2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 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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28 * @version $Revision$
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30 public class IdentifyFile
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35 * @param file DOCUMENT ME!
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36 * @param protocol DOCUMENT ME!
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38 * @return DOCUMENT ME!
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40 public String Identify(String file, String protocol)
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42 String reply = "PFAM";
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43 String error = "FILE NOT FOUND";
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46 BufferedReader reader = null;
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48 if (protocol.equals(AppletFormatAdapter.FILE))
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50 reader = new BufferedReader(new FileReader(file));
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52 else if (protocol.equals(AppletFormatAdapter.URL))
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54 error = "URL NOT FOUND";
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55 URL url = new URL(file);
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56 reader = new BufferedReader(new InputStreamReader(
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60 else if (protocol.equals(AppletFormatAdapter.PASTE))
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62 reader = new BufferedReader(new StringReader(file));
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64 else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
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66 java.io.InputStream is = getClass().getResourceAsStream("/" +
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68 reader = new BufferedReader(new java.io.InputStreamReader(is));
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73 while ( (data = reader.readLine()) != null)
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75 data = data.toUpperCase();
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77 if ( (data.indexOf("# STOCKHOLM") > -1))
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84 if ( (data.indexOf("#") == 0) || (data.length() < 1))
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89 if (data.indexOf("PILEUP") > -1)
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96 if ( (data.indexOf("//") == 0) ||
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97 ( (data.indexOf("!!") > -1) &&
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98 (data.indexOf("!!") < data.indexOf(
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99 "_MULTIPLE_ALIGNMENT "))))
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105 else if (data.indexOf("CLUSTAL") > -1)
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111 else if ( (data.indexOf(">P1;") > -1) ||
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112 (data.indexOf(">DL;") > -1))
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118 else if (data.indexOf(">") > -1)
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120 // could be BLC file, read next line to confirm
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121 data = reader.readLine();
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123 if (data.indexOf(">") > -1)
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129 //Is this a single line BLC file?
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131 String data2 = reader.readLine();
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133 && data.indexOf("*") > -1
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134 && data.indexOf("*") == data2.indexOf("*"))
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146 else if (data.indexOf("HEADER") == 0 ||
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147 data.indexOf("ATOM") == 0)
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152 else if (data.indexOf(":") < data.indexOf(",")) // && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))
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154 // file looks like a concise JNet file
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155 reply = "JnetFile";
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162 catch (Exception ex)
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164 System.err.println("File Identification failed!\n" + ex);
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