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