runner/compbio/pipeline/_jpred/Pairwise.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.pipeline._jpred;\r
  19 \r
  20 import java.io.BufferedInputStream;\r
  21 import java.io.File;\r
  22 import java.io.FileInputStream;\r
  23 import java.io.FileNotFoundException;\r
  24 import java.io.IOException;\r
  25 import java.util.HashSet;\r
  26 import java.util.List;\r
  27 import java.util.Set;\r
  28 \r
  29 import compbio.data.sequence.FastaSequence;\r
  30 import compbio.data.sequence.SequenceUtil;\r
  31 \r
  32 public class Pairwise {\r
  33 \r
  34         private final List<FastaSequence> sequences; \r
  35         final Set<PScore> pscores; \r
  36         \r
  37         public Pairwise(List<FastaSequence> sequences) {\r
  38                 this.sequences = sequences;\r
  39                 pscores = new HashSet<PScore>(); \r
  40         }\r
  41 \r
  42         void compare() {\r
  43                 for (int i = 0; i < sequences.size(); i++) {\r
  44                         FastaSequence seq1 = sequences.get(i); \r
  45                         System.out.println(seq1.getId());\r
  46                         for (int j = i+1; j < sequences.size(); j++) {\r
  47                                 FastaSequence seq2 = sequences.get(j);\r
  48                                 PScore pscore = new PScore();\r
  49                                 pscore.name = seq1.getId();\r
  50                                 pscore.otherName = seq2.getId();\r
  51                                 pscores.add(pscore);\r
  52                                 compare(pscore, seq1.getSequence(), seq2.getSequence());\r
  53                         }\r
  54                 }\r
  55         }\r
  56 \r
  57         void compare(PScore pscore, String seq1, String seq2) { \r
  58                 char[] chars1 = seq1.trim().toUpperCase().toCharArray(); \r
  59                 char[] chars2 = seq2.trim().toUpperCase().toCharArray();\r
  60                 if(chars1.length != chars2.length) { \r
  61                         throw new IllegalArgumentException("Different lenght sequence are provided but same expected! \n Sequence 1: \n" + pscore.name+ \r
  62                                         "\n Length:"+chars1.length +"\n "+ \r
  63                                         "Sequence 2: \n " + pscore.otherName + \r
  64                                         " \n Lenght: " + chars2.length ); \r
  65                 }\r
  66                 compare(pscore, chars1, chars2); \r
  67         }\r
  68         \r
  69         void compare(PScore pscore, char[] seq1, char[] seq2) { \r
  70                 int sameResedue = 0; \r
  71                 for (int i = 0; i < seq1.length; i++) {\r
  72                         if(seq1[i]==seq2[i]) { \r
  73                                 sameResedue++;\r
  74                         }\r
  75                 }\r
  76                 pscore.score = (double)sameResedue /seq1.length;\r
  77                 System.out.println(pscore.score*100);\r
  78         }\r
  79         \r
  80         public static final void main(String[]  args) throws FileNotFoundException, IOException {\r
  81                 File in = new File(args[0]);\r
  82                 List<FastaSequence> fslist = SequenceUtil.readFasta(new BufferedInputStream(new FileInputStream(in)));\r
  83                 Pairwise pair = new Pairwise(fslist);\r
  84                 pair.compare(); \r
  85                 System.out.println(pair.pscores);\r
  86         }\r
  87 }\r