Add check for unsorted index groups in selections.

Selections did not work properly if an index group was used that
did not have the atom indices in strictly ascending order.
Added a check for this, and tests that check that this now gives an
error.

Refactored the way index group references are resolved such that the
logic and the related error messages are now only in one place:
selelem.cpp.  This resolves TODOs about improving the error messages.
Also made this piece of code to use exceptions for error reporting.

Related to #651 and #655.

Change-Id: I2318823b1be74775d0a0f8bd4a3c58b0aed1aba1

diff --git a/src/gromacs/selection/parser.cpp b/src/gromacs/selection/parser.cpp
index 5986ba6eb7a5be5c43c0c668bb28681fd1f7b343..1aa00baa5fd9bbd0b12342007171b75c5f14b295 100644 (file)
--- a/src/gromacs/selection/parser.cpp
+++ b/src/gromacs/selection/parser.cpp
@@ -583,16 +583,16 @@ static const yytype_int8 yyrhs[] =
 /* YYRLINE[YYN] -- source line where rule number YYN was defined.  */
 static const yytype_uint16 yyrline[] =
 {
-       0,   199,   199,   204,   215,   216,   238,   244,   250,   262,
-     275,   281,   288,   295,   302,   313,   322,   327,   338,   339,
-     346,   347,   361,   362,   366,   367,   370,   371,   374,   375,
-     383,   394,   405,   416,   420,   431,   439,   449,   450,   455,
-     456,   457,   461,   469,   477,   485,   496,   511,   522,   536,
-     544,   555,   561,   567,   573,   579,   585,   591,   598,   609,
-     624,   633,   637,   647,   661,   669,   677,   690,   692,   698,
-     703,   714,   723,   724,   729,   734,   742,   753,   754,   758,
-     764,   772,   782,   788,   794,   800,   806,   810,   816,   822,
-     829,   833,   839,   845
+       0,   199,   199,   204,   215,   216,   238,   244,   250,   261,
+     273,   279,   286,   293,   300,   311,   320,   325,   336,   337,
+     344,   345,   359,   360,   364,   365,   368,   369,   372,   373,
+     381,   392,   403,   414,   418,   429,   436,   445,   446,   451,
+     452,   453,   457,   465,   473,   481,   492,   507,   518,   532,
+     540,   551,   557,   563,   569,   575,   581,   587,   594,   605,
+     620,   629,   633,   643,   657,   665,   673,   686,   688,   694,
+     699,   710,   719,   720,   725,   730,   738,   749,   750,   754,
+     760,   768,   778,   784,   790,   796,   802,   806,   812,   818,
+     825,   829,   835,   841
 };
 #endif
 
@@ -1993,7 +1993,6 @@ yyreduce:
                  BEGIN_ACTION;
                  SelectionTreeElementPointer s
                         = _gmx_sel_init_group_by_id((yyvsp[(1) - (1)].i), scanner);
-                 if (!s) YYERROR;
                  SelectionTreeElementPointer p
                         = _gmx_sel_init_position(s, NULL, scanner);
                  if (!p) YYERROR;
@@ -2004,13 +2003,12 @@ yyreduce:
 
   case 9:
 /* Line 1787 of yacc.c  */
-#line 263 "parser.y"
+#line 262 "parser.y"
     {
                  BEGIN_ACTION;
                  scoped_ptr_sfree nameGuard((yyvsp[(1) - (1)].str));
                  SelectionTreeElementPointer s
                         = _gmx_sel_init_group_by_name((yyvsp[(1) - (1)].str), scanner);
-                 if (!s) YYERROR;
                  SelectionTreeElementPointer p
                         = _gmx_sel_init_position(s, NULL, scanner);
                  if (!p) YYERROR;
@@ -2021,7 +2019,7 @@ yyreduce:
 
   case 10:
 /* Line 1787 of yacc.c  */
-#line 276 "parser.y"
+#line 274 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.sel), _gmx_sel_init_selection(NULL, get((yyvsp[(1) - (1)].sel)), scanner));
@@ -2031,7 +2029,7 @@ yyreduce:
 
   case 11:
 /* Line 1787 of yacc.c  */
-#line 282 "parser.y"
+#line 280 "parser.y"
     {
                  BEGIN_ACTION;
                  scoped_ptr_sfree nameGuard((yyvsp[(1) - (2)].str));
@@ -2042,7 +2040,7 @@ yyreduce:
 
   case 12:
 /* Line 1787 of yacc.c  */
-#line 289 "parser.y"
+#line 287 "parser.y"
     {
                  BEGIN_ACTION;
                  scoped_ptr_sfree nameGuard((yyvsp[(1) - (3)].str));
@@ -2053,7 +2051,7 @@ yyreduce:
 
   case 13:
 /* Line 1787 of yacc.c  */
-#line 296 "parser.y"
+#line 294 "parser.y"
     {
                  BEGIN_ACTION;
                  scoped_ptr_sfree nameGuard((yyvsp[(1) - (3)].str));
@@ -2064,7 +2062,7 @@ yyreduce:
 
   case 14:
 /* Line 1787 of yacc.c  */
-#line 303 "parser.y"
+#line 301 "parser.y"
     {
                  BEGIN_ACTION;
                  scoped_ptr_sfree nameGuard((yyvsp[(1) - (3)].str));
@@ -2075,7 +2073,7 @@ yyreduce:
 
   case 15:
 /* Line 1787 of yacc.c  */
-#line 314 "parser.y"
+#line 312 "parser.y"
     {
                  BEGIN_ACTION;
                  _gmx_sel_handle_help_cmd(get((yyvsp[(2) - (2)].vlist)), scanner);
@@ -2085,7 +2083,7 @@ yyreduce:
 
   case 16:
 /* Line 1787 of yacc.c  */
-#line 322 "parser.y"
+#line 320 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.vlist), SelectionParserValue::createList());
@@ -2095,7 +2093,7 @@ yyreduce:
 
   case 17:
 /* Line 1787 of yacc.c  */
-#line 328 "parser.y"
+#line 326 "parser.y"
     {
                  BEGIN_ACTION;
                  SelectionParserValueListPointer list(get((yyvsp[(1) - (2)].vlist)));
@@ -2107,13 +2105,13 @@ yyreduce:
 
   case 18:
 /* Line 1787 of yacc.c  */
-#line 338 "parser.y"
+#line 336 "parser.y"
     { (yyval.sel) = (yyvsp[(1) - (1)].sel); }
     break;
 
   case 19:
 /* Line 1787 of yacc.c  */
-#line 340 "parser.y"
+#line 338 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.sel), _gmx_sel_init_position(get((yyvsp[(1) - (1)].sel)), NULL, scanner));
@@ -2124,13 +2122,13 @@ yyreduce:
 
   case 20:
 /* Line 1787 of yacc.c  */
-#line 346 "parser.y"
+#line 344 "parser.y"
     { (yyval.sel) = (yyvsp[(2) - (3)].sel); }
     break;
 
   case 21:
 /* Line 1787 of yacc.c  */
-#line 348 "parser.y"
+#line 346 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.sel), _gmx_sel_init_modifier((yyvsp[(2) - (3)].meth), get((yyvsp[(3) - (3)].plist)), get((yyvsp[(1) - (3)].sel)), scanner));
@@ -2141,55 +2139,55 @@ yyreduce:
 
   case 22:
 /* Line 1787 of yacc.c  */
-#line 361 "parser.y"
+#line 359 "parser.y"
     { (yyval.i) = (yyvsp[(1) - (1)].i); }
     break;
 
   case 23:
 /* Line 1787 of yacc.c  */
-#line 362 "parser.y"
+#line 360 "parser.y"
     { (yyval.i) = -(yyvsp[(2) - (2)].i); }
     break;
 
   case 24:
 /* Line 1787 of yacc.c  */
-#line 366 "parser.y"
+#line 364 "parser.y"
     { (yyval.r) = (yyvsp[(1) - (1)].r); }
     break;
 
   case 25:
 /* Line 1787 of yacc.c  */
-#line 367 "parser.y"
+#line 365 "parser.y"
     { (yyval.r) = -(yyvsp[(2) - (2)].r); }
     break;
 
   case 26:
 /* Line 1787 of yacc.c  */
-#line 370 "parser.y"
+#line 368 "parser.y"
     { (yyval.r) = (yyvsp[(1) - (1)].i); }
     break;
 
   case 27:
 /* Line 1787 of yacc.c  */
-#line 371 "parser.y"
+#line 369 "parser.y"
     { (yyval.r) = (yyvsp[(1) - (1)].r); }
     break;
 
   case 28:
 /* Line 1787 of yacc.c  */
-#line 374 "parser.y"
+#line 372 "parser.y"
     { (yyval.str) = (yyvsp[(1) - (1)].str); }
     break;
 
   case 29:
 /* Line 1787 of yacc.c  */
-#line 375 "parser.y"
+#line 373 "parser.y"
     { (yyval.str) = (yyvsp[(1) - (1)].str); }
     break;
 
   case 30:
 /* Line 1787 of yacc.c  */
-#line 384 "parser.y"
+#line 382 "parser.y"
     {
                  BEGIN_ACTION;
                  SelectionTreeElementPointer arg(get((yyvsp[(2) - (2)].sel)));
@@ -2204,7 +2202,7 @@ yyreduce:
 
   case 31:
 /* Line 1787 of yacc.c  */
-#line 395 "parser.y"
+#line 393 "parser.y"
     {
                  BEGIN_ACTION;
                  SelectionTreeElementPointer arg1(get((yyvsp[(1) - (3)].sel))), arg2(get((yyvsp[(3) - (3)].sel)));
@@ -2219,7 +2217,7 @@ yyreduce:
 
   case 32:
 /* Line 1787 of yacc.c  */
-#line 406 "parser.y"
+#line 404 "parser.y"
     {
                  BEGIN_ACTION;
                  SelectionTreeElementPointer arg1(get((yyvsp[(1) - (3)].sel))), arg2(get((yyvsp[(3) - (3)].sel)));
@@ -2234,13 +2232,13 @@ yyreduce:
 
   case 33:
 /* Line 1787 of yacc.c  */
-#line 416 "parser.y"
+#line 414 "parser.y"
     { (yyval.sel) = (yyvsp[(2) - (3)].sel); }
     break;
 
   case 34:
 /* Line 1787 of yacc.c  */
-#line 421 "parser.y"
+#line 419 "parser.y"
     {
                  BEGIN_ACTION;
                  scoped_ptr_sfree opGuard((yyvsp[(2) - (3)].str));
@@ -2252,60 +2250,58 @@ yyreduce:
 
   case 35:
 /* Line 1787 of yacc.c  */
-#line 432 "parser.y"
+#line 430 "parser.y"
     {
                  BEGIN_ACTION;
                  scoped_ptr_sfree nameGuard((yyvsp[(2) - (2)].str));
                  set((yyval.sel), _gmx_sel_init_group_by_name((yyvsp[(2) - (2)].str), scanner));
-                 CHECK_SEL((yyval.sel));
                  END_ACTION;
              }
     break;
 
   case 36:
 /* Line 1787 of yacc.c  */
-#line 440 "parser.y"
+#line 437 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.sel), _gmx_sel_init_group_by_id((yyvsp[(2) - (2)].i), scanner));
-                 CHECK_SEL((yyval.sel));
                  END_ACTION;
              }
     break;
 
   case 37:
 /* Line 1787 of yacc.c  */
-#line 449 "parser.y"
+#line 445 "parser.y"
     { (yyval.str) = NULL; }
     break;
 
   case 38:
 /* Line 1787 of yacc.c  */
-#line 450 "parser.y"
+#line 446 "parser.y"
     { (yyval.str) = (yyvsp[(1) - (1)].str);   }
     break;
 
   case 39:
 /* Line 1787 of yacc.c  */
-#line 455 "parser.y"
+#line 451 "parser.y"
     { (yyval.smt) = gmx::eStringMatchType_RegularExpression; }
     break;
 
   case 40:
 /* Line 1787 of yacc.c  */
-#line 456 "parser.y"
+#line 452 "parser.y"
     { (yyval.smt) = gmx::eStringMatchType_Wildcard; }
     break;
 
   case 41:
 /* Line 1787 of yacc.c  */
-#line 457 "parser.y"
+#line 453 "parser.y"
     { (yyval.smt) = gmx::eStringMatchType_Exact; }
     break;
 
   case 42:
 /* Line 1787 of yacc.c  */
-#line 462 "parser.y"
+#line 458 "parser.y"
     {
                  BEGIN_ACTION;
                  scoped_ptr_sfree posmodGuard((yyvsp[(1) - (2)].str));
@@ -2317,7 +2313,7 @@ yyreduce:
 
   case 43:
 /* Line 1787 of yacc.c  */
-#line 470 "parser.y"
+#line 466 "parser.y"
     {
                  BEGIN_ACTION;
                  scoped_ptr_sfree posmodGuard((yyvsp[(1) - (3)].str));
@@ -2329,7 +2325,7 @@ yyreduce:
 
   case 44:
 /* Line 1787 of yacc.c  */
-#line 478 "parser.y"
+#line 474 "parser.y"
     {
                  BEGIN_ACTION;
                  scoped_ptr_sfree posmodGuard((yyvsp[(1) - (4)].str));
@@ -2341,7 +2337,7 @@ yyreduce:
 
   case 45:
 /* Line 1787 of yacc.c  */
-#line 486 "parser.y"
+#line 482 "parser.y"
     {
                  BEGIN_ACTION;
                  scoped_ptr_sfree posmodGuard((yyvsp[(1) - (3)].str));
@@ -2353,7 +2349,7 @@ yyreduce:
 
   case 46:
 /* Line 1787 of yacc.c  */
-#line 497 "parser.y"
+#line 493 "parser.y"
     {
                  BEGIN_ACTION;
                  scoped_ptr_sfree posmodGuard((yyvsp[(1) - (3)].str));
@@ -2365,7 +2361,7 @@ yyreduce:
 
   case 47:
 /* Line 1787 of yacc.c  */
-#line 512 "parser.y"
+#line 508 "parser.y"
     {
                  BEGIN_ACTION;
                  SelectionTreeElementPointer sel(
@@ -2380,7 +2376,7 @@ yyreduce:
 
   case 48:
 /* Line 1787 of yacc.c  */
-#line 523 "parser.y"
+#line 519 "parser.y"
     {
                  BEGIN_ACTION;
                  SelectionTreeElementPointer sel(
@@ -2395,7 +2391,7 @@ yyreduce:
 
   case 49:
 /* Line 1787 of yacc.c  */
-#line 537 "parser.y"
+#line 533 "parser.y"
     {
                  BEGIN_ACTION;
                  scoped_ptr_sfree posmodGuard((yyvsp[(1) - (2)].str));
@@ -2407,7 +2403,7 @@ yyreduce:
 
   case 50:
 /* Line 1787 of yacc.c  */
-#line 545 "parser.y"
+#line 541 "parser.y"
     {
                  BEGIN_ACTION;
                  scoped_ptr_sfree posmodGuard((yyvsp[(1) - (3)].str));
@@ -2419,7 +2415,7 @@ yyreduce:
 
   case 51:
 /* Line 1787 of yacc.c  */
-#line 556 "parser.y"
+#line 552 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '+', scanner));
@@ -2429,7 +2425,7 @@ yyreduce:
 
   case 52:
 /* Line 1787 of yacc.c  */
-#line 562 "parser.y"
+#line 558 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '-', scanner));
@@ -2439,7 +2435,7 @@ yyreduce:
 
   case 53:
 /* Line 1787 of yacc.c  */
-#line 568 "parser.y"
+#line 564 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '*', scanner));
@@ -2449,7 +2445,7 @@ yyreduce:
 
   case 54:
 /* Line 1787 of yacc.c  */
-#line 574 "parser.y"
+#line 570 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '/', scanner));
@@ -2459,7 +2455,7 @@ yyreduce:
 
   case 55:
 /* Line 1787 of yacc.c  */
-#line 580 "parser.y"
+#line 576 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(2) - (2)].sel)), SelectionTreeElementPointer(), '-', scanner));
@@ -2469,7 +2465,7 @@ yyreduce:
 
   case 56:
 /* Line 1787 of yacc.c  */
-#line 586 "parser.y"
+#line 582 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '^', scanner));
@@ -2479,13 +2475,13 @@ yyreduce:
 
   case 57:
 /* Line 1787 of yacc.c  */
-#line 591 "parser.y"
+#line 587 "parser.y"
     { (yyval.sel) = (yyvsp[(2) - (3)].sel); }
     break;
 
   case 58:
 /* Line 1787 of yacc.c  */
-#line 599 "parser.y"
+#line 595 "parser.y"
     {
                  BEGIN_ACTION;
                  SelectionTreeElementPointer sel(
@@ -2500,7 +2496,7 @@ yyreduce:
 
   case 59:
 /* Line 1787 of yacc.c  */
-#line 610 "parser.y"
+#line 606 "parser.y"
     {
                  BEGIN_ACTION;
                  scoped_ptr_sfree posmodGuard((yyvsp[(1) - (2)].str));
@@ -2512,7 +2508,7 @@ yyreduce:
 
   case 60:
 /* Line 1787 of yacc.c  */
-#line 625 "parser.y"
+#line 621 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.sel), _gmx_sel_init_const_position((yyvsp[(2) - (7)].r), (yyvsp[(4) - (7)].r), (yyvsp[(6) - (7)].r)));
@@ -2522,13 +2518,13 @@ yyreduce:
 
   case 61:
 /* Line 1787 of yacc.c  */
-#line 633 "parser.y"
+#line 629 "parser.y"
     { (yyval.sel) = (yyvsp[(2) - (3)].sel); }
     break;
 
   case 62:
 /* Line 1787 of yacc.c  */
-#line 638 "parser.y"
+#line 634 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.sel), _gmx_sel_init_method((yyvsp[(1) - (2)].meth), get((yyvsp[(2) - (2)].plist)), NULL, scanner));
@@ -2539,7 +2535,7 @@ yyreduce:
 
   case 63:
 /* Line 1787 of yacc.c  */
-#line 648 "parser.y"
+#line 644 "parser.y"
     {
                  BEGIN_ACTION;
                  scoped_ptr_sfree keywordGuard((yyvsp[(1) - (3)].str));
@@ -2551,7 +2547,7 @@ yyreduce:
 
   case 64:
 /* Line 1787 of yacc.c  */
-#line 662 "parser.y"
+#line 658 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.sel), _gmx_sel_init_variable_ref(get((yyvsp[(1) - (1)].sel))));
@@ -2561,7 +2557,7 @@ yyreduce:
 
   case 65:
 /* Line 1787 of yacc.c  */
-#line 670 "parser.y"
+#line 666 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.sel), _gmx_sel_init_variable_ref(get((yyvsp[(1) - (1)].sel))));
@@ -2571,7 +2567,7 @@ yyreduce:
 
   case 66:
 /* Line 1787 of yacc.c  */
-#line 678 "parser.y"
+#line 674 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.sel), _gmx_sel_init_variable_ref(get((yyvsp[(1) - (1)].sel))));
@@ -2581,19 +2577,19 @@ yyreduce:
 
   case 67:
 /* Line 1787 of yacc.c  */
-#line 691 "parser.y"
+#line 687 "parser.y"
     { (yyval.plist) = (yyvsp[(1) - (1)].plist); }
     break;
 
   case 68:
 /* Line 1787 of yacc.c  */
-#line 693 "parser.y"
+#line 689 "parser.y"
     { (yyval.plist) = (yyvsp[(1) - (2)].plist); }
     break;
 
   case 69:
 /* Line 1787 of yacc.c  */
-#line 698 "parser.y"
+#line 694 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.plist), SelectionParserParameter::createList());
@@ -2603,7 +2599,7 @@ yyreduce:
 
   case 70:
 /* Line 1787 of yacc.c  */
-#line 704 "parser.y"
+#line 700 "parser.y"
     {
                  BEGIN_ACTION;
                  SelectionParserParameterListPointer list(get((yyvsp[(1) - (2)].plist)));
@@ -2615,7 +2611,7 @@ yyreduce:
 
   case 71:
 /* Line 1787 of yacc.c  */
-#line 715 "parser.y"
+#line 711 "parser.y"
     {
                  BEGIN_ACTION;
                  scoped_ptr_sfree nameGuard((yyvsp[(1) - (2)].str));
@@ -2626,19 +2622,19 @@ yyreduce:
 
   case 72:
 /* Line 1787 of yacc.c  */
-#line 723 "parser.y"
+#line 719 "parser.y"
     { (yyval.vlist) = (yyvsp[(1) - (1)].vlist);   }
     break;
 
   case 73:
 /* Line 1787 of yacc.c  */
-#line 724 "parser.y"
+#line 720 "parser.y"
     { (yyval.vlist) = (yyvsp[(2) - (3)].vlist);   }
     break;
 
   case 74:
 /* Line 1787 of yacc.c  */
-#line 729 "parser.y"
+#line 725 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.vlist), SelectionParserValue::createList());
@@ -2648,7 +2644,7 @@ yyreduce:
 
   case 75:
 /* Line 1787 of yacc.c  */
-#line 735 "parser.y"
+#line 731 "parser.y"
     {
                  BEGIN_ACTION;
                  SelectionParserValueListPointer list(get((yyvsp[(1) - (2)].vlist)));
@@ -2660,7 +2656,7 @@ yyreduce:
 
   case 76:
 /* Line 1787 of yacc.c  */
-#line 743 "parser.y"
+#line 739 "parser.y"
     {
                  BEGIN_ACTION;
                  SelectionParserValueListPointer list(get((yyvsp[(1) - (3)].vlist)));
@@ -2672,19 +2668,19 @@ yyreduce:
 
   case 77:
 /* Line 1787 of yacc.c  */
-#line 753 "parser.y"
+#line 749 "parser.y"
     { (yyval.vlist) = (yyvsp[(1) - (1)].vlist); }
     break;
 
   case 78:
 /* Line 1787 of yacc.c  */
-#line 754 "parser.y"
+#line 750 "parser.y"
     { (yyval.vlist) = (yyvsp[(2) - (3)].vlist); }
     break;
 
   case 79:
 /* Line 1787 of yacc.c  */
-#line 759 "parser.y"
+#line 755 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.vlist), SelectionParserValue::createList(get((yyvsp[(1) - (1)].val))));
@@ -2694,7 +2690,7 @@ yyreduce:
 
   case 80:
 /* Line 1787 of yacc.c  */
-#line 765 "parser.y"
+#line 761 "parser.y"
     {
                  BEGIN_ACTION;
                  SelectionParserValueListPointer list(get((yyvsp[(1) - (2)].vlist)));
@@ -2706,7 +2702,7 @@ yyreduce:
 
   case 81:
 /* Line 1787 of yacc.c  */
-#line 773 "parser.y"
+#line 769 "parser.y"
     {
                  BEGIN_ACTION;
                  SelectionParserValueListPointer list(get((yyvsp[(1) - (3)].vlist)));
@@ -2718,7 +2714,7 @@ yyreduce:
 
   case 82:
 /* Line 1787 of yacc.c  */
-#line 783 "parser.y"
+#line 779 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.val), SelectionParserValue::createExpr(get((yyvsp[(1) - (1)].sel))));
@@ -2728,7 +2724,7 @@ yyreduce:
 
   case 83:
 /* Line 1787 of yacc.c  */
-#line 789 "parser.y"
+#line 785 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.val), SelectionParserValue::createExpr(get((yyvsp[(1) - (1)].sel))));
@@ -2738,7 +2734,7 @@ yyreduce:
 
   case 84:
 /* Line 1787 of yacc.c  */
-#line 795 "parser.y"
+#line 791 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.val), SelectionParserValue::createExpr(get((yyvsp[(1) - (1)].sel))));
@@ -2748,7 +2744,7 @@ yyreduce:
 
   case 85:
 /* Line 1787 of yacc.c  */
-#line 801 "parser.y"
+#line 797 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.val), SelectionParserValue::createExpr(get((yyvsp[(1) - (1)].sel))));
@@ -2758,13 +2754,13 @@ yyreduce:
 
   case 86:
 /* Line 1787 of yacc.c  */
-#line 806 "parser.y"
+#line 802 "parser.y"
     { (yyval.val) = (yyvsp[(1) - (1)].val); }
     break;
 
   case 87:
 /* Line 1787 of yacc.c  */
-#line 811 "parser.y"
+#line 807 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.val), SelectionParserValue::createInteger((yyvsp[(1) - (1)].i)));
@@ -2774,7 +2770,7 @@ yyreduce:
 
   case 88:
 /* Line 1787 of yacc.c  */
-#line 817 "parser.y"
+#line 813 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.val), SelectionParserValue::createReal((yyvsp[(1) - (1)].r)));
@@ -2784,7 +2780,7 @@ yyreduce:
 
   case 89:
 /* Line 1787 of yacc.c  */
-#line 823 "parser.y"
+#line 819 "parser.y"
     {
                  BEGIN_ACTION;
                  scoped_ptr_sfree stringGuard((yyvsp[(1) - (1)].str));
@@ -2795,13 +2791,13 @@ yyreduce:
 
   case 90:
 /* Line 1787 of yacc.c  */
-#line 829 "parser.y"
+#line 825 "parser.y"
     { (yyval.val) = (yyvsp[(1) - (1)].val); }
     break;
 
   case 91:
 /* Line 1787 of yacc.c  */
-#line 834 "parser.y"
+#line 830 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.val), SelectionParserValue::createIntegerRange((yyvsp[(1) - (3)].i), (yyvsp[(3) - (3)].i)));
@@ -2811,7 +2807,7 @@ yyreduce:
 
   case 92:
 /* Line 1787 of yacc.c  */
-#line 840 "parser.y"
+#line 836 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.val), SelectionParserValue::createRealRange((yyvsp[(1) - (3)].i), (yyvsp[(3) - (3)].r)));
@@ -2821,7 +2817,7 @@ yyreduce:
 
   case 93:
 /* Line 1787 of yacc.c  */
-#line 846 "parser.y"
+#line 842 "parser.y"
     {
                  BEGIN_ACTION;
                  set((yyval.val), SelectionParserValue::createRealRange((yyvsp[(1) - (3)].r), (yyvsp[(3) - (3)].r)));
@@ -2831,7 +2827,7 @@ yyreduce:
 
 
 /* Line 1787 of yacc.c  */
-#line 2835 "parser.cpp"
+#line 2831 "parser.cpp"
       default: break;
     }
   /* User semantic actions sometimes alter yychar, and that requires

diff --git a/src/gromacs/selection/parser.y b/src/gromacs/selection/parser.y
index dd5f95db1cda08607c442278da4abbb7ae1c8016..81f140a4e3c24fabbaec17f48d8f2f6c66bff707 100644 (file)
--- a/src/gromacs/selection/parser.y
+++ b/src/gromacs/selection/parser.y
@@ -252,7 +252,6 @@ cmd_plain:   /* empty */
                  BEGIN_ACTION;
                  SelectionTreeElementPointer s
                         = _gmx_sel_init_group_by_id($1, scanner);
-                 if (!s) YYERROR;
                  SelectionTreeElementPointer p
                         = _gmx_sel_init_position(s, NULL, scanner);
                  if (!p) YYERROR;
@@ -265,7 +264,6 @@ cmd_plain:   /* empty */
                  scoped_ptr_sfree nameGuard($1);
                  SelectionTreeElementPointer s
                         = _gmx_sel_init_group_by_name($1, scanner);
-                 if (!s) YYERROR;
                  SelectionTreeElementPointer p
                         = _gmx_sel_init_position(s, NULL, scanner);
                  if (!p) YYERROR;
@@ -433,14 +431,12 @@ sel_expr:    GROUP string
                  BEGIN_ACTION;
                  scoped_ptr_sfree nameGuard($2);
                  set($$, _gmx_sel_init_group_by_name($2, scanner));
-                 CHECK_SEL($$);
                  END_ACTION;
              }
            | GROUP TOK_INT
              {
                  BEGIN_ACTION;
                  set($$, _gmx_sel_init_group_by_id($2, scanner));
-                 CHECK_SEL($$);
                  END_ACTION;
              }
 ;

diff --git a/src/gromacs/selection/parsetree.cpp b/src/gromacs/selection/parsetree.cpp
index a52346a951acfc9850b5c198c3fbd5c1821a1793..b98cbba819d6618519dba2d48c0f8957a13aad18 100644 (file)
--- a/src/gromacs/selection/parsetree.cpp
+++ b/src/gromacs/selection/parsetree.cpp
@@ -237,6 +237,7 @@
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/file.h"
 #include "gromacs/utility/messagestringcollector.h"
+#include "gromacs/utility/stringutil.h"
 
 #include "keywords.h"
 #include "parsetree.h"
@@ -915,8 +916,7 @@ _gmx_sel_init_const_position(real x, real y, real z)
 /*!
  * \param[in] name  Name of an index group to search for.
  * \param[in] scanner Scanner data structure.
- * \returns   The created constant selection element, or NULL if no matching
- *     index group found.
+ * \returns   The created selection element.
  *
  * See gmx_ana_indexgrps_find() for information on how \p name is matched
  * against the index groups.
@@ -924,67 +924,42 @@ _gmx_sel_init_const_position(real x, real y, real z)
 SelectionTreeElementPointer
 _gmx_sel_init_group_by_name(const char *name, yyscan_t scanner)
 {
-    gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
 
-    if (!_gmx_sel_lexer_has_groups_set(scanner))
-    {
-        SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_GROUPREF));
-        _gmx_selelem_set_vtype(sel, GROUP_VALUE);
-        sel->setName(name);
-        sel->u.gref.name = strdup(name);
-        sel->u.gref.id   = -1;
-        return sel;
-    }
-    if (!grps)
-    {
-        _gmx_selparser_error(scanner, "No index groups set; cannot match 'group %s'", name);
-        return SelectionTreeElementPointer();
-    }
-    SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_CONST));
+    SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_GROUPREF));
     _gmx_selelem_set_vtype(sel, GROUP_VALUE);
-    std::string                 foundName;
-    if (!gmx_ana_indexgrps_find(&sel->u.cgrp, &foundName, grps, name))
+    sel->setName(gmx::formatString("group \"%s\"", name));
+    sel->u.gref.name = strdup(name);
+    sel->u.gref.id   = -1;
+
+    if (_gmx_sel_lexer_has_groups_set(scanner))
     {
-        _gmx_selparser_error(scanner, "Cannot match 'group %s'", name);
-        return SelectionTreeElementPointer();
+        gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
+        sel->resolveIndexGroupReference(grps);
     }
-    sel->setName(foundName);
+
     return sel;
 }
 
 /*!
  * \param[in] id    Zero-based index number of the group to extract.
  * \param[in] scanner Scanner data structure.
- * \returns   The created constant selection element, or NULL if no matching
- *     index group found.
+ * \returns   The created selection element.
  */
 SelectionTreeElementPointer
 _gmx_sel_init_group_by_id(int id, yyscan_t scanner)
 {
-    gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
-
-    if (!_gmx_sel_lexer_has_groups_set(scanner))
-    {
-        SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_GROUPREF));
-        _gmx_selelem_set_vtype(sel, GROUP_VALUE);
-        sel->u.gref.name = NULL;
-        sel->u.gref.id   = id;
-        return sel;
-    }
-    if (!grps)
-    {
-        _gmx_selparser_error(scanner, "No index groups set; cannot match 'group %d'", id);
-        return SelectionTreeElementPointer();
-    }
-    SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_CONST));
+    SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_GROUPREF));
     _gmx_selelem_set_vtype(sel, GROUP_VALUE);
-    std::string                 foundName;
-    if (!gmx_ana_indexgrps_extract(&sel->u.cgrp, &foundName, grps, id))
+    sel->setName(gmx::formatString("group %d", id));
+    sel->u.gref.name = NULL;
+    sel->u.gref.id   = id;
+
+    if (_gmx_sel_lexer_has_groups_set(scanner))
     {
-        _gmx_selparser_error(scanner, "Cannot match 'group %d'", id);
-        return SelectionTreeElementPointer();
+        gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
+        sel->resolveIndexGroupReference(grps);
     }
-    sel->setName(foundName);
+
     return sel;
 }
 

diff --git a/src/gromacs/selection/selectioncollection-impl.h b/src/gromacs/selection/selectioncollection-impl.h
index 6d0dc6ce439eb3eb837e65cce8611c4635789cfe..d423b3e0db9d71cd20768e13732e15816983d024 100644 (file)
--- a/src/gromacs/selection/selectioncollection-impl.h
+++ b/src/gromacs/selection/selectioncollection-impl.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013, 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.
@@ -111,7 +111,7 @@ struct gmx_ana_selcollection_t
 namespace gmx
 {
 
