// Copyright 2012 Georg-August-Universität Göttingen, Germany // // Licensed under the Apache License, Version 2.0 (the "License"); // you may not use this file except in compliance with the License. // You may obtain a copy of the License at // // http://www.apache.org/licenses/LICENSE-2.0 // // Unless required by applicable law or agreed to in writing, software // distributed under the License is distributed on an "AS IS" BASIS, // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // See the License for the specific language governing permissions and // limitations under the License. package de.ugoe.cs.autoquest.plugin.alignment.commands; import java.io.File; import java.io.FilenameFilter; import java.util.Collection; import java.util.Iterator; import java.util.LinkedList; import java.util.List; import java.util.logging.Level; import de.ugoe.cs.autoquest.CommandHelpers; import de.ugoe.cs.autoquest.eventcore.Event; import de.ugoe.cs.autoquest.plugin.alignment.SmithWaterman; import de.ugoe.cs.autoquest.plugin.alignment.seqgen.RandomSequenceGenerator; import de.ugoe.cs.autoquest.plugin.alignment.seqgen.SimpleSequenceGenerator; import de.ugoe.cs.autoquest.plugin.alignment.substitution.DifferenceSubstitutionMatrix; import de.ugoe.cs.autoquest.plugin.alignment.substitution.NearbySubstitutionMatrix; import de.ugoe.cs.autoquest.tasktrees.manager.TaskTreeManager; import de.ugoe.cs.autoquest.tasktrees.taskequality.TaskEquality; import de.ugoe.cs.autoquest.tasktrees.temporalrelation.TaskInstanceComparator; import de.ugoe.cs.autoquest.tasktrees.temporalrelation.TaskHandlingStrategy; import de.ugoe.cs.autoquest.tasktrees.treeifc.ITask; import de.ugoe.cs.autoquest.tasktrees.treeifc.ITaskBuilder; import de.ugoe.cs.autoquest.tasktrees.treeifc.ITaskInstance; import de.ugoe.cs.autoquest.tasktrees.treeifc.IUserSession; import de.ugoe.cs.autoquest.tasktrees.treeimpl.TaskBuilder; import de.ugoe.cs.autoquest.usageprofiles.SymbolMap; import de.ugoe.cs.util.console.Command; import de.ugoe.cs.util.console.Console; import de.ugoe.cs.util.console.GlobalDataContainer; /** *
* Command to generate a binary alignment of two sequences *
* * @author Steffen Herbold * @version 1.0 */ public class CMDbinaryAlignment implements Command { /* * (non-Javadoc) * * @see de.ugoe.cs.util.console.Command#run(java.util.List) */ public void run(List