Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / trajectoryanalysis / modules / select.h

diff --git a/src/gromacs/trajectoryanalysis/modules/select.h b/src/gromacs/trajectoryanalysis/modules/select.h
index b25b476c2b1646dc261c81c2936005cc679e64c1..62b26a34af0aed34046a5f6bcdfcb2b16b3913f3 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/select.h
+++ b/src/gromacs/trajectoryanalysis/modules/select.h
@@ -1,10 +1,10 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2011,2012,2013, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 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.
  *
  * GROMACS is free software; you can redistribute it and/or
  * modify it under the terms of the GNU Lesser General Public License
@@ -42,72 +42,20 @@
 #ifndef GMX_TRAJECTORYANALYSIS_MODULES_SELECT_H
 #define GMX_TRAJECTORYANALYSIS_MODULES_SELECT_H
 
-#include <string>
-#include <vector>
-
-#include "../analysismodule.h"
-#include "gromacs/analysisdata/analysisdata.h"
-#include "gromacs/analysisdata/modules/average.h"
-#include "gromacs/analysisdata/modules/lifetime.h"
-#include "gromacs/selection/selection.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
 
 namespace gmx
 {
 
-class SelectionOptionInfo;
-
 namespace analysismodules
 {
 
-class Select : public TrajectoryAnalysisModule
+class SelectInfo
 {
     public:
         static const char name[];
         static const char shortDescription[];
-
-        Select();
-        virtual ~Select();
-
-        virtual void initOptions(Options                    *options,
-                                 TrajectoryAnalysisSettings *settings);
-        virtual void optionsFinished(Options                    *options,
-                                     TrajectoryAnalysisSettings *settings);
-        virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
-                                  const TopologyInformation        &top);
-
-        virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
-                                  TrajectoryAnalysisModuleData *pdata);
-
-        virtual void finishAnalysis(int nframes);
-        virtual void writeOutput();
-
-    private:
-        SelectionList                       sel_;
-        SelectionOptionInfo                *selOpt_;
-
-        std::string                         fnSize_;
-        std::string                         fnFrac_;
-        std::string                         fnIndex_;
-        std::string                         fnNdx_;
-        std::string                         fnMask_;
-        std::string                         fnOccupancy_;
-        std::string                         fnPDB_;
-        std::string                         fnLifetime_;
-        bool                                bTotNorm_;
-        bool                                bFracNorm_;
-        bool                                bResInd_;
-        bool                                bCumulativeLifetimes_;
-        std::string                         resNumberType_;
-        std::string                         pdbAtoms_;
-
-        const TopologyInformation          *top_;
-        std::vector<int>                    totsize_;
-        AnalysisData                        sdata_;
-        AnalysisData                        cdata_;
-        AnalysisData                        idata_;
-        AnalysisData                        mdata_;
-        AnalysisDataAverageModulePointer    occupancyModule_;
-        AnalysisDataLifetimeModulePointer   lifetimeModule_;
+        static TrajectoryAnalysisModulePointer create();
 };
 
 } // namespace analysismodules