libpappsomspp
Library for mass spectrometry
pappso::XtandemHyperscore Class Reference

#include <xtandemhyperscore.h>

Public Types

using AaFactorMap = std::map< char, pappso_double >
 

Public Member Functions

 XtandemHyperscore (const MassSpectrum &spectrum, pappso::PeptideSp peptideSp, unsigned int parent_charge, PrecisionPtr precision, std::list< PeptideIon > ion_list, bool refine_spectrum_synthesis)
 
 XtandemHyperscore (const XtandemHyperscore &other)
 
 ~XtandemHyperscore ()
 
pappso_double getHyperscore () const
 
unsigned int getMatchedIons (PeptideIon ion_type) const
 

Private Member Functions

unsigned int getXtandemPredictedIonIntensityFactor (const QString &sequence, PeptideDirection ion_direction, unsigned int ion_size) const
 

Private Attributes

bool _refine_spectrum_synthesis
 
pappso_double _proto_hyperscore
 
std::map< PeptideIon, unsigned int > _ion_count
 

Static Private Attributes

static AaFactorMap _aa_ion_factor_y
 
static AaFactorMap _aa_ion_factor_b
 

Detailed Description

Definition at line 42 of file xtandemhyperscore.h.

Member Typedef Documentation

◆ AaFactorMap

Definition at line 45 of file xtandemhyperscore.h.

Constructor & Destructor Documentation

◆ XtandemHyperscore() [1/2]

pappso::XtandemHyperscore::XtandemHyperscore ( const MassSpectrum spectrum,
pappso::PeptideSp  peptideSp,
unsigned int  parent_charge,
PrecisionPtr  precision,
std::list< PeptideIon ion_list,
bool  refine_spectrum_synthesis 
)

Definition at line 51 of file xtandemhyperscore.cpp.

57 : _refine_spectrum_synthesis(refine_spectrum_synthesis)
58{
59 try
60 {
61 /*
62 if ((peptide_ion_sp.get()->getPeptideIonType() == PeptideIon::c) ||
63 (peptide_ion_sp.get()->getPeptideIonType() == PeptideIon::z)) {
64 if(current_max_charge > 2) {
65 current_max_charge--;
66 }
67 }*/
68 unsigned int max_charge = parent_charge;
69 if(parent_charge > 1)
70 {
71 max_charge = parent_charge - 1;
72 }
73 PeptideSpectrumMatch psm(
74 spectrum, peptideSp, max_charge, precision, ion_list);
75
77 {PeptideIon::b, 0},
78 {PeptideIon::bo, 0},
80 {PeptideIon::c, 0},
81 {PeptideIon::y, 0},
82 {PeptideIon::yo, 0},
84 {PeptideIon::z, 0}};
85
86 std::map<PeptideIon, unsigned int> ion_count;
87 for(auto &&ion_type : ion_list)
88 {
89 ion_count.insert(std::pair<PeptideIon, unsigned int>(ion_type, 0));
90 }
91
92 std::map<unsigned int, pappso_double> charge_dot_product;
93 std::map<unsigned int, std::map<PeptideIon, unsigned int>>
94 charge_ion_count;
95 for(unsigned int i = 1; i <= max_charge; i++)
96 {
97 charge_dot_product.insert(
98 std::pair<unsigned int, pappso_double>(i, 0));
99 charge_ion_count.insert(
100 std::pair<unsigned int, std::map<PeptideIon, unsigned int>>(
101 i, ion_count));
102 }
103 QString sequence = peptideSp.get()->getSequence();
104 for(auto &&peptide_ion_match : psm)
105 {
106 PeptideIon ion_type = peptide_ion_match.getPeptideIonType();
107 unsigned int charge = peptide_ion_match.getCharge();
108 charge_dot_product[charge] +=
109 peptide_ion_match.getPeak().y *
111 sequence,
112 peptide_ion_match.getPeptideIonDirection(),
113 peptide_ion_match.getPeptideFragmentIonSp().get()->size());
114 charge_ion_count[charge][ion_type] += 1;
115 _ion_count[ion_type] += 1;
116 }
117
118 qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
119 << " _ion_count[PeptideIon::y]=" << _ion_count[PeptideIon::y];
120 // take the 2 best component
121 pappso_double sum_intensity = 0;
122 for(unsigned int i = 1; i <= max_charge; i++)
123 {
124 sum_intensity += charge_dot_product[i];
125 }
126 for(auto count : _ion_count)
127 {
128 sum_intensity *= factorial(count.second);
129 }
130
131 _proto_hyperscore = sum_intensity;
132 }
133 catch(PappsoException &exception_pappso)
134 {
135 QString errorStr =
136 QObject::tr("ERROR computing hyperscore, PAPPSO exception:\n%1")
137 .arg(exception_pappso.qwhat());
138 qDebug() << "XtandemHyperscore::XtandemHyperscore PappsoException :\n"
139 << errorStr;
140 throw PappsoException(errorStr);
141 }
142 catch(std::exception &exception_std)
143 {
144 QString errorStr =
145 QObject::tr("ERROR computing hyperscore, std exception:\n%1")
146 .arg(exception_std.what());
147 qDebug() << "XtandemHyperscore::XtandemHyperscore std::exception :\n"
148 << errorStr;
149 throw PappsoException(errorStr);
150 }
151}
unsigned int getXtandemPredictedIonIntensityFactor(const QString &sequence, PeptideDirection ion_direction, unsigned int ion_size) const
std::map< PeptideIon, unsigned int > _ion_count
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
Definition: types.h:400
@ a
Nter aldimine ions.
@ y
Cter amino ions.
@ c
Nter amino ions.
@ ystar
Cter amino ions + NH3 loss.
@ yo
Cter amino ions + H2O loss.
@ bstar
Nter acylium ions + NH3 loss.
@ b
Nter acylium ions.
@ bo
Nter acylium ions + H2O loss.
@ z
Cter carbocations.
double pappso_double
A type definition for doubles.
Definition: types.h:49
unsigned int factorial(unsigned int n)

