A RetroSearch Logo

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Search Query:

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/SpectrumSet_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/ms/omssa/SpectrumSet.cpp Source File

121  bool

GotOne(

false

);

125  bool

GotThisOne(

false

);

129  if

(!DTA || DTA.eof()) {

141  if

(Max > 0 && Count > Max) {

142  ERR_POST

(

Info

<<

"LoadMultDTA: too many spectra in xml"

);

147  CRegexp

RxpGetNum(

"\\sid\\s*=\\s*(\"(\\S+)\"|(\\S+)\b)"

);

149  if

((Match = RxpGetNum.

GetMatch

(

Line

.c_str(), 0, 2)) !=

""

||

150

(Match = RxpGetNum.

GetMatch

(

Line

.c_str(), 0, 3)) !=

""

) {

153

MySpectrum->SetNumber(iIndex);

157  CRegexp

RxpGetName(

"\\sname\\s*=\\s*(\"(\\S+)\"|(\\S+)\b)"

);

158  if

((Match = RxpGetName.

GetMatch

(

Line

.c_str(), 0, 2)) !=

""

||

159

(Match = RxpGetName.

GetMatch

(

Line

.c_str(), 0, 3)) !=

""

) {

165

}

while

(

Line

.size() < 3 && !DTA.eof());

170  ERR_POST

(

Info

<<

"LoadMultDTA: not able to get header"

);

187  Set

().push_back(MySpectrum);

189

}

while

(DTA && !DTA.eof());

196

}

catch

(NCBI_NS_STD::exception& e) {

197  ERR_POST

(

Info

<<

"Exception in CSpectrumSet::LoadMultDTA: "

<< e.what());

200  ERR_POST

(

Info

<<

"Exception in CSpectrumSet::LoadMultDTA: "

);

214  bool

GotOne(

false

);

218  bool

GotThisOne(

false

);

220  if

(Max > 0 && Count > Max)

224

MySpectrum->SetNumber(iIndex);

229

}

while

(

Line

.size() < 3 && !DTA.eof());

241  if

(!DTA || DTA.eof()) {

250  while

(

Line

.size() > 1) {

260  Set

().push_back(MySpectrum);

262

}

while

(DTA && !DTA.eof());

267

}

catch

(NCBI_NS_STD::exception& e) {

268  ERR_POST

(

Info

<<

"Exception in CSpectrumSet::LoadMultBlankLineDTA: "

<< e.what());

271  ERR_POST

(

Info

<<

"Exception in CSpectrumSet::LoadMultBlankLineDTA: "

);

286  double

precursor(0.0L);

288  if

(!(DTA >> precursor) || precursor < 0) {

300  if

(!(DTA >>

dummy

)

) {

303

MySpectrum->SetCharge().push_back(

static_cast <int>

(

dummy

));

309

MySpectrum->SetPrecursormz(

MSSCALE2INT

(precursor));

329  for

(

i

= 0;

i

< InputPeaks.size(); ++

i

) {

330  if

(InputPeaks[

i

].Intensity > MaxI) MaxI = InputPeaks[

i

].Intensity;

335  if

(MaxI > 0.0) Scale = 1000000000.0/MaxI;

338

Scale = pow(10.0, floor(

log10

(Scale)));

339

MySpectrum->SetIscale(Scale);

342  for

(

i

= 0;

i

< InputPeaks.size(); ++

i

) {

344

MySpectrum->SetMz().push_back(InputPeaks[

i

].mz);

346

MySpectrum->SetAbundance().push_back(

static_cast <int>

(InputPeaks[

i

].Intensity*Scale));

368

InputPeaks.push_back(InputPeak);

379  bool

GotOne(

false

);

386

MySpectrum->SetNumber(1);

391

}

while

(

Line

.size() < 3 && !DTA.eof());

407  Set

().push_back(MySpectrum);

410

}

catch

(NCBI_NS_STD::exception& e) {

411  ERR_POST

(

Info

<<

"Exception in CSpectrumSet::LoadDTA: "

<< e.what());

414  ERR_POST

(

Info

<<

"Exception in CSpectrumSet::LoadDTA: "

);

418  if

(!GotOne)

return

1;

431  bool

GotOne(

false

);

437  if

(Max > 0 && Count > Max)

440

MySpectrum->SetNumber(iIndex);

447  else if

(retval == 1) {

452  if

(retval != -1 && retval != -2)

Set

().push_back(MySpectrum);

454

}

while

(DTA && !DTA.eof() && retval != -1);

