String releaseDate;
 
 	/** Constructor to set the default values for floats */
-	public MmtfBean() {
+	public MmtfEncodedStructure() {
 
 		/** The mmtf version. Set here. */
 		mmtfVersion = "0.1";

mmtf-common/src/main/java/org/rcsb/mmtf/sedeserializers/MmtfBeanSeDeMessagePackImpl.java

@@ -5,23 +5,23 @@
 import java.io.OutputStream;
 
 import org.msgpack.jackson.dataformat.MessagePackFactory;
-import org.rcsb.mmtf.dataholders.MmtfBean;
+import org.rcsb.mmtf.dataholders.MmtfEncodedStructure;
 
 import com.fasterxml.jackson.annotation.JsonInclude.Include;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 /**
- * A message pack implementation of the mmtf serializer / deserializer
+ * A message pack implementation of the mmtf serializer / deserializer.
  * @author Anthony Bradley
  *
  */
 public class MmtfBeanSeDeMessagePackImpl implements MmtfBeanSeDerializerInterface {
 
 	@Override
-	public MmtfBean deserialize(InputStream byteArray){
-		MmtfBean mmtfBean = null;
+	public MmtfEncodedStructure deserialize(InputStream byteArray){
+		MmtfEncodedStructure mmtfBean = null;
 		try {
-			mmtfBean = new ObjectMapper(new MessagePackFactory()).readValue(byteArray, MmtfBean.class);
+			mmtfBean = new ObjectMapper(new MessagePackFactory()).readValue(byteArray, MmtfEncodedStructure.class);
 		} catch (IOException e) {
 			// TODO Auto-generated catch block
 			e.printStackTrace();
@@ -30,7 +30,7 @@ public MmtfBean deserialize(InputStream byteArray){
 	}
 
 	@Override
-	public void serialize(MmtfBean object, OutputStream outputStream) {
+	public void serialize(MmtfEncodedStructure object, OutputStream outputStream) {
 		ObjectMapper objectMapper = new ObjectMapper(new MessagePackFactory());
 		objectMapper.setSerializationInclusion(Include.NON_NULL);
 		try {

mmtf-common/src/main/java/org/rcsb/mmtf/sedeserializers/MmtfBeanSeDerializerInterface.java

@@ -3,17 +3,27 @@
 import java.io.InputStream;
 import java.io.OutputStream;
 
-import org.rcsb.mmtf.dataholders.MmtfBean;
+import org.rcsb.mmtf.dataholders.MmtfEncodedStructure;
 
 /**
- * An interface to carry out serializing / deserializing to mmtfBean
+ * An interface to carry out serializing / deserializing to mmtfBean.
  * @author Anthony Bradley
  *
  */
 public interface MmtfBeanSeDerializerInterface {
 
-	public void serialize(MmtfBean mmtfBean, OutputStream outputStream);
+	/**
+	 * Serialize an mmtfBean to a generic output stream.
+	 * @param mmtfBean the compressed data
+	 * @param outputStream the ouput stream to write to
+	 */
+	public void serialize(MmtfEncodedStructure mmtfBean, OutputStream outputStream);
 
-	public MmtfBean deserialize(InputStream dataInputStream);
+	/**
+	 * Deserialize and input stream from an input stream.
+	 * @param dataInputStream the inputstream to deserialize
+	 * @return the compressed structure data.
+	 */
+	public MmtfEncodedStructure deserialize(InputStream dataInputStream);
 
 }

mmtf-common/src/test/java/org/rcsb/mmtf/dataholders/TestDataHolders.java

@@ -33,8 +33,8 @@ public void testBeans() throws IllegalAccessException, IllegalArgumentException,
 		PodamFactory factory = new PodamFactoryImpl();
 		// Tests if setters are set appropriately
 		ReflectionAssert.assertPropertiesNotNull("Some properties null.", 
-				factory.manufacturePojo(MmtfBean.class));
-		testData(MmtfBean.class, factory.manufacturePojo(MmtfBean.class));
+				factory.manufacturePojo(MmtfEncodedStructure.class));
+		testData(MmtfEncodedStructure.class, factory.manufacturePojo(MmtfEncodedStructure.class));
 
