From 407e6d4914c247a24e018f8decb6f8eb53d1df16 Mon Sep 17 00:00:00 2001
From: abradle <anthony.richard.bradley@gmail.com>
Date: Wed, 13 Apr 2016 04:16:12 -0700
Subject: [PATCH] Refactoring of the names of the interfaces and
 decoder/encoder classes.

---
 ...erInterface.java => DataTransferInterface.java} |  2 +-
 ...ataInterface.java => DecodedDataInterface.java} |  2 +-
 .../{DataApiToReader.java => DecoderToReader.java} | 14 +++++++-------
 .../java/org/rcsb/mmtf/decoder/DecoderUtils.java   | 14 +++++++-------
 .../{BeanToDataApi.java => DefaultDecoder.java}    |  6 +++---
 .../{DataApiToBean.java => DefaultEncoder.java}    |  6 +++---
 .../java/org/rcsb/mmtf/encoder/EncoderUtils.java   |  8 ++++----
 .../{WriterToDataApi.java => WriterToEncoder.java} |  6 +++---
 .../java/org/rcsb/mmtf/encoder/WriterUtils.java    |  6 +++---
 9 files changed, 32 insertions(+), 32 deletions(-)
 rename mmtf-api/src/main/java/org/rcsb/mmtf/api/{MmtfDecoderInterface.java => DataTransferInterface.java} (99%)
 rename mmtf-api/src/main/java/org/rcsb/mmtf/api/{MmtfDecodedDataInterface.java => DecodedDataInterface.java} (99%)
 rename mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/{DataApiToReader.java => DecoderToReader.java} (95%)
 rename mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/{BeanToDataApi.java => DefaultDecoder.java} (98%)
 rename mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/{DataApiToBean.java => DefaultEncoder.java} (97%)
 rename mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/{WriterToDataApi.java => WriterToEncoder.java} (98%)

diff --git a/mmtf-api/src/main/java/org/rcsb/mmtf/api/MmtfDecoderInterface.java b/mmtf-api/src/main/java/org/rcsb/mmtf/api/DataTransferInterface.java
similarity index 99%
rename from mmtf-api/src/main/java/org/rcsb/mmtf/api/MmtfDecoderInterface.java
rename to mmtf-api/src/main/java/org/rcsb/mmtf/api/DataTransferInterface.java
index 7dd5718..fcb06f1 100644
--- a/mmtf-api/src/main/java/org/rcsb/mmtf/api/MmtfDecoderInterface.java
+++ b/mmtf-api/src/main/java/org/rcsb/mmtf/api/DataTransferInterface.java
@@ -5,7 +5,7 @@
  *
  * @author Anthony Bradley
  */
-public interface MmtfDecoderInterface {
+public interface DataTransferInterface {
 
 	/**
 	 * Used before any additions to do any required pre-processing.
diff --git a/mmtf-api/src/main/java/org/rcsb/mmtf/api/MmtfDecodedDataInterface.java b/mmtf-api/src/main/java/org/rcsb/mmtf/api/DecodedDataInterface.java
similarity index 99%
rename from mmtf-api/src/main/java/org/rcsb/mmtf/api/MmtfDecodedDataInterface.java
rename to mmtf-api/src/main/java/org/rcsb/mmtf/api/DecodedDataInterface.java
index d335852..dcd5d5d 100644
--- a/mmtf-api/src/main/java/org/rcsb/mmtf/api/MmtfDecodedDataInterface.java
+++ b/mmtf-api/src/main/java/org/rcsb/mmtf/api/DecodedDataInterface.java
@@ -22,7 +22,7 @@
  * @author Anthony Bradley
  * @author Jose Duarte
  */
-public interface MmtfDecodedDataInterface {
+public interface DecodedDataInterface {
 
 	/**
 	 * Returns an array containing the X coordinates of the atoms in Angstroms.
diff --git a/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DataApiToReader.java b/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DecoderToReader.java
similarity index 95%
rename from mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DataApiToReader.java
rename to mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DecoderToReader.java
index ba481a1..c92a8f9 100644
--- a/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DataApiToReader.java
+++ b/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DecoderToReader.java
@@ -3,8 +3,8 @@
 import java.util.HashSet;
 import java.util.Set;
 
-import org.rcsb.mmtf.api.MmtfDecodedDataInterface;
-import org.rcsb.mmtf.api.MmtfDecoderInterface;
+import org.rcsb.mmtf.api.DecodedDataInterface;
+import org.rcsb.mmtf.api.DataTransferInterface;
 
