Removing ParseException

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

@@ -1,148 +1,144 @@
-package org.rcsb.mmtf.decoder;
-
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-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;
-import org.rcsb.mmtf.serialization.MessagePackSerialization;
-import org.rcsb.mmtf.utils.CodecUtils;
-
-/**
- * A class of static utility methods for reading data.
- *
- * @author Anthony Bradley
- *
- */
-public class ReaderUtils {
-
-	/**
-	 * 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.
-	 *
-	 * @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 ParseException, IOException {
-		// Get these as an inputstream
-		byte[] bytes = getByteArrayFromUrl(pdbCode);
-		// Now return the gzip deflated and deserialized byte array
-		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 {
-		URL url = new URL(getUrl(pdbCode));
-		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);
-			}
-			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 {
-		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);
-			}
-			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, ParseException {
-		// Now return the gzip deflated and deserialized byte array
-		try (InputStream is = new ByteArrayInputStream(readFile(filePath))) {
-			return getDataFromInputStream(is);
-		}
-	}
-
-	/**
-	 * 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)
-		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
-	 */
-	public static String getUrl(String pdbId) {
-		return CodecUtils.BASE_URL + pdbId;
-	}
-}
+package org.rcsb.mmtf.decoder;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URL;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.zip.GZIPInputStream;
+
+import org.rcsb.mmtf.dataholders.MmtfStructure;
+import org.rcsb.mmtf.serialization.MessagePackSerialization;
+import org.rcsb.mmtf.utils.CodecUtils;
+
+/**
+ * A class of static utility methods for reading data.
+ *
+ * @author Anthony Bradley
+ *
+ */
+public class ReaderUtils {
+
+	/**
+	 * 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.
+	 *
+	 * @param pdbCode the pdb code for the desired structure.
+	 * @return the MMTFBean of the deserialized data
+	 * @throws IOException if the data cannot be read from the URL
+	 */
+	public static MmtfStructure getDataFromUrl(String pdbCode)
+		throws IOException {
+		// Get these as an inputstream
+		byte[] bytes = getByteArrayFromUrl(pdbCode);
+		// Now return the gzip deflated and deserialized byte array
+		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 {
+		URL url = new URL(getUrl(pdbCode));
+		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);
+			}
+			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 {
+		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);
+			}
+			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
+	 */
+	public static MmtfStructure getDataFromFile(Path filePath)
+		throws IOException {
+		// Now return the gzip deflated and deserialized byte array
+		try (InputStream is = new ByteArrayInputStream(readFile(filePath))) {
+			return getDataFromInputStream(is);
+		}
+	}
+
+	/**
+	 * 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.io.IOException if the inStream cannot be read
+	 */
+	public static MmtfStructure getDataFromInputStream(InputStream inStream)
+		throws 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
+	 */
+	public static String getUrl(String pdbId) {
+		return CodecUtils.BASE_URL + pdbId;
+	}
+}