Fixed issues around reduced format

README.md

@@ -29,7 +29,7 @@ Quick getting started.
 
 1) Get the data for a PDB structure and print the number of chains:
 ```java
-StructureDataInterface dataInterface = new GenericDecoder(ReaderUtils.getDataFromUrl("4cup"));
+StructureDataInterface dataInterface = new GenericDecoder(ReaderUtils.getDataFromUrl("4CUP"));
 System.out.println("PDB Code: "+dataInterface.getStructureId()+" has "+dataInterface.getNumChains()+" chains");
 ```
 

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

@@ -66,12 +66,6 @@ public static void addXtalographicInfo(StructureDataInterface dataApi, Structure
 	 */
 	public static void addEntityInfo(StructureDataInterface dataApi, StructureAdapterInterface structInflator) {
 		for (int i=0; i<dataApi.getNumEntities(); i++) {
-			String[] chainIdList = new String[dataApi.getEntityChainIndexList(i).length];
-			int counter = 0;
-			for (int chainInd : dataApi.getEntityChainIndexList(i)) {
-				chainIdList[counter] = dataApi.getChainIds()[chainInd];
-				counter++;
-			}
 			structInflator.setEntityInfo(dataApi.getEntityChainIndexList(i), dataApi.getEntitySequence(i), dataApi.getEntityDescription(i), dataApi.getEntityType(i));
 		}			
 	}

mmtf-codec/src/main/java/org/rcsb/mmtf/decoder/GenericDecoder.java

@@ -1,5 +1,6 @@
 package org.rcsb.mmtf.decoder;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -18,7 +19,8 @@
  * @author Anthony Bradley
  *
  */
-public class GenericDecoder  implements StructureDataInterface {
+public class GenericDecoder  implements StructureDataInterface, Serializable {
+	private static final long serialVersionUID = 1109812420718081496L;
 
 	/**
 	 * Constructor for the default decoder.

mmtf-codec/src/main/java/org/rcsb/mmtf/decoder/StructureDataToAdapter.java

@@ -1,14 +1,18 @@
 package org.rcsb.mmtf.decoder;
 
 import org.rcsb.mmtf.api.StructureDataInterface;
+
+import java.io.Serializable;
+
 import org.rcsb.mmtf.api.StructureAdapterInterface;
 
 /**
  * Pass data from a {@link StructureDataInterface} into a {@link StructureAdapterInterface}.
  * @author Anthony Bradley
  *
  */
-public class StructureDataToAdapter {
+public class StructureDataToAdapter implements Serializable {
+	private static final long serialVersionUID = 1304850018382353781L;
 
 	/** The struct inflator. */
 	private StructureAdapterInterface structInflator;

mmtf-codec/src/main/java/org/rcsb/mmtf/encoder/AdapterToStructureData.java

@@ -89,7 +89,7 @@ public class AdapterToStructureData implements StructureDataInterface, Structure
 	/** The mmtf version */
 	private String mmtfVersion = MmtfStructure.VERSION;
 
-	/** The mmtf prodcuer */
+	/** The mmtf producer */
 	private String mmtfProducer = "UNKNOWN";
 
 	/** The list of entities in this structure. */
@@ -139,14 +139,15 @@ public class AdapterToStructureData implements StructureDataInterface, Structure
 	private int modelIndex = 0;
 	/** Add the atom information for the current group */
 	private Group pdbGroup;
-	/** A List for Entities as the number of entities is not defined*/
-	private List<Entity> entities;
 	/** The total number of bonds in the structure */
 	private int totalNumBonds;
 	/** The list of groups */
 	private List<Group> pdbGroupList;
 	/** The NCS operation matrix list */
 	private double[][] ncsOperMatrixList;
+
+	/** Temporary list of entities */
+	private transient List<Entity> entities;
 
