[1448] | 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 | import java.util.ArrayList;
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| 18 | import java.util.Collection;
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| 19 | import java.util.Collections;
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| 20 | import java.util.Comparator;
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| 21 | import java.util.Iterator;
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| 22 | import java.util.LinkedList;
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| 23 | import java.util.List;
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| 24 | import java.util.logging.Level;
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| 25 |
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| 26 | import de.ugoe.cs.autoquest.eventcore.Event;
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| 27 | import de.ugoe.cs.autoquest.plugin.alignment.SmithWaterman;
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| 28 | import de.ugoe.cs.autoquest.plugin.alignment.seqgen.SimpleSequenceGenerator;
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| 29 | import de.ugoe.cs.autoquest.plugin.alignment.substitution.NearbySubstitutionMatrix;
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| 30 | import de.ugoe.cs.autoquest.plugin.alignment.substitution.ObjectDistanceSubstitionMatrix;
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| 31 | import de.ugoe.cs.util.console.Command;
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| 32 | import de.ugoe.cs.util.console.Console;
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| 33 | import de.ugoe.cs.util.console.GlobalDataContainer;
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| 34 |
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| 35 | /**
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| 36 | * <p>
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| 37 | * Command to generate a binary alignment of two sequences
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| 38 | * </p>
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| 39 | *
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| 40 | * @author Ralph Krimmel
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| 41 | * @version 1.0
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| 42 | */
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| 43 | public class CMDsequenceStats implements Command {
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| 44 |
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| 45 | /*
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| 46 | * (non-Javadoc)
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| 47 | *
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| 48 | * @see de.ugoe.cs.util.console.Command#run(java.util.List)
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| 49 | */
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| 50 | @SuppressWarnings("unchecked")
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| 51 | public void run(List<Object> parameters) {
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| 52 | String sequencesName = "sequences";
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| 53 | double standarddev = 0.0;
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| 54 | double mean = 0;
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| 55 | double median = 0;
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| 56 | double sum = 0;
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| 57 |
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| 58 | try {
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| 59 | sequencesName = (String) parameters.get(0);
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| 60 | } catch (Exception e) {
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| 61 | throw new IllegalArgumentException();
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| 62 | }
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| 63 |
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| 64 | Collection<List<Event>> sequences = new LinkedList<List<Event>>();
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| 65 | Object obj = GlobalDataContainer.getInstance().getData(sequencesName);
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| 66 | if (obj != null) {
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| 67 |
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| 68 | if (obj.getClass().equals(sequences.getClass())) {
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| 69 | sequences = (Collection<List<Event>>) obj;
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| 70 | }
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| 71 |
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| 72 |
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| 73 | Console.println("Number of sequences: " + sequences.size());
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| 74 | //Calculate the mean size
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| 75 | for(Iterator<List<Event>> iter = sequences.iterator();iter.hasNext();) {
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| 76 | sum += iter.next().size();
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| 77 |
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| 78 | }
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| 79 | mean = sum/sequences.size();
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| 80 |
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| 81 |
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| 82 | //Calculate the median
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| 83 | List<List<Event>> list = new ArrayList<List<Event>>(sequences);
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| 84 | Collections.sort(list,new SizeComparator());
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| 85 |
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| 86 | Console.println("Mean size: " +mean);
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| 87 | Console.println("Median size: " + list.get(Math.round(list.size()/2)).size());
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| 88 |
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| 89 | }
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| 90 | }
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| 91 |
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| 92 | class SizeComparator implements Comparator<List<Event>> {
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| 93 | @Override
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| 94 | public int compare(List<Event> a, List<Event> b) {
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| 95 | return a.size() < b.size() ? -1 : a.size() == b.size() ? 0 : 1;
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| 96 | }
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| 97 | }
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| 98 | /*
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| 99 | * (non-Javadoc)
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| 100 | *
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| 101 | * @see de.ugoe.cs.util.console.Command#help()
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| 102 | */
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| 103 | @Override
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| 104 | public String help() {
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| 105 | return "sequenceStats <sequence name>";
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| 106 | }
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| 107 |
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| 108 | }
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