JWS-29 patch fixes bug - wierd workaround since "^\\s*>" caused scanner to advance...

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