-class MessageStringCollector;
+class ExceptionInitializer;
 
 /*! \internal \brief
  * Private implemention class for SelectionCollection.
@@ -140,18 +140,16 @@ class SelectionCollection::Impl
          *
          * \param[in]    root    Root of selection tree to process.
          * \param        errors  Object for reporting any error messages.
+         * \throws std::bad_alloc if out of memory.
          *
          * Recursively searches the selection tree for unresolved external
          * references.  If one is found, finds the referenced group in
          * \a grps_ and replaces the reference with a constant element that
          * contains the atoms from the referenced group.  Any failures to
          * resolve references are reported to \p errors.
-         *
-         * Does not throw currently, but this is subject to change when more
-         * underlying code is converted to C++.
          */
         void resolveExternalGroups(const gmx::SelectionTreeElementPointer &root,
-                                   MessageStringCollector                 *errors);
+                                   ExceptionInitializer                   *errors);
 
         //! Internal data, used for interfacing with old C code.
         gmx_ana_selcollection_t sc_;

diff --git a/src/gromacs/selection/selectioncollection.cpp b/src/gromacs/selection/selectioncollection.cpp
index 71ea23a42a240197a83a38e83966d675b018bd68..62865880f6326d57dbfd2221288d2925fe2c6e28 100644 (file)
--- a/src/gromacs/selection/selectioncollection.cpp
+++ b/src/gromacs/selection/selectioncollection.cpp
@@ -300,45 +300,18 @@ early_termination:
 
 void SelectionCollection::Impl::resolveExternalGroups(
         const SelectionTreeElementPointer &root,
-        MessageStringCollector            *errors)
+        ExceptionInitializer              *errors)
 {
 
     if (root->type == SEL_GROUPREF)
     {
-        bool        bOk = true;
-        std::string foundName;
-        if (grps_ == NULL)
+        try
         {
-            // TODO: Improve error messages
-            errors->append("Unknown group referenced in a selection");
-            bOk = false;
+            root->resolveIndexGroupReference(grps_);
         }
-        else if (root->u.gref.name != NULL)
+        catch (const UserInputError &)
         {
-            char *name = root->u.gref.name;
-            bOk = gmx_ana_indexgrps_find(&root->u.cgrp, &foundName, grps_, name);
-            sfree(name);
-            if (!bOk)
-            {
-                root->u.gref.name = NULL;
-                // TODO: Improve error messages
-                errors->append("Unknown group referenced in a selection");
-            }
-        }
-        else
-        {
-            if (!gmx_ana_indexgrps_extract(&root->u.cgrp, &foundName, grps_,
-                                           root->u.gref.id))
-            {
-                // TODO: Improve error messages
-                errors->append("Unknown group referenced in a selection");
-                bOk = false;
-            }
-        }
-        if (bOk)
-        {
-            root->type = SEL_CONST;
-            root->setName(foundName);
+            errors->addCurrentExceptionAsNested();
         }
     }
 
@@ -466,16 +439,16 @@ SelectionCollection::setIndexGroups(gmx_ana_indexgrps_t *grps)
     impl_->grps_               = grps;
     impl_->bExternalGroupsSet_ = true;
 
-    MessageStringCollector      errors;
+    ExceptionInitializer        errors("Unknown index group references encountered");
     SelectionTreeElementPointer root = impl_->sc_.root;
     while (root)
     {
         impl_->resolveExternalGroups(root, &errors);
         root = root->next;
     }
-    if (!errors.isEmpty())
+    if (errors.hasNestedExceptions())
     {
-        GMX_THROW(InvalidInputError(errors.toString()));
+        GMX_THROW(InconsistentInputError(errors));
     }
     for (size_t i = 0; i < impl_->sc_.sel.size(); ++i)
     {

diff --git a/src/gromacs/selection/selectioncollection.h b/src/gromacs/selection/selectioncollection.h
index 2e8947fb1bf5d043dc70567c50142703fc47d0af..a00ae0484b30b0ba2b222655b00a2af63a16332e 100644 (file)
--- a/src/gromacs/selection/selectioncollection.h
+++ b/src/gromacs/selection/selectioncollection.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, 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.
@@ -223,14 +223,14 @@ class SelectionCollection
          *
          * \param[in]  grps  Index groups to use for the selections.
          * \throws  std::bad_alloc if out of memory.
-         * \throws  InvalidInputError if a group reference cannot be resolved.
+         * \throws  InconsistentInputError if a group reference cannot be resolved.
          *
          * Only the first call to this method can have a non-NULL \p grps.
          * At this point, any selections that have already been provided are
          * searched for references to external groups, and the references are
          * replaced by the contents of the groups.  If any referenced group
          * cannot be found in \p grps (or if \p grps is NULL and there are any
-         * references), InvalidInputError is thrown.
+         * references), InconsistentInputError is thrown.
          *
          * The selection collection keeps a reference to \p grps until this
          * method is called with a NULL \p grps.

