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 a7cdac9f287b90c1fb28de97b953791d04e2113d..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, 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
@@ -42,69 +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/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_;
-        bool                             bDump_;
-        bool                             bTotNorm_;
-        bool                             bFracNorm_;
-        bool                             bResInd_;
-        std::string                      resNumberType_;
-        std::string                      pdbAtoms_;
-
-        const TopologyInformation       *top_;
-        std::vector<int>                 totsize_;
-        AnalysisData                     sdata_;
-        AnalysisData                     cdata_;
-        AnalysisData                     idata_;
-        AnalysisData                     mdata_;
-        AnalysisDataAverageModulePointer occupancyModule_;
+        static TrajectoryAnalysisModulePointer create();
 };
 
 } // namespace analysismodules