 		ReflectionAssert.assertPropertiesNotNull("Some properties null.", 
 				factory.manufacturePojo(BioAssemblyData.class));

mmtf-common/src/test/java/org/rcsb/mmtf/sedeserializers/TestMessagePack.java

@@ -6,7 +6,7 @@
 import java.io.ByteArrayOutputStream;
 
 import org.junit.Test;
-import org.rcsb.mmtf.dataholders.MmtfBean;
+import org.rcsb.mmtf.dataholders.MmtfEncodedStructure;
 
 import uk.co.jemos.podam.api.PodamFactory;
 import uk.co.jemos.podam.api.PodamFactoryImpl;
@@ -27,7 +27,7 @@ public void testDeserialize()  {
 		MmtfBeanSeDeMessagePackImpl mmtfBeanSeDeMessagePackImpl = new MmtfBeanSeDeMessagePackImpl();
 		byte[] source = new byte[] {(byte) (char) 129, (byte) (char)162, (byte) (char)100, (byte) (char)111, (byte) (char)1};
 		ByteArrayInputStream bis = new ByteArrayInputStream(source);
-		MmtfBean mmtfBean = mmtfBeanSeDeMessagePackImpl.deserialize(bis);
+		MmtfEncodedStructure mmtfBean = mmtfBeanSeDeMessagePackImpl.deserialize(bis);
 		assertNotNull(mmtfBean);
 	}
 
@@ -38,7 +38,7 @@ public void testDeserialize()  {
 	public void testSerialize() {
 		MmtfBeanSeDeMessagePackImpl mmtfBeanSeDeMessagePackImpl = new MmtfBeanSeDeMessagePackImpl();
 		PodamFactory factory = new PodamFactoryImpl();
-		MmtfBean mmtfBean = factory.manufacturePojo(MmtfBean.class);
+		MmtfEncodedStructure mmtfBean = factory.manufacturePojo(MmtfEncodedStructure.class);
 		ByteArrayOutputStream bos = new ByteArrayOutputStream();
 		mmtfBeanSeDeMessagePackImpl.serialize(mmtfBean, bos);
 		assertNotNull(bos.toByteArray());

mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DefaultDecoder.java

@@ -6,7 +6,7 @@
 import org.rcsb.mmtf.api.StructureDataInterface;
 import org.rcsb.mmtf.dataholders.BioAssemblyData;
 import org.rcsb.mmtf.dataholders.Entity;
-import org.rcsb.mmtf.dataholders.MmtfBean;
+import org.rcsb.mmtf.dataholders.MmtfEncodedStructure;
 import org.rcsb.mmtf.dataholders.PDBGroup;
 
 /**
@@ -20,38 +20,38 @@ public class DefaultDecoder implements StructureDataInterface {
 	 * Constructor for the default decoder.
 	 * @param inputData The input mmtfBean data to be decompressed.
 	 */
-	public DefaultDecoder(MmtfBean inputData) {
+	public DefaultDecoder(MmtfEncodedStructure inputData) {
 		groupList = ArrayConverters.convertFourByteToIntegers(inputData.getGroupTypeList());
 		// Decode the coordinate  and B-factor arrays.
 		cartnX = ArrayConverters.convertIntsToFloats(
 				ArrayDecoders.deltaDecode(
 						ArrayConverters.combineIntegers(
 								ArrayConverters.convertTwoByteToIntegers(inputData.getxCoordSmall()),
 								ArrayConverters.convertFourByteToIntegers(inputData.getxCoordBig()))),
-				MmtfBean.COORD_DIVIDER);
+				MmtfEncodedStructure.COORD_DIVIDER);
 		cartnY = ArrayConverters.convertIntsToFloats(
 				ArrayDecoders.deltaDecode(
 						ArrayConverters.combineIntegers(
 								ArrayConverters.convertTwoByteToIntegers(inputData.getyCoordSmall()),
 								ArrayConverters.convertFourByteToIntegers(inputData.getyCoordBig()))),
-				MmtfBean.COORD_DIVIDER);
+				MmtfEncodedStructure.COORD_DIVIDER);
 		cartnZ = ArrayConverters.convertIntsToFloats(
 				ArrayDecoders.deltaDecode(
 						ArrayConverters.combineIntegers(
 								ArrayConverters.convertTwoByteToIntegers(inputData.getzCoordSmall()),
 								ArrayConverters.convertFourByteToIntegers(inputData.getzCoordBig()))),
-				MmtfBean.COORD_DIVIDER);
+				MmtfEncodedStructure.COORD_DIVIDER);
 		bFactor = ArrayConverters.convertIntsToFloats(
 				ArrayDecoders.deltaDecode(
 						ArrayConverters.combineIntegers(
 								ArrayConverters.convertTwoByteToIntegers(inputData.getbFactorSmall()),
 								ArrayConverters.convertFourByteToIntegers(inputData.getbFactorBig()))),
-				MmtfBean.OCCUPANCY_BFACTOR_DIVIDER);
+				MmtfEncodedStructure.OCCUPANCY_BFACTOR_DIVIDER);
 		// Run length decode the occupancy array
 		occupancy = ArrayConverters.convertIntsToFloats(
 				ArrayDecoders.runlengthDecode(
 						ArrayConverters.convertFourByteToIntegers(inputData.getOccupancyList())), 
-				MmtfBean.OCCUPANCY_BFACTOR_DIVIDER);
+				MmtfEncodedStructure.OCCUPANCY_BFACTOR_DIVIDER);
 		// Run length and delta 
 		atomId = ArrayDecoders.deltaDecode(
 				ArrayDecoders.runlengthDecode(
@@ -340,23 +340,23 @@ public int getNumAtoms() {
 	@Override
 	public float getRfree() {
 		if (rFree==null|| rFree ==0.0f) {
-			return MmtfBean.UNAVAILABLE_R_VALUE;
+			return MmtfEncodedStructure.UNAVAILABLE_R_VALUE;
 		}
 		return rFree;
 	}
 
