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