1 /* Copyright (c) 2009 Peter Troshin
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3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
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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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19 package compbio.runner.msa;
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21 import java.io.FileNotFoundException;
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22 import java.io.IOException;
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23 import java.util.Arrays;
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24 import java.util.List;
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26 import org.apache.log4j.Logger;
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28 import compbio.data.sequence.Alignment;
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29 import compbio.data.sequence.UnknownFileFormatException;
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30 import compbio.engine.client.PipedExecutable;
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31 import compbio.engine.client.SkeletalExecutable;
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32 import compbio.metadata.ResultNotAvailableException;
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33 import compbio.runner.Util;
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35 public class Probcons extends SkeletalExecutable<Probcons>
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37 PipedExecutable<Probcons> {
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39 private static Logger log = Logger.getLogger(Probcons.class);
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41 private final static String ANNOTATION = "annotation.txt";
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43 public static final String KEY_VALUE_SEPARATOR = Util.SPACE;
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47 * @param workDirectory
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50 addParameters(Arrays.asList("-v", "-clustalw", "-annot", ANNOTATION));
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52 * Could either have probabilities or the alignment, but not both "-t",
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57 @SuppressWarnings("unchecked")
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59 public Alignment getResults(String workDirectory)
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60 throws ResultNotAvailableException {
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62 return Util.readClustalFile(workDirectory, getOutput());
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63 } catch (FileNotFoundException e) {
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64 log.error(e.getMessage(), e.getCause());
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65 throw new ResultNotAvailableException(e);
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66 } catch (IOException e) {
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67 log.error(e.getMessage(), e.getCause());
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68 throw new ResultNotAvailableException(e);
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69 } catch (UnknownFileFormatException e) {
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70 log.error(e.getMessage(), e.getCause());
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71 throw new ResultNotAvailableException(e);
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72 } catch (NullPointerException e) {
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73 log.error(e.getMessage(), e.getCause());
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74 throw new ResultNotAvailableException(e);
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79 public List<String> getCreatedFiles() {
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80 return Arrays.asList(getOutput(), ANNOTATION, getError());
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84 public Probcons setInput(String inFile) {
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85 String input = getInput();
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86 super.setInput(inFile);
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87 // TODO replace with setLast
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88 cbuilder.setParam(inFile);
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92 @SuppressWarnings("unchecked")
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94 public Class<Probcons> getType() {
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95 return (Class<Probcons>) this.getClass();
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