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.ClusterNativeSpecExecutable;
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31 import compbio.engine.client.CommandBuilder;
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32 import compbio.engine.client.Executable;
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33 import compbio.engine.client.PipedExecutable;
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34 import compbio.engine.client.SkeletalExecutable;
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35 import compbio.engine.conf.PropertyHelperManager;
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36 import compbio.metadata.ResultNotAvailableException;
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37 import compbio.runner.Util;
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38 import compbio.util.PropertyHelper;
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40 public class Tcoffee extends SkeletalExecutable<Tcoffee>
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42 PipedExecutable<Tcoffee>,
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43 ClusterNativeSpecExecutable<Tcoffee> {
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45 private static Logger log = Logger.getLogger(Tcoffee.class);
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47 private static PropertyHelper ph = PropertyHelperManager
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48 .getPropertyHelper();
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50 public static final String KEY_VALUE_SEPARATOR = "=";
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53 * Number of cores to use, defaults to 1 for local execution or the value of
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54 * "tcoffee.cluster.cpunum" property for cluster execution
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56 private int ncoreNumber = 0;
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59 * Number of cores parameter name
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61 private final static String ncorePrm = "-n_core";
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65 * @param workDirectory
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68 super(KEY_VALUE_SEPARATOR);
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70 * Use "-quiet" to disable sdtout and progress to stderr inorder=input -
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71 * prevent t-coffee from sorting sequences
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73 addParameters(Arrays.asList("-output=clustalw"));
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74 setInput(super.inputFile);
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78 public Tcoffee setInput(String inFile) {
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79 super.setInput(inFile);
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80 cbuilder.setParam("-seq", inFile);
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84 @SuppressWarnings("unchecked")
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86 public Alignment getResults(String workDirectory)
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87 throws ResultNotAvailableException {
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89 return Util.readClustalFile(workDirectory, getOutput());
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90 } catch (FileNotFoundException e) {
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91 log.error(e.getMessage(), e.getCause());
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92 throw new ResultNotAvailableException(e);
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93 } catch (IOException e) {
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94 log.error(e.getMessage(), e.getCause());
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95 throw new ResultNotAvailableException(e);
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96 } catch (UnknownFileFormatException e) {
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97 log.error(e.getMessage(), e.getCause());
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98 throw new ResultNotAvailableException(e);
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99 } catch (NullPointerException e) {
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100 log.error(e.getMessage(), e.getCause());
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101 throw new ResultNotAvailableException(e);
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106 public List<String> getCreatedFiles() {
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107 return Arrays.asList(getOutput());
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110 public void setNCore(int ncoreNumber) {
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111 if (ncoreNumber < 1 || ncoreNumber > 100) {
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112 throw new IndexOutOfBoundsException(
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113 "Number of cores must be within 1 and 100 ");
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115 this.ncoreNumber = ncoreNumber;
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116 cbuilder.setParam(ncorePrm, Integer.toString(getNCore()));
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120 return ncoreNumber;
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124 public CommandBuilder<Tcoffee> getParameters(ExecProvider provider) {
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125 // Limit number of cores to 1 for ANY execution which does not set
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126 // Ncores explicitly using setNCore method
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127 if (ncoreNumber == 0) {
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130 if (provider == Executable.ExecProvider.Cluster) {
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131 int cpunum = SkeletalExecutable.getClusterCpuNum(getType());
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136 return super.getParameters(provider);
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140 public String getNativeSpecs() {
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141 return getClusterSettings();
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144 @SuppressWarnings("unchecked")
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146 public Class<Tcoffee> getType() {
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147 return (Class<Tcoffee>) this.getClass();
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