 	@Override
 	public float getResolution() {
 		if (resolution==null || resolution==0.0f) {
-			return MmtfBean.UNAVAILABLE_RESOLUTION_VALUE;
+			return MmtfEncodedStructure.UNAVAILABLE_RESOLUTION_VALUE;
 		}
 		return resolution;
 	}
 
 	@Override
 	public float getRwork() {
 		if (rWork==null|| rWork ==0.0f) {
-			return MmtfBean.UNAVAILABLE_R_VALUE;
+			return MmtfEncodedStructure.UNAVAILABLE_R_VALUE;
 		}
 		return rWork;
 	}

mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/ReaderUtils.java

@@ -9,7 +9,7 @@
 import java.nio.file.Path;
 import java.util.zip.GZIPInputStream;
 
-import org.rcsb.mmtf.dataholders.MmtfBean;
+import org.rcsb.mmtf.dataholders.MmtfEncodedStructure;
 import org.rcsb.mmtf.sedeserializers.MmtfBeanSeDeMessagePackImpl;
 import org.rcsb.mmtf.utils.CodecUtils;
 
@@ -30,7 +30,7 @@ public class ReaderUtils {
 	 * @return the MMTFBean of the deserialized data
 	 * @throws IOException if the data cannot be read from the URL
 	 */
-	public static MmtfBean getDataFromUrl(String pdbCode) throws IOException {	
+	public static MmtfEncodedStructure getDataFromUrl(String pdbCode) throws IOException {	
 		// Get these as an inputstream
 		ByteArrayOutputStream baos = new ByteArrayOutputStream();
 		InputStream is = null;
@@ -90,7 +90,7 @@ public static byte[] deflateGzip(byte[] inputBytes) throws IOException {
 	 * @return the deserialized mmtfBean
 	 * @throws IOException an error reading the file 
 	 */
-	public static MmtfBean getDataFromFile(Path filePath) throws IOException {
+	public static MmtfEncodedStructure getDataFromFile(Path filePath) throws IOException {
 		// Now return the gzip deflated and deserialized byte array
 		MmtfBeanSeDeMessagePackImpl mmtfBeanSeDeMessagePackImpl = new MmtfBeanSeDeMessagePackImpl();
 		return mmtfBeanSeDeMessagePackImpl.deserialize(new ByteArrayInputStream(readFile(filePath)));

mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DecoderToReader.java → mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/StructureDataToAdapter.java

@@ -9,7 +9,7 @@
  * @author Anthony Bradley
  *
  */
-public class DecoderToReader {
+public class StructureDataToAdapter {
 
