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NCBI C++ ToolKit: src/objtools/cleanup/cleanup_utils.hpp Source File

1 #ifndef OBJECTS_GENERAL___CLEANUP_UTILS__HPP 2 #define OBJECTS_GENERAL___CLEANUP_UTILS__HPP 61  bool

changed =

false

;

98 template

<

typename

C>

101  bool

changed =

false

;

102  typename

C::iterator it = str_cont.begin();

103  while

(it != str_cont.end()) {

108

it = str_cont.erase(it);

117 template

<

typename

C>

120  bool

changed =

false

;

121  typename

C::iterator it = str_cont.begin();

122  while

(it != str_cont.end()) {

127

it = str_cont.erase(it);

144 template

<

typename

Cont>

147  bool

changed =

false

;

148  typedef typename

Cont::iterator iterator;

149

iterator l_it =

l

.begin();

150  while

(l_it !=

l

.end()) {

151

iterator dup_it = case_insensitive ?

153

find(

l

.begin(), l_it, *l_it );

154  if

(dup_it != l_it) {

155

l_it =

l

.erase(l_it);

165 #define TRUNCATE_SPACES(o, x) \ 166  if ((o).IsSet##x()) { \ 167  size_t n = (o).Get##x().size(); \ 168  NStr::TruncateSpacesInPlace((o).Set##x()); \ 169  if (n != (o).Get##x().size() ) { \ 170  ChangeMade(CCleanupChange::eTrimSpaces); \ 172  if (NStr::IsBlank((o).Get##x())) { \ 174  ChangeMade(CCleanupChange::eTrimSpaces); \ 178 #define TRUNCATE_CHOICE_SPACES(o, x) \ 180  size_t n = (o).Get##x().size(); \ 181  NStr::TruncateSpacesInPlace((o).Set##x()); \ 182  if (n != (o).Get##x().size() ) { \ 183  ChangeMade(CCleanupChange::eTrimSpaces); \ 185  if (NStr::IsBlank((o).Get##x())) { \ 187  ChangeMade(CCleanupChange::eTrimSpaces); \ 191 #define CONVERT_QUOTES(x) \ 193  if (ConvertDoubleQuotes(Set##x()) ) { \ 194  ChangeMade(CCleanupChange::eCleanDoubleQuotes); \ 198 #define COMPRESS_STRING_MEMBER(o, x) \ 199  if ((o).IsSet##x()) { \ 200  const size_t old_len = (o).Set##x().length(); \ 201  CompressSpaces((o).Set##x()); \ 202  if( old_len != (o).Set##x().length() ) { \ 203  ChangeMade(CCleanupChange::eTrimSpaces); \ 205  if (NStr::IsBlank((o).Get##x())) { \ 207  ChangeMade(CCleanupChange::eTrimSpaces); \ 211 #define CLEAN_STRING_MEMBER(o, x) \ 212  if ((o).IsSet##x()) { \ 213  if (CleanVisString((o).Set##x()) ) { \ 214  ChangeMade(CCleanupChange::eTrimSpaces); \ 216  if (NStr::IsBlank((o).Get##x())) { \ 218  ChangeMade(CCleanupChange::eTrimSpaces); \ 223 #define CLEAN_AND_COMPRESS_STRING_MEMBER(o, x) \ 224  do { COMPRESS_STRING_MEMBER(o, x); CLEAN_STRING_MEMBER(o, x); } while(false) 226 #define CLEAN_STRING_MEMBER_JUNK(o, x) \ 227 if ((o).IsSet##x()) { \ 228  if (CleanVisStringJunk((o).Set##x()) ) { \ 229  ChangeMade(CCleanupChange::eTrimSpaces); \ 231  if (NStr::IsBlank((o).Get##x())) { \ 233  ChangeMade(CCleanupChange::eTrimSpaces); \ 238 #define CLEAN_AND_COMPRESS_STRING_MEMBER_JUNK(o, x) \ 239  do { COMPRESS_STRING_MEMBER(o, x); CLEAN_STRING_MEMBER_JUNK(o, x); } while(false) 241 #define EXTENDED_CLEAN_STRING_MEMBER(o, x) \ 242 if ((o).IsSet##x()) { \ 243  CleanVisString((o).Set##x()); \ 244  if (NStr::IsBlank((o).Get##x())) { \ 246  ChangeMade(CCleanupChange::eTrimSpaces); \ 250 #define CLEAN_STRING_CHOICE(o, x) \ 251  if (CleanVisString((o).Set##x()) ) { \ 252  ChangeMade(CCleanupChange::eTrimSpaces); \ 254  if (NStr::IsBlank((o).Get##x())) { \ 256  ChangeMade(CCleanupChange::eTrimSpaces); \ 259 #define CLEAN_STRING_LIST(o, x) \ 260  if ((o).IsSet##x()) { \ 261  if (CleanVisStringContainer((o).Set##x()) ) { \ 262  ChangeMade(CCleanupChange::eTrimSpaces); \ 264  if ((o).Get##x().empty()) { \ 266  ChangeMade(CCleanupChange::eTrimSpaces); \ 270 #define CLEAN_STRING_LIST_JUNK(o, x) \ 271 if ((o).IsSet##x()) { \ 272  if (CleanVisStringContainerJunk((o).Set##x()) ) { \ 273  ChangeMade(CCleanupChange::eTrimSpaces); \ 275  if ((o).Get##x().empty()) { \ 277  ChangeMade(CCleanupChange::eTrimSpaces); \ 281 #define EXTENDED_CLEAN_STRING_LIST(o, x) \ 282  if ((o).IsSet##x()) { \ 283  CleanVisStringList((o).Set##x()); \ 284  if ((o).Get##x().empty()) { \ 286  ChangeMade(CCleanupChange::eTrimSpaces); \ 291 #define CLEAN_INTERNAL_STRING(o, x) \ 292  if (o.IsSet##x()) { \ 293  if ( CleanVisString(o.Set##x()) ) { \ 294  ChangeMade(CCleanupChange::eTrimSpaces); \ 296  if (NStr::IsBlank(o.Get##x())) { \ 298  ChangeMade(CCleanupChange::eTrimSpaces); \ 302 #define MERGEABLE_STRING_VALUE(o1, o2, x) \ 303  if ((o1).CanGet##x() && (o2).CanGet##x() \ 304  && !NStr::IsBlank ((o1).Get##x()) \ 305  && !NStr::IsBlank ((o2).Get##x()) \ 306  && !NStr::Equal ((o1).Get##x(), (o2).Get##x())) { \ 310 #define MERGEABLE_STRING_LIST(o1, o2, x) \ 311  if ((o1).CanGet##x() && (o2).CanGet##x() \ 312  && (o1).Get##x().size() > 0 \ 313  && (o2).Get##x().size() > 0) { \ 314  list <string>::const_iterator it1 = (o1).Get##x().begin(); \ 315  list <string>::const_iterator it2 = (o2).Get##x().begin(); \ 316  while (it1 != (o1).Get##x().end() && it2 != (o2).Get##x().end()) { \ 317  if (!NStr::Equal ((*it1), (*it2))) { \ 322  if (it1 != (o1).Get##x().end() || it2 != (o2).Get##x().end()) { \ 327 #define MERGEABLE_INT_VALUE(o1, o2, x) \ 328  (!(o1).CanGet##x() || !(o2).CanGet##x() \ 329  || (o1).Get##x() == 0 \ 330  || (o2).Get##x() == 0 \ 331  || (o1).Get##x() == (o2).Get##x()) 333 #define MATCH_STRING_VALUE(o1, o2, x) \ 334  ((!(o1).CanGet##x() && !(o2).CanGet##x()) \ 335  || ((o1).CanGet##x() && (o2).CanGet##x() \ 336  && NStr::Equal((o1).Get##x(), (o2).Get##x()))) 338 #define MATCH_STRING_LIST(o1, o2, x) \ 339  if (((o1).CanGet##x() && (o1).Get##x().size() > 0 && !(o2).CanGet##x()) \ 340  || (!(o1).CanGet##x() && (o2).CanGet##x() && (o2).Get##x().size() > 0)) { \ 342  } else if ((o1).CanGet##x() && (o2).CanGet##x()) { \ 343  list <string>::const_iterator it1 = (o1).Get##x().begin(); \ 344  list <string>::const_iterator it2 = (o2).Get##x().begin(); \ 345  while (it1 != (o1).Get##x().end() && it2 != (o2).Get##x().end()) { \ 346  if (!NStr::Equal ((*it1), (*it2))) { \ 351  if (it1 != (o1).Get##x().end() || it2 != (o2).Get##x().end()) { \ 356 #define MATCH_INT_VALUE(o1, o2, x) \ 357  ((!(o1).CanGet##x() && !(o2).CanGet##x()) \ 358  || ((o1).CanGet##x() && (o2).CanGet##x() \ 359  && (o1).Get##x() == (o2).Get##x()) \ 360  || ((o1).CanGet##x() && (o1).Get##x() == 0 \ 361  && !(o2).CanGet##x()) \ 362  || ((o2).CanGet##x() && (o2).Get##x() == 0 \ 363  && !(o1).CanGet##x())) 365 #define MATCH_BOOL_VALUE(o1, o2, x) \ 366  if (!(o1).IsSet##x()) { \ 367  if ((o2).IsSet##x()) { \ 370  } else if (!(o2).IsSet##x()) { \ 372  } else if (((o1).Get##x() && !(o2).Get##x()) \ 373  || (!(o2).Get##x() && (o2).Get##x())) { \ 395 template

<

class

Iter,

class

Comp>

412 template

<

class

Iter>

@Auth_list.hpp User-defined methods of the data storage class.

@Pubdesc.hpp User-defined methods of the data storage class.

bool RemoveSpacesBetweenTildes(string &str)

remove white space between pairs of tildes.

bool is_sorted(Iter first, Iter last, Comp comp)

bool CleanVisStringContainer(C &str_cont)

bool CleanDoubleQuote(string &str)

Change double to single quotes.

bool RemoveDupsNoSort(Cont &l, bool case_insensitive=false)

bool CleanVisString(string &str)

bool CleanVisStringContainerJunk(C &str_cont)

CRef< CSeq_loc > ReadLocFromText(const string &text, const CSeq_id *id, CScope *scope)

bool s_OrgrefSynCompare(const string &syn1, const string &syn2)

bool s_DbtagEqual(const CRef< CDbtag > &dbt1, const CRef< CDbtag > &dbt2)

void TrimInternalSemicolons(string &str)

remove duplicate internal semicolons.

bool s_DbtagCompare(const CRef< CDbtag > &dbt1, const CRef< CDbtag > &dbt2)

char x_ValidAminoAcid(string_view abbrev)

bool s_OrgrefSynEqual(const string &syn1, const string &syn2)

bool RemoveSpaces(string &str)

remove all spaces from a string

bool Asn2gnbkCompressSpaces(string &val)

weird space compression from C Toolkit

bool TrimSpacesSemicolonsAndCommas(string &val)

bool CleanVisStringJunk(string &str, bool allow_ellipses=false)

bool ConvertDoubleQuotes(string &str)

Cleaning functions may return true if they have changed something.

Include a standard set of the NCBI C++ Toolkit most basic headers.

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static DLIST_TYPE *DLIST_NAME() last(DLIST_LIST_TYPE *list)

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

static const char * str(char *buf, int n)

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static void text(MDB_val *v)

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

SCaseInsensitiveStrComp(const string &str)

bool operator()(string &s)

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