diff --git a/src/gromacs/selection/selelem.cpp b/src/gromacs/selection/selelem.cpp
index f496ea8b505f55518257503979a495b2f0136384..e1996fd80b34c36e8a19f01f8ff477bee73d34da 100644 (file)
--- a/src/gromacs/selection/selelem.cpp
+++ b/src/gromacs/selection/selelem.cpp
@@ -49,6 +49,7 @@
 #include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/stringutil.h"
 
 #include "keywords.h"
 #include "mempool.h"
@@ -330,6 +331,59 @@ void SelectionTreeElement::fillNameIfMissing(const char *selectionText)
     }
 }
 
+void SelectionTreeElement::resolveIndexGroupReference(gmx_ana_indexgrps_t *grps)
+{
+    GMX_RELEASE_ASSERT(type == SEL_GROUPREF,
+                       "Should only be called for index group reference elements");
+    if (grps == NULL)
+    {
+        std::string message = formatString(
+                    "Cannot match '%s', because index groups are not available.",
+                    name().c_str());
+        GMX_THROW(InconsistentInputError(message));
+    }
+
+    gmx_ana_index_t foundGroup;
+    std::string     foundName;
+    if (u.gref.name != NULL)
+    {
+        if (!gmx_ana_indexgrps_find(&foundGroup, &foundName, grps, u.gref.name))
+        {
+            std::string message = formatString(
+                        "Cannot match '%s', because no such index group can be found.",
+                        name().c_str());
+            GMX_THROW(InconsistentInputError(message));
+        }
+    }
+    else
+    {
+        if (!gmx_ana_indexgrps_extract(&foundGroup, &foundName, grps, u.gref.id))
+        {
+            std::string message = formatString(
+                        "Cannot match '%s', because no such index group can be found.",
+                        name().c_str());
+            GMX_THROW(InconsistentInputError(message));
+        }
+    }
+
+    if (!gmx_ana_index_check_sorted(&foundGroup))
+    {
+        gmx_ana_index_deinit(&foundGroup);
+        std::string message = formatString(
+                    "Group '%s' ('%s') cannot be used in selections, "
+                    "because atom indices in it are not sorted and/or "
+                    "it contains duplicate atoms.",
+                    foundName.c_str(), name().c_str());
+        GMX_THROW(InconsistentInputError(message));
+    }
+
+    sfree(u.gref.name);
+    type = SEL_CONST;
+    gmx_ana_index_set(&u.cgrp, foundGroup.isize, foundGroup.index,
+                      foundGroup.nalloc_index);
+    setName(foundName);
+}
+
 } // namespace gmx
 
 /*!

diff --git a/src/gromacs/selection/selelem.h b/src/gromacs/selection/selelem.h
index 9f4691e30194cfd525d0b6a989a12c13e40790d9..c89adf0ecb0bf1a199afbe4cefcc6a95ab686457 100644 (file)
--- a/src/gromacs/selection/selelem.h
+++ b/src/gromacs/selection/selelem.h
@@ -319,6 +319,16 @@ class SelectionTreeElement
          */
         void fillNameIfMissing(const char *selectionText);
 
+        /*! \brief
+         * Resolved an unresolved reference to an index group.
+         *
+         * \param[in] grps  Index groups to use to resolve the reference.
+         * \throws    std::bad_alloc if out of memory.
+         * \throws    InconsistentInputError if the reference cannot be
+         *     resolved.
+         */
+        void resolveIndexGroupReference(gmx_ana_indexgrps_t *grps);
+
         //! Type of the element.
         e_selelem_t                         type;
         /*! \brief

diff --git a/src/gromacs/selection/tests/selectioncollection.cpp b/src/gromacs/selection/tests/selectioncollection.cpp
index 521514e60870c3e65e9297e67f2d806c520d8cd8..04716ae3d61c10c26efbff065c2ffc3b21311d68 100644 (file)
--- a/src/gromacs/selection/tests/selectioncollection.cpp
+++ b/src/gromacs/selection/tests/selectioncollection.cpp
@@ -476,22 +476,22 @@ TEST_F(SelectionCollectionTest, HandlesHelpKeywordInInvalidContext)
 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser1)
 {
     ASSERT_NO_THROW_GMX(sc_.setIndexGroups(NULL));
-    EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InvalidInputError);
-    EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InvalidInputError);
+    EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
+    EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 }
 
 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser2)
 {
     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
-    EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InvalidInputError);
-    EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InvalidInputError);
+    EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
+    EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 }
 
 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed1)
 {
     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"foo\""));
     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
-    EXPECT_THROW_GMX(sc_.setIndexGroups(NULL), gmx::InvalidInputError);
+    EXPECT_THROW_GMX(sc_.setIndexGroups(NULL), gmx::InconsistentInputError);
     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 }
 
@@ -499,7 +499,22 @@ TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed2)
 {
     ASSERT_NO_THROW_GMX(sc_.parseFromString("group 4; group \"foo\""));
     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
-    EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InvalidInputError);
+    EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
+    EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
+}
+
+TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReference)
+{
+    ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
+    EXPECT_THROW_GMX(sc_.parseFromString("group \"GrpUnsorted\""),
+                     gmx::InconsistentInputError);
+    EXPECT_THROW_GMX(sc_.parseFromString("2"), gmx::InconsistentInputError);
+}
+
+TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReferenceDelayed)
+{
+    ASSERT_NO_THROW_GMX(sc_.parseFromString("group 2; group \"GrpUnsorted\""));
+    EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 }