References _ion_count, _proto_hyperscore, pappso::a, pappso::b, pappso::bo, pappso::bstar, pappso::c, pappso::factorial(), getXtandemPredictedIonIntensityFactor(), pappso::PappsoException::qwhat(), pappso::y, pappso::yo, pappso::ystar, and pappso::z.

◆ XtandemHyperscore() [2/2]

pappso::XtandemHyperscore::XtandemHyperscore ( const XtandemHyperscore other)

Definition at line 153 of file xtandemhyperscore.cpp.

154{
155 _ion_count = other._ion_count;
156 _proto_hyperscore = other._proto_hyperscore;
157 _refine_spectrum_synthesis = other._refine_spectrum_synthesis;
158}

References _ion_count, _proto_hyperscore, and _refine_spectrum_synthesis.

◆ ~XtandemHyperscore()

pappso::XtandemHyperscore::~XtandemHyperscore ( )

Definition at line 165 of file xtandemhyperscore.cpp.

166{
167}

Member Function Documentation

◆ getHyperscore()

pappso_double pappso::XtandemHyperscore::getHyperscore ( ) const

Definition at line 261 of file xtandemhyperscore.cpp.

262{
263 try
264 {
265 qDebug() << " _proto_hyperscore=" << _proto_hyperscore;
266 double hyperscore = (log10(_proto_hyperscore) * 4);
267 if(hyperscore < 0)
268 return 0;
269 return hyperscore;
270 }
271 catch(PappsoException &exception_pappso)
272 {
273 QString errorStr =
274 QObject::tr("ERROR in getHyperscore, PAPPSO exception:\n%1")
275 .arg(exception_pappso.qwhat());
276 qDebug() << "XtandemHyperscore::getHyperscore PappsoException :\n"
277 << errorStr;
278 throw PappsoException(errorStr);
279 }
280 catch(std::exception &exception_std)
281 {
282 QString errorStr =
283 QObject::tr("ERROR in getHyperscore, std exception:\n%1")
284 .arg(exception_std.what());
285 qDebug() << "XtandemHyperscore::getHyperscore std::exception :\n"
286 << errorStr;
287 throw PappsoException(errorStr);
288 }
289}

References _proto_hyperscore, pappso::log10, and pappso::PappsoException::qwhat().

◆ getMatchedIons()

unsigned int pappso::XtandemHyperscore::getMatchedIons ( PeptideIon  ion_type) const

Definition at line 161 of file xtandemhyperscore.cpp.

162{
163 return _ion_count.at(ion_type);
164}

References _ion_count.

◆ getXtandemPredictedIonIntensityFactor()

unsigned int pappso::XtandemHyperscore::getXtandemPredictedIonIntensityFactor ( const QString &  sequence,
PeptideDirection  ion_direction,
unsigned int  ion_size 
) const
private

Definition at line 201 of file xtandemhyperscore.cpp.

