2 * Copyright (c) 2009 Peter Troshin JAva Bioinformatics Analysis Web Services
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3 * (JABAWS) @version: 1.0 This library is free software; you can redistribute it
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4 * and/or modify it under the terms of the Apache License version 2 as published
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5 * by the Apache Software Foundation This library is distributed in the hope
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6 * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
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7 * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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8 * Apache License for more details. A copy of the license is in
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9 * apache_license.txt. It is also available here:
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10 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt Any republication or
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11 * derived work distributed in source code form must include this copyright and
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15 package compbio.runner.conservation;
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17 import java.io.File;
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18 import java.io.FileInputStream;
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19 import java.io.FileNotFoundException;
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20 import java.io.IOException;
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21 import java.io.InputStream;
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22 import java.util.Arrays;
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23 import java.util.HashSet;
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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.SMERFSConstraints;
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29 import compbio.data.sequence.Score;
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30 import compbio.data.sequence.SequenceUtil;
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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.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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42 * java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
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47 public class AACon extends SkeletalExecutable<AACon> {
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49 private static Logger log = Logger.getLogger(AACon.class);
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52 * Number of cores to use, defaults to 1 for local execution or the value of
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53 * "jronn.cluster.cpunum" property for cluster execution
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55 private int ncoreNumber = 0;
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57 private final String ncorePrm = "-t=";
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59 // Cache for Limits information
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60 private static LimitsManager<AACon> limits;
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62 public static final String KEY_VALUE_SEPARATOR = "=";
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63 public static final String STAT_FILE = "stat.txt";
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65 private final int windowWidth = SMERFSConstraints.DEFAULT_WINDOW_SIZE;
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66 private final SMERFSConstraints colScoreMethod = SMERFSConstraints.MID_SCORE;
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67 private final double gapTreshold = SMERFSConstraints.DEFAULT_GAP_THRESHOLD;
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70 addParameters(Arrays.asList("-jar", getLibPath(), "-d=" + STAT_FILE,
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71 "-f=RESULT_NO_ALIGNMENT"));
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73 // HashMap<Method, float[]>
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75 public HashSet<Score> getResults(String workDirectory)
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76 throws ResultNotAvailableException {
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77 HashSet<Score> annotations = null;
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79 InputStream inStream = new FileInputStream(new File(workDirectory,
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81 annotations = SequenceUtil.readAAConResults(inStream);
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83 } catch (FileNotFoundException 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 (IOException 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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89 } catch (NullPointerException e) {
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90 log.error(e.getMessage(), e.getCause());
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91 throw new ResultNotAvailableException(e);
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96 private static String getLibPath() {
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98 String settings = ph.getProperty("aacon.jar.file");
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99 if (compbio.util.Util.isEmpty(settings)) {
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100 throw new NullPointerException(
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101 "Please define aacon.jar.file property in Executable.properties file"
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102 + "and initialize it with the location of jronn jar file");
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104 if (new File(settings).isAbsolute()) {
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105 // the jar can be found so no actions necessary
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106 // no further actions is necessary
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109 return compbio.engine.client.Util.convertToAbsolute(settings);
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113 public List<String> getCreatedFiles() {
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114 return Arrays.asList(getOutput(), getError());
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118 public AACon setInput(String inFile) {
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119 super.setInput(inFile);
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120 cbuilder.setParam("-i=" + inFile);
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125 public AACon setOutput(String outFile) {
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126 super.setOutput(outFile);
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127 cbuilder.setParam("-o=" + outFile);
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132 public Limit<AACon> getLimit(String presetName) {
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133 if (limits == null) {
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134 limits = getLimits();
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136 Limit<AACon> limit = null;
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137 if (limits != null) {
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138 // this returns default limit if preset is undefined!
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139 limit = limits.getLimitByName(presetName);
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141 // If limit is not defined for a particular preset, then return default
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143 if (limit == null) {
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144 log.debug("Limit for the preset " + presetName
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145 + " is not found. Using default");
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146 limit = limits.getDefaultLimit();
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152 public LimitsManager<AACon> getLimits() {
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153 // synchronise on static field
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154 synchronized (log) {
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155 if (limits == null) {
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156 limits = Util.getLimits(this.getClass());
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163 public Class<? extends Executable<?>> getType() {
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164 return this.getClass();
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167 public static String getStatFile() {
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171 public void setNCore(int ncoreNumber) {
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172 if (ncoreNumber < 1 || ncoreNumber > 100) {
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173 throw new IndexOutOfBoundsException(
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174 "Number of cores must be within 1 and 100 ");
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176 this.ncoreNumber = ncoreNumber;
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177 cbuilder.setParam(ncorePrm + Integer.toString(getNCore()));
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181 return ncoreNumber;
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185 public CommandBuilder<AACon> getParameters(ExecProvider provider) {
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186 // If number of cores is provided, set it for the cluster execution
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188 if (provider == Executable.ExecProvider.Cluster) {
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189 int cpunum = SkeletalExecutable.getClusterCpuNum(getType());
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190 cpunum = (cpunum == 0) ? 1 : cpunum;
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193 // Limit number of cores to 1 for ANY execution which does not set
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194 // Ncores explicitly using setNCore method or is run on local VM
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195 if (ncoreNumber == 0) {
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199 return super.getParameters(provider);
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