Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / trajectoryanalysis / analysismodule.h

diff --git a/src/gromacs/trajectoryanalysis/analysismodule.h b/src/gromacs/trajectoryanalysis/analysismodule.h
index 367efad64d8b12c90a89e1761760cb39dfaaf6ce..a3846214b7ea14b2282c5857d3e6bd6c0a12c02d 100644 (file)
--- a/src/gromacs/trajectoryanalysis/analysismodule.h
+++ b/src/gromacs/trajectoryanalysis/analysismodule.h
@@ -1,39 +1,43 @@
 /*
+ * This file is part of the GROMACS molecular simulation package.
  *
- *                This source code is part of
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
  *
- *                 G   R   O   M   A   C   S
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
  *
- *          GROningen MAchine for Chemical Simulations
+ * GROMACS 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
+ * Lesser General Public License for more details.
  *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * 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.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  *
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
  *
  * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
+ * the research papers on the package. Check out http://www.gromacs.org.
  */
 /*! \file
  * \brief
  * Declares gmx::TrajectoryAnalysisModule and
  * gmx::TrajectoryAnalysisModuleData.
  *
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
  * \inpublicapi
  * \ingroup module_trajectoryanalysis
  */
@@ -43,11 +47,13 @@
 #include <string>
 #include <vector>
 
-#include "../legacyheaders/typedefs.h"
+#include <boost/shared_ptr.hpp>
+
+#include "gromacs/selection/selection.h" // For gmx::SelectionList
+#include "gromacs/utility/common.h"
 
-#include "../selection/selection.h" // For gmx::SelectionList
-#include "../utility/common.h"
-#include "../utility/uniqueptr.h"
+struct t_pbc;
+struct t_trxframe;
 
 namespace gmx
 {
@@ -104,6 +110,8 @@ class TrajectoryAnalysisModuleData
          *
          * \p data should have previously been registered with
          * TrajectoryAnalysisModule::registerAnalysisDataset().
+         * If \p data has zero columns in all data sets, the returned data
+         * handle is invalid.
          *
          * Does not throw.
          */
@@ -170,7 +178,7 @@ class TrajectoryAnalysisModuleData
 };
 
 //! Smart pointer to manage a TrajectoryAnalysisModuleData object.
-typedef gmx_unique_ptr<TrajectoryAnalysisModuleData>::type
+typedef boost::shared_ptr<TrajectoryAnalysisModuleData>
     TrajectoryAnalysisModuleDataPointer;
 
 /*! \brief
@@ -287,7 +295,8 @@ class TrajectoryAnalysisModule
          *
          * The default implementation does nothing.
          */
-        virtual void initAfterFirstFrame(const t_trxframe &fr);
+        virtual void initAfterFirstFrame(const TrajectoryAnalysisSettings &settings,
+                                         const t_trxframe                 &fr);
 
         /*! \brief
          * Starts the analysis of frames.
@@ -489,7 +498,7 @@ class TrajectoryAnalysisModule
 };
 
 //! Smart pointer to manage a TrajectoryAnalysisModule.
-typedef gmx_unique_ptr<TrajectoryAnalysisModule>::type
+typedef boost::shared_ptr<TrajectoryAnalysisModule>
     TrajectoryAnalysisModulePointer;
 
 } // namespace gmx