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.Executable;
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31 import compbio.engine.client.PipedExecutable;
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32 import compbio.engine.client.SkeletalExecutable;
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33 import compbio.metadata.Limit;
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34 import compbio.metadata.LimitsManager;
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35 import compbio.metadata.ResultNotAvailableException;
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36 import compbio.runner.Util;
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38 public class Probcons extends SkeletalExecutable<Probcons> implements
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39 PipedExecutable<Probcons> {
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41 private static Logger log = Logger.getLogger(Probcons.class);
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43 // Cache for Limits information
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44 private static LimitsManager<Probcons> limits;
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45 private final static String ANNOTATION = "annotation.txt";
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47 public static final String KEY_VALUE_SEPARATOR = Util.SPACE;
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51 * @param workDirectory
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54 addParameters(Arrays.asList("-v", "-clustalw", "-annot", ANNOTATION));
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56 * Could either have probabilities or the alignment, but not both "-t",
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61 @SuppressWarnings("unchecked")
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63 public Alignment getResults(String workDirectory)
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64 throws ResultNotAvailableException {
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66 return Util.readClustalFile(workDirectory, getOutput());
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67 } catch (FileNotFoundException e) {
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68 log.error(e.getMessage(), e.getCause());
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69 throw new ResultNotAvailableException(e);
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70 } catch (IOException e) {
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71 log.error(e.getMessage(), e.getCause());
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72 throw new ResultNotAvailableException(e);
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73 } catch (UnknownFileFormatException e) {
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74 log.error(e.getMessage(), e.getCause());
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75 throw new ResultNotAvailableException(e);
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76 } catch (NullPointerException e) {
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77 log.error(e.getMessage(), e.getCause());
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78 throw new ResultNotAvailableException(e);
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83 public List<String> getCreatedFiles() {
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84 return Arrays.asList(getOutput(), ANNOTATION, getError());
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88 public Probcons setInput(String inFile) {
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89 String input = getInput();
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90 super.setInput(inFile);
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91 // TODO replace with setLast
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92 cbuilder.setParam(inFile);
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97 public Limit<Probcons> getLimit(String presetName) {
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98 if (limits == null) {
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99 limits = getLimits();
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101 Limit<Probcons> limit = null;
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102 if (limits != null) {
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103 // this returns default limit if preset is undefined!
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104 limit = limits.getLimitByName(presetName);
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106 // If limit is not defined for a particular preset, then return default
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108 if (limit == null) {
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109 log.debug("Limit for the preset " + presetName
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110 + " is not found. Using default");
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111 limit = limits.getDefaultLimit();
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117 public LimitsManager<Probcons> getLimits() {
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118 // synchronise on static field
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119 synchronized (log) {
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120 if (limits == null) {
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121 limits = Util.getLimits(this.getClass());
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128 public Class<? extends Executable<?>> getType() {
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129 return this.getClass();
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