Speedup

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

@@ -73,6 +73,10 @@ public GenericDecoder(MmtfStructure inputData) {
 		numGroups = inputData.getNumGroups();
 		numChains = inputData.getNumChains();
 		numModels = inputData.getNumModels();
+		numIntergroupBonds = interGroupBondOrders.length;
+		for(int groupIndex : groupList) {
+			numIntergroupBonds += groupMap[groupIndex].getBondOrderList().length;
+		}
 		ncsOperMatrixList = inputData.getNcsOperatorList();
 	}
 
@@ -183,6 +187,8 @@ public GenericDecoder(MmtfStructure inputData) {
 
 	private int numGroups;
 
+	private int numIntergroupBonds;
+
 	private double[][] ncsOperMatrixList;
 
 
@@ -452,10 +458,6 @@ public String getDepositionDate() {
 
 	@Override
 	public int getNumBonds() {		
-		int numIntergroupBonds = interGroupBondOrders.length;
-		for(int groupIndex : groupList) {
-			numIntergroupBonds+=groupMap[groupIndex].getBondOrderList().length;
-		}
 		return numIntergroupBonds;
 	}
 

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

@@ -7,6 +7,7 @@
 import java.net.URL;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.text.ParseException;
 import java.util.zip.GZIPInputStream;
 
 import org.rcsb.mmtf.dataholders.MmtfStructure;
@@ -15,110 +16,129 @@
 
 /**
  * A class of static utility methods for reading data.
+ *
  * @author Anthony Bradley
  *
  */
 public class ReaderUtils {
 
-	/** The size of a chunk for a byte buffer. */
+	/**
+	 * The size of a chunk for a byte buffer.
+	 */
 	private static final int BYTE_BUFFER_CHUNK_SIZE = 4096;
 
 	/**
-	 * Find the message pack byte array from the web using the input code and a base url.
-	 * Caches the file if possible.
+	 * Find the message pack byte array from the web using the input code and a base url. Caches the
+	 * file if possible.
+	 *
 	 * @param pdbCode the pdb code for the desired structure.
 	 * @return the MMTFBean of the deserialized data
+	 * @throws java.text.ParseException if MessagePack cannot be parsed
 	 * @throws IOException if the data cannot be read from the URL
 	 */
-	public static MmtfStructure getDataFromUrl(String pdbCode) throws IOException {	
+	public static MmtfStructure getDataFromUrl(String pdbCode)
+		throws ParseException, IOException {
 		// Get these as an inputstream
-		byte[] byteArr = getByteArrayFromUrl(pdbCode);
+		byte[] bytes = getByteArrayFromUrl(pdbCode);
 		// Now return the gzip deflated and deserialized byte array
-		MessagePackSerialization mmtfBeanSeDeMessagePackImpl = new MessagePackSerialization();
-		return mmtfBeanSeDeMessagePackImpl.deserialize(new ByteArrayInputStream(deflateGzip(byteArr)));
+		MessagePackSerialization mmtfBeanSeDeMessagePackImpl
+			= new MessagePackSerialization();
+		return mmtfBeanSeDeMessagePackImpl.deserialize(new ByteArrayInputStream(
+			deflateGzip(bytes)));
 	}
 
 	/**
 	 * Get the GZIP compressed and messagepack serialized data from the MMTF servers
+	 *
 	 * @param pdbCode the PDB code for the data required
 	 * @return the byte array (GZIP compressed) of the data from the URL
 	 * @throws IOException an error reading the URL
 	 */
-	public static byte[] getByteArrayFromUrl(String pdbCode)  throws IOException {
-		ByteArrayOutputStream baos = new ByteArrayOutputStream();
-		InputStream inputStream = null;
+	public static byte[] getByteArrayFromUrl(String pdbCode)
+		throws IOException {
 		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.
+		try (InputStream inputStream = url.openStream();
+			ByteArrayOutputStream baos = new ByteArrayOutputStream();) {
+			byte[] byteChunk = new byte[BYTE_BUFFER_CHUNK_SIZE];
+			// Or whatever size you want to read in at a time.
 			int n;
 			while ((n = inputStream.read(byteChunk)) > 0) {
 				baos.write(byteChunk, 0, n);
 			}
-		} finally {
-			if (inputStream != null) { inputStream.close(); }
-		}
 			return baos.toByteArray();
 		}
+	}
 
