From f55e379f8941bc5589a5fa24f77dc6b4e69635d6 Mon Sep 17 00:00:00 2001
From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Wed, 27 Apr 2011 23:22:08 +0000
Subject: [PATCH] A wee improvement

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4042 e3abac25-378b-4346-85de-24260fe3988d
---
 datamodel/compbio/data/sequence/FastaReader.java |   34 +++++++++++++++++++---
 1 file changed, 30 insertions(+), 4 deletions(-)

diff --git a/datamodel/compbio/data/sequence/FastaReader.java b/datamodel/compbio/data/sequence/FastaReader.java
index 10eec8f..4b6fd66 100644
--- a/datamodel/compbio/data/sequence/FastaReader.java
+++ b/datamodel/compbio/data/sequence/FastaReader.java
@@ -58,14 +58,28 @@ public class FastaReader implements Iterator<FastaSequence> {
 	 *            read from
 	 * @throws FileNotFoundException
 	 *             if the input file is not found
+	 * @throws IllegalStateException
+	 *             if the close method was called on this instance
+	 * 
 	 */
-	public FastaReader(final String input) throws FileNotFoundException {
-		this.input = new Scanner(new File(input), "UTF8");
-		this.input.useDelimiter("\\s*>");
-	}
+	public FastaReader(final String inputFile) throws FileNotFoundException {
+		input = new Scanner(new File(inputFile), "UTF8");
+		input.useDelimiter("\\s*>");
+		Runtime.getRuntime().addShutdownHook(new Thread() {
 
+			@Override
+			public void run() {
+				if (input != null) {
+					input.close();
+				}
+			}
+		});
+	}
 	/**
 	 * {@inheritDoc}
+	 * 
+	 * @throws IllegalStateException
+	 *             if the close method was called on this instance
 	 */
 	@Override
 	public boolean hasNext() {
@@ -77,6 +91,8 @@ public class FastaReader implements Iterator<FastaSequence> {
 	 * 
 	 * @throws AssertionError
 	 *             if the header or the sequence is missing
+	 * @throws IllegalStateException
+	 *             if the close method was called on this instance
 	 */
 	@Override
 	public FastaSequence next() {
@@ -91,6 +107,16 @@ public class FastaReader implements Iterator<FastaSequence> {
 		throw new UnsupportedOperationException();
 	}
 
+	/**
+	 * Call this method to close the connection to the input file if you want to
+	 * free up the resources. The connection will be closed on the JVM shutdown
+	 * if this method was not called explicitly. No further reading on this
+	 * instance of the FastaReader will be possible after calling this method.
+	 */
+	public void close() {
+		input.close();
+	}
+
 	private static FastaSequence toFastaSequence(final String singleFastaEntry) {
 		final Scanner sc = new Scanner(singleFastaEntry);
 		// Use new line delimiter
-- 
1.7.10.2