webservices/compbio/ws/client/IOHelper.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 package compbio.ws.client;\r
  19 \r
  20 import static compbio.ws.client.Constraints.pseparator;\r
  21 \r
  22 import java.io.BufferedReader;\r
  23 import java.io.File;\r
  24 import java.io.FileReader;\r
  25 import java.io.FileWriter;\r
  26 import java.io.IOException;\r
  27 import java.io.Writer;\r
  28 import java.util.ArrayList;\r
  29 import java.util.List;\r
  30 \r
  31 import compbio.data.sequence.Alignment;\r
  32 import compbio.data.sequence.ClustalAlignmentUtil;\r
  33 import compbio.data.sequence.ScoreManager;\r
  34 \r
  35 public class IOHelper {\r
  36 \r
  37         /**\r
  38          * Checks -i options and return the File if one was provided, null otherwise\r
  39          * \r
  40          * @param cmd\r
  41          * @param key\r
  42          * @param mustExist\r
  43          * @return\r
  44          * @throws IOException\r
  45          */\r
  46         static File getFile(String[] cmd, String key, boolean mustExist)\r
  47                         throws IOException {\r
  48                 assert key != null && key.trim().length() != 0;\r
  49                 for (int i = 0; i < cmd.length; i++) {\r
  50                         String filename = cmd[i];\r
  51                         filename = filename.trim();\r
  52                         if (filename.toLowerCase().startsWith(key + pseparator)) {\r
  53                                 filename = filename.substring((key + pseparator).length());\r
  54                                 File file = new File(filename);\r
  55                                 if (mustExist && !file.exists()) {\r
  56                                         System.out.println(key + " file " + file.getAbsolutePath()\r
  57                                                         + " does not exist");\r
  58                                         return null;\r
  59                                 }\r
  60                                 if (!mustExist && !file.exists()) {\r
  61                                         file.createNewFile();\r
  62                                 }\r
  63                                 if (!file.canRead()) {\r
  64                                         System.out.println("Cannot read " + key + " file "\r
  65                                                         + file.getAbsolutePath());\r
  66                                         return null;\r
  67                                 }\r
  68                                 return file;\r
  69                         }\r
  70                 }\r
  71                 return null;\r
  72         }\r
  73 \r
  74         /**\r
  75          * Load parameters from file\r
  76          * \r
  77          * @throws IOException\r
  78          */\r
  79         static List<String> loadParameters(File paramsfile) throws IOException {\r
  80                 assert paramsfile != null && paramsfile.exists();\r
  81                 BufferedReader reader = new BufferedReader(new FileReader(paramsfile));\r
  82                 String line = null;\r
  83                 ArrayList<String> params = new ArrayList<String>();\r
  84                 while ((line = reader.readLine()) != null) {\r
  85                         line = line.trim();\r
  86                         if (line.length() == 0)\r
  87                                 continue;\r
  88                         params.add(line);\r
  89                 }\r
  90                 return params;\r
  91         }\r
  92 \r
  93         static Writer getWriter(File file) throws IOException {\r
  94                 assert file != null && file.exists();\r
  95                 return new FileWriter(file);\r
  96         }\r
  97 \r
  98         /**\r
  99          * Outputs clustal formatted alignment into the file represented by the\r
 100          * outStream\r
 101          * \r
 102          * @param outStream\r
 103          * @param align\r
 104          *            the alignment to output\r
 105          */\r
 106         static void writeOut(Writer writer, Alignment align) {\r
 107                 try {\r
 108                         ClustalAlignmentUtil.writeClustalAlignment(writer, align);\r
 109                 } catch (IOException e) {\r
 110                         System.err\r
 111                                         .println("Problems writing output file! Stack trace is below: ");\r
 112                         e.printStackTrace();\r
 113                 } finally {\r
 114                         if (writer != null) {\r
 115                                 try {\r
 116                                         writer.close();\r
 117                                 } catch (IOException ignored) {\r
 118                                         // e.printStackTrace();\r
 119                                 }\r
 120                         }\r
 121                 }\r
 122         }\r
 123 \r
 124         /**\r
 125          * Outputs AAcon results into the file represented by the outStream\r
 126          * \r
 127          * @param outStream\r
 128          * @param result\r
 129          *            the AACon scores to output\r
 130          */\r
 131         static void writeOut(Writer writer, ScoreManager results) {\r
 132                 if (results == null) {\r
 133                         return;\r
 134                 }\r
 135                 try {\r
 136                         results.writeOut(writer);\r
 137                 } catch (IOException e) {\r
 138                         System.err\r
 139                                         .println("Problems writing output file! Stack trace is below: ");\r
 140                         e.printStackTrace();\r
 141                 } finally {\r
 142                         if (writer != null) {\r
 143                                 try {\r
 144                                         writer.close();\r
 145                                 } catch (IOException ignored) {\r
 146                                         // e.printStackTrace();\r
 147                                 }\r
 148                         }\r
 149                 }\r
 150         }\r
 151 \r
 152 }\r