src/jalview/io/IdentifyFile.java

   1 /*
   2 * Jalview - A Sequence Alignment Editor and Viewer
   3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4 *
   5 * This program is free software; you can redistribute it and/or
   6 * modify it under the terms of the GNU General Public License
   7 * as published by the Free Software Foundation; either version 2
   8 * of the License, or (at your option) any later version.
   9 *
  10 * This program is distributed in the hope that it will be useful,
  11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13 * GNU General Public License for more details.
  14 *
  15 * You should have received a copy of the GNU General Public License
  16 * along with this program; if not, write to the Free Software
  17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18 */
  19 package jalview.io;
  20
  21 import java.io.*;
  22
  23 import java.net.*;
  24
  25
  26 /**
  27  * DOCUMENT ME!
  28  *
  29  * @author $author$
  30  * @version $Revision$
  31  */
  32 public class IdentifyFile
  33 {
  34     /**
  35      * DOCUMENT ME!
  36      *
  37      * @param file DOCUMENT ME!
  38      * @param protocol DOCUMENT ME!
  39      *
  40      * @return DOCUMENT ME!
  41      */
  42     public String Identify(String file, String protocol)
  43     {
  44         String reply = "PFAM";
  45         String error =  "FILE NOT FOUND";
  46         try
  47         {
  48             BufferedReader reader = null;
  49
  50             if (protocol.equals(AppletFormatAdapter.FILE))
  51             {
  52               reader = new BufferedReader(new FileReader(file));
  53             }
  54             else if (protocol.equals(AppletFormatAdapter.URL))
  55             {
  56               error = "URL NOT FOUND";
  57               URL url = new URL(file);
  58               reader = new BufferedReader(new InputStreamReader(
  59                   url.openStream()));
  60
  61             }
  62             else if (protocol.equals(AppletFormatAdapter.PASTE))
  63             {
  64               reader = new BufferedReader(new StringReader(file));
  65             }
  66             else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
  67             {
  68               java.io.InputStream is = getClass().getResourceAsStream("/" +
  69                   file);
  70               reader = new BufferedReader(new java.io.InputStreamReader(is));
  71             }
  72
  73             String data;
  74
  75             while ((data = reader.readLine()) != null)
  76             {
  77                 data = data.toUpperCase();
  78
  79                 if ( (data.indexOf("# STOCKHOLM") > -1))
  80                 {
  81                   reply = "STH";
  82
  83                   break;
  84                 }
  85
  86                 if ((data.indexOf("#") == 0) || (data.length() < 1))
  87                 {
  88                     continue;
  89                 }
  90
  91                 if (data.indexOf("PILEUP") > -1)
  92                 {
  93                     reply = "PileUp";
  94
  95                     break;
  96                 }
  97
  98                 if ((data.indexOf("//") == 0) ||
  99                         ((data.indexOf("!!") > -1) &&
 100                         (data.indexOf("!!") < data.indexOf(
 101                             "_MULTIPLE_ALIGNMENT "))))
 102                 {
 103                     reply = "MSF";
 104
 105                     break;
 106                 }
 107                 else if (data.indexOf("CLUSTAL") > -1)
 108                 {
 109                     reply = "CLUSTAL";
 110
 111                     break;
 112                 }
 113                 else if ((data.indexOf(">P1;") > -1) ||
 114                         (data.indexOf(">DL;") > -1))
 115                 {
 116                     reply = "PIR";
 117
 118                     break;
 119                 }
 120                 else if (data.indexOf(">") > -1)
 121                 {
 122                     // could be BLC file, read next line to confirm
 123                     data = reader.readLine();
 124
 125                     if (data.indexOf(">") > -1 || data.indexOf("*") >-1 )
 126                     {
 127                         reply = "BLC";
 128                     }
 129                     else
 130                     {
 131                         reply = "FASTA";
 132                     }
 133
 134                     break;
 135                   }
 136                   else if (data.indexOf("HEADER") > -1 ||
 137                            data.indexOf("ATOM") > -1)
 138                   {
 139                     reply = "PDB";
 140                     break;
 141                   }
 142                   else if (data.indexOf(":") < data.indexOf(",")) //  && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))
 143                   {
 144                     // file looks like a concise JNet file
 145                     reply = "JnetFile";
 146                     break;
 147                   }
 148             }
 149
 150             reader.close();
 151         }
 152         catch (Exception ex)
 153         {
 154             System.err.println("File Identification failed!\n" + ex);
 155             return error;
 156         }
 157
 158         return reply;
 159     }
 160 }