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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuUtils_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/structure/cd_utils/cuUtils.cpp Source File

81  if

(SeqID.

Empty

()) {

82

Str +=

"<Empty Sequence>"

;

84

}

else if

(!SeqID->

IsGi

() && !SeqID->

IsPdb

()) {

85

Str +=

"<Non-gi/pdb Sequence Types Unsupported>"

;

89  if

(SeqID->

IsGi

()) {

90

GI = SeqID->

GetGi

();

91

Str += NStr::NumericToString<TGi>(GI);

92

}

else if

(SeqID->

IsPdb

()) {

97

sprintf(

buf

,

"pdb %s_%c"

,pPDB_ID.

GetMol

().

Get

().c_str(),chain);

99  if

(chain==

' '

)

buf

[

len

-2]=0;

113  if

(SeqID.

Empty

()) {

114  return "<Empty Sequence>"

;

120  if

(SeqID->

IsGi

()) {

121

GI = SeqID->

GetGi

();

122

Str = NStr::NumericToString<TGi>(GI);

123

}

else if

(SeqID->

IsPdb

()) {

126

}

else if

(SeqID->

IsOther

()) {

128

}

else if

(SeqID->

IsLocal

()) {

138  if

( (

int

)Str.size() <

Len

) {

139

Str.append(

Len

- Str.size(),

' '

);

154

list< CRef< CCdd_id > >::const_iterator

i

, ibegin, iend;

156

ibegin = cdd.

GetId

().

Get

().begin();

158  for

(

i

= ibegin;

i

!= iend; ++

i

) {

174  string

s =

"Accession "

+

id

.GetGid().GetAccession();

175  if

(

id

.GetGid().IsSetDatabase()) {

176

s.append(

" Database "

+

id

.GetGid().GetDatabase());

178  if

(

id

.GetGid().IsSetRelease()) {

179

s.append(

" Release "

+

id

.GetGid().GetRelease());

181  if

(

id

.GetGid().IsSetVersion()) {

186  return "Unset/Unknown Cdd_id"

;

210  static const std::string

allowed =

"-ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789[],(){}<>."

;

212  for

(

i

=0;

i

<prosite.size();

i

++) {

213  if

(allowed.find(

toupper

((

unsigned char

) prosite[

i

])) == std::string::npos)

break

;

215  if

(

i

!= prosite.size())

throw "invalid ProSite character"

;

216  if

(prosite[prosite.size() - 1] !=

'.'

)

throw "ProSite pattern must end with '.'"

;

221  bool

inGroup =

false

;

222  for

(

i

=0;

i

<prosite.size();

i

++) {

225  bool

characterHandled =

true

;

226  switch

(prosite[

i

]) {

227  case '-'

:

case '.'

:

case '>'

:

232  if

(prosite[

i

] ==

'>'

) *regex +=

'$'

;

238

characterHandled =

false

;

241  if

(characterHandled)

continue

;

243

(

isalpha

((

unsigned char

) prosite[

i

]) &&

toupper

((

unsigned char

) prosite[

i

]) !=

'X'

) ||

244

prosite[

i

] ==

'['

|| prosite[

i

] ==

'{'

)) {

250  switch

(prosite[

i

]) {

263  case 'X'

:

case 'x'

:

267

*regex +=

toupper

((

unsigned char

) prosite[

i

]);

273  catch

(

const char

*err) {

274

*errString =

string

(err);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

bool Prosite2Regex(const std::string &prosite, std::string *regex, std::string *errString)

string CddIdString(const CCdd &cdd)

bool SameCDAccession(const CCdd_id &id1, const CCdd_id &id2)

const int CDTreeColorCycle[]

void Make_GI_or_PDB_String_CN3D(const CRef< CSeq_id > SeqID, std::string &Str)

string GetSeqIDStr(const CRef< CSeq_id > &SeqID)

const int kNumColorsInCDTreeColorCycle

string Make_SeqID_String(const CRef< CSeq_id > SeqID, bool Pad, int Len)

const TPrim & Get(void) const

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#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 string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

const TId & GetId(void) const

Get the Id member data.

const TAccession & GetAccession(void) const

Get the Accession member data.

E_Choice Which(void) const

Which variant is currently selected.

const TGid & GetGid(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

E_Choice

Choice variants.

@ e_Gid

holds accession/version pairs

@ e_Uid

for synchronization with Entrez holds PSSM-Ids

bool IsStr(void) const

Check if variant Str is selected.

bool IsId(void) const

Check if variant Id is selected.

const TStr & GetStr(void) const

Get the variant data.

TId GetId(void) const

Get the variant data.

TChain GetChain(void) const

Get the Chain member data.

const TPdb & GetPdb(void) const

Get the variant data.

bool IsOther(void) const

Check if variant Other is selected.

bool IsPdb(void) const

Check if variant Pdb is selected.

TGi GetGi(void) const

Get the variant data.

const TMol & GetMol(void) const

Get the Mol member data.

const TOther & GetOther(void) const

Get the variant data.

const TLocal & GetLocal(void) const

Get the variant data.

bool IsLocal(void) const

Check if variant Local is selected.

bool IsGi(void) const

Check if variant Gi is selected.

const TAccession & GetAccession(void) const

Get the Accession member data.

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