1 /* Copyright (c) 2009 Peter Troshin
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3 * Jalview Web Services @version: 2.0
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5 * This library is free software; you can redistribute it and/or modify it under the terms of the
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6 * Apache License version 2 as published by the Apache Software Foundation
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8 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
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9 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
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10 * License for more details.
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12 * A copy of the license is in apache_license.txt. It is also available here:
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13 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
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15 * Any republication or derived work distributed in source code form
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16 * must include this copyright and license notice.
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18 package compbio.runner._impl;
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20 import java.util.Arrays;
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21 import java.util.List;
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23 import compbio.runner._SkeletalCommandBuilder;
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28 * DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops fold_rem465 sequence_file
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29 print 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out'
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31 new DisEMBL is at /homes/pvtroshin/soft/DisEMBL-1.4raw
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32 This is not a standard DisEMBL! The script has been modified!
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33 DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops fold_rem465 [mode] < fasta_file > out
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34 print 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 < fasta_file'
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35 print 'Mode: "default"(nothing) or "scores" which will give scores per residue in TAB separated format'
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37 public class Disembl extends _SkeletalCommandBuilder {
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39 private static final String command = "/homes/pvtroshin/soft/DisEMBL-1.4raw/DisEMBL.py";
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40 static final List<String> params = Arrays.asList(new String[] { "8", "8",
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41 "4", "1.2", "1.4", "1.2", "scores" });
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43 private final String workDirectory;
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45 public Disembl(String workDirectory) {
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46 this.workDirectory = workDirectory;
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49 public static List<String> getTestArgs() {
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53 public String getCommand(ExecProvider provider) {
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57 public static String getTestCommand() {
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61 public String getCommandName() {
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66 public List<String> getCreatedFiles() {
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67 // TODO Auto-generated method stub
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72 public String getInput() {
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73 // TODO Auto-generated method stub
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