X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datamodel%2Fcompbio%2Fdata%2Fsequence%2FFastaReader.java;h=6c3e9432fb416ae9abd1c4c5c59ac92df6f41f64;hb=8ce6db56df6c0a1c2baca2fc2d33bcb10067c6cd;hp=2e1357f18788dc0a862ecf1aa7e2b59eababb8a5;hpb=53217f65cb529e859838b528e4ac81a7169e2519;p=jabaws.git

diff --git a/datamodel/compbio/data/sequence/FastaReader.java b/datamodel/compbio/data/sequence/FastaReader.java
index 2e1357f..6c3e943 100644
--- a/datamodel/compbio/data/sequence/FastaReader.java
+++ b/datamodel/compbio/data/sequence/FastaReader.java
@@ -19,8 +19,12 @@ package compbio.data.sequence;
 
 import java.io.File;
 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;
 
@@ -66,11 +70,14 @@ 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
 	 * 
-	 * @param input
+	 * @param inputFile
 	 *            the file containing the list of FASTA formatted sequences to
 	 *            read from
 	 * @throws FileNotFoundException
@@ -81,7 +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
@@ -92,6 +99,19 @@ public class FastaReader implements Iterator<FastaSequence> {
 			}
 		});
 	}
+
+	/**
+	 * This class will not close the incoming stream! So the client should do
+	 * so.
+	 * 
+	 * @param inputStream
+	 * @throws FileNotFoundException
+	 */
+	public FastaReader(final InputStream inputStream)
+			throws FileNotFoundException {
+		input = new Scanner(inputStream);
+		input.useDelimiter(DELIM);
+	}
 	/**
 	 * {@inheritDoc}
 	 * 
@@ -110,10 +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);
 	}
 
 	/**