 	/**
 	 * Deflate a gzip byte array.
+	 *
 	 * @param inputBytes a gzip compressed byte array
 	 * @return a deflated byte array
 	 * @throws IOException error in gzip input stream
 	 */
 	public static byte[] deflateGzip(byte[] inputBytes) throws IOException {
-		// Start the byte input stream
-		ByteArrayInputStream byteInputStream = new ByteArrayInputStream(inputBytes);
-		GZIPInputStream gzipInputStream;
-		ByteArrayOutputStream byteArrayOutputStream = null;
-		try {
-			gzipInputStream = new GZIPInputStream(byteInputStream);
-
-			byteArrayOutputStream = new ByteArrayOutputStream();
-			// Make a buffer
+		ByteArrayOutputStream byteArrayOutputStream
+			= new ByteArrayOutputStream();
+		try (GZIPInputStream gzipInputStream = new GZIPInputStream(
+			new ByteArrayInputStream(inputBytes))) {
 			byte[] buffer = new byte[BYTE_BUFFER_CHUNK_SIZE];
-
 			while (gzipInputStream.available() == 1) {
 				int size = gzipInputStream.read(buffer);
 				if (size == -1) {
 					break;
 				}
 				byteArrayOutputStream.write(buffer, 0, size);
 			}
-
-		} finally {
-			if (byteArrayOutputStream != null) {
-				byteArrayOutputStream.close();
-			}			
-		}
 			return byteArrayOutputStream.toByteArray();
 		}
+	}
 
 	/**
 	 * A function to get MMTF data from a file path.
+	 *
 	 * @param filePath the full path of the file to be read
 	 * @return the deserialized {@link MmtfStructure}
 	 * @throws IOException an error reading the file
+	 * @throws java.text.ParseException if MessagePack cannot be parsed
 	 */
-	public static MmtfStructure getDataFromFile(Path filePath) throws IOException {
+	public static MmtfStructure getDataFromFile(Path filePath)
+		throws IOException, ParseException {
+		// Now return the gzip deflated and deserialized byte array
+		try (InputStream is = new ByteArrayInputStream(readFile(filePath))) {
+			return getDataFromInputStream(is);
+		}
+	}
 
-		return getDataFromInputStream(Files.newInputStream(filePath));
+	/**
+	 * Read a byte array from a file
+	 *
+	 * @param path the input file path
+	 * @return the returned byte array
+	 * @throws IOException an error reading the file
+	 */
+	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
+	 * @throws java.text.ParseException if MessagePack cannot be parsed
+	 * @throws java.io.IOException if the inStream cannot be read
 	 */
-	public static MmtfStructure getDataFromInputStream(InputStream inStream) {
-		MessagePackSerialization mmtfBeanSeDeMessagePackImpl = new MessagePackSerialization();
+	public static MmtfStructure getDataFromInputStream(InputStream inStream)
+		throws ParseException, IOException {
+		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
 	 */

mmtf-codec/src/test/java/org/rcsb/mmtf/codec/TestRoundTrip.java

@@ -4,7 +4,7 @@
 
 import java.io.IOException;
 import java.nio.file.Path;
-import java.nio.file.Paths;
+import java.text.ParseException;
 
 import org.junit.Test;
 import org.rcsb.mmtf.api.StructureDataInterface;
@@ -24,7 +24,7 @@ public class TestRoundTrip {
 	 * @throws IOException error reading the file from the resource
 	 */
 	@Test
-	public void testGenericGeneric() throws IOException {
+	public void testGenericGeneric() throws IOException, ParseException {
 		Utils.compare(getDefaultFullData());
 	}
 
@@ -58,9 +58,8 @@ public void testArrayRoundTrip() {
 	 * @return a {@link StructureDataInterface} for the full data.
 	 * @throws IOException
 	 */
-	private StructureDataInterface getDefaultFullData() throws IOException {
-		ClassLoader classLoader = getClass().getClassLoader();
-		Path inFile = Paths.get(classLoader.getResource("mmtf/4cup.mmtf").getFile());
-		return new GenericDecoder(ReaderUtils.getDataFromFile(inFile));
+	private StructureDataInterface getDefaultFullData() throws IOException, ParseException {
+		Path p = Utils.getResource("/mmtf/4cup.mmtf");
+		return new GenericDecoder(ReaderUtils.getDataFromFile(p));
 	}
 }