205{
206 unsigned int Pi(1);
207
208 char last_aa_nter('_'), last_aa_cter('_');
209
210 if(ion_direction == PeptideDirection::Nter)
211 {
212 last_aa_nter = sequence[ion_size - 1].toLatin1();
213 last_aa_cter = sequence[ion_size].toLatin1();
214 if(ion_size == 2)
215 {
216 if(last_aa_nter == 'P')
217 {
218 Pi *= 10;
219 }
220 else
221 {
222 Pi *= 3;
223 }
224 }
225 }
226 else
227 {
228 unsigned int offset(sequence.size() - ion_size);
229 last_aa_nter = sequence[offset - 1].toLatin1();
230 last_aa_cter = sequence[offset].toLatin1();
231 if((offset) == 2)
232 {
233 if(last_aa_nter == 'P')
234 {
235 Pi *= 10;
236 }
237 else
238 {
239 Pi *= 3;
240 }
241 }
242 }
243 // QDebug << " last_aa_nter=" << QChar(last_aa_nter) << "
244 // _aa_ion_factor_b[last_aa_nter]="s ;
245 qDebug() << PeptideFragment::getPeptideIonDirectionName(ion_direction)
246 << " last_aa_nter=" << last_aa_nter
247 << " _aa_ion_factor_b[last_aa_nter]="
248 << _aa_ion_factor_b[last_aa_nter] << " last_aa_cter=" << last_aa_cter
249 << " _aa_ion_factor_y[last_aa_cter]="
250 << _aa_ion_factor_y[last_aa_cter];
252 {
253 Pi *= _aa_ion_factor_b[last_aa_nter] * _aa_ion_factor_y[last_aa_cter];
254 }
255
256 return Pi;
257}
static const QString getPeptideIonDirectionName(PeptideDirection direction)
static AaFactorMap _aa_ion_factor_y
static AaFactorMap _aa_ion_factor_b

References _aa_ion_factor_b, _aa_ion_factor_y, _refine_spectrum_synthesis, pappso::PeptideFragment::getPeptideIonDirectionName(), and pappso::Nter.

Referenced by XtandemHyperscore().

Member Data Documentation

◆ _aa_ion_factor_b

XtandemHyperscore::AaFactorMap pappso::XtandemHyperscore::_aa_ion_factor_b
staticprivate
Initial value:
= [] {
for(long c = 64; c < 126; c++)
{
ret.insert(std::pair<char, pappso_double>(c, pappso_double(1.0)));
}
ret['D'] = pappso_double(5.0);
ret['N'] = pappso_double(2.0);
ret['V'] = pappso_double(3.0);
ret['E'] = pappso_double(3.0);
ret['Q'] = pappso_double(2.0);
ret['I'] = pappso_double(3.0);
ret['L'] = pappso_double(3.0);
return ret;
}()
std::map< char, pappso_double > AaFactorMap

Definition at line 70 of file xtandemhyperscore.h.

Referenced by getXtandemPredictedIonIntensityFactor().

◆ _aa_ion_factor_y

XtandemHyperscore::AaFactorMap pappso::XtandemHyperscore::_aa_ion_factor_y
staticprivate
Initial value:
= [] {
for(long c = 64; c < 126; c++)
{
ret.insert(std::pair<char, pappso_double>(c, pappso_double(1.0)));
}
ret['P'] = pappso_double(5.0);
return ret;
}()

Definition at line 69 of file xtandemhyperscore.h.

Referenced by getXtandemPredictedIonIntensityFactor().

◆ _ion_count

std::map<PeptideIon, unsigned int> pappso::XtandemHyperscore::_ion_count
private

Definition at line 67 of file xtandemhyperscore.h.

Referenced by XtandemHyperscore(), and getMatchedIons().

◆ _proto_hyperscore

pappso_double pappso::XtandemHyperscore::_proto_hyperscore
private

Definition at line 66 of file xtandemhyperscore.h.

Referenced by XtandemHyperscore(), and getHyperscore().

◆ _refine_spectrum_synthesis

bool pappso::XtandemHyperscore::_refine_spectrum_synthesis
private

Definition at line 59 of file xtandemhyperscore.h.

Referenced by XtandemHyperscore(), and getXtandemPredictedIonIntensityFactor().


The documentation for this class was generated from the following files: