1 /********************
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2 * 2004 Jalview Reengineered
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14 public class IdentifyFile
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16 public static String Identify(String file, String protocol)
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18 String reply = "PFAM";
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21 BufferedReader reader = null;
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23 if(protocol.equals("File"))
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24 reader = new BufferedReader(new FileReader(file));
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26 else if (protocol.equals("URL"))
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28 reply = "URL NOT FOUND";
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29 URL url = new URL(file);
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30 reader = new BufferedReader(new InputStreamReader( url.openStream() ) );
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33 else if( protocol.equals("Paste"))
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34 reader = new BufferedReader( new StringReader(file) );
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38 while( (data=reader.readLine())!=null)
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40 data = data.toUpperCase();
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41 if(data.indexOf("#")==0 || data.length()<1)
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44 if(data.indexOf("PILEUP")>-1)
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49 if((data.indexOf("!!")>-1)
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50 && (data.indexOf("!!")<data.indexOf("_MULTIPLE_ALIGNMENT ")))
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55 else if(data.indexOf("CLUSTAL")>-1)
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60 else if(data.indexOf(">P1;")>-1 || data.indexOf(">DL;")>-1)
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65 else if(data.indexOf(">")>-1)
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67 // could be BLC file, read next line to confirm
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68 data = reader.readLine();
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69 if(data.indexOf(">")>-1)
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79 catch(Exception ex){
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80 System.err.println("File Identification failed!"); ex.printStackTrace();}
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