1 | // Copyright 2012 Georg-August-Universität Göttingen, Germany
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2 | //
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3 | // Licensed under the Apache License, Version 2.0 (the "License");
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4 | // you may not use this file except in compliance with the License.
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5 | // You may obtain a copy of the License at
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6 | //
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7 | // http://www.apache.org/licenses/LICENSE-2.0
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8 | //
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9 | // Unless required by applicable law or agreed to in writing, software
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10 | // distributed under the License is distributed on an "AS IS" BASIS,
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11 | // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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12 | // See the License for the specific language governing permissions and
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13 | // limitations under the License.
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14 |
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15 | package de.ugoe.cs.autoquest.plugin.alignment.commands;
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16 |
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17 |
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18 | import java.util.Collection;
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19 | import java.util.LinkedList;
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20 | import java.util.List;
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21 |
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22 | import de.ugoe.cs.autoquest.eventcore.Event;
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23 | import de.ugoe.cs.autoquest.plugin.alignment.SmithWaterman;
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24 | import de.ugoe.cs.autoquest.plugin.alignment.seqgen.SimpleSequenceGenerator;
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25 | import de.ugoe.cs.autoquest.plugin.alignment.substitution.NearbySubstitutionMatrix;
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26 | import de.ugoe.cs.autoquest.plugin.alignment.substitution.ObjectDistanceSubstitionMatrix;
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27 | import de.ugoe.cs.util.console.Command;
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28 | import de.ugoe.cs.util.console.Console;
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29 | import de.ugoe.cs.util.console.GlobalDataContainer;
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30 |
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31 | /**
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32 | * <p>
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33 | * Command to generate a binary alignment of two sequences
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34 | * </p>
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35 | *
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36 | * @author Ralph Krimmel
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37 | * @version 1.0
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38 | */
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39 | public class CMDbinaryAlignment implements Command {
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40 |
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41 | /*
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42 | * (non-Javadoc)
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43 | *
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44 | * @see de.ugoe.cs.util.console.Command#run(java.util.List)
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45 | */
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46 | public void run(List<Object> parameters) {
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47 | String sequencesName;
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48 | String algorithm;
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49 | try {
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50 | sequencesName = (String) parameters.get(0);
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51 | if (parameters.size() > 1) {
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52 | algorithm = (String) parameters.get(1);
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53 | }
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54 | } catch (Exception e) {
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55 | throw new IllegalArgumentException();
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56 | }
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57 |
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58 | Collection<List<Event>> sequences = new LinkedList<List<Event>>();
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59 | Object obj = GlobalDataContainer.getInstance().getData(sequencesName);
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60 | if(obj.getClass().equals(sequences.getClass())) {
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61 | sequences = (Collection<List<Event>>) obj;
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62 | }
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63 |
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64 |
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65 |
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66 |
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67 |
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68 | if(sequences != null) {
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69 | Console.println("Number of sequences: " + sequences.size());
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70 |
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71 | SimpleSequenceGenerator gen = new SimpleSequenceGenerator();
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72 | gen.generate(sequences);
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73 | int[] seq1 = gen.get(0);
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74 | int[] seq2 = gen.get(0);
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75 | ObjectDistanceSubstitionMatrix submat = new ObjectDistanceSubstitionMatrix();
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76 | submat.generate(sequences);
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77 | SmithWaterman sw = new SmithWaterman(seq1, seq2,
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78 | new NearbySubstitutionMatrix(seq1, seq2, 10));
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79 |
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80 | sw.printDPMatrix();
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81 | System.out.println();
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82 | //sw.printAlignments();
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83 | // sw.getMatches();
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84 | }
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85 | }
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86 |
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87 |
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88 | /*
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89 | * (non-Javadoc)
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90 | *
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91 | * @see de.ugoe.cs.util.console.Command#help()
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92 | */
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93 | @Override
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94 | public String help() {
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95 | return "binaryAlignment <sequencesName> {<algorithm>}";
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96 | }
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97 |
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98 | }
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