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 2722c5065f621ab0433c257e1411a1dcdb14d1e7..a3846214b7ea14b2282c5857d3e6bd6c0a12c02d 100644 (file)
--- a/src/gromacs/trajectoryanalysis/analysismodule.h
+++ b/src/gromacs/trajectoryanalysis/analysismodule.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012, by the GROMACS development team, led by
+ * 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.
@@ -47,11 +47,13 @@
 #include <string>
 #include <vector>
 
-#include "../legacyheaders/typedefs.h"
+#include <boost/shared_ptr.hpp>
 
-#include "../selection/selection.h" // For gmx::SelectionList
-#include "../utility/common.h"
-#include "../utility/uniqueptr.h"
+#include "gromacs/selection/selection.h" // For gmx::SelectionList
+#include "gromacs/utility/common.h"
+
+struct t_pbc;
+struct t_trxframe;
 
 namespace gmx
 {
@@ -108,6 +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.
          */
@@ -174,7 +178,7 @@ class TrajectoryAnalysisModuleData
 };
 
 //! Smart pointer to manage a TrajectoryAnalysisModuleData object.
-typedef gmx_unique_ptr<TrajectoryAnalysisModuleData>::type
+typedef boost::shared_ptr<TrajectoryAnalysisModuleData>
     TrajectoryAnalysisModuleDataPointer;
 
 /*! \brief
@@ -291,7 +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.
@@ -493,7 +498,7 @@ class TrajectoryAnalysisModule
 };
 
 //! Smart pointer to manage a TrajectoryAnalysisModule.
-typedef gmx_unique_ptr<TrajectoryAnalysisModule>::type
+typedef boost::shared_ptr<TrajectoryAnalysisModule>
     TrajectoryAnalysisModulePointer;
 
 } // namespace gmx