import java.io.IOException;\r
import java.io.OutputStream;\r
import java.util.ArrayList;\r
+import java.util.HashSet;\r
import java.util.List;\r
-import java.util.Set;\r
+import java.util.Map;\r
\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.ClustalAlignmentUtil;\r
* @param result\r
* the AACon scores to output\r
*/\r
- static void writeOut(OutputStream outStream, Set<Score> result) {\r
+ static void writeOut(OutputStream outStream,\r
+ Map<String, HashSet<Score>> result) {\r
try {\r
- Score.write(result, outStream);\r
+ for (Map.Entry<String, HashSet<Score>> entry : result.entrySet()) {\r
+ System.out.println(">" + entry.getKey());\r
+ Score.write(entry.getValue(), outStream);\r
+ }\r
} catch (IOException e) {\r
System.err\r
.println("Problems writing output file! Stack trace is below: ");\r