 
 	@Override
@@ -413,48 +414,53 @@ public String getDepositionDate() {
 	public void initStructure(int totalNumBonds, int totalNumAtoms, int totalNumGroups, 
 			int totalNumChains, int totalNumModels, String structureId) {
 		this.totalNumBonds = totalNumBonds;
-		// Intitialise the bond level info
+		// Initialize the bond level info
 		interGroupBondIndices = new ArrayList<>();
 		interGroupBondOrders = new ArrayList<>();
-		// Intitialise the atom level arrays
+		// Initialize the atom level arrays
 		cartnX = new float[totalNumAtoms];
 		cartnY= new float[totalNumAtoms];
 		cartnZ = new float[totalNumAtoms];
 		occupancy = new float[totalNumAtoms];
 		bFactor = new float[totalNumAtoms];
 		atomId = new int[totalNumAtoms];	
 		altId = new char[totalNumAtoms];
-		// Initialise the group level data
+		// Initialize the group level data
 		groupNum = new int[totalNumGroups];
-		// List for storing the group level information
-		pdbGroupList = new ArrayList<>();
 		insertionCodeList = new char[totalNumGroups];
 		seqResGroupList = new int[totalNumGroups];
 		secStructInfo = new int[totalNumGroups];
-		// Intialise the chain level data 	 	
+		// List for storing the group level information
+		pdbGroupList = new ArrayList<>();
+		// Initialize the chain level data 	 	
 		chainList = new String[totalNumChains];
 		publicChainIds = new String[totalNumChains];
 		groupsPerChain = new int[totalNumChains];
-		// Initialise the model level information
+		// Initialize the model level information
 		numModels = totalNumModels;
 		// Set the name
 		pdbId = structureId;
 		bioAssembly = new ArrayList<>();
-		entities = new ArrayList<>();
 		chainsPerModel = new int[totalNumModels];
+
+		// temporary data structure
+		entities = new ArrayList<>();
 	}
 
 	@Override
 	public void finalizeStructure() {
 		// Convert the entities array to a list
 		entityList = entities.toArray(new Entity[0]);
+		// clear temporary data structure to avoid "memory leak"
+		entities.clear();
+
 		// Cleanup the group list
 		groupMap = new ArrayList<>(new HashSet<>(pdbGroupList));
 		groupList = new int[pdbGroupList.size()];
 		for(int i=0; i<pdbGroupList.size(); i++){		
 			// Find the index of this groups information.
 			groupList[i] = groupMap.indexOf(pdbGroupList.get(i));
-		}
+		}	
 	}
 
 	@Override
@@ -581,6 +587,10 @@ public void setHeaderInfo(float rFree, float rWork, float resolution, String tit
 
 
 	}
+
+	public void setMmtfProducer(String mmtfProducer) {
+		this.mmtfProducer = mmtfProducer;
+	}
 
 	private Group getGroup(int groupInd) {
 		return groupMap.get(groupInd);
@@ -612,5 +622,4 @@ public double[][] getNcsOperatorList() {
 	public String getBioassemblyName(int bioassemblyIndex) {
 		return bioAssembly.get(bioassemblyIndex).getName();
 	}
-
 }

mmtf-codec/src/main/java/org/rcsb/mmtf/encoder/GenericEncoder.java

@@ -1,5 +1,7 @@
 package org.rcsb.mmtf.encoder;
 
+import java.io.Serializable;
+
 import org.rcsb.mmtf.api.StructureDataInterface;
 import org.rcsb.mmtf.codec.CharCodecs;
 import org.rcsb.mmtf.codec.FloatCodecs;
@@ -12,9 +14,8 @@
  * @author Anthony Bradley
  *
  */
-public class GenericEncoder implements EncoderInterface {
-
-
+public class GenericEncoder implements EncoderInterface, Serializable {
+	private static final long serialVersionUID = 4128892132322015448L;
 	private MmtfStructure mmtfBean;
 	private int coordDivider = MmtfStructure.COORD_DIVIDER;
 	private int bfactorOccDivider = MmtfStructure.OCCUPANCY_BFACTOR_DIVIDER;