Refactored variables to mmtf-common.

rcsb · Apr 20, 2016 · 4cd80bb · 4cd80bb
1 parent c68ff53
commit 4cd80bb
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Showing 4 changed files with 20 additions and 13 deletions.
diff --git a/mmtf-common/src/main/java/org/rcsb/mmtf/utils/CodecUtils.java b/mmtf-common/src/main/java/org/rcsb/mmtf/utils/CodecUtils.java
@@ -3,11 +3,20 @@
 import java.util.List;
 
 /**
- * A utility class of static methods for the codec project.
+ * A utility class of static methods and constants
+ * for the codec project.
  * @author Anthony Bradley
  *
  */
 public class CodecUtils {
+
+
+	/** The base url. */
+	public static final String BASE_URL = "http://mmtf.rcsb.org/v0/full/";
+
+
+	/** The maximum number of chars in a chain entry. */
+	public static final int MAX_CHARS_PER_CHAIN_ENTRY= 4;
 
 	/**
 	 * Convert an integer list to an integer array

diff --git a/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/ArrayConverters.java b/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/ArrayConverters.java
@@ -2,6 +2,8 @@
 
 import java.nio.ByteBuffer;
 
+import org.rcsb.mmtf.utils.CodecUtils;
+
 /**
  * Class of functions to convert arrays to readable types.
  * e.g. byte arrays to integer arrays.
@@ -10,9 +12,6 @@
  */
 public class ArrayConverters {
 
-	/** The maximum number of chars in a chain entry. */
-	private static final int MAX_CHARS_PER_CHAIN_ENTRY = 4;
-
 	/**
 	 * Find all the chain ids from a single byte array. Each byte encodes a different ASCII character.
 	 * @param currentChainList the byte array of the chain list input. Each chain takes up 4 bytes.
@@ -144,21 +143,21 @@ public static char[] convertIntegerToChar(int[] integerArray) {
 	private static String getChainId(byte[] byteArr, int chainIndex) {
 		int incrementor = 0;
 		StringBuilder sb = new StringBuilder();
-		byte chainIdOne = byteArr[chainIndex * MAX_CHARS_PER_CHAIN_ENTRY + incrementor];
+		byte chainIdOne = byteArr[chainIndex * CodecUtils.MAX_CHARS_PER_CHAIN_ENTRY + incrementor];
 		sb.append((char) chainIdOne);
 		// Now get the next byte
 		incrementor += 1;
-		byte chainIdTwo = byteArr[chainIndex * MAX_CHARS_PER_CHAIN_ENTRY + incrementor];
+		byte chainIdTwo = byteArr[chainIndex * CodecUtils.MAX_CHARS_PER_CHAIN_ENTRY + incrementor];
 		if (chainIdTwo != (byte) 0) {
 			sb.append((char) chainIdTwo);
 		}
 		incrementor += 1;
-		byte chainIdThree = byteArr[chainIndex * MAX_CHARS_PER_CHAIN_ENTRY + incrementor];
+		byte chainIdThree = byteArr[chainIndex * CodecUtils.MAX_CHARS_PER_CHAIN_ENTRY + incrementor];
 		if (chainIdThree != (byte) 0) {
 			sb.append((char) chainIdThree);
 		}
 		incrementor += 1;
-		byte chainIdFour = byteArr[chainIndex * MAX_CHARS_PER_CHAIN_ENTRY + incrementor];
+		byte chainIdFour = byteArr[chainIndex * CodecUtils.MAX_CHARS_PER_CHAIN_ENTRY + incrementor];
 		if (chainIdFour != (byte) 0) {
 			sb.append((char) chainIdFour);
 		}

diff --git a/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DecoderToReader.java b/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DecoderToReader.java
@@ -62,7 +62,7 @@ public DecoderToReader(StructureDataInterface inputApi, StructureAdapterInterfac
 	/**
 	 * Add the main atomic information to the data model
 	 */
-	private final void addAtomicInformation() {
+	private void addAtomicInformation() {
 		for (int modelChains: dataApi.getChainsPerModel()) {
 			structInflator.setModelInfo(modelCounter, modelChains);
 			int totChainsThisModel = chainCounter + modelChains;

diff --git a/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/ReaderUtils.java b/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/ReaderUtils.java
@@ -11,16 +11,15 @@
 
 import org.rcsb.mmtf.dataholders.MmtfBean;
 import org.rcsb.mmtf.deserializers.MessagePackDeserializer;
+import org.rcsb.mmtf.utils.CodecUtils;
 
 /**
  * A class of static utility methods for reading data.
  * @author Anthony Bradley
  *
  */
 public class ReaderUtils {
-
-	/** The base url. */
-	public static final String BASE_URL = "http://mmtf.rcsb.org/v0/full/";
+
 	/** The size of a chunk for a byte buffer. */
 	private static final int BYTE_BUFFER_CHUNK_SIZE = 4096;
 
@@ -35,7 +34,7 @@ public static MmtfBean getDataFromUrl(String pdbCode) throws IOException {
 		// Get these as an inputstream
 		ByteArrayOutputStream baos = new ByteArrayOutputStream();
 		InputStream is = null;
-		URL url = new URL(BASE_URL + pdbCode);
+		URL url = new URL(CodecUtils.BASE_URL + pdbCode);
 		try {
 			is = url.openStream();
 			byte[] byteChunk = new byte[BYTE_BUFFER_CHUNK_SIZE]; // Or whatever size you want to read in at a time.