From 8ce6db56df6c0a1c2baca2fc2d33bcb10067c6cd Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 1 Jun 2012 12:53:39 +0100
Subject: [PATCH] JWS-29 patch fixes bug - wierd workaround since "^\\s*>"
 caused scanner to advance to end of file rather than start
 of next FASTA header

---
 datamodel/compbio/data/sequence/FastaReader.java |   21 +++++++++++++++++----
 1 file changed, 17 insertions(+), 4 deletions(-)

diff --git a/datamodel/compbio/data/sequence/FastaReader.java b/datamodel/compbio/data/sequence/FastaReader.java
index 1641d34..6c3e943 100644
--- a/datamodel/compbio/data/sequence/FastaReader.java
+++ b/datamodel/compbio/data/sequence/FastaReader.java
@@ -22,6 +22,9 @@ import java.io.FileNotFoundException;
 import java.io.InputStream;
 import java.util.Iterator;
 import java.util.Scanner;
+import java.util.regex.MatchResult;
+
+import javax.vecmath.MismatchedSizeException;
 
 import compbio.util.Util;
 
@@ -67,7 +70,10 @@ import compbio.util.Util;
 public class FastaReader implements Iterator<FastaSequence> {
 
 	private final Scanner input;
-
+	/**
+	 * Delimiter for the scanner
+	 */
+	private final String DELIM=">";
 	/**
 	 * Header data can contain non-ASCII symbols and read in UTF8
 	 * 
@@ -82,7 +88,7 @@ public class FastaReader implements Iterator<FastaSequence> {
 	 */
 	public FastaReader(final String inputFile) throws FileNotFoundException {
 		input = new Scanner(new File(inputFile), "UTF8");
-		input.useDelimiter("\\s*>");
+		input.useDelimiter(DELIM);
 		Runtime.getRuntime().addShutdownHook(new Thread() {
 
 			@Override
@@ -104,7 +110,7 @@ public class FastaReader implements Iterator<FastaSequence> {
 	public FastaReader(final InputStream inputStream)
 			throws FileNotFoundException {
 		input = new Scanner(inputStream);
-		input.useDelimiter("\\s*>");
+		input.useDelimiter(DELIM);
 	}
 	/**
 	 * {@inheritDoc}
@@ -124,10 +130,17 @@ public class FastaReader implements Iterator<FastaSequence> {
 	 *             if the header or the sequence is missing
 	 * @throws IllegalStateException
 	 *             if the close method was called on this instance
+	 *             @throws MismatchException - if there were no more FastaSequence's.
 	 */
 	@Override
 	public FastaSequence next() {
-		return FastaReader.toFastaSequence(input.next());
+		String fastaHeader=input.next();
+		while (fastaHeader.indexOf("\n")<0 && input.hasNext())
+		{
+			fastaHeader = fastaHeader.concat(">");
+			fastaHeader = fastaHeader.concat(input.next());
+		}
+		return FastaReader.toFastaSequence(fastaHeader);
 	}
 
 	/**
-- 
1.7.10.2