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