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.disorder;
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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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25 import org.apache.log4j.Logger;
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27 import com.sun.xml.internal.bind.api.impl.NameConverter.Standard;
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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.PipedExecutable;
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32 import compbio.engine.client.SkeletalExecutable;
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33 import compbio.metadata.Limit;
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34 import compbio.metadata.LimitsManager;
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35 import compbio.metadata.ResultNotAvailableException;
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36 import compbio.runner.Util;
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39 * @see Standard DisEMBL DisEMBL.py smooth_frame peak_frame join_frame
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40 * fold_coils fold_hotloops fold_rem465 sequence_file print 'A default run
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41 * would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out'
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43 * new DisEMBL is at /homes/pvtroshin/soft/DisEMBL-1.4raw This is not a
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44 * standard DisEMBL! The script has been modified! DisEMBL.py smooth_frame
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45 * peak_frame join_frame fold_coils fold_hotloops fold_rem465 [mode] <
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46 * fasta_file > out print 'A default run would be: ./DisEMBL.py 8 8 4 1.2
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47 * 1.4 1.2 < fasta_file' print 'Mode: "default"(nothing) or "scores" which
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48 * will give scores per residue in TAB separated format'
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51 public class Disembl extends SkeletalExecutable<Disembl> implements
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52 PipedExecutable<Disembl> {
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54 private static Logger log = Logger.getLogger(Disembl.class);
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56 // Cache for Limits information
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57 private static LimitsManager<Disembl> limits;
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59 public static final String KEY_VALUE_SEPARATOR = Util.SPACE;
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62 // remove default input to prevent it to appear in the parameters list
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63 // that could happen if the parameters are set first
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64 // super.setInput("");
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65 addParameters(Arrays.asList("8", "8", "4", "1.2", "1.4", "1.2",
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69 @SuppressWarnings("unchecked")
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70 public Alignment getResults(String workDirectory)
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71 throws ResultNotAvailableException {
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73 return Util.readClustalFile(workDirectory, getOutput());
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74 } catch (FileNotFoundException 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 (IOException 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 (UnknownFileFormatException 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 (NullPointerException 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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90 public Disembl setInput(String inFile) {
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91 super.setInput(inFile);
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92 cbuilder.setLast(inFile);
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97 public Limit<Disembl> getLimit(String presetName) {
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98 if (limits == null) {
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99 limits = getLimits();
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102 Limit<Disembl> limit = null;
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103 if (limits != null) {
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104 // this returns default limit if preset is undefined!
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105 limit = limits.getLimitByName(presetName);
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107 // If limit is not defined for a particular preset, then return default
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109 if (limit == null) {
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110 log.debug("Limit for the preset " + presetName
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111 + " is not found. Using default");
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112 limit = limits.getDefaultLimit();
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118 public LimitsManager<Disembl> getLimits() {
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119 // synchronise on static field
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120 synchronized (log) {
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121 if (limits == null) {
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122 limits = Util.getLimits(this.getClass());
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129 public Class<? extends Executable<?>> getType() {
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130 return this.getClass();
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