459

}

catch

(NCBI_NS_STD::exception& e) {

460  ERR_POST

(

Info

<<

"Exception in CSpectrumSet::LoadMGF: "

<< e.what());

463  ERR_POST

(

Info

<<

"Exception in CSpectrumSet::LoadMGF: "

);

477  bool

GotMass(

false

);

483  if

(!DTA || DTA.eof())

490  if

(!DTA || DTA.eof())

493

MySpectrum->SetIds().push_back(

500  string

LastLine(

Line

.substr(8,

Line

.size()-8));

503  if

(istr >> precursor) {

504

MySpectrum->SetPrecursormz(

MSSCALE2INT

(precursor));

509  string

LastLine(

Line

.substr(7,

Line

.size()-7));

518

MySpectrum->SetCharge().clear();

523

MySpectrum->SetCharge().push_back(charge);

525

}

while

(charge != 0);

532

}

while

(

Line

.substr(0, 1).find_first_not_of(

"0123456789.-"

) == 0 ||

Line

.empty());

537  if

(MySpectrum->SetCharge().empty())

538

MySpectrum->SetCharge().push_back(1);

541  if

(!DTA || DTA.eof())

546  if

(

Line

.size() <= 1)

549  if

(

Line

.find_first_of(

"#;/!"

) == 0)

552  if

(!

GetDTABody

(istr, InputPeaks))

return

1;

User-defined methods of the data storage class.

static CNcbiIstream & MyGetline(CNcbiIstream &is, string &str)

deque< TInputPeak > TInputPeaks

for holding a spectrum

int LoadFile(const EMSSpectrumFileType FileType, CNcbiIstream &DTA, int Max=0)

wrapper for various file loaders

bool GetDTAHeader(CNcbiIstream &DTA, CRef< CMSSpectrum > &MySpectrum, bool isPKL=false)

Read in the header of a DTA file.

int LoadMultDTA(CNcbiIstream &DTA, int Max=0)

load in multiple dta files with <dta> tag separators

int GetMGFBlock(CNcbiIstream &DTA, CRef< CMSSpectrum > &MySpectrum)

Read in an ms/ms block in an mgf file.

bool Peaks2Spectrum(const TInputPeaks &InputPeaks, CRef< CMSSpectrum > &MySpectrum) const

Convert peak list to spectrum.

int LoadMGF(CNcbiIstream &DTA, int Max=0)

load mgf file

bool GetDTABody(CNcbiIstream &DTA, TInputPeaks &InputPeaks)

Read in the body of a dta like file.

int LoadMultBlankLineDTA(CNcbiIstream &DTA, int Max=0, bool isPKL=false)

load multiple dta's separated by a blank line

int LoadDTA(CNcbiIstream &DTA)

load in a single dta file

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

The NCBI C++ standard methods for dealing with std::string.

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

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void Info(CExceptionArgs_Base &args)

CTempString GetMatch(CTempString str, size_t offset=0, size_t idx=0, TMatch flags=fMatch_default, bool noreturn=false)

Get matching pattern and subpatterns.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

CNcbiIstream & NcbiGetline(CNcbiIstream &is, string &str, char delim, string::size_type *count=NULL)

Read from "is" to "str" up to the delimiter symbol "delim" (or EOF)

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static string PrintableString(const CTempString str, TPrintableMode mode=fNewLine_Quote|fNonAscii_Passthru)

Get a printable version of the specified string.

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

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

Convert string to int.

static int Compare(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Compare of a substring with another string.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

Tdata & Set(void)

Assign a value to data member.

EMSSpectrumFileType

Access to EMSSpectrumFileType's attributes (values, names) as defined in spec.

@ eMSSpectrumFileType_pks

@ eMSSpectrumFileType_mgf

@ eMSSpectrumFileType_sciex

@ eMSSpectrumFileType_omxbz2

bzip2 omx file

@ eMSSpectrumFileType_dtablank

@ eMSSpectrumFileType_pkl

@ eMSSpectrumFileType_omx

xml for iterative search

@ eMSSpectrumFileType_dtaxml

@ eMSSpectrumFileType_dta

@ eMSSpectrumFileType_unknown

@ eMSSpectrumFileType_asc

@ eMSSpectrumFileType_oms

asn.1 binary for iterative search

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

struct for holding a single peak

int mz

scaled m/z value for peak

float Intensity

unscaled intensity

C++ wrappers for the Perl-compatible regular expression (PCRE) library.

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4