 	/** The struct inflator. */
 	private StructureAdapterInterface structInflator;
@@ -30,7 +30,7 @@ public class DecoderToReader {
 	 * @param inputApi the interface to the decoded data
 	 * @param inputInflator the interface to put the data into the client object
 	 */
-	public DecoderToReader(StructureDataInterface inputApi, StructureAdapterInterface inputInflator){
+	public StructureDataToAdapter(StructureDataInterface inputApi, StructureAdapterInterface inputInflator){
 		// Set the counters to zero
 		modelCounter = 0;
 		chainCounter = 0;

mmtf-decoder/src/test/java/org/rcsb/mmtf/decoder/TestDefaultDecoder.java

@@ -9,7 +9,7 @@
 import java.lang.reflect.InvocationTargetException;
 
 import org.junit.Test;
-import org.rcsb.mmtf.dataholders.MmtfBean;
+import org.rcsb.mmtf.dataholders.MmtfEncodedStructure;
 import org.unitils.reflectionassert.ReflectionAssert;
 
 import uk.co.jemos.podam.api.PodamFactory;
@@ -33,11 +33,11 @@ public class TestDefaultDecoder {
 	@Test
 	public void testDecodeAllFields() throws IOException, IntrospectionException, IllegalAccessException, IllegalArgumentException, InvocationTargetException {
 		PodamFactory factory = new PodamFactoryImpl();
-		MmtfBean mmtfBean = factory.manufacturePojo(MmtfBean.class);
+		MmtfEncodedStructure mmtfBean = factory.manufacturePojo(MmtfEncodedStructure.class);
 		DefaultDecoder defaultDecoder = new DefaultDecoder(mmtfBean);
 		ReflectionAssert.assertPropertiesNotNull("Some properties null after decoding", defaultDecoder);
 		for(PropertyDescriptor propertyDescriptor : 
-			Introspector.getBeanInfo(MmtfBean.class).getPropertyDescriptors()){
+			Introspector.getBeanInfo(MmtfEncodedStructure.class).getPropertyDescriptors()){
 			assertNotNull(propertyDescriptor.getReadMethod().invoke(mmtfBean));
 		}
 		// Check the decoder has been populated to
@@ -56,7 +56,7 @@ public void testDecodeAllFields() throws IOException, IntrospectionException, Il
 	@Test
 	public void testReader() {
 		DummyApiImpl dummyApiImpl = new DummyApiImpl();
-		new DecoderToReader(dummyApiImpl, new DummyTransferImpl());
+		new StructureDataToAdapter(dummyApiImpl, new DummyTransferImpl());
 	}
 
 }

mmtf-decoder/src/test/java/org/rcsb/mmtf/decoder/TestReaderUtils.java

@@ -1,7 +1,7 @@
 package org.rcsb.mmtf.decoder;
 
 import org.junit.Test;
-import org.rcsb.mmtf.dataholders.MmtfBean;
+import org.rcsb.mmtf.dataholders.MmtfEncodedStructure;
 
 import static org.junit.Assert.assertArrayEquals;
 import static org.junit.Assert.assertEquals;
@@ -81,7 +81,7 @@ public void testGzipDecompressText() throws IOException {
 	@Test 
 	public void testReadFromFile() throws IOException {
 		ClassLoader classLoader = getClass().getClassLoader();
-		MmtfBean mmtfBean = ReaderUtils.getDataFromFile(Paths.get(classLoader.getResource("mmtf/4cup.mmtf").getFile()));
+		MmtfEncodedStructure mmtfBean = ReaderUtils.getDataFromFile(Paths.get(classLoader.getResource("mmtf/4cup.mmtf").getFile()));
 		assertNotEquals(mmtfBean, null);
 		assertEquals(mmtfBean.getDepositionDate(), "2014-03-21");
 	}

mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/WriterToEncoder.java → mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/AdapterToStructureData.java

@@ -17,7 +17,7 @@
  * @author Anthony Bradley
  *
  */
-public class WriterToEncoder implements StructureDataInterface, StructureAdapterInterface {
+public class AdapterToStructureData implements StructureDataInterface, StructureAdapterInterface {
 
 
 	/** The X coordinates */
@@ -29,10 +29,10 @@ public class WriterToEncoder implements StructureDataInterface, StructureAdapter
 	/** The Z coordinates */
 	private float[] cartnZ;
 
-	/** The X coordinates */
+	/** The B factors */
 	private float[] bFactor;
 
-	/** The Y coordinates */
+	/** The occupancy */
 	private float[] occupancy;
 
 	/** The atom id. */