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.SkeletalExecutable;
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32 import compbio.metadata.Limit;
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33 import compbio.metadata.LimitsManager;
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34 import compbio.metadata.ResultNotAvailableException;
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35 import compbio.runner.Util;
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37 public class ClustalW extends SkeletalExecutable<ClustalW> {
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39 private static Logger log = Logger.getLogger(ClustalW.class);
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40 private static final String EXEC_STAT_FILE = "stat.log";
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41 private static final String TREE_FILE_EXT = ".dnd";
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43 public static final String KEY_VALUE_SEPARATOR = "=";
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45 // Cache for Limits information
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46 private static LimitsManager<ClustalW> limits;
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49 super(KEY_VALUE_SEPARATOR);
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50 addParameters(Arrays.asList("-OUTORDER=ALIGNED", "-QUIET", "-STATS="
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52 // set default in, outs and err files
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53 this.setInput(super.inputFile);
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54 this.setOutput(super.outputFile);
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55 this.setError(super.errorFile);
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59 public ClustalW setOutput(String outFile) {
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60 super.setOutput(outFile);
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61 cbuilder.setParam("-OUTFILE=" + outFile);
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66 public ClustalW setInput(String inFile) {
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67 super.setInput(inFile);
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68 cbuilder.setParam("-INFILE=" + inFile);
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72 @SuppressWarnings("unchecked")
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73 public Alignment getResults(String workDirectory)
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74 throws ResultNotAvailableException {
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76 return Util.readClustalFile(workDirectory, getOutput());
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77 } catch (FileNotFoundException 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 (IOException 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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83 } catch (UnknownFileFormatException e) {
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84 log.error(e.getMessage(), e.getCause());
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85 throw new ResultNotAvailableException(e);
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86 } catch (NullPointerException e) {
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87 log.error(e.getMessage(), e.getCause());
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88 throw new ResultNotAvailableException(e);
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93 public List<String> getCreatedFiles() {
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94 return Arrays.asList(getOutput(), EXEC_STAT_FILE,
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95 convertInputNameToTreeName());
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99 * Clustal output tree with same name as input file but .dnd extension e.g.
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100 * this methods do similar conversion TO122.fasta -> TO122.dnd or
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101 * TO122.fasta.in -> TO122.fasta.dnd It does not seems that there is any
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102 * limits on the name length
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106 private String convertInputNameToTreeName() {
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107 assert super.getInput() != null;
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108 int dotIdx = getInput().lastIndexOf(".");
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109 String treeFileName = "";
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111 treeFileName = getInput().substring(0, dotIdx);
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113 return treeFileName + TREE_FILE_EXT;
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116 public static String getStatFile() {
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117 return EXEC_STAT_FILE;
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121 public Limit<ClustalW> getLimit(String presetName) {
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123 if (limits == null) {
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124 limits = getLimits();
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127 Limit<ClustalW> limit = null;
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128 if (limits != null) {
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129 // this returns default limit if preset is undefined!
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130 limit = limits.getLimitByName(presetName);
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132 // If limit is not defined for a particular preset, then return default
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134 if (limit == null) {
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135 log.debug("Limit for the preset " + presetName
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136 + " is not found. Using default");
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137 limit = limits.getDefaultLimit();
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143 public LimitsManager<ClustalW> getLimits() {
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144 // synchronise on static field
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145 synchronized (log) {
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146 if (limits == null) {
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147 limits = Util.getLimits(this.getClass());
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154 public Class<? extends Executable<?>> getType() {
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155 return this.getClass();
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