[927] | 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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[1303] | 15 | package de.ugoe.cs.autoquest.plugin.alignment.commands;
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[205] | 16 |
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| 17 | import java.io.File;
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[425] | 18 | import java.io.FilenameFilter;
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[205] | 19 | import java.util.Collection;
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| 20 | import java.util.LinkedList;
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| 21 | import java.util.List;
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[639] | 22 | import java.util.logging.Level;
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[205] | 23 |
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[922] | 24 | import de.ugoe.cs.autoquest.CommandHelpers;
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| 25 | import de.ugoe.cs.autoquest.eventcore.Event;
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[205] | 26 | import de.ugoe.cs.util.console.Command;
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| 27 | import de.ugoe.cs.util.console.Console;
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[667] | 28 | import de.ugoe.cs.util.console.GlobalDataContainer;
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[205] | 29 |
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[206] | 30 | /**
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| 31 | * <p>
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[1303] | 32 | * Command to generate a binary alignment of two sequences
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[206] | 33 | * </p>
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| 34 | *
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| 35 | * @author Steffen Herbold
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| 36 | * @version 1.0
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| 37 | */
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[1303] | 38 | public class CMDbinaryAligment implements Command {
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[205] | 39 |
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[206] | 40 | /*
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| 41 | * (non-Javadoc)
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| 42 | *
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| 43 | * @see de.ugoe.cs.util.console.Command#run(java.util.List)
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| 44 | */
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[205] | 45 | @Override
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| 46 | public void run(List<Object> parameters) {
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[227] | 47 | String sequencesName;
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[1303] | 48 | String algorithm;
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[205] | 49 | try {
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[1303] | 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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[205] | 53 | }
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| 54 | } catch (Exception e) {
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[766] | 55 | throw new IllegalArgumentException();
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[205] | 56 | }
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[206] | 57 |
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[425] | 58 |
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[556] | 59 | Collection<List<Event>> sequences = new LinkedList<List<Event>>();
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[1303] | 60 |
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[206] | 61 |
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[205] | 62 | }
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| 63 |
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[206] | 64 | /*
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| 65 | * (non-Javadoc)
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| 66 | *
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| 67 | * @see de.ugoe.cs.util.console.Command#help()
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| 68 | */
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[205] | 69 | @Override
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[664] | 70 | public String help() {
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[1303] | 71 | return "binaryAlignment <sequencesName> {<algorithm>}";
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[205] | 72 | }
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| 73 |
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| 74 | }
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