Update to DecoderToReader and downstream refactoring. As per Jose's s…

…uggestions.

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

@@ -1,8 +1,5 @@
 package org.rcsb.mmtf.decoder;
 
-import java.util.HashSet;
-import java.util.Set;
-
 import org.rcsb.mmtf.api.StructureDataInterface;
 import org.rcsb.mmtf.api.StructureAdapterInterface;
 
@@ -21,19 +18,25 @@ public class DecoderToReader {
 	private StructureDataInterface dataApi;
 
 	// Intialises the counters.
-	private int modelCounter = 0;
-	private int chainCounter = 0;
-	private int groupCounter = 0;
-	private int atomCounter = 0;
-	private int currentAtomIndex = 0;
-	private Set<String> chainIdSet;
+	private int modelCounter;
+	private int chainCounter;
+	private int groupCounter;
+	private int atomInGroupCounter;
+	private int atomInStructureCounter;
+
 
 	/**
 	 * Passes data from the data interface to the inflator interface.
 	 * @param inputApi the interface to the decoded data
 	 * @param inputInflator the interface to put the data into the client object
 	 */
-	public void read(StructureDataInterface inputApi, StructureAdapterInterface inputInflator){
+	public DecoderToReader(StructureDataInterface inputApi, StructureAdapterInterface inputInflator){
+		// Set the counters to zero
+		modelCounter = 0;
+		chainCounter = 0;
+		groupCounter = 0;
+		atomInGroupCounter = 0;
+		atomInStructureCounter = 0;
 		// Set the api and the inflator
 		dataApi = inputApi;
 		structInflator = inputInflator;
@@ -55,15 +58,13 @@ public void read(StructureDataInterface inputApi, StructureAdapterInterface inpu
 		// Now do any required cleanup
 		structInflator.finalizeStructure();
 	}
-	
+
 	/**
 	 * Add the main atomic information to the data model
 	 */
 	private final void addAtomicInformation() {
 		for (int modelChains: dataApi.getChainsPerModel()) {
 			structInflator.setModelInfo(modelCounter, modelChains);
-			// A list to check if we need to set or update the chains
-			chainIdSet = new HashSet<>();
 			int totChainsThisModel = chainCounter + modelChains;
 			int lastChainCounter = chainCounter;
 			for (int chainIndex = lastChainCounter; chainIndex < totChainsThisModel;  chainIndex++) {
@@ -83,12 +84,7 @@ private void addOrUpdateChainInfo(int chainIndex) {
 		String currentChainName = dataApi.getChainNames()[chainIndex];
 		int groupsThisChain = dataApi.getGroupsPerChain()[chainIndex];
 		// If we've already seen this chain -> just update it
-		if (chainIdSet.contains(currentChainId)) {
-			structInflator.setChainInfo(currentChainId, currentChainName, groupsThisChain);
-		} else {
-			structInflator.setChainInfo(currentChainId, currentChainName, groupsThisChain);
-			chainIdSet.add(currentChainId);
-		}
+		structInflator.setChainInfo(currentChainId, currentChainName, groupsThisChain);
 		int nextInd = groupCounter + groupsThisChain;
 		int lastGroupCount = groupCounter;
 		// Now iteratr over the group
@@ -115,13 +111,13 @@ private int addGroup(int currentGroupIndex) {
 				dataApi.getGroupChemCompType(groupInd), atomCount, dataApi.getNumBonds(), dataApi.getGroupSingleLetterCode(groupInd),
 				dataApi.getGroupSequenceIndices()[currentGroupIndex], dataApi.getSecStructList()[currentGroupIndex]);
 		// A counter for the atom information
-		atomCounter = 0;
+		atomInGroupCounter = 0;
 		// Now read the next atoms
 		for (int i = 0; i < atomCount; i++) {
-			addAtomData(dataApi.getGroupAtomNames(groupInd), dataApi.getGroupElementNames(groupInd), dataApi.getGroupAtomCharges(groupInd), currentAtomIndex);  
-			currentAtomIndex++;
+			addAtomData(dataApi.getGroupAtomNames(groupInd), dataApi.getGroupElementNames(groupInd), dataApi.getGroupAtomCharges(groupInd), atomInStructureCounter);  
+			atomInStructureCounter++;
 			// Now increment the atom counter for this group
-			atomCounter++;
+			atomInGroupCounter++;
 		}
 		addGroupBonds(dataApi.getGroupBondIndices(groupInd), dataApi.getGroupBondOrders(groupInd));
 		return atomCount;
@@ -137,9 +133,9 @@ private int addGroup(int currentGroupIndex) {
 	private void addAtomData(String[] atomNames, String[] elementNames, int[] atomCharges, 
 			int currentAtomIndex) {
 		// Now get all the relevant atom level information here
-		String atomName = atomNames[atomCounter];
-		String element = elementNames[atomCounter];
-		int charge = atomCharges[atomCounter];
+		String atomName = atomNames[atomInGroupCounter];
+		String element = elementNames[atomInGroupCounter];
+		int charge = atomCharges[atomInGroupCounter];
 		char alternativeLocationId = dataApi.getAltLocIds()[currentAtomIndex];
 		int serialNumber = dataApi.getAtomIds()[currentAtomIndex];
 		float x = dataApi.getxCoords()[currentAtomIndex];

