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NCBI C++ ToolKit: src/app/cn3d/cn3d_tools.cpp Source File

36 #if defined(__WXMSW__) 40 #elif defined(__WXGTK__) 43 #elif defined(__WXMAC__) 48 #include "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/Headers/InternetConfig.h" 62 #include <wx/msw/winundef.h> 66 #include <wx/fileconf.h> 112

wxFont *font = wxFont::New(

113

#

if

defined(__WXMSW__)

115

#elif defined(__WXGTK__)

117

#elif defined(__WXMAC__)

120

wxSWISS, wxNORMAL, wxBOLD,

false

);

121  if

(font && font->Ok())

124  ERRORMSG

(

"Can't create default structure window font"

);

126  if

(font)

delete

font;

130

#

if

defined(__WXMSW__)

132

#elif defined(__WXGTK__)

134

#elif defined(__WXMAC__)

137

wxROMAN, wxNORMAL, wxNORMAL,

false

);

138  if

(font && font->Ok())

141  ERRORMSG

(

"Can't create default sequence window font"

);

142  if

(font)

delete

font;

158  "( netscape -noraise -remote 'openURL(<URL>,new-window)' || netscape '<URL>' ) >/dev/null 2>&1 &" 203

wxString regStr =

registry

.

Get

(section, name).c_str();

204  return

(regStr.size() > 0 && regStr.ToLong(&

value

));

210

wxString regStr =

registry

.

Get

(section, name).c_str();

211  return

(regStr.size() > 0 && regStr.ToDouble(&

value

));

217  return

(regStr.size() > 0 && (

218  toupper

((

unsigned char

) regStr[0]) ==

'T'

||

toupper

((

unsigned char

) regStr[0]) ==

'F'

||

219  toupper

((

unsigned char

) regStr[0]) ==

'Y'

||

toupper

((

unsigned char

) regStr[0]) ==

'N'

));

225  return

(regStr.size() > 0);

230

wxString regStr =

registry

.

Get

(section, name).c_str();

232  if

(regStr.size() == 0 || !regStr.ToLong(&

l

)) {

233  WARNINGMSG

(

"Can't get long from registry: "

<< section <<

", "

<< name);

242

wxString regStr =

registry

.

Get

(section, name).c_str();

243  if

(regStr.size() == 0 || !regStr.ToDouble(

value

)) {

244  WARNINGMSG

(

"Can't get double from registry: "

<< section <<

", "

<< name);

253  if

(regStr.size() == 0 || !(

254  toupper

((

unsigned char

) regStr[0]) ==

'T'

||

toupper

((

unsigned char

) regStr[0]) ==

'F'

||

255  toupper

((

unsigned char

) regStr[0]) ==

'Y'

||

toupper

((

unsigned char

) regStr[0]) ==

'N'

)) {

256  WARNINGMSG

(

"Can't get boolean from registry: "

<< section <<

", "

<< name);

259

*

value

= (

toupper

((

unsigned char

) regStr[0]) ==

'T'

||

toupper

((

unsigned char

) regStr[0]) ==

'Y'

);

266  if

(regStr.size() == 0) {

267  WARNINGMSG

(

"Can't get string from registry: "

<< section <<

", "

<< name);

278  ERRORMSG

(

"registry Set("

<< section <<

", "

<< name <<

") failed"

);

288  ERRORMSG

(

"registry Set("

<< section <<

", "

<< name <<

") failed"

);

298

regStr =

value

?

"yes"

:

"no"

;

300

regStr =

value

?

"true"

:

"false"

;

303  ERRORMSG

(

"registry Set("

<< section <<

", "

<< name <<

") failed"

);

313  ERRORMSG

(

"registry Set("

<< section <<

", "

<< name <<

") failed"

);

338  if

(getenv(

"CN3D_HOME"

) !=

NULL

)

342  if

(wxIsAbsolutePath(argv0))

344  else if

(wxPathOnly(argv0) ==

""

)

353

wxFileName::SplitPath(wxFileConfig::GetLocalFileName(

"unused"

), &localDir,

NULL

,

NULL

);

354

wxString prefsDirLocal = localDir + wxFILE_SEP_PATH +

"Cn3D_User"

;

355

wxString prefsDirProg = wxString(

programDir

.c_str()) + wxFILE_SEP_PATH +

"Cn3D_User"

;

356  if

(wxDirExists(prefsDirLocal))

358  else if

(wxDirExists(prefsDirProg))

362  if

(wxMkdir(prefsDirLocal) && wxDirExists(prefsDirLocal))

364  else if

(wxMkdir(prefsDirProg) && wxDirExists(prefsDirProg))

368  WARNINGMSG

(

"Can't create Cn3D_User folder at either:" 369

<<

"\n "

<< prefsDirLocal

370

<<

"\nor "

<< prefsDirProg);

389 static bool

MSWin_OpenDocument(

const char

* doc_name)

391  int

status = (

int

) ShellExecute(0,

"open"

, doc_name,

NULL

,

NULL

, SW_SHOWNORMAL);

393  ERRORMSG

(

"Unable to open document \""

<< doc_name <<

"\", error = "

<< status);

402 static

OSStatus MacLaunchURL(ConstStr255Param urlStr,

long int len

)

409

err = ICStart(&inst,

'Cn3D'

);

412

err = ICFindConfigFile(inst, 0, nil);

423

endSel = (

len

> 0 &&

len

<= 255) ?

len

: 255;

424

err = ICLaunchURL(inst,

"\p"

, urlStr, endSel, &startSel, &endSel);

435  INFOMSG

(

"launching url "

<< url);

437 #if defined(__WXMSW__) 438  if

(!MSWin_OpenDocument(url)) {

439  ERRORMSG

(

"Unable to launch browser"

);

442 #elif defined(__WXGTK__) 446  while

((pos=

command

.find(

"<URL>"

, pos)) != string::npos)

451 #elif defined(__WXMAC__) 455  unsigned int i

= 0,

l

= strlen(url);

456  unsigned char

uc_url[

l

+1];

457  for

(;

i

<

l

&&

i

< 255; ++

i

) uc_url[

i

] = (

unsigned char

) *(url +

i

);

459

MacLaunchURL(uc_url,

l

);

467  static const string

host(

"eutils.ncbi.nlm.nih.gov"

), path(

"/entrez/eutils/efetch.fcgi"

);

468  string

args =

string

(

"rettype=asn.1&retmode=binary&maxplex=1&id="

) + id;

473  string

db = (

round

== 1) ?

