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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/MSResponse_8cpp_source.html below:

NCBI C++ ToolKit: src/objects/omssa/MSResponse.cpp Source File

62 if

(retval.find_first_of(

",\""

) < retval.size()) retval =

"\""

+ retval +

"\""

;

72

os <<

"Spectrum number, Filename/id, Peptide, E-value, Mass, gi, Accession, Start, Stop, Defline, Mods, Charge, Theo Mass, P-value, NIST score"

<< endl;

75

CMSResponse::THitsets::const_iterator iHits;

87

CMSHitSet::THits::const_iterator iHit;

88

CMSHits::TPephits::const_iterator iPephit;

89 for

(iHit = HitSet->GetHits().begin(); iHit != HitSet->GetHits().end(); iHit++)

92 if

(HitSet->GetIds().begin() != HitSet->GetIds().end())

93 id

= *(HitSet->GetIds().begin());

94 double

NISTScore (0.0L);

95 if

((*iHit)->CanGetScores()) {

97 if

((*iNISTScore)->GetName() ==

"NIST Score"

)

98

NISTScore = (*iNISTScore)->GetValue();

102 for

(iPephit = (*iHit)->GetPephits().begin(); iPephit != (*iHit)->GetPephits().end(); iPephit++)

105

(*iHit)->MakePepString(PepString);

107

(*iHit)->MakeModString(ModString, ModSet);

108 string

Accession(

""

);

109 if

((*iPephit)->CanGetAccession())

110

Accession =

CSVString

((*iPephit)->GetAccession());

112 if

((*iPephit)->CanGetGi())

113

Gi = (*iPephit)->GetGi();

114

os << HitSet->GetNumber() <<

","

CSVString

(

id

) <<

","

116

(*iHit)->GetEvalue() <<

","

<< (*iHit)->GetMass()/fMZ_scale <<

","

117

Gi <<

","

<< Accession <<

","

118

(*iPephit)->GetStart() + 1 <<

","

<< (*iPephit)->GetStop() + 1 <<

","

120 ","

<< (*iHit)->GetCharge() <<

121 ","

<< (*iHit)->GetTheomass()/fMZ_scale <<

122 ","

<< (*iHit)->GetPvalue() <<

123 ","

<< NISTScore << endl;

133 const double

Threshold)

const 138 if

((*iHit)->GetEvalue() <= Threshold) {

139

OidSet.

insert

((*iPepHit)->GetOid());

151 if

((*iHitSet)->GetNumber() == Number)

return

*iHitSet;

User-defined methods of the data storage class.

void PrintCSV(ostream &os, CRef< CMSModSpecSet > ModSet)

void GetOidsBelowThreshold(TOidSet &OidSet, const double Threshold) const

insert oids into oidset if hit is below threhold

CRef< CMSHitSet > FindHitSet(const int Number) const

Find hitset with given number.

string CSVString(const string &in)

iterator_bool insert(const value_type &val)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Replace occurrences of a substring within a string.

list< CRef< CMSScoreSet > > TScores

vector< CRef< CMSHits > > THits

TScale GetScale(void) const

Get the Scale member data.

const THitsets & GetHitsets(void) const

Get the Hitsets member data.

bool CanGetScale(void) const

Check if it is safe to call GetScale method.

vector< CRef< CMSHitSet > > THitsets

bool CanGetError(void) const

Check if it is safe to call GetError method.

bool CanGetHitsets(void) const

Check if it is safe to call GetHitsets method.

list< CRef< CMSPepHit > > TPephits

@ eMSHitError_notenuffpeaks

not enough peaks to search

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

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