Sort all includes in src/gromacs

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

diff --git a/src/gromacs/selection/parsetree.cpp b/src/gromacs/selection/parsetree.cpp
index 3035805bd4e11ce0f19f0631faff4351c6952f91..14d5d27dbdaddb8dc4d518fd3bbd6f7130c6ad4a 100644 (file)
--- a/src/gromacs/selection/parsetree.cpp
+++ b/src/gromacs/selection/parsetree.cpp
@@ -219,16 +219,18 @@
  * Each element has exactly two children (one for unary negation elements),
  * which are in the order given in the input.
  */
-#include <stdio.h>
+#include "gmxpre.h"
+
+#include "parsetree.h"
+
 #include <stdarg.h>
+#include <stdio.h>
 
 #include <boost/exception_ptr.hpp>
 #include <boost/shared_ptr.hpp>
 
-#include "gromacs/fileio/futil.h"
-#include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/selection.h"
-#include "gromacs/selection/selmethod.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/file.h"
 #include "gromacs/utility/messagestringcollector.h"
@@ -236,13 +238,13 @@
 #include "gromacs/utility/stringutil.h"
 
 #include "keywords.h"
-#include "parsetree.h"
+#include "poscalc.h"
+#include "scanner.h"
 #include "selectioncollection-impl.h"
 #include "selelem.h"
+#include "selmethod.h"
 #include "symrec.h"
 
-#include "scanner.h"
-
 using gmx::SelectionParserValue;
 using gmx::SelectionParserValueList;
 using gmx::SelectionParserValueListPointer;
@@ -580,7 +582,7 @@ _gmx_sel_init_arithmetic(const gmx::SelectionTreeElementPointer &left,
     buf[0] = op;
     buf[1] = 0;
     sel->setName(buf);
-    sel->u.arith.opstr = strdup(buf);
+    sel->u.arith.opstr = gmx_strdup(buf);
     sel->child         = left;
     sel->child->next   = right;
     return sel;
@@ -911,13 +913,14 @@ _gmx_sel_init_group_by_name(const char *name, yyscan_t scanner)
     SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_GROUPREF));
     _gmx_selelem_set_vtype(sel, GROUP_VALUE);
     sel->setName(gmx::formatString("group \"%s\"", name));
-    sel->u.gref.name = strdup(name);
+    sel->u.gref.name = gmx_strdup(name);
     sel->u.gref.id   = -1;
 
     if (_gmx_sel_lexer_has_groups_set(scanner))
     {
-        gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
-        sel->resolveIndexGroupReference(grps);
+        gmx_ana_indexgrps_t     *grps = _gmx_sel_lexer_indexgrps(scanner);
+        gmx_ana_selcollection_t *sc   = _gmx_sel_lexer_selcollection(scanner);
+        sel->resolveIndexGroupReference(grps, sc->gall.isize);
     }
 
     return sel;
@@ -939,8 +942,9 @@ _gmx_sel_init_group_by_id(int id, yyscan_t scanner)
 
     if (_gmx_sel_lexer_has_groups_set(scanner))
     {
-        gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
-        sel->resolveIndexGroupReference(grps);
+        gmx_ana_indexgrps_t     *grps = _gmx_sel_lexer_indexgrps(scanner);
+        gmx_ana_selcollection_t *sc   = _gmx_sel_lexer_selcollection(scanner);
+        sel->resolveIndexGroupReference(grps, sc->gall.isize);
     }
 
     return sel;
@@ -1002,6 +1006,12 @@ _gmx_sel_init_selection(const char                             *name,
     }
     /* Update the flags */
     _gmx_selelem_update_flags(root);
+    gmx::ExceptionInitializer errors("Invalid index group reference(s)");
+    root->checkUnsortedAtoms(true, &errors);
+    if (errors.hasNestedExceptions())
+    {
+        GMX_THROW(gmx::InconsistentInputError(errors));
+    }
 
     root->fillNameIfMissing(_gmx_sel_lexer_pselstr(scanner));
 
@@ -1041,30 +1051,36 @@ _gmx_sel_assign_variable(const char                             *name,
     {
         /* If so, just assign the constant value to the variable */
         sc->symtab->addVariable(name, expr);
-        goto finish;
     }
     /* Check if we are assigning a variable to another variable */
-    if (expr->type == SEL_SUBEXPRREF)
+    else if (expr->type == SEL_SUBEXPRREF)
     {
         /* If so, make a simple alias */
         sc->symtab->addVariable(name, expr->child);
-        goto finish;
     }
-    /* Create the root element */
-    root.reset(new SelectionTreeElement(SEL_ROOT));
-    root->setName(name);
-    /* Create the subexpression element */
-    root->child.reset(new SelectionTreeElement(SEL_SUBEXPR));
-    root->child->setName(name);
-    _gmx_selelem_set_vtype(root->child, expr->v.type);
-    root->child->child  = expr;
-    /* Update flags */
-    _gmx_selelem_update_flags(root);
-    /* Add the variable to the symbol table */
-    sc->symtab->addVariable(name, root->child);
-finish:
+    else
+    {
+        /* Create the root element */
+        root.reset(new SelectionTreeElement(SEL_ROOT));
+        root->setName(name);
+        /* Create the subexpression element */
+        root->child.reset(new SelectionTreeElement(SEL_SUBEXPR));
+        root->child->setName(name);
+        _gmx_selelem_set_vtype(root->child, expr->v.type);
+        root->child->child  = expr;
+        /* Update flags */
+        _gmx_selelem_update_flags(root);
+        gmx::ExceptionInitializer errors("Invalid index group reference(s)");
+        root->checkUnsortedAtoms(true, &errors);
+        if (errors.hasNestedExceptions())
+        {
+            GMX_THROW(gmx::InconsistentInputError(errors));
+        }
+        /* Add the variable to the symbol table */
+        sc->symtab->addVariable(name, root->child);
+    }
     srenew(sc->varstrs, sc->nvars + 1);
-    sc->varstrs[sc->nvars] = strdup(pselstr);
+    sc->varstrs[sc->nvars] = gmx_strdup(pselstr);
     ++sc->nvars;
     if (_gmx_sel_is_lexer_interactive(scanner))
     {