text: /**
   * UGENE - Integrated Bioinformatics Tools.
   * Copyright (C) 2008-2020 UniPro <ugene@unipro.ru>
   * http://ugene.net
   *
   * This program is free software; you can redistribute it and/or
   * modify it under the terms of the GNU General Public License
   * as published by the Free Software Foundation; either version 2
   * of the License, or (at your option) any later version.
   *
   * This program is distributed in the hope that it will be useful,
   * but WITHOUT ANY WARRANTY; without even the implied warranty of
   * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
   * GNU General Public License for more details.
   *
   * You should have received a copy of the GNU General Public License
   * along with this program; if not, write to the Free Software
   * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
   * MA 02110-1301, USA.
   */
  
  #ifndef _U2_TCOFFEE_SUPPORT_TASK_H
  #define _U2_TCOFFEE_SUPPORT_TASK_H
  
  #include <U2Core/ExternalToolRunTask.h>
  #include <U2Core/GObjectReference.h>
  #include <U2Core/IOAdapter.h>
  #include <U2Core/MultipleSequenceAlignment.h>
  #include <U2Core/SaveDocumentTask.h>
  #include <U2Core/Task.h>
  
  #include "utils/ExportTasks.h"
  
  namespace U2 {
  
  class TCoffeeSupportTaskSettings {
  public:
      TCoffeeSupportTaskSettings() {
          reset();
      }
      void reset();
  
      float gapOpenPenalty;
      float gapExtenstionPenalty;
      int numIterations;
      QString inputFilePath;
      QString outputFilePath;
  };
  
  class LoadDocumentTask;
  
  class TCoffeeSupportTask : public ExternalToolSupportTask {
      Q_OBJECT
      Q_DISABLE_COPY(TCoffeeSupportTask)
  public:
      TCoffeeSupportTask(const MultipleSequenceAlignment &_inputMsa, const GObjectReference &_objRef, const TCoffeeSupportTaskSettings &_settings);
      ~TCoffeeSupportTask();
  
      void prepare();
      Task::ReportResult report();
  
      QList<Task *> onSubTaskFinished(Task *subTask);
  
      MultipleSequenceAlignment resultMA;
  
  private:
      MultipleSequenceAlignment inputMsa;
      GObjectReference objRef;
      QPointer<Document> tmpDoc;
      QString url;
  
      SaveMSA2SequencesTask *saveTemporaryDocumentTask;
      ExternalToolRunTask *tCoffeeTask;
      LoadDocumentTask *loadTmpDocumentTask;
      TCoffeeSupportTaskSettings settings;
      QPointer<StateLock> lock;
  };
  
  class MultipleSequenceAlignmentObject;
  
  class TCoffeeWithExtFileSpecifySupportTask : public Task {
      Q_OBJECT
      Q_DISABLE_COPY(TCoffeeWithExtFileSpecifySupportTask)
  public:
      TCoffeeWithExtFileSpecifySupportTask(const TCoffeeSupportTaskSettings &settings);
      ~TCoffeeWithExtFileSpecifySupportTask();
      void prepare();
      Task::ReportResult report();
  
      QList<Task *> onSubTaskFinished(Task *subTask);
  
  private:
      MultipleSequenceAlignmentObject *mAObject;
      Document *currentDocument;
      bool cleanDoc;
  
      SaveDocumentTask *saveDocumentTask;
      LoadDocumentTask *loadDocumentTask;
      TCoffeeSupportTask *tCoffeeSupportTask;
      TCoffeeSupportTaskSettings settings;
  };
  
  class TCoffeeLogParser : public ExternalToolLogParser {
  public:
      TCoffeeLogParser();
  
      int getProgress();
      void parseOutput(const QString &partOfLog);
      void parseErrOutput(const QString &partOfLog);
  
  private:
      QString lastErrLine;
      int progress;
  };
  
  }    // namespace U2
  #endif    // _U2_TCOFFEE_SUPPORT_TASK_H
  