\r
import java.io.BufferedReader;\r
import java.io.File;\r
-import java.io.FileNotFoundException;\r
-import java.io.FileOutputStream;\r
import java.io.FileReader;\r
+import java.io.FileWriter;\r
import java.io.IOException;\r
-import java.io.OutputStream;\r
+import java.io.Writer;\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
return params;\r
}\r
\r
- static OutputStream getOutStream(File file) {\r
+ static Writer getWriter(File file) throws IOException {\r
assert file != null && file.exists();\r
- try {\r
- return new FileOutputStream(file);\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- }\r
- return null;\r
+ return new FileWriter(file);\r
}\r
\r
/**\r
* @param align\r
* the alignment to output\r
*/\r
- static void writeOut(OutputStream outStream, Alignment align) {\r
+ static void writeOut(Writer writer, Alignment align) {\r
try {\r
- ClustalAlignmentUtil.writeClustalAlignment(outStream, align);\r
+ ClustalAlignmentUtil.writeClustalAlignment(writer, align);\r
} catch (IOException e) {\r
System.err\r
.println("Problems writing output file! Stack trace is below: ");\r
e.printStackTrace();\r
} finally {\r
- if (outStream != null) {\r
+ if (writer != null) {\r
try {\r
- outStream.close();\r
+ writer.close();\r
} catch (IOException ignored) {\r
// e.printStackTrace();\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(Writer writer, 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(writer);\r
} catch (IOException e) {\r
System.err\r
.println("Problems writing output file! Stack trace is below: ");\r
e.printStackTrace();\r
} finally {\r
- if (outStream != null) {\r
+ if (writer != null) {\r
try {\r
- outStream.close();\r
+ writer.close();\r
} catch (IOException ignored) {\r
// e.printStackTrace();\r
}\r