Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / selection / params.cpp

diff --git a/src/gromacs/selection/params.cpp b/src/gromacs/selection/params.cpp
index 18dc7560ece0c75966d06bff05746d47f9359ae7..9c76fe7aea3d034e84c0512489df720e0eafa18e 100644 (file)
--- a/src/gromacs/selection/params.cpp
+++ b/src/gromacs/selection/params.cpp
@@ -1,10 +1,10 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012, 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) 2009,2010,2011,2012,2013,2014, 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.
  *
  * GROMACS is free software; you can redistribute it and/or
  * modify it under the terms of the GNU Lesser General Public License
@@ -39,25 +39,25 @@
  * \author Teemu Murtola <teemu.murtola@gmail.com>
  * \ingroup module_selection
  */
+#include "gmxpre.h"
+
 #include <algorithm>
 #include <string>
 
-#include "gromacs/legacyheaders/smalloc.h"
-#include "gromacs/legacyheaders/string2.h"
-#include "gromacs/legacyheaders/vec.h"
-
+#include "gromacs/math/vec.h"
 #include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
-#include "gromacs/selection/selparam.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/messagestringcollector.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
 #include "parsetree.h"
-#include "position.h"
 #include "scanner.h"
 #include "selelem.h"
+#include "selmethod.h"
+#include "selparam.h"
 
 using gmx::SelectionParserValue;
 using gmx::SelectionParserValueList;
@@ -541,7 +541,7 @@ parse_values_varnum(const SelectionParserValueList    &values,
                 param->val.u.r[i++] = value->u.r.r1;
                 break;
             case STR_VALUE:
-                param->val.u.s[i++] = strdup(value->stringValue().c_str());
+                param->val.u.s[i++] = gmx_strdup(value->stringValue().c_str());
                 break;
             case POS_VALUE:  copy_rvec(value->u.x, param->val.u.p->x[i++]); break;
             default: /* Should not be reached */
@@ -617,7 +617,7 @@ add_child(const SelectionTreeElementPointer &root, gmx_ana_selparam_t *param,
         // FIXME: Use exceptions.
         return SelectionTreeElementPointer();
     }
-    _gmx_selelem_update_flags(child, scanner);
+    _gmx_selelem_update_flags(child);
     if ((child->flags & SEL_DYNAMIC) && !(param->flags & SPAR_DYNAMIC))
     {
         _gmx_selparser_error(scanner, "dynamic values not supported");
@@ -866,7 +866,7 @@ parse_values_std(const SelectionParserValueList &values,
                     param->val.u.r[i] = value->u.r.r1;
                     break;
                 case STR_VALUE:
-                    param->val.u.s[i] = strdup(value->stringValue().c_str());
+                    param->val.u.s[i] = gmx_strdup(value->stringValue().c_str());
                     break;
                 case POS_VALUE:
                     gmx_ana_pos_init_const(&param->val.u.p[i], value->u.x);
@@ -1053,9 +1053,10 @@ convert_const_values(SelectionParserValueList *values)
  * have been processed, no matter is there was an error or not.
  */
 bool
-_gmx_sel_parse_params(const SelectionParserParameterList &pparams,
+_gmx_sel_parse_params(const gmx::SelectionParserParameterList &pparams,
                       int nparam, gmx_ana_selparam_t *params,
-                      const SelectionTreeElementPointer &root, void *scanner)
+                      const gmx::SelectionTreeElementPointer &root,
+                      void *scanner)
 {
     gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
     gmx_ana_selparam_t          *oparam;