 /**
  * Decode an MMTF structure using a structure inflator. 
@@ -12,13 +12,13 @@
  * @author Anthony Bradley
  *
  */
-public class DataApiToReader {
+public class DecoderToReader {
 
 	/** The struct inflator. */
-	private MmtfDecoderInterface structInflator;
+	private DataTransferInterface structInflator;
 
 	/** The api to the data */
-	private MmtfDecodedDataInterface dataApi;
+	private DecodedDataInterface dataApi;
 
 	// Intialises the counters.
 	private int modelCounter = 0;
@@ -28,14 +28,14 @@ public class DataApiToReader {
 	private int currentAtomIndex = 0;
 	private Set<String> chainIdSet;
 
-	public DataApiToReader(){
+	public DecoderToReader(){
 
 	}
 
 	/**
 	 * Passes data from the data interface to the inflator interface.
 	 */
-	public void read(MmtfDecodedDataInterface inputApi, MmtfDecoderInterface inputInflator){
+	public void read(DecodedDataInterface inputApi, DataTransferInterface inputInflator){
 		// Set the api and the inflator
 		dataApi = inputApi;
 		structInflator = inputInflator;
diff --git a/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DecoderUtils.java b/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DecoderUtils.java
index c6c0c3e..f9d5bcb 100644
--- a/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DecoderUtils.java
+++ b/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DecoderUtils.java
@@ -1,14 +1,14 @@
 package org.rcsb.mmtf.decoder;
 
-import org.rcsb.mmtf.api.MmtfDecodedDataInterface;
-import org.rcsb.mmtf.api.MmtfDecoderInterface;
+import org.rcsb.mmtf.api.DecodedDataInterface;
+import org.rcsb.mmtf.api.DataTransferInterface;
 
 public class DecoderUtils {
 
 	/**
 	 * Parses the bioassembly data and inputs it to the structure inflator
 	 */
-	public static void generateBioAssembly(MmtfDecodedDataInterface dataApi, MmtfDecoderInterface structInflator) {
+	public static void generateBioAssembly(DecodedDataInterface dataApi, DataTransferInterface structInflator) {
 		for (int i=0; i<dataApi.getNumBioassemblies(); i++) {
 			for(int j=0; j<dataApi.getNumTransInBioassembly(i); j++) {
 				structInflator.setBioAssemblyTrans(i+1, dataApi.getChainIndexListForTransform(i, j), dataApi.getMatrixForTransform(i,j));    
@@ -20,7 +20,7 @@ public static void generateBioAssembly(MmtfDecodedDataInterface dataApi, MmtfDec
 	 * Generate inter group bonds
 	 * Bond indices are specified within the whole structure and start at 0.
 	 */
-	public static void addInterGroupBonds(MmtfDecodedDataInterface dataApi, MmtfDecoderInterface structInflator) {
+	public static void addInterGroupBonds(DecodedDataInterface dataApi, DataTransferInterface structInflator) {
 		for (int i = 0; i < dataApi.getInterGroupBondOrders().length; i++) {
 			structInflator.setInterGroupBond(dataApi.getInterGroupBondIndices()[i * 2],
 					dataApi.getInterGroupBondIndices()[i * 2 + 1], dataApi.getInterGroupBondOrders()[i]);
@@ -30,7 +30,7 @@ public static void addInterGroupBonds(MmtfDecodedDataInterface dataApi, MmtfDeco
 	/**
 	 * Add ancilliary header information to the structure
 	 */
-	public static void addHeaderInfo(MmtfDecodedDataInterface dataApi, MmtfDecoderInterface structInflator) {
+	public static void addHeaderInfo(DecodedDataInterface dataApi, DataTransferInterface structInflator) {
 		structInflator.setHeaderInfo(dataApi.getRfree(),dataApi.getRwork(), dataApi.getResolution(), 
 				dataApi.getTitle(), dataApi.getDepositionDate(), dataApi.getReleaseDate(), dataApi.getExperimentalMethods());		
 	}
@@ -41,7 +41,7 @@ public static void addHeaderInfo(MmtfDecodedDataInterface dataApi, MmtfDecoderIn
 	 * @param dataApi
 	 * @param structInflator
 	 */
-	public static void addXtalographicInfo(MmtfDecodedDataInterface dataApi, MmtfDecoderInterface structInflator) {
+	public static void addXtalographicInfo(DecodedDataInterface dataApi, DataTransferInterface structInflator) {
 		if(dataApi.getUnitCell()!=null){
 			structInflator.setXtalInfo(dataApi.getSpaceGroup(), dataApi.getUnitCell());    
 		}		
@@ -52,7 +52,7 @@ public static void addXtalographicInfo(MmtfDecodedDataInterface dataApi, MmtfDec
 	 * @param dataApi
 	 * @param structInflator
 	 */
-	public static void addEntityInfo(MmtfDecodedDataInterface dataApi, MmtfDecoderInterface structInflator) {
+	public static void addEntityInfo(DecodedDataInterface dataApi, DataTransferInterface structInflator) {
 		for (int i=0; i<dataApi.getNumEntities(); i++) {
 			String[] chainIdList = new String[dataApi.getEntityChainIndexList(i).length];
 			int counter = 0;
diff --git a/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/BeanToDataApi.java b/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DefaultDecoder.java
similarity index 98%
rename from mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/BeanToDataApi.java
rename to mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DefaultDecoder.java
index b8ed1c3..1f1eaad 100644
--- a/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/BeanToDataApi.java
+++ b/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DefaultDecoder.java
@@ -4,7 +4,7 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import org.rcsb.mmtf.api.MmtfDecodedDataInterface;
+import org.rcsb.mmtf.api.DecodedDataInterface;
 import org.rcsb.mmtf.dataholders.BioAssemblyData;
 import org.rcsb.mmtf.dataholders.Entity;
 import org.rcsb.mmtf.dataholders.MmtfBean;
@@ -15,9 +15,9 @@
  * @author Anthony Bradley
  *
  */
-public class BeanToDataApi implements MmtfDecodedDataInterface {
+public class DefaultDecoder implements DecodedDataInterface {
 
-	public BeanToDataApi(MmtfBean inputData) throws IOException {
+	public DefaultDecoder(MmtfBean inputData) throws IOException {
 		groupList = ArrayConverters.convertFourByteToIntegers(inputData.getGroupTypeList());
 		// Decode the coordinate  and B-factor arrays.
 		cartnX = ArrayConverters.convertIntsToFloats(
diff --git a/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/DataApiToBean.java b/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/DefaultEncoder.java
similarity index 97%
rename from mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/DataApiToBean.java
rename to mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/DefaultEncoder.java
index ee37041..1a86f52 100644
--- a/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/DataApiToBean.java
+++ b/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/DefaultEncoder.java
@@ -3,7 +3,7 @@
 import java.io.IOException;
 import java.util.List;
 
-import org.rcsb.mmtf.api.MmtfDecodedDataInterface;
+import org.rcsb.mmtf.api.DecodedDataInterface;
 import org.rcsb.mmtf.dataholders.MmtfBean;
 import org.rcsb.mmtf.encoder.ArrayConverters;
 import org.rcsb.mmtf.encoder.ArrayEncoders;
@@ -14,11 +14,11 @@
  * @author Anthony Bradley
  *
  */
-public class DataApiToBean {
+public class DefaultEncoder {
 
 	private MmtfBean mmtfBean;
 
-	public DataApiToBean(MmtfDecodedDataInterface mmtfDecodedDataInterface) throws IOException {
+	public DefaultEncoder(DecodedDataInterface mmtfDecodedDataInterface) throws IOException {
 		mmtfBean = new MmtfBean();
 		// Set the group types
 		mmtfBean.setGroupTypeList(
diff --git a/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/EncoderUtils.java b/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/EncoderUtils.java
index 203266e..10c8943 100644
--- a/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/EncoderUtils.java
+++ b/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/EncoderUtils.java
@@ -3,7 +3,7 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import org.rcsb.mmtf.api.MmtfDecodedDataInterface;
+import org.rcsb.mmtf.api.DecodedDataInterface;
 import org.rcsb.mmtf.dataholders.BioAssemblyData;
 import org.rcsb.mmtf.dataholders.BioAssemblyTrans;
 import org.rcsb.mmtf.dataholders.Entity;
@@ -17,7 +17,7 @@ public class EncoderUtils {
 	 * @param mmtfDecodedDataInterface the input interface
 	 * @return a list of all the groups in the molecule
 	 */
-	public static PDBGroup[] generateGroupMap(MmtfDecodedDataInterface mmtfDecodedDataInterface) {
+	public static PDBGroup[] generateGroupMap(DecodedDataInterface mmtfDecodedDataInterface) {
 		int[] groupTypeIndices = mmtfDecodedDataInterface.getGroupTypeIndices();
 		int maxIndex = CodecUtils.findMaxInIntArray(groupTypeIndices);
 		PDBGroup[] outGroupList = new PDBGroup[maxIndex+1];
@@ -42,7 +42,7 @@ public static PDBGroup[] generateGroupMap(MmtfDecodedDataInterface mmtfDecodedDa
 	 * @param mmtfDecodedDataInterface the interface from where to find the data
 	 * @return a list of bioassembly information
 	 */
-	public static List<BioAssemblyData> generateBioassemblies(MmtfDecodedDataInterface mmtfDecodedDataInterface) {
+	public static List<BioAssemblyData> generateBioassemblies(DecodedDataInterface mmtfDecodedDataInterface) {
 		int numBioassemblies = mmtfDecodedDataInterface.getNumBioassemblies();
 		List<BioAssemblyData> outList = new ArrayList<>();
 		for (int i=0; i<numBioassemblies; i++) {
@@ -68,7 +68,7 @@ public static List<BioAssemblyData> generateBioassemblies(MmtfDecodedDataInterfa
 	 * @param mmtfDecodedDataInterface the input interface
 	 * @return the list of entities
 	 */
-	public static Entity[] generateEntityList(MmtfDecodedDataInterface mmtfDecodedDataInterface) {
+	public static Entity[] generateEntityList(DecodedDataInterface mmtfDecodedDataInterface) {
 		int numEntities =  mmtfDecodedDataInterface.getNumEntities();
 		Entity[] outList = new Entity[numEntities];
 		for (int i=0; i<numEntities;i++) {
diff --git a/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/WriterToDataApi.java b/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/WriterToEncoder.java
similarity index 98%
rename from mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/WriterToDataApi.java
rename to mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/WriterToEncoder.java
index 1daac00..895476e 100644
--- a/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/WriterToDataApi.java
+++ b/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/WriterToEncoder.java
@@ -4,8 +4,8 @@
 import java.util.HashSet;
 import java.util.List;
 
-import org.rcsb.mmtf.api.MmtfDecodedDataInterface;
-import org.rcsb.mmtf.api.MmtfDecoderInterface;
+import org.rcsb.mmtf.api.DecodedDataInterface;
+import org.rcsb.mmtf.api.DataTransferInterface;
 import org.rcsb.mmtf.dataholders.BioAssemblyData;
 import org.rcsb.mmtf.dataholders.BioAssemblyTrans;
 import org.rcsb.mmtf.dataholders.Entity;
@@ -17,7 +17,7 @@
  * @author Anthony Bradley
  *
  */
-public class WriterToDataApi implements MmtfDecodedDataInterface, MmtfDecoderInterface {
+public class WriterToEncoder implements DecodedDataInterface, DataTransferInterface {
 
 
 	/** The X coordinates */
diff --git a/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/WriterUtils.java b/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/WriterUtils.java
index 1b1cc3d..b864d9c 100644
--- a/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/WriterUtils.java
+++ b/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/WriterUtils.java
@@ -13,7 +13,7 @@ public class WriterUtils {
 	 * @param path
 	 * @throws IOException 
 	 */
-	public static void writeDataToFile(WriterToDataApi inflatorToGet, String path) throws IOException {
+	public static void writeDataToFile(WriterToEncoder inflatorToGet, String path) throws IOException {
 		byte[] byteArray = getDataAsByteArr(inflatorToGet);
 		FileOutputStream fos = new FileOutputStream(path);
 		fos.write(byteArray);
@@ -21,10 +21,10 @@ public static void writeDataToFile(WriterToDataApi inflatorToGet, String path) t
 	}
 	
 	
-	public static byte[] getDataAsByteArr(WriterToDataApi inflatorToGet) throws IOException {
+	public static byte[] getDataAsByteArr(WriterToEncoder inflatorToGet) throws IOException {
 		MessagePackSerializer messagePackSerializer = new MessagePackSerializer();
 		// Get to bean
-		DataApiToBean getToBean = new DataApiToBean(inflatorToGet);
+		DefaultEncoder getToBean = new DefaultEncoder(inflatorToGet);
 		return messagePackSerializer.serialize(getToBean.getMmtfBean());
 	}