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