1 /* Copyright (c) 2011 Peter Troshin
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3 * JAva Bioinformatics Analysis Web Services (JABAWS) @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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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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31 import compbio.engine.client.PipedExecutable;
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32 import compbio.engine.client.SkeletalExecutable;
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33 import compbio.metadata.ResultNotAvailableException;
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34 import compbio.runner.Util;
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41 public class Mafft extends SkeletalExecutable<Mafft>
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43 PipedExecutable<Mafft> {
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45 * TODO get rid of piping: Mafft now supports --out option for output file.
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46 * Multi-threading supported with e.g. "thread 4" only for Linux, so JABAWS
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47 * will not support it for now, it also need editing of mafft makefile
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51 private static Logger log = Logger.getLogger(Mafft.class);
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53 private static String autoOption = "--auto";
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55 private final String MATRIX_PAR_NAME = "--aamatrix";
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57 public static final String KEY_VALUE_SEPARATOR = Util.SPACE;
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60 // remove default input to prevent it to appear in the parameters list
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61 // that could happen if the parameters are set first
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62 // super.setInput("");
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63 addParameters(Arrays.asList("--clustalout", autoOption));
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66 @SuppressWarnings("unchecked")
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67 public Alignment getResults(String workDirectory)
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68 throws ResultNotAvailableException {
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70 return Util.readClustalFile(workDirectory, getOutput());
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71 } catch (FileNotFoundException e) {
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72 log.error(e.getMessage(), e.getCause());
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73 throw new ResultNotAvailableException(e);
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74 } catch (IOException e) {
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75 log.error(e.getMessage(), e.getCause());
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76 throw new ResultNotAvailableException(e);
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77 } catch (UnknownFileFormatException e) {
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78 log.error(e.getMessage(), e.getCause());
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79 throw new ResultNotAvailableException(e);
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80 } catch (NullPointerException e) {
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81 log.error(e.getMessage(), e.getCause());
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82 throw new ResultNotAvailableException(e);
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87 public Mafft setInput(String inFile) {
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88 super.setInput(inFile);
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89 cbuilder.setLast(inFile);
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94 * Mafft input must always be the last parameter!
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97 public Mafft addParameters(List<String> parameters) {
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98 cbuilder.addParams(parameters);
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99 cbuilder.removeParam(autoOption);
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105 @SuppressWarnings("unchecked")
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107 public Class<Mafft> getType() {
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108 return (Class<Mafft>) this.getClass();
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112 * @Override public List<String> getParameters(
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113 * compbio.runner.Executable.ExecProvider provider) { for (int i = 0; i <
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114 * param.size(); i++) { String par = param.get(i); if
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115 * (isMatrixParameter(par)) { String matrixName = getValue(i); if (new
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116 * File(matrixName).isAbsolute()) { // Matrix can be found so no actions
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117 * necessary // This method has been called already and the matrix name //
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118 * is modified to contain full path // no further actions is necessary
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119 * break; } String matrixPath = Util.getExecProperty("matrix.path", this);
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120 * String absMatrixPath = Util.convertToAbsolute(matrixPath); param.remove(i
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121 * + 1); param.remove(i); super.addParameter(MATRIX_PAR_NAME);
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122 * super.addParameter(absMatrixPath + File.separator + matrixName); break; }
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123 * } return super.getParameters(provider); }
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125 * boolean isMatrixParameter(String parameter) { assert
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126 * !compbio.util.Util.isEmpty(parameter); if
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127 * (parameter.toUpperCase().startsWith(MATRIX_PAR_NAME)) { return true; }
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130 * String getValue(int i) { return param.get(i + 1); }
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