Refactored client class to accomodate new WS interface and reduce the complexity

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

diff --git a/webservices/compbio/ws/client/IOHelper.java b/webservices/compbio/ws/client/IOHelper.java
new file mode 100644 (file)
index 0000000..af9a52c
--- /dev/null
+++ b/webservices/compbio/ws/client/IOHelper.java
@@ -0,0 +1,112 @@
+package compbio.ws.client;\r
+\r
+import static compbio.ws.client.Constraints.pseparator;\r
+\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.IOException;\r
+import java.io.OutputStream;\r
+import java.util.ArrayList;\r
+import java.util.List;\r
+\r
+import compbio.data.sequence.Alignment;\r
+import compbio.data.sequence.ClustalAlignmentUtil;\r
+\r
+public class IOHelper {\r
+\r
+       /**\r
+        * Checks -i options and return the File if one was provided, null otherwise\r
+        * \r
+        * @param cmd\r
+        * @param key\r
+        * @param mustExist\r
+        * @return\r
+        * @throws IOException\r
+        */\r
+       static File getFile(String[] cmd, String key, boolean mustExist)\r
+                       throws IOException {\r
+               assert key != null && key.trim().length() != 0;\r
+               for (int i = 0; i < cmd.length; i++) {\r
+                       String filename = cmd[i];\r
+                       filename = filename.trim();\r
+                       if (filename.toLowerCase().startsWith(key + pseparator)) {\r
+                               filename = filename.substring((key + pseparator).length());\r
+                               File file = new File(filename);\r
+                               if (mustExist && !file.exists()) {\r
+                                       System.out.println(key + " file " + file.getAbsolutePath()\r
+                                                       + " does not exist");\r
+                                       return null;\r
+                               }\r
+                               if (!mustExist && !file.exists()) {\r
+                                       file.createNewFile();\r
+                               }\r
+                               if (!file.canRead()) {\r
+                                       System.out.println("Cannot read " + key + " file "\r
+                                                       + file.getAbsolutePath());\r
+                                       return null;\r
+                               }\r
+                               return file;\r
+                       }\r
+               }\r
+               return null;\r
+       }\r
+\r
+       /**\r
+        * Load parameters from file\r
+        * \r
+        * @throws IOException\r
+        */\r
+       static List<String> loadParameters(File paramsfile) throws IOException {\r
+               assert paramsfile != null && paramsfile.exists();\r
+               BufferedReader reader = new BufferedReader(new FileReader(paramsfile));\r
+               String line = null;\r
+               ArrayList<String> params = new ArrayList<String>();\r
+               while ((line = reader.readLine()) != null) {\r
+                       line = line.trim();\r
+                       if (line.length() == 0)\r
+                               continue;\r
+                       params.add(line);\r
+               }\r
+               return params;\r
+       }\r
+\r
+       static OutputStream getOutStream(File file) {\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
+       }\r
+\r
+       /**\r
+        * Outputs clustal formatted alignment into the file represented by the\r
+        * outStream\r
+        * \r
+        * @param outStream\r
+        * @param align\r
+        *            the alignment to output\r
+        */\r
+       static void writeOut(OutputStream outStream, Alignment align) {\r
+               try {\r
+                       ClustalAlignmentUtil.writeClustalAlignment(outStream, 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
+                               try {\r
+                                       outStream.close();\r
+                               } catch (IOException ignored) {\r
+                                       // e.printStackTrace();\r
+                               }\r
+                       }\r
+               }\r
+       }\r
+\r
+}\r