src/jalview/io/IdentifyFile.java

   1 /********************\r
   2  * 2004 Jalview Reengineered\r
   3  * Barton Group\r
   4  * Dundee University\r
   5  *\r
   6  * AM Waterhouse\r
   7  *******************/\r
   8 \r
   9 package jalview.io;\r
  10 \r
  11 import java.io.*;\r
  12 import java.net.*;\r
  13 \r
  14 public class IdentifyFile\r
  15 {\r
  16   public static String Identify(String file, String protocol)\r
  17   {\r
  18     String reply = "PFAM";\r
  19     try{\r
  20 \r
  21       BufferedReader reader = null;\r
  22 \r
  23       if(protocol.equals("File"))\r
  24         reader = new BufferedReader(new FileReader(file));\r
  25 \r
  26       else if (protocol.equals("URL"))\r
  27       {\r
  28         reply = "URL NOT FOUND";\r
  29         URL url = new URL(file);\r
  30         reader = new BufferedReader(new InputStreamReader( url.openStream() ) );\r
  31         reply = "error";\r
  32       }\r
  33       else if( protocol.equals("Paste"))\r
  34         reader = new BufferedReader( new StringReader(file) );\r
  35 \r
  36 \r
  37       String data;\r
  38       while( (data=reader.readLine())!=null)\r
  39       {\r
  40         data = data.toUpperCase();\r
  41         if(data.indexOf("#")==0 || data.length()<1)\r
  42           continue;\r
  43 \r
  44         if(data.indexOf("PILEUP")>-1)\r
  45         {\r
  46           reply = "PileUp";\r
  47           break;\r
  48         }\r
  49         if((data.indexOf("!!")>-1)\r
  50            && (data.indexOf("!!")<data.indexOf("_MULTIPLE_ALIGNMENT ")))\r
  51         {\r
  52           reply = "MSF";\r
  53           break;\r
  54         }\r
  55         else if(data.indexOf("CLUSTAL")>-1)\r
  56         {\r
  57           reply = "CLUSTAL";\r
  58           break;\r
  59         }\r
  60         else if(data.indexOf(">P1;")>-1 || data.indexOf(">DL;")>-1)\r
  61         {\r
  62           reply = "PIR";\r
  63           break;\r
  64         }\r
  65         else if(data.indexOf(">")>-1)\r
  66         {\r
  67           // could be BLC file, read next line to confirm\r
  68           data = reader.readLine();\r
  69           if(data.indexOf(">")>-1)\r
  70             reply = "BLC";\r
  71           else\r
  72             reply = "FASTA";\r
  73 \r
  74             break;\r
  75         }\r
  76       }\r
  77       reader.close();\r
  78     }\r
  79     catch(Exception ex){\r
  80       System.err.println("File Identification failed!"); ex.printStackTrace();}\r
  81 \r
  82     return reply;\r
  83   }\r
  84 \r
  85 \r
  86 }\r