More work to disorder prediction client & services.

[jabaws.git] / webservices / compbio / ws / client / IOHelper.java

diff --git a/webservices/compbio/ws/client/IOHelper.java b/webservices/compbio/ws/client/IOHelper.java
index 8fbf763..88b695a 100644 (file)
--- a/webservices/compbio/ws/client/IOHelper.java
+++ b/webservices/compbio/ws/client/IOHelper.java
@@ -4,11 +4,10 @@ import static compbio.ws.client.Constraints.pseparator;
 \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.List;\r
 \r
@@ -74,14 +73,9 @@ public class IOHelper {
                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
@@ -92,17 +86,17 @@ public class IOHelper {
         * @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
@@ -117,17 +111,17 @@ public class IOHelper {
         * @param result\r
         *            the AACon scores to output\r
         */\r
-       static void writeOut(OutputStream outStream, ScoreManager results) {\r
+       static void writeOut(Writer writer, ScoreManager results) {\r
                try {\r
-                       results.writeOut(outStream);\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