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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26 public class IdentifyFile {
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27 public static String Identify(String file, String protocol) {
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28 String reply = "PFAM";
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31 BufferedReader reader = null;
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33 if (protocol.equals("File")) {
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34 reader = new BufferedReader(new FileReader(file));
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36 else if (protocol.equals("URL")) {
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37 reply = "URL NOT FOUND";
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39 URL url = new URL(file);
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40 reader = new BufferedReader(new InputStreamReader(
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43 } else if (protocol.equals("Paste")) {
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44 reader = new BufferedReader(new StringReader(file));
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49 while ((data = reader.readLine()) != null) {
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50 data = data.toUpperCase();
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52 if ((data.indexOf("#") == 0) || (data.length() < 1)) {
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56 if (data.indexOf("PILEUP") > -1) {
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62 if ((data.indexOf("//") == 0) ||
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63 ((data.indexOf("!!") > -1) &&
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64 (data.indexOf("!!") < data.indexOf(
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65 "_MULTIPLE_ALIGNMENT ")))) {
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69 } else if (data.indexOf("CLUSTAL") > -1) {
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73 } else if ((data.indexOf(">P1;") > -1) ||
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74 (data.indexOf(">DL;") > -1)) {
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78 } 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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82 if (data.indexOf(">") > -1) {
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93 } catch (Exception ex) {
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94 System.err.println("File Identification failed!\n" + ex);
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