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 static compbio.runner._impl.BlastParameters.parAlView;
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21 import static compbio.runner._impl.BlastParameters.parDatabase;
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23 import java.util.Arrays;
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24 import java.util.List;
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26 import compbio.runner._SkeletalCommandBuilder;
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28 public class RPSBlast extends _SkeletalCommandBuilder {
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31 Pfam, Cdd, Cog, Smart, Kog, Tirg
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34 private static final String command = Environment.getBlastBinDir()
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37 private final String workDirectory;
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39 public RPSBlast(String workDirectory) {
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40 this.workDirectory = workDirectory;
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44 // "$blast_dir/rpsblast -i $input -d $dblocat/$dbnam -m 9 -a 1 -o $output_dir/$outfile.rpsblastout";
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45 // Could be static, but interface declaration requires to be overriden
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46 public String getCommand(ExecProvider provider) {
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50 public static String getTestCommand() {
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54 public static String getCommandName() {
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58 static List<String> getTestArgs() {
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59 return Arrays.asList(new String[] {
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60 parDatabase + Environment.getRPSBlastDatabasesDir() + DB.Smart,
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64 String getDefaultEvalue() {
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69 public List<String> getCreatedFiles() {
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70 // TODO Auto-generated method stub
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75 public String getInput() {
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76 // TODO Auto-generated method stub
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