X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datamodel%2Fcompbio%2Fdata%2Fsequence%2FClustalAlignmentUtil.java;h=fc44c441b464106fb7a11dd19c1a7078cce89243;hb=ba2d4e920e433bd080f448248e7dacade69a27a0;hp=2d1a616b95fa40b88bf2ae2753e470fb4433af52;hpb=73ca89ba470d6251d2f37ae6b7f443f133c35ab9;p=jabaws.git

diff --git a/datamodel/compbio/data/sequence/ClustalAlignmentUtil.java b/datamodel/compbio/data/sequence/ClustalAlignmentUtil.java
index 2d1a616..fc44c44 100644
--- a/datamodel/compbio/data/sequence/ClustalAlignmentUtil.java
+++ b/datamodel/compbio/data/sequence/ClustalAlignmentUtil.java
@@ -24,9 +24,7 @@ import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
+import java.io.Writer;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -202,17 +200,15 @@ public final class ClustalAlignmentUtil {
 	 * consensus. Potential bug - records 60 chars length alignment where
 	 * Clustal would have recorded 50 chars.
 	 * 
-	 * @param outStream
+	 * @param out
 	 * 
 	 * @param alignment
 	 * @throws IOException
 	 */
-	public static void writeClustalAlignment(final OutputStream outStream,
+	public static void writeClustalAlignment(final Writer out,
 			final Alignment alignment) throws IOException {
 		List<FastaSequence> seqs = alignment.getSequences();
 
-		PrintWriter out = new PrintWriter(new OutputStreamWriter(outStream));
-
 		out.write("CLUSTAL\n\n\n");
 
 		int max = 0;
@@ -249,10 +245,10 @@ public final class ClustalAlignmentUtil {
 				// display at most 30 characters in the name, keep the names
 				// 6 spaces away from the alignment for longest sequence names,
 				// and more than this for shorter names
-				out.format(
+				out.write(String.format(
 						"%-" + maxidLength + "s" + spacer,
 						(name.length() > maxNameLength ? name.substring(0,
-								maxidLength) : name));
+								maxidLength) : name)));
 				int start = i * oneLineAlignmentLength;
 				int end = start + oneLineAlignmentLength;