webservices/compbio/ws/client/IOHelper.java

   1 package compbio.ws.client;\r
   2 \r
   3 import static compbio.ws.client.Constraints.pseparator;\r
   4 \r
   5 import java.io.BufferedReader;\r
   6 import java.io.File;\r
   7 import java.io.FileNotFoundException;\r
   8 import java.io.FileOutputStream;\r
   9 import java.io.FileReader;\r
  10 import java.io.IOException;\r
  11 import java.io.OutputStream;\r
  12 import java.util.ArrayList;\r
  13 import java.util.List;\r
  14 \r
  15 import compbio.data.sequence.Alignment;\r
  16 import compbio.data.sequence.ClustalAlignmentUtil;\r
  17 \r
  18 public class IOHelper {\r
  19 \r
  20         /**\r
  21          * Checks -i options and return the File if one was provided, null otherwise\r
  22          * \r
  23          * @param cmd\r
  24          * @param key\r
  25          * @param mustExist\r
  26          * @return\r
  27          * @throws IOException\r
  28          */\r
  29         static File getFile(String[] cmd, String key, boolean mustExist)\r
  30                         throws IOException {\r
  31                 assert key != null && key.trim().length() != 0;\r
  32                 for (int i = 0; i < cmd.length; i++) {\r
  33                         String filename = cmd[i];\r
  34                         filename = filename.trim();\r
  35                         if (filename.toLowerCase().startsWith(key + pseparator)) {\r
  36                                 filename = filename.substring((key + pseparator).length());\r
  37                                 File file = new File(filename);\r
  38                                 if (mustExist && !file.exists()) {\r
  39                                         System.out.println(key + " file " + file.getAbsolutePath()\r
  40                                                         + " does not exist");\r
  41                                         return null;\r
  42                                 }\r
  43                                 if (!mustExist && !file.exists()) {\r
  44                                         file.createNewFile();\r
  45                                 }\r
  46                                 if (!file.canRead()) {\r
  47                                         System.out.println("Cannot read " + key + " file "\r
  48                                                         + file.getAbsolutePath());\r
  49                                         return null;\r
  50                                 }\r
  51                                 return file;\r
  52                         }\r
  53                 }\r
  54                 return null;\r
  55         }\r
  56 \r
  57         /**\r
  58          * Load parameters from file\r
  59          * \r
  60          * @throws IOException\r
  61          */\r
  62         static List<String> loadParameters(File paramsfile) throws IOException {\r
  63                 assert paramsfile != null && paramsfile.exists();\r
  64                 BufferedReader reader = new BufferedReader(new FileReader(paramsfile));\r
  65                 String line = null;\r
  66                 ArrayList<String> params = new ArrayList<String>();\r
  67                 while ((line = reader.readLine()) != null) {\r
  68                         line = line.trim();\r
  69                         if (line.length() == 0)\r
  70                                 continue;\r
  71                         params.add(line);\r
  72                 }\r
  73                 return params;\r
  74         }\r
  75 \r
  76         static OutputStream getOutStream(File file) {\r
  77                 assert file != null && file.exists();\r
  78                 try {\r
  79                         return new FileOutputStream(file);\r
  80                 } catch (FileNotFoundException e) {\r
  81                         e.printStackTrace();\r
  82                 }\r
  83                 return null;\r
  84         }\r
  85 \r
  86         /**\r
  87          * Outputs clustal formatted alignment into the file represented by the\r
  88          * outStream\r
  89          * \r
  90          * @param outStream\r
  91          * @param align\r
  92          *            the alignment to output\r
  93          */\r
  94         static void writeOut(OutputStream outStream, Alignment align) {\r
  95                 try {\r
  96                         ClustalAlignmentUtil.writeClustalAlignment(outStream, align);\r
  97                 } catch (IOException e) {\r
  98                         System.err\r
  99                                         .println("Problems writing output file! Stack trace is below: ");\r
 100                         e.printStackTrace();\r
 101                 } finally {\r
 102                         if (outStream != null) {\r
 103                                 try {\r
 104                                         outStream.close();\r
 105                                 } catch (IOException ignored) {\r
 106                                         // e.printStackTrace();\r
 107                                 }\r
 108                         }\r
 109                 }\r
 110         }\r
 111 \r
 112 }\r