src/jalview/io/IdentifyFile.java

   1 /*\r
   2 * Jalview - A Sequence Alignment Editor and Viewer\r
   3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4 *\r
   5 * This program is free software; you can redistribute it and/or\r
   6 * modify it under the terms of the GNU General Public License\r
   7 * as published by the Free Software Foundation; either version 2\r
   8 * of the License, or (at your option) any later version.\r
   9 *\r
  10 * This program is distributed in the hope that it will be useful,\r
  11 * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13 * GNU General Public License for more details.\r
  14 *\r
  15 * You should have received a copy of the GNU General Public License\r
  16 * along with this program; if not, write to the Free Software\r
  17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18 */\r
  19 package jalview.io;\r
  20 \r
  21 import java.io.*;\r
  22 \r
  23 import java.net.*;\r
  24 \r
  25 \r
  26 /**\r
  27  * DOCUMENT ME!\r
  28  *\r
  29  * @author $author$\r
  30  * @version $Revision$\r
  31  */\r
  32 public class IdentifyFile\r
  33 {\r
  34     /**\r
  35      * DOCUMENT ME!\r
  36      *\r
  37      * @param file DOCUMENT ME!\r
  38      * @param protocol DOCUMENT ME!\r
  39      *\r
  40      * @return DOCUMENT ME!\r
  41      */\r
  42     public String Identify(String file, String protocol)\r
  43     {\r
  44         String reply = "PFAM";\r
  45         String error =  "FILE NOT FOUND";\r
  46         try\r
  47         {\r
  48             BufferedReader reader = null;\r
  49 \r
  50             if (protocol.equals(AppletFormatAdapter.FILE))\r
  51             {\r
  52               reader = new BufferedReader(new FileReader(file));\r
  53             }\r
  54             else if (protocol.equals(AppletFormatAdapter.URL))\r
  55             {\r
  56               error = "URL NOT FOUND";\r
  57               URL url = new URL(file);\r
  58               reader = new BufferedReader(new InputStreamReader(\r
  59                   url.openStream()));\r
  60 \r
  61             }\r
  62             else if (protocol.equals(AppletFormatAdapter.PASTE))\r
  63             {\r
  64               reader = new BufferedReader(new StringReader(file));\r
  65             }\r
  66             else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))\r
  67             {\r
  68               java.io.InputStream is = getClass().getResourceAsStream("/" +\r
  69                   file);\r
  70               reader = new BufferedReader(new java.io.InputStreamReader(is));\r
  71             }\r
  72 \r
  73             String data;\r
  74 \r
  75             while ((data = reader.readLine()) != null)\r
  76             {\r
  77                 data = data.toUpperCase();\r
  78 \r
  79                 if ( (data.indexOf("# STOCKHOLM") > -1))\r
  80                 {\r
  81                   reply = "STH";\r
  82 \r
  83                   break;\r
  84                 }\r
  85 \r
  86                 if ((data.indexOf("#") == 0) || (data.length() < 1))\r
  87                 {\r
  88                     continue;\r
  89                 }\r
  90 \r
  91                 if (data.indexOf("PILEUP") > -1)\r
  92                 {\r
  93                     reply = "PileUp";\r
  94 \r
  95                     break;\r
  96                 }\r
  97 \r
  98                 if ((data.indexOf("//") == 0) ||\r
  99                         ((data.indexOf("!!") > -1) &&\r
 100                         (data.indexOf("!!") < data.indexOf(\r
 101                             "_MULTIPLE_ALIGNMENT "))))\r
 102                 {\r
 103                     reply = "MSF";\r
 104 \r
 105                     break;\r
 106                 }\r
 107                 else if (data.indexOf("CLUSTAL") > -1)\r
 108                 {\r
 109                     reply = "CLUSTAL";\r
 110 \r
 111                     break;\r
 112                 }\r
 113                 else if ((data.indexOf(">P1;") > -1) ||\r
 114                         (data.indexOf(">DL;") > -1))\r
 115                 {\r
 116                     reply = "PIR";\r
 117 \r
 118                     break;\r
 119                 }\r
 120                 else if (data.indexOf(">") > -1)\r
 121                 {\r
 122                     // could be BLC file, read next line to confirm\r
 123                     data = reader.readLine();\r
 124 \r
 125                     if (data.indexOf(">") > -1)\r
 126                     {\r
 127                         reply = "BLC";\r
 128                     }\r
 129                     else\r
 130                     {\r
 131                       //Is this a single line BLC file?\r
 132                       reader.readLine();\r
 133                       String data2 = reader.readLine();\r
 134                       if ( data2 != null\r
 135                            && data.indexOf("*")>-1\r
 136                            && data.indexOf("*")==data2.indexOf("*"))\r
 137                       {\r
 138                         reply = "BLC";\r
 139                       }\r
 140                       else\r
 141                       {\r
 142                         reply = "FASTA";\r
 143                       }\r
 144                     }\r
 145 \r
 146                     break;\r
 147                   }\r
 148                   else if (data.indexOf("HEADER") == 0 ||\r
 149                            data.indexOf("ATOM") == 0)\r
 150                   {\r
 151                     reply = "PDB";\r
 152                     break;\r
 153                   }\r
 154                   else if (data.indexOf(":") < data.indexOf(",")) //  && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))\r
 155                   {\r
 156                     // file looks like a concise JNet file\r
 157                     reply = "JnetFile";\r
 158                     break;\r
 159                   }\r
 160             }\r
 161 \r
 162             reader.close();\r
 163         }\r
 164         catch (Exception ex)\r
 165         {\r
 166             System.err.println("File Identification failed!\n" + ex);\r
 167             return error;\r
 168         }\r
 169 \r
 170         return reply;\r
 171     }\r
 172 }\r