mmtf-codec/src/test/java/org/rcsb/mmtf/codec/Utils.java

@@ -6,10 +6,15 @@
 import java.beans.IntrospectionException;
 import java.beans.Introspector;
 import java.beans.PropertyDescriptor;
+import java.io.File;
+import java.io.IOException;
 import java.lang.reflect.InvocationTargetException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 
 import org.rcsb.mmtf.api.StructureDataInterface;
 import org.rcsb.mmtf.decoder.GenericDecoder;
+import org.rcsb.mmtf.decoder.ReaderUtils;
 import org.rcsb.mmtf.encoder.GenericEncoder;
 
 /**
@@ -72,4 +77,12 @@ public static void compareStructDataInfs(StructureDataInterface interfaceOne, St
 		assertArrayEquals(interfaceOne.getInterGroupBondIndices(), interfaceTwo.getInterGroupBondIndices());
 		assertArrayEquals(interfaceOne.getInterGroupBondOrders(), interfaceTwo.getInterGroupBondOrders());
 	}
+
+	/**
+	 * path = "/mmtf/4cup.mmtf"
+	 */
+	public static Path getResource(String p) throws IOException {			
+		File f = new File(Utils.class.getClass().getResource(p).getFile());
+		return Paths.get(f.getAbsolutePath());
+	}
 }

mmtf-codec/src/test/java/org/rcsb/mmtf/decoder/TestGenericDecoder.java

@@ -7,9 +7,10 @@
 import java.beans.PropertyDescriptor;
 import java.io.IOException;
 import java.lang.reflect.InvocationTargetException;
-import java.nio.file.Paths;
+import java.text.ParseException;
 
 import org.junit.Test;
+import org.rcsb.mmtf.codec.Utils;
 import org.rcsb.mmtf.dataholders.MmtfStructure;
 import org.unitils.reflectionassert.ReflectionAssert;
 
@@ -29,11 +30,13 @@ public class TestGenericDecoder {
 	 * @throws IllegalAccessException  an error with introspection
 	 */
 	@Test
-	public void testDecodeAllFields() throws IOException, IllegalAccessException, IllegalArgumentException, InvocationTargetException, IntrospectionException {
+	public void testDecodeAllFields() throws IOException, ParseException, IllegalAccessException,
+		IllegalArgumentException, InvocationTargetException, IntrospectionException {
 		ClassLoader classLoader = getClass().getClassLoader();
-		MmtfStructure mmtfBean = ReaderUtils.getDataFromFile(Paths.get(classLoader.getResource("mmtf/4cup.mmtf").getFile()));
+		MmtfStructure mmtfBean = ReaderUtils.getDataFromFile(Utils.getResource("/mmtf/4cup.mmtf"));
 		GenericDecoder genericDecoder = new GenericDecoder(mmtfBean);
-		ReflectionAssert.assertPropertiesNotNull("Some properties null after decoding", genericDecoder);
+		ReflectionAssert.assertPropertiesNotNull("Some properties null after decoding", 
+			genericDecoder);
 		for(PropertyDescriptor propertyDescriptor : 
 			Introspector.getBeanInfo(MmtfStructure.class).getPropertyDescriptors()){
 			assertNotNull(propertyDescriptor.getReadMethod().invoke(mmtfBean));

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

@@ -9,7 +9,8 @@
 
 
 import java.io.IOException;
-import java.nio.file.Paths;
+import java.text.ParseException;
+import org.rcsb.mmtf.codec.Utils;
 
 /**
  * Test the reader utils class functions work.
@@ -81,9 +82,9 @@ public void testGzipDecompressText() throws IOException {
 	 * @throws IOException error accesing the file
 	 */
 	@Test 
-	public void testReadFromFile() throws IOException {
+	public void testReadFromFile() throws IOException, ParseException {
 		ClassLoader classLoader = getClass().getClassLoader();
-		MmtfStructure mmtfBean = ReaderUtils.getDataFromFile(Paths.get(classLoader.getResource("mmtf/4cup.mmtf").getFile()));
+		MmtfStructure mmtfBean = ReaderUtils.getDataFromFile(Utils.getResource("/mmtf/4cup.mmtf"));
 		assertNotEquals(mmtfBean, null);
 		assertEquals(mmtfBean.getDepositionDate(), "2014-03-21");
 	}