2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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25 public class IdentifyFile
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27 public static String Identify(String file, String protocol)
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29 String reply = "PFAM";
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32 BufferedReader reader = null;
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34 if(protocol.equals("File"))
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35 reader = new BufferedReader(new FileReader(file));
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37 else if (protocol.equals("URL"))
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39 reply = "URL NOT FOUND";
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40 URL url = new URL(file);
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41 reader = new BufferedReader(new InputStreamReader( url.openStream() ) );
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44 else if( protocol.equals("Paste"))
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45 reader = new BufferedReader( new StringReader(file) );
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49 while( (data=reader.readLine())!=null)
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51 data = data.toUpperCase();
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52 if(data.indexOf("#")==0 || data.length()<1)
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55 if(data.indexOf("PILEUP")>-1)
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60 if((data.indexOf("//")==0)
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61 || ((data.indexOf("!!")>-1)
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62 && (data.indexOf("!!")<data.indexOf("_MULTIPLE_ALIGNMENT "))))
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67 else if(data.indexOf("CLUSTAL")>-1)
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72 else if(data.indexOf(">P1;")>-1 || data.indexOf(">DL;")>-1)
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77 else if(data.indexOf(">")>-1)
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79 // could be BLC file, read next line to confirm
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80 data = reader.readLine();
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81 if(data.indexOf(">")>-1)
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91 catch(Exception ex){
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92 System.err.println("File Identification failed!\n"+ex);}
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