runner/compbio/pipeline/_jpred/BlastParser.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  Jalview Web Services @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 import java.io.*;\r
  20 import java.util.*;\r
  21 \r
  22 import javax.xml.stream.XMLInputFactory;\r
  23 import javax.xml.stream.XMLStreamException;\r
  24 import javax.xml.stream.XMLStreamReader;\r
  25 \r
  26 \r
  27 public class BlastParser {\r
  28         \r
  29         static class Psiseq {\r
  30                 String id;\r
  31                 String seq;\r
  32         }\r
  33         /**\r
  34          * args[0] is assumed to be the name of a Blast output file\r
  35          * @throws XMLStreamException \r
  36          * @throws FileNotFoundException \r
  37          */\r
  38         public static void main(String[] args) throws FileNotFoundException, XMLStreamException {\r
  39                 XMLInputFactory f = XMLInputFactory.newInstance();\r
  40                 XMLStreamReader r = f.createXMLStreamReader( new BufferedInputStream(new FileInputStream(new File(args[0]))));\r
  41                 List<Psiseq> pl = new ArrayList<Psiseq>();\r
  42                 Psiseq psi = null;\r
  43                 while(r.hasNext()) {\r
  44                         int idx = r.next(); \r
  45                         //System.out.println(idx);\r
  46 \r
  47                         if(r.isStartElement()) {\r
  48                                 String name = r.getLocalName();\r
  49                                 if(name.equals("Hit") ) {\r
  50                                         psi = new Psiseq();\r
  51                                 }\r
  52                                 if(name.equals("Hit_id") ) {\r
  53                                         //System.out.println(r.getElementText());\r
  54                                         psi.id = r.getElementText();\r
  55                                         System.out.println(psi.id);\r
  56                                 } \r
  57                                 if(name.equals("Hsp_hseq")) {\r
  58                                         psi.seq = r.getElementText();\r
  59                                         System.out.println(psi.seq);\r
  60                                 } \r
  61                         }\r
  62                         \r
  63                         if(r.isEndElement()) {\r
  64                                 String name = r.getLocalName();\r
  65                                 if(name.equals("Hit") ) {\r
  66                                         pl.add(psi);\r
  67                                         psi = null;\r
  68                                 }\r
  69                         }\r
  70 \r
  71                 } \r
  72 \r
  73         }\r
  74 }\r