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

@@ -10,6 +10,7 @@
  */
 public class DecoderUtils {
 
+
 	/**
 	 * Parses the bioassembly data and inputs it to the structure inflator
 	 * @param dataApi the interface to the decoded data

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

@@ -111,8 +111,7 @@ public static byte[] deflateGzip(byte[] inputBytes){
 	 */
 	public static MmtfBean getDataFromFile(String filePath) throws IOException {
 		// Now return the gzip deflated and deserialized byte array
-		MessagePackDeserializer messagePackDeserializer = new MessagePackDeserializer();
-		return messagePackDeserializer.deserialize(readFile(filePath));
+		return new MessagePackDeserializer().deserialize(readFile(filePath));
 	}
 
 	/**

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

@@ -9,7 +9,6 @@
 import java.lang.reflect.InvocationTargetException;
 
 import org.junit.Test;
-import org.rcsb.mmtf.api.StructureAdapterInterface;
 import org.rcsb.mmtf.dataholders.MmtfBean;
 import org.unitils.reflectionassert.ReflectionAssert;
 
@@ -57,9 +56,7 @@ public void testDecodeAllFields() throws IOException, IntrospectionException, Il
 	@Test
 	public void testReader() {
 		DummyApiImpl dummyApiImpl = new DummyApiImpl();
-		DecoderToReader decoderToReader = new DecoderToReader();
-		StructureAdapterInterface inputInflator = new DummyTransferImpl();
-		decoderToReader.read(dummyApiImpl, inputInflator);
+		new DecoderToReader(dummyApiImpl, new DummyTransferImpl());
 	}
 
 }

mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/WriterUtils.java

@@ -3,6 +3,7 @@
 import java.io.FileOutputStream;
 import java.io.IOException;
 
+import org.rcsb.mmtf.api.StructureDataInterface;
 import org.rcsb.mmtf.serializers.MessagePackSerializer;
 
 /**
@@ -18,7 +19,7 @@ public class WriterUtils {
 	 * @param path the full path to write to
 	 * @throws IOException an error related to byte array transfers
 	 */
-	public static void writeDataToFile(WriterToEncoder writerToEncoder, String path) throws IOException {
+	public static void writeDataToFile(StructureDataInterface writerToEncoder, String path) throws IOException {
 		byte[] byteArray = getDataAsByteArr(writerToEncoder);
 		FileOutputStream fos = new FileOutputStream(path);
 		fos.write(byteArray);
@@ -32,7 +33,7 @@ public static void writeDataToFile(WriterToEncoder writerToEncoder, String path)
 	 * @return a byte array of the data
 	 * @throws IOException an error related to byte array transfers
 	 */
-	public static byte[] getDataAsByteArr(WriterToEncoder writerToEncoder) throws IOException {
+	public static byte[] getDataAsByteArr(StructureDataInterface writerToEncoder) throws IOException {
 		MessagePackSerializer messagePackSerializer = new MessagePackSerializer();
 		// Get to bean
 		DefaultEncoder getToBean = new DefaultEncoder(writerToEncoder);