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 javax.xml.bind.annotation.XmlTransient;
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28 import org.apache.log4j.Logger;
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30 import compbio.data.sequence.Alignment;
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31 import compbio.data.sequence.UnknownFileFormatException;
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32 import compbio.engine.client.Executable;
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33 import compbio.engine.client.SkeletalExecutable;
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34 import compbio.metadata.Limit;
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35 import compbio.metadata.LimitsManager;
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36 import compbio.metadata.ResultNotAvailableException;
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37 import compbio.runner.Util;
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39 public class Muscle extends SkeletalExecutable<Muscle> {
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42 * Tell JAXB to ignore this while marshalling
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45 private static Logger log = Logger.getLogger(Muscle.class);
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47 // Cache for Limits information
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48 private static LimitsManager<Muscle> limits;
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50 private static final String EXEC_STAT_FILE = "stat.log";
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52 public static final String KEY_VALUE_SEPARATOR = Util.SPACE;
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55 * Default options are
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57 * -clwstrict - write output in clustal format
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59 * @param workDirectory
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63 * The –quiet command-line option disables writing progress messages to
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64 * standard error. If the –verbose command-line option is specified, a
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65 * progress message will be written to the log file when each iteration
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66 * completes. So –quiet and –verbose are not contradictory."-quiet",
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69 addParameters(Arrays.asList("-clwstrict", "-quiet", "-verbose"));
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70 cbuilder.setParam("-log", EXEC_STAT_FILE);
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74 public Muscle setOutput(String outFile) {
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75 super.setOutput(outFile);
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76 cbuilder.setParam("-out", outFile);
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81 public Muscle setInput(String inFile) {
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82 super.setInput(inFile);
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83 cbuilder.setParam("-in", inFile);
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87 @SuppressWarnings("unchecked")
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89 public Alignment getResults(String workDirectory)
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90 throws ResultNotAvailableException {
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92 return Util.readClustalFile(workDirectory, getOutput());
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93 } catch (FileNotFoundException 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 (IOException 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 (UnknownFileFormatException 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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102 } catch (NullPointerException e) {
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103 log.error(e.getMessage(), e.getCause());
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104 throw new ResultNotAvailableException(e);
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109 public List<String> getCreatedFiles() {
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110 return Arrays.asList(getOutput(), EXEC_STAT_FILE);
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113 public static String getStatFile() {
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114 return EXEC_STAT_FILE;
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118 public Limit<Muscle> getLimit(String presetName) {
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120 if (limits == null) {
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121 limits = getLimits();
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124 Limit<Muscle> limit = null;
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125 if (limits != null) {
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126 // this returns default limit if preset is undefined!
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127 limit = limits.getLimitByName(presetName);
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129 // If limit is not defined for a particular preset, then return default
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131 if (limit == null) {
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132 log.debug("Limit for the preset " + presetName
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133 + " is not found. Using default");
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134 limit = limits.getDefaultLimit();
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140 public LimitsManager<Muscle> getLimits() {
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141 // synchronise on static field
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142 synchronized (log) {
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143 if (limits == null) {
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144 limits = Util.getLimits(this.getClass());
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151 public Class<? extends Executable<?>> getType() {
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152 return this.getClass();
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