"protein"

:

"nucleotide"

;

474  INFOMSG

(

"Trying to load sequence from URL "

<< host << path <<

'?'

<< (args +

"&db="

+ db));

478  if

(seqEntry.

IsSeq

())

483  WARNINGMSG

(

"FetchSequenceViaHTTP() - confused by SeqEntry format"

);

485  WARNINGMSG

(

"FetchSequenceViaHTTP() - HTTP Bioseq retrieval failed, err: "

<< err);

497  static

Char2UChar charMap;

499  if

(charMap.size() == 0) {

504

Char2UChar::const_iterator

n

= charMap.find(

toupper

((

unsigned char

)

r

));

505  if

(

n

!= charMap.end())

508  return

charMap.find(

'X'

)->second;

515  ERRORMSG

(

"LookupCharacterFromNCBIStdaaNumber() - valid values are 0 - 27"

);

523  static const string

allowed =

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

;

525  for

(

i

=0;

i

<prosite.size(); ++

i

)

526  if

(allowed.find(

toupper

((

unsigned char

) prosite[

i

])) == string::npos)

break

;

527  if

(

i

!= prosite.size())

throw "invalid ProSite character"

;

528  if

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

'.'

)

throw "ProSite pattern must end with '.'"

;

534  bool

inGroup =

false

;

535  for

(

unsigned int i

=0;

i

<prosite.size(); ++

i

) {

538  bool

characterHandled =

true

;

539  switch

(prosite[

i

]) {

540  case '-'

:

case '.'

:

case '>'

:

545  if

(prosite[

i

] ==

'>'

) *regex +=

'$'

;

551

characterHandled =

false

;

554  if

(characterHandled)

continue

;

556

(

isalpha

((

unsigned char

) prosite[

i

]) &&

toupper

((

unsigned char

) prosite[

i

]) !=

'X'

) ||

557

prosite[

i

] ==

'['

|| prosite[

i

] ==

'{'

|| prosite[

i

] ==

'#'

)) {

564  switch

(prosite[

i

]) {

577  case 'X'

:

case 'x'

:

584

*regex +=

toupper

((

unsigned char

) prosite[

i

]);

590  catch

(

const char

*err) {

591  ERRORMSG

(

"Prosite2Regex() - "

<< err);

601  static const string

allowed =

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

;

605  for

(

i

=0;

i

<prosite.size(); ++

i

)

606  if

(allowed.find(

toupper

((

unsigned char

) prosite[

i

])) == string::npos)

break

;

607  if

(

i

!= prosite.size())

return

0;

609  bool

hasOnlyX =

true

, stopParsing =

false

;

610  bool

inBraces =

false

, inBrackets =

false

, inParens =

false

;

611  unsigned int

length = 0;

613  string

betweenParens;

615  for

(

i

=0;

i

< prosite.size() && !stopParsing; ++

i

) {

618  bool

characterHandled =

true

;

619  switch

(prosite[

i

]) {

620  case '-'

:

case '.'

:

case '>'

:

case '<'

:

623

characterHandled =

false

;

626  if

(inParens && prosite[

i

] !=

')'

&& !characterHandled) betweenParens += prosite[

i

];

627  if

(characterHandled)

continue

;

629  if

(hasOnlyX &&

isalpha

((

unsigned char

) prosite[

i

]) &&

toupper

((

unsigned char

) prosite[

i

]) !=

'X'

) {

634  switch

(prosite[

i

]) {

644

length += nFromParens - 1;

649

betweenParens.erase();

666  if

(!inParens && !inBraces && !inBrackets) ++length;

672  if

(inParens || inBrackets || inBraces) length = 0;

675  if

(hasOnlyX) length = 0;

679  if

(stopParsing) length = 0;

bool GetAsnDataViaHTTPS(const std::string &host, const std::string &path, const std::string &args, ASNClass *asnObject, std::string *err, bool binaryData=true)

bool IsWindowedMode(void)

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

std::ofstream out("events_result.xml")

main entry point for tests

void Reset(void)

Reset reference object.

bool Empty(void) const THROWS_NONE

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

virtual const string & Get(const string &section, const string &name, TFlags flags=0) const

Get the parameter value.

IRWRegistry * Read(CNcbiIstream &is, TFlags flags=0, const string &path=kEmptyStr)

Read and parse the stream "is", and merge its content with current Registry entries.

bool Write(CNcbiOstream &os, TFlags flags=0) const

Write the registry content to output stream.

bool Set(const string &section, const string &name, const string &value, TFlags flags=0, const string &comment=kEmptyStr)

Set the configuration parameter value.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

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

Convert int to string.

@ fConvErr_NoThrow

Do not throw an exception on error.

TSet & SetSet(void)

Select the variant.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

unsigned int

A callback function used to compare two keys in a database.

const struct ncbi::grid::netcache::search::fields::SIZE size

const GenericPointer< typename T::ValueType > T2 value

Process information in the NCBI Registry, including working with configuration files.

std::istream & in(std::istream &in_, double &x_)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

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

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