From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Thu, 28 Apr 2011 10:47:29 +0000 (+0000)
Subject: FastaReader build into the datamodel
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=53217f65cb529e859838b528e4ac81a7169e2519;p=jabaws.git

FastaReader build into the datamodel

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4045 e3abac25-378b-4346-85de-24260fe3988d
---

diff --git a/build.xml b/build.xml
index 9b30d3a..fc99421 100644
--- a/build.xml
+++ b/build.xml
@@ -8,8 +8,8 @@
 	<!-- Distributive file names-->
 	<property name="distdir" value="website/archive"/>
 	<mkdir dir="${distdir}" />
-	<property name="datamodel" value="${distdir}/datamodel-1.1.jar"/>
-	<property name="datamodel-src" value="${distdir}/datamodel-src-1.1.jar"/>
+	<property name="datamodel" value="${distdir}/datamodel-1.2.jar"/>
+	<property name="datamodel-src" value="${distdir}/datamodel-src-1.2.jar"/>
 	<property name="min-jaba-client" value="${distdir}/min-jaba-client.jar"/>
 	<property name="aacon-ws-client" value="${distdir}/aacon-ws-client.jar"/>
 	<property name="full-jaba-client" value="${distdir}/full-jaba-client.jar"/>
diff --git a/datamodel/compbio/data/sequence/FastaReader.java b/datamodel/compbio/data/sequence/FastaReader.java
index ed91e93..2e1357f 100644
--- a/datamodel/compbio/data/sequence/FastaReader.java
+++ b/datamodel/compbio/data/sequence/FastaReader.java
@@ -135,26 +135,24 @@ public class FastaReader implements Iterator<FastaSequence> {
 	}
 
 	private static FastaSequence toFastaSequence(final String singleFastaEntry) {
-		final Scanner sc = new Scanner(singleFastaEntry);
-		// Use new line delimiter
-		sc.useDelimiter("\n");
-		if (!sc.hasNext()) {
+
+		assert !Util.isEmpty(singleFastaEntry) : "Empty String where FASTA sequence is expected!";
+
+		int nlineidx = singleFastaEntry.indexOf("\n");
+		if (nlineidx < 0) {
 			throw new AssertionError(
 					"The FASTA sequence must contain the header information"
 							+ " separated by the new line from the sequence. Given sequence does not appear to "
 							+ "contain the header! Given data:\n "
 							+ singleFastaEntry);
 		}
-		String header = sc.next();
+		String header = singleFastaEntry.substring(0, nlineidx);
+
 		// Get rid of the new line chars (should cover common cases)
 		header = header.replaceAll("\r", "");
 
-		sc.useDelimiter("\\s*");
-		final StringBuilder sb = new StringBuilder();
-		while (sc.hasNext()) {
-			sb.append(sc.next());
-		}
-		final String sequence = sb.toString();
+		String sequence = singleFastaEntry.substring(nlineidx);
+
 		if (Util.isEmpty(sequence)) {
 			throw new AssertionError(
 					"Empty sequences are not allowed! Please make sure the "
diff --git a/website/archive/datamodel-1.2.jar b/website/archive/datamodel-1.2.jar
new file mode 100644
index 0000000..4c7cffc
Binary files /dev/null and b/website/archive/datamodel-1.2.jar differ
diff --git a/website/archive/datamodel-src-1.2.jar b/website/archive/datamodel-src-1.2.jar
new file mode 100644
index 0000000..6b324de
Binary files /dev/null and b/website/archive/datamodel-src-1.2.jar differ