testsrc/compbio/data/sequence/FastaGeneratorManager.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     \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 \r
  19 package compbio.data.sequence;\r
  20 \r
  21 import java.io.IOException;\r
  22 import java.util.List;\r
  23 \r
  24 import compbio.util.FileUtil;\r
  25 \r
  26 public class FastaGeneratorManager {\r
  27 \r
  28         public static void main(String[] args) throws IOException {\r
  29                 FastaSequenceGenerator fgen = new FastaSequenceGenerator(\r
  30                                 FastaSequenceGenerator.SeqType.PROTEIN, 50);\r
  31 \r
  32                 List<FastaSequence> fslist = fgen.generateFasta(400);\r
  33                 writeToFile(fslist, "SmallProtein.fasta");\r
  34 \r
  35                 fgen = new FastaSequenceGenerator(\r
  36                                 FastaSequenceGenerator.SeqType.PROTEIN, 200);\r
  37 \r
  38                 fslist = fgen.generateFasta(500);\r
  39                 writeToFile(fslist, "200x500Protein.fasta");\r
  40 \r
  41                 fgen = new FastaSequenceGenerator(FastaSequenceGenerator.SeqType.DNA,\r
  42                                 1000);\r
  43                 fslist = fgen.generateFasta(3000);\r
  44                 writeToFile(fslist, "1000x3000Dna.fasta");\r
  45 \r
  46                 fgen = new FastaSequenceGenerator(FastaSequenceGenerator.SeqType.DNA,\r
  47                                 50000);\r
  48                 fslist = fgen.generateFasta(300);\r
  49                 writeToFile(fslist, "50000x300Dna.fasta");\r
  50                 System.out.println("Done");\r
  51         }\r
  52 \r
  53         static void writeToFile(List<FastaSequence> fastalist, String filepath)\r
  54                         throws IOException {\r
  55                 StringBuilder sb = new StringBuilder();\r
  56                 for (FastaSequence fs : fastalist) {\r
  57                         sb.append(fs.getOnelineFasta() + "\n");\r
  58                 }\r
  59                 FileUtil.writeToFile(sb.toString(), filepath);\r
  60         }\r
  61 }\r