Javadoc fixes

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

diff --git a/datamodel/compbio/data/sequence/ClustalAlignmentUtil.java b/datamodel/compbio/data/sequence/ClustalAlignmentUtil.java
index 2d1a616..fc44c44 100644 (file)
--- 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;\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
@@ -202,17 +200,15 @@ public final class ClustalAlignmentUtil {
         * consensus. Potential bug - records 60 chars length alignment where\r
         * Clustal would have recorded 50 chars.\r
         * \r
-        * @param outStream\r
+        * @param out\r
         * \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
@@ -249,10 +245,10 @@ public final class ClustalAlignmentUtil {
                                // 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