import java.io.IOException;\r
import java.io.InputStream;\r
import java.io.InputStreamReader;\r
-import java.io.OutputStream;\r
-import java.io.OutputStreamWriter;\r
-import java.io.PrintWriter;\r
+import java.io.Writer;\r
import java.util.ArrayList;\r
import java.util.Arrays;\r
import java.util.HashMap;\r
* @param alignment\r
* @throws IOException\r
*/\r
- public static void writeClustalAlignment(final OutputStream outStream,\r
+ public static void writeClustalAlignment(final Writer out,\r
final Alignment alignment) throws IOException {\r
List<FastaSequence> seqs = alignment.getSequences();\r
\r
- PrintWriter out = new PrintWriter(new OutputStreamWriter(outStream));\r
-\r
out.write("CLUSTAL\n\n\n");\r
\r
int max = 0;\r
// display at most 30 characters in the name, keep the names\r
// 6 spaces away from the alignment for longest sequence names,\r
// and more than this for shorter names\r
- out.format(\r
+ out.write(String.format(\r
"%-" + maxidLength + "s" + spacer,\r
(name.length() > maxNameLength ? name.substring(0,\r
- maxidLength) : name));\r
+ maxidLength) : name)));\r
int start = i * oneLineAlignmentLength;\r
int end = start + oneLineAlignmentLength;\r
\r