FastaReader build into the datamodel

[jabaws.git] / datamodel / compbio / data / sequence / FastaReader.java

diff --git a/datamodel/compbio/data/sequence/FastaReader.java b/datamodel/compbio/data/sequence/FastaReader.java
index ed91e93..2e1357f 100644 (file)
--- a/datamodel/compbio/data/sequence/FastaReader.java
+++ b/datamodel/compbio/data/sequence/FastaReader.java
@@ -135,26 +135,24 @@ public class FastaReader implements Iterator<FastaSequence> {
        }\r
 \r
        private static FastaSequence toFastaSequence(final String singleFastaEntry) {\r
-               final Scanner sc = new Scanner(singleFastaEntry);\r
-               // Use new line delimiter\r
-               sc.useDelimiter("\n");\r
-               if (!sc.hasNext()) {\r
+\r
+               assert !Util.isEmpty(singleFastaEntry) : "Empty String where FASTA sequence is expected!";\r
+\r
+               int nlineidx = singleFastaEntry.indexOf("\n");\r
+               if (nlineidx < 0) {\r
                        throw new AssertionError(\r
                                        "The FASTA sequence must contain the header information"\r
                                                        + " separated by the new line from the sequence. Given sequence does not appear to "\r
                                                        + "contain the header! Given data:\n "\r
                                                        + singleFastaEntry);\r
                }\r
-               String header = sc.next();\r
+               String header = singleFastaEntry.substring(0, nlineidx);\r
+\r
                // Get rid of the new line chars (should cover common cases)\r
                header = header.replaceAll("\r", "");\r
 \r
-               sc.useDelimiter("\\s*");\r
-               final StringBuilder sb = new StringBuilder();\r
-               while (sc.hasNext()) {\r
-                       sb.append(sc.next());\r
-               }\r
-               final String sequence = sb.toString();\r
+               String sequence = singleFastaEntry.substring(nlineidx);\r
+\r
                if (Util.isEmpty(sequence)) {\r
                        throw new AssertionError(\r
                                        "Empty sequences are not allowed! Please make sure the "\r