Added API functions to get the URL as a String and the data as an Inp…

…utStream

CHANGELOG.md

@@ -71,3 +71,8 @@ All notable changes to this project will be documented in this file, following t
  - Cleanup of WriterUtils
  - Updated version string in MmtfStructure
  - Updated test data
+
+
+## v1.0.3 - 2016-09-13
+### Added
+ - API functions to get the URL as a string and the data as an inputstream

README.md

@@ -1,7 +1,7 @@
 [![Build Status](https://travis-ci.org/rcsb/mmtf-java.svg?branch=master)](https://travis-ci.org/rcsb/mmtf-java)
 [![Coverage Status](https://coveralls.io/repos/github/rcsb/mmtf-java/badge.svg?branch=master)](https://coveralls.io/github/rcsb/mmtf-java?branch=master)
 [![Dependency Status](https://www.versioneye.com/user/projects/56feb8e5fcd19a0039f1553c/badge.svg?style=flat)](https://www.versioneye.com/user/projects/56feb8e5fcd19a0039f1553c)
-[![Version](http://img.shields.io/badge/version-1.0.2-blue.svg?style=flat)](https://github.com/rcsb/mmtf-java/) [![License](http://img.shields.io/badge/license-Apache 2.0-blue.svg?style=flat)](https://github.com/rcsb/mmtf-java/blob/master/LICENSE.txt)
+[![Version](http://img.shields.io/badge/version-1.0.3-blue.svg?style=flat)](https://github.com/rcsb/mmtf-java/) [![License](http://img.shields.io/badge/license-Apache 2.0-blue.svg?style=flat)](https://github.com/rcsb/mmtf-java/blob/master/LICENSE.txt)
 [![Changelog](https://img.shields.io/badge/changelog--lightgrey.svg?style=flat)](https://github.com/rcsb/mmtf-java/blob/master/CHANGELOG.md)
 
 
@@ -16,12 +16,12 @@ The alpha release is available on Maven central.
 		<dependency>
 			<groupId>org.rcsb</groupId>
 			<artifactId>mmtf-codec</artifactId>
-			<version>1.0.2</version>
+			<version>1.0.3</version>
 		</dependency>
         <dependency>
             <groupId>org.rcsb</groupId>
             <artifactId>mmtf-api</artifactId>
-            <version>1.0.2</version>
+            <version>1.0.3</version>
         </dependency>
 ```
 

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

@@ -47,7 +47,7 @@ public static MmtfStructure getDataFromUrl(String pdbCode) throws IOException {
 	public static byte[] getByteArrayFromUrl(String pdbCode)  throws IOException {
 		ByteArrayOutputStream baos = new ByteArrayOutputStream();
 		InputStream inputStream = null;
-		URL url = new URL(CodecUtils.BASE_URL + pdbCode);
+		URL url = new URL(getUrl(pdbCode));
 		try {
 			inputStream = url.openStream();
 			byte[] byteChunk = new byte[BYTE_BUFFER_CHUNK_SIZE]; // Or whatever size you want to read in at a time.
@@ -103,8 +103,7 @@ public static byte[] deflateGzip(byte[] inputBytes) throws IOException {
 	 */
 	public static MmtfStructure getDataFromFile(Path filePath) throws IOException {
 		// Now return the gzip deflated and deserialized byte array
-		MessagePackSerialization mmtfBeanSeDeMessagePackImpl = new MessagePackSerialization();
-		return mmtfBeanSeDeMessagePackImpl.deserialize(new ByteArrayInputStream(readFile(filePath)));
+		return getDataFromInputStream(new ByteArrayInputStream(readFile(filePath)));
 	}
 
 	/**
@@ -117,4 +116,24 @@ private static byte[] readFile(Path path) throws IOException {
 		byte[] data = Files.readAllBytes(path);
 		return data;
 	}
+
+	/**
+	 * Read an input stream to an {@link MmtfStructure} object.
+	 * @param inStream the {@link InputStream} to read.
+	 * @return the {@link MmtfStructure} to be returned 
+	 */
+	public static MmtfStructure getDataFromInputStream(InputStream inStream) {
+		MessagePackSerialization mmtfBeanSeDeMessagePackImpl = new MessagePackSerialization();
+		return mmtfBeanSeDeMessagePackImpl.deserialize(inStream);
+
+	}
+
+	/**
+	 * Get the URL to return a given PDB id
+	 * @param pdbId the input PDB id
+	 * @return the URL {@link String} to get data from
+	 */
+	public static String getUrl(String pdbId) {
+		return CodecUtils.BASE_URL